-- dump date 20111121_015502 -- class Genbank::misc_feature -- table misc_feature_note -- id note 579112000001 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 579112000002 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 579112000003 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 579112000004 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 579112000005 G1 box; other site 579112000006 GTP/Mg2+ binding site [chemical binding]; other site 579112000007 Switch I region; other site 579112000008 G2 box; other site 579112000009 Switch II region; other site 579112000010 G3 box; other site 579112000011 G4 box; other site 579112000012 G5 box; other site 579112000013 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 579112000014 membrane protein insertase; Provisional; Region: PRK01318 579112000015 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 579112000016 Domain of unknown function DUF37; Region: DUF37; cl00506 579112000017 Ribonuclease P; Region: Ribonuclease_P; cl00457 579112000018 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 579112000019 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 579112000020 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 579112000021 Walker A/P-loop; other site 579112000022 ATP binding site [chemical binding]; other site 579112000023 Q-loop/lid; other site 579112000024 ABC transporter signature motif; other site 579112000025 Walker B; other site 579112000026 D-loop; other site 579112000027 H-loop/switch region; other site 579112000028 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...; Region: TM_PBP2; cd06261 579112000029 dimer interface [polypeptide binding]; other site 579112000030 conserved gate region; other site 579112000031 putative PBP binding loops; other site 579112000032 ABC-ATPase subunit interface; other site 579112000033 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 579112000034 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...; Region: PBPb; cd00134 579112000035 substrate binding pocket [chemical binding]; other site 579112000036 membrane-bound complex binding site; other site 579112000037 hinge residues; other site 579112000038 hypothetical protein; Validated; Region: PRK06672 579112000039 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 579112000040 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...; Region: AAA; cd00009 579112000041 Walker A motif; other site 579112000042 ATP binding site [chemical binding]; other site 579112000043 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112000044 Walker B motif; other site 579112000045 arginine finger; other site 579112000046 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 579112000047 DnaA box-binding interface [nucleotide binding]; other site 579112000048 DNA polymerase III subunit beta; Validated; Region: PRK05643 579112000049 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...; Region: beta_clamp; cd00140 579112000050 putative DNA binding surface [nucleotide binding]; other site 579112000051 dimer interface [polypeptide binding]; other site 579112000052 beta-clamp/clamp loader binding surface; other site 579112000053 beta-clamp/translesion DNA polymerase binding surface; other site 579112000054 recombination protein F; Reviewed; Region: recF; PRK00064 579112000055 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112000056 Walker A/P-loop; other site 579112000057 ATP binding site [chemical binding]; other site 579112000058 Q-loop/lid; other site 579112000059 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112000060 ABC transporter signature motif; other site 579112000061 Walker B; other site 579112000062 D-loop; other site 579112000063 H-loop/switch region; other site 579112000064 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 579112000065 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 579112000066 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 579112000067 anchoring element; other site 579112000068 dimer interface [polypeptide binding]; other site 579112000069 ATP binding site [chemical binding]; other site 579112000070 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...; Region: TOPRIM_TopoIIA_GyrB; cd03366 579112000071 active site 579112000072 putative metal-binding site [ion binding]; other site 579112000073 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 579112000074 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 579112000075 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein...; Region: ACD_IbpA-B_like; cd06470 579112000076 putative dimer interface [polypeptide binding]; other site 579112000077 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 579112000078 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112000079 homodimer interface [polypeptide binding]; other site 579112000080 catalytic residue [active] 579112000081 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 579112000082 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 579112000083 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 579112000084 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 579112000085 dimer interface [polypeptide binding]; other site 579112000086 motif 1; other site 579112000087 active site 579112000088 motif 2; other site 579112000089 motif 3; other site 579112000090 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 579112000091 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 579112000092 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 579112000093 CPxP motif; other site 579112000094 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 579112000095 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 579112000096 NADP binding site [chemical binding]; other site 579112000097 dimer interface [polypeptide binding]; other site 579112000098 threonine dehydratase; Reviewed; Region: PRK09224 579112000099 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 579112000100 tetramer interface [polypeptide binding]; other site 579112000101 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112000102 catalytic residue [active] 579112000103 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 579112000104 putative Ile/Val binding site [chemical binding]; other site 579112000105 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 579112000106 putative Ile/Val binding site [chemical binding]; other site 579112000107 Dehydratase family; Region: ILVD_EDD; cl00340 579112000108 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 579112000109 branched-chain amino acid aminotransferase; Provisional; Region: PRK12479 579112000110 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 alpha-...; Region: BCAT_beta_family; cd01557 579112000111 homodimer interface [polypeptide binding]; other site 579112000112 substrate-cofactor binding pocket; other site 579112000113 catalytic residue [active] 579112000114 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-...; Region: CBS_pair; cl09141 579112000115 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 579112000116 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 579112000117 PYR/PP interface [polypeptide binding]; other site 579112000118 dimer interface [polypeptide binding]; other site 579112000119 TPP binding site [chemical binding]; other site 579112000120 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 579112000121 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 579112000122 TPP-binding site [chemical binding]; other site 579112000123 dimer interface [polypeptide binding]; other site 579112000124 Mg chelatase-related protein; Region: TIGR00368 579112000125 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...; Region: AAA; cd00009 579112000126 Walker A motif; other site 579112000127 ATP binding site [chemical binding]; other site 579112000128 Walker B motif; other site 579112000129 arginine finger; other site 579112000130 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 579112000131 putative acyl-acceptor binding pocket; other site 579112000132 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 579112000133 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 579112000134 catalytic residues [active] 579112000135 hinge region; other site 579112000136 alpha helical domain; other site 579112000137 Phosphotransferase enzyme family; Region: APH; pfam01636 579112000138 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 579112000139 active site 579112000140 ATP binding site [chemical binding]; other site 579112000141 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 579112000142 4Fe-4S binding domain; Region: Fer4_5; pfam12801 579112000143 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 alpha-; Region: HCP_like; cl14655 579112000144 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 579112000145 Protein of unknown function (DUF1040); Region: DUF1040; cl01176 579112000146 Sporulation control protein [General function prediction only]; Region: Spo0M; COG4326 579112000147 SpoOM protein; Region: Spo0M; pfam07070 579112000148 Haemolysin-III related; Region: HlyIII; cl03831 579112000149 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 579112000150 Cation transport protein; Region: TrkH; cl10514 579112000151 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 579112000152 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 579112000153 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112000154 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; cl09110 579112000155 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112000156 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; cl09110 579112000157 16S rRNA methyltransferase B; Provisional; Region: PRK10901 579112000158 N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological...; Region: Methyltransferase_Sun; cd00620 579112000159 putative RNA binding site [nucleotide binding]; other site 579112000160 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 579112000161 S-adenosylmethionine binding site [chemical binding]; other site 579112000162 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 579112000163 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 579112000164 putative active site [active] 579112000165 substrate binding site [chemical binding]; other site 579112000166 putative cosubstrate binding site; other site 579112000167 catalytic site [active] 579112000168 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 579112000169 substrate binding site [chemical binding]; other site 579112000170 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(...; Region: Pep_deformylase; cd00487 579112000171 active site 579112000172 catalytic residues [active] 579112000173 metal binding site [ion binding]; metal-binding site 579112000174 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 579112000175 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 579112000176 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 579112000177 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 579112000178 Protein of unknown function (DUF494); Region: DUF494; cl01103 579112000179 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 579112000180 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 579112000181 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 579112000182 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 579112000183 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112000184 AIR carboxylase; Region: AIRC; cl00310 579112000185 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 579112000186 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 579112000187 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 579112000188 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 579112000189 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 579112000190 shikimate binding site; other site 579112000191 NAD(P) binding site [chemical binding]; other site 579112000192 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 579112000193 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 579112000194 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 579112000195 trimer interface [polypeptide binding]; other site 579112000196 putative metal binding site [ion binding]; other site 579112000197 CrcB-like protein; Region: CRCB; cl09114 579112000198 ThiC family; Region: ThiC; cl08031 579112000199 thiamine-phosphate pyrophosphorylase; Reviewed; Region: thiE; PRK12290 579112000200 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- (beta-...; Region: TMP_TenI; cd00564 579112000201 thiamine phosphate binding site [chemical binding]; other site 579112000202 active site 579112000203 pyrophosphate binding site [ion binding]; other site 579112000204 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...; Region: ThiF_MoeB_HesA_family; cd00757 579112000205 thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily; Region: adenyl_thiF; TIGR02356 579112000206 ATP binding site [chemical binding]; other site 579112000207 substrate interface [chemical binding]; other site 579112000208 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 579112000209 thiS-thiF/thiG interaction site; other site 579112000210 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 579112000211 ThiS interaction site; other site 579112000212 putative active site [active] 579112000213 tetramer interface [polypeptide binding]; other site 579112000214 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 579112000215 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 579112000216 FeS/SAM binding site; other site 579112000217 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 579112000218 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 579112000219 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 579112000220 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 579112000221 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 579112000222 active site 579112000223 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 579112000224 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112000225 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 579112000226 substrate binding pocket [chemical binding]; other site 579112000227 dimerization interface [polypeptide binding]; other site 579112000228 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 579112000229 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 579112000230 putative substrate translocation pore; other site 579112000231 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 579112000232 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112000233 PAS domain S-box; Region: sensory_box; TIGR00229 579112000234 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112000235 putative active site [active] 579112000236 heme pocket [chemical binding]; other site 579112000237 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112000238 metal binding site [ion binding]; metal-binding site 579112000239 active site 579112000240 I-site; other site 579112000241 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 579112000242 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112000243 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 579112000244 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 579112000245 Ligand Binding Site [chemical binding]; other site 579112000246 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 579112000247 Ferritin-like domain; Region: Ferritin; pfam00210 579112000248 ferroxidase diiron center [ion binding]; other site 579112000249 Universal stress protein B (UspB); Region: UspB; cl11669 579112000250 Predicted flavoproteins [General function prediction only]; Region: COG2081 579112000251 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112000252 EamA-like transporter family; Region: EamA; cl01037 579112000253 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 579112000254 EamA-like transporter family; Region: EamA; cl01037 579112000255 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 579112000256 RmuC family; Region: RmuC; pfam02646 579112000257 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 579112000258 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 579112000259 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 579112000260 SCP-2 sterol transfer family; Region: SCP2; cl01225 579112000261 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 579112000262 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 579112000263 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 579112000264 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 579112000265 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 579112000266 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 579112000267 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 579112000268 MatE; Region: MatE; cl10513 579112000269 MatE; Region: MatE; cl10513 579112000270 Leucine carboxyl methyltransferase; Region: LCM; cl01306 579112000271 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112000272 LexA repressor; Validated; Region: PRK00215 579112000273 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 (...; Region: S24_LexA-like; cd06529 579112000274 Catalytic site [active] 579112000275 Glycerol-3-phosphate O-acyltransferase [Lipid metabolism]; Region: PlsB; COG2937 579112000276 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 579112000277 putative acyl-acceptor binding pocket; other site 579112000278 UbiA prenyltransferase family; Region: UbiA; cl00337 579112000279 UTRA domain; Region: UTRA; cl01230 579112000280 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 579112000281 PAS fold; Region: PAS_4; pfam08448 579112000282 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112000283 putative active site [active] 579112000284 heme pocket [chemical binding]; other site 579112000285 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112000286 PAS fold; Region: PAS_3; pfam08447 579112000287 putative active site [active] 579112000288 heme pocket [chemical binding]; other site 579112000289 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112000290 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112000291 intramembrane serine protease GlpG; Provisional; Region: PRK10907 579112000292 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 579112000293 Rhomboid family; Region: Rhomboid; cl11446 579112000294 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 579112000295 active site residue [active] 579112000296 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 579112000297 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 579112000298 active site 579112000299 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 579112000300 dimer interface [polypeptide binding]; other site 579112000301 allosteric magnesium binding site [ion binding]; other site 579112000302 active site 579112000303 aspartate-rich active site metal binding site; other site 579112000304 Schiff base residues; other site 579112000305 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112000306 Coenzyme A binding pocket [chemical binding]; other site 579112000307 DNA polymerase I; Provisional; Region: PRK05755 579112000308 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 579112000309 active site 579112000310 metal binding site 1 [ion binding]; metal-binding site 579112000311 putative 5' ssDNA interaction site; other site 579112000312 metal binding site 3; metal-binding site 579112000313 metal binding site 2 [ion binding]; metal-binding site 579112000314 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 579112000315 putative DNA binding site [nucleotide binding]; other site 579112000316 putative metal binding site [ion binding]; other site 579112000317 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 579112000318 active site 579112000319 catalytic site [active] 579112000320 substrate binding site [chemical binding]; other site 579112000321 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 579112000322 active site 579112000323 DNA binding site [nucleotide binding] 579112000324 catalytic site [active] 579112000325 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 579112000326 G1 box; other site 579112000327 GTP/Mg2+ binding site [chemical binding]; other site 579112000328 Switch I region; other site 579112000329 G2 box; other site 579112000330 G3 box; other site 579112000331 Switch II region; other site 579112000332 G4 box; other site 579112000333 G5 box; other site 579112000334 Cytochrome c; Region: Cytochrom_C; cl11414 579112000335 Cytochrome c; Region: Cytochrom_C; cl11414 579112000336 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112000337 Protein of unknown function, DUF414; Region: DUF414; cl01172 579112000338 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 579112000339 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 579112000340 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 579112000341 FeS/SAM binding site; other site 579112000342 HemN C-terminal region; Region: HemN_C; pfam06969 579112000343 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 579112000344 HemY protein N-terminus; Region: HemY_N; pfam07219 579112000345 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 579112000346 TPR motif; other site 579112000347 binding surface 579112000348 HemX; Region: HemX; cl14667 579112000349 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 579112000350 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...; Region: HemD; cd06578 579112000351 active site 579112000352 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 579112000353 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 579112000354 domain interfaces; other site 579112000355 active site 579112000356 Adenylate cyclase [Nucleotide transport and metabolism]; Region: CyaA; COG3072 579112000357 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 579112000358 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 579112000359 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 579112000360 putative iron binding site [ion binding]; other site 579112000361 diaminopimelate decarboxylase; Region: lysA; TIGR01048 579112000362 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 579112000363 active site 579112000364 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 579112000365 substrate binding site [chemical binding]; other site 579112000366 catalytic residues [active] 579112000367 dimer interface [polypeptide binding]; other site 579112000368 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 579112000369 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 579112000370 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 579112000371 Protein of unknown function, DUF484; Region: DUF484; cl01228 579112000372 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 579112000373 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 579112000374 DNA binding site [nucleotide binding] 579112000375 Int/Topo IB signature motif; other site 579112000376 active site 579112000377 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; cl11391 579112000378 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 579112000379 Uncharacterized conserved protein [Function unknown]; Region: COG3287 579112000380 FIST N domain; Region: FIST; cl10701 579112000381 FIST C domain; Region: FIST_C; pfam10442 579112000382 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112000383 metal binding site [ion binding]; metal-binding site 579112000384 active site 579112000385 I-site; other site 579112000386 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 579112000387 DTW domain; Region: DTW; cl01221 579112000388 Predicted membrane protein [Function unknown]; Region: COG3650 579112000389 putative hydrolase; Provisional; Region: PRK10976 579112000390 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 579112000391 active site 579112000392 motif I; other site 579112000393 motif II; other site 579112000394 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; cl11391 579112000395 lysophospholipase L2; Provisional; Region: PRK10749 579112000396 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 579112000397 LysE type translocator; Region: LysE; cl00565 579112000398 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 579112000399 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 579112000400 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112000401 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 579112000402 dimerization interface [polypeptide binding]; other site 579112000403 DPS ferroxidase diiron center [ion binding]; other site 579112000404 ion pore; other site 579112000405 Protein of unknown function (DUF2500); Region: DUF2500; pfam10694 579112000406 YhhN-like protein; Region: YhhN; cl01505 579112000407 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 579112000408 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 579112000409 S-adenosylmethionine binding site [chemical binding]; other site 579112000410 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 579112000411 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 579112000412 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 579112000413 P loop; other site 579112000414 GTP binding site [chemical binding]; other site 579112000415 cell division protein FtsE; Provisional; Region: PRK10908 579112000416 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112000417 Walker A/P-loop; other site 579112000418 ATP binding site [chemical binding]; other site 579112000419 Q-loop/lid; other site 579112000420 ABC transporter signature motif; other site 579112000421 Walker B; other site 579112000422 D-loop; other site 579112000423 H-loop/switch region; other site 579112000424 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 579112000425 FtsX-like permease family; Region: FtsX; pfam02687 579112000426 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 579112000427 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 579112000428 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 579112000429 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...; Region: Sigma70_r4; cd06171 579112000430 DNA binding residues [nucleotide binding] 579112000431 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 579112000432 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112000433 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 579112000434 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 579112000435 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112000436 Protein of unknown function (DUF1422); Region: DUF1422; cl11649 579112000437 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 579112000438 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112000439 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 579112000440 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112000441 N-terminal plug; other site 579112000442 ligand-binding site [chemical binding]; other site 579112000443 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 579112000444 Peptidase S8 family domain in ProteinaseK-like proteins; Region: Peptidases_S8_PCSK9_ProteinaseK_like; cd04077 579112000445 calcium binding site 2 [ion binding]; other site 579112000446 active site 579112000447 catalytic triad [active] 579112000448 calcium binding site 1 [ion binding]; other site 579112000449 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 579112000450 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 579112000451 RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA...; Region: RRM; cd00590 579112000452 RNA/DNA binding site [nucleotide binding]; other site 579112000453 RRM dimerization site [polypeptide binding]; other site 579112000454 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112000455 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 579112000456 The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; Region: PBP2_IlvY; cd08430 579112000457 putative dimerization interface [polypeptide binding]; other site 579112000458 ketol-acid reductoisomerase; Validated; Region: PRK05225 579112000459 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112000460 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 579112000461 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 579112000462 Membrane fusogenic activity; Region: BMFP; cl01115 579112000463 multidrug efflux protein; Reviewed; Region: PRK09579 579112000464 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 579112000465 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112000466 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112000467 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 579112000468 UvrD/REP helicase; Region: UvrD-helicase; cl14126 579112000469 Cytochrome c; Region: Cytochrom_C; cl11414 579112000470 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 579112000471 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112000472 Walker A/P-loop; other site 579112000473 ATP binding site [chemical binding]; other site 579112000474 Q-loop/lid; other site 579112000475 ABC transporter signature motif; other site 579112000476 Walker B; other site 579112000477 D-loop; other site 579112000478 H-loop/switch region; other site 579112000479 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112000480 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112000481 Walker A/P-loop; other site 579112000482 ATP binding site [chemical binding]; other site 579112000483 Q-loop/lid; other site 579112000484 ABC transporter signature motif; other site 579112000485 Walker B; other site 579112000486 D-loop; other site 579112000487 H-loop/switch region; other site 579112000488 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112000489 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 579112000490 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 579112000491 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 579112000492 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...; Region: TM_PBP2; cd06261 579112000493 dimer interface [polypeptide binding]; other site 579112000494 conserved gate region; other site 579112000495 putative PBP binding loops; other site 579112000496 ABC-ATPase subunit interface; other site 579112000497 dipeptide transporter; Provisional; Region: PRK10913 579112000498 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...; Region: TM_PBP2; cd06261 579112000499 dimer interface [polypeptide binding]; other site 579112000500 conserved gate region; other site 579112000501 putative PBP binding loops; other site 579112000502 ABC-ATPase subunit interface; other site 579112000503 glutathione reductase; Validated; Region: PRK06116 579112000504 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112000505 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 579112000506 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 579112000507 oligopeptidase A; Provisional; Region: PRK10911 579112000508 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 579112000509 active site 579112000510 Zn binding site [ion binding]; other site 579112000511 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 579112000512 UvrD/REP helicase; Region: UvrD-helicase; cl14126 579112000513 LysE type translocator; Region: LysE; cl00565 579112000514 Cupin domain; Region: Cupin_2; cl09118 579112000515 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112000516 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112000517 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 579112000518 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 579112000519 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 579112000520 ATP binding site [chemical binding]; other site 579112000521 putative Mg++ binding site [ion binding]; other site 579112000522 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 579112000523 nucleotide binding region [chemical binding]; other site 579112000524 ATP-binding site [chemical binding]; other site 579112000525 RQC domain; Region: RQC; cl09632 579112000526 HRDC domain; Region: HRDC; cl02578 579112000527 Protein of unknown function (DUF3630); Region: DUF3630; pfam12305 579112000528 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 579112000529 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 579112000530 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112000531 Walker A/P-loop; other site 579112000532 ATP binding site [chemical binding]; other site 579112000533 Q-loop/lid; other site 579112000534 ABC transporter signature motif; other site 579112000535 Walker B; other site 579112000536 D-loop; other site 579112000537 H-loop/switch region; other site 579112000538 ferrichrome receptor precursor protein; Provisional; Region: PRK14050 579112000539 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112000540 N-terminal plug; other site 579112000541 ligand-binding site [chemical binding]; other site 579112000542 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 579112000543 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 579112000544 Walker A/P-loop; other site 579112000545 ATP binding site [chemical binding]; other site 579112000546 Q-loop/lid; other site 579112000547 ABC transporter signature motif; other site 579112000548 Walker B; other site 579112000549 D-loop; other site 579112000550 H-loop/switch region; other site 579112000551 iron-dicitrate transporter substrate-binding subunit; Provisional; Region: fecB; PRK11411 579112000552 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor...; Region: FhuD; cd01146 579112000553 siderophore binding site; other site 579112000554 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 579112000555 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112000556 ABC-ATPase subunit interface; other site 579112000557 dimer interface [polypeptide binding]; other site 579112000558 putative PBP binding regions; other site 579112000559 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112000560 ABC-ATPase subunit interface; other site 579112000561 dimer interface [polypeptide binding]; other site 579112000562 putative PBP binding regions; other site 579112000563 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11557 579112000564 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...; Region: SIS_RpiR; cd05013 579112000565 putative active site [active] 579112000566 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 579112000567 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 579112000568 putative active site [active] 579112000569 PTS system N-acetylmuramic acid transporter subunits EIIBC; Reviewed; Region: murP; PRK09586 579112000570 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...; Region: PTS_IIB_glc; cd00212 579112000571 active site turn [active] 579112000572 phosphorylation site [posttranslational modification] 579112000573 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112000574 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 579112000575 hypothetical protein; Provisional; Region: PRK11820 579112000576 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 579112000577 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 579112000578 ribonuclease PH; Reviewed; Region: rph; PRK00173 579112000579 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 579112000580 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 579112000581 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 579112000582 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 579112000583 putative acyl-acceptor binding pocket; other site 579112000584 division inhibitor protein; Provisional; Region: slmA; PRK09480 579112000585 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112000586 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 579112000587 Flavoprotein; Region: Flavoprotein; cl08021 579112000588 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 579112000589 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 579112000590 Cache domain; Region: Cache_2; cl07034 579112000591 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 579112000592 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 connected by an extended linker. The...; Region: HAMP; cd06225 579112000593 dimerization interface [polypeptide binding]; other site 579112000594 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112000595 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112000596 hypothetical protein; Reviewed; Region: PRK00024 579112000597 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 579112000598 MPN+ (JAMM) motif; other site 579112000599 Zinc-binding site [ion binding]; other site 579112000600 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 579112000601 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 579112000602 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 579112000603 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 579112000604 DNA binding site [nucleotide binding] 579112000605 catalytic residue [active] 579112000606 H2TH interface [polypeptide binding]; other site 579112000607 putative catalytic residues [active] 579112000608 turnover-facilitating residue; other site 579112000609 intercalation triad [nucleotide binding]; other site 579112000610 8OG recognition residue [nucleotide binding]; other site 579112000611 putative reading head residues; other site 579112000612 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 579112000613 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 579112000614 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 579112000615 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 579112000616 active site 579112000617 (T/H)XGH motif; other site 579112000618 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 579112000619 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 579112000620 putative active site [active] 579112000621 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 579112000622 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 579112000623 putative metal binding site [ion binding]; other site 579112000624 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 579112000625 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 579112000626 putative active site [active] 579112000627 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 579112000628 ATP binding site [chemical binding]; other site 579112000629 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 579112000630 WavE lipopolysaccharide synthesis; Region: WavE; pfam07507 579112000631 WavE lipopolysaccharide synthesis; Region: WavE; pfam07507 579112000632 GT2_BcbE_like is likely involved in the biosynthesis of the polysaccharide capsule; Region: GT2_BcE_like; cd04183 579112000633 Ligand binding site [chemical binding]; other site 579112000634 Phosphotransferase enzyme family; Region: APH; pfam01636 579112000635 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; cl11391 579112000636 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 579112000637 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 579112000638 Mannosyltransferase OCH1 and related enzymes [Cell envelope biogenesis, outer membrane]; Region: OCH1; COG3774 579112000639 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 579112000640 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 579112000641 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 579112000642 putative active site [active] 579112000643 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 579112000644 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 579112000645 putative active site [active] 579112000646 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 579112000647 O-Antigen ligase; Region: Wzy_C; cl04850 579112000648 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 6-...; Region: LbH_MAT_like; cd04647 579112000649 trimer interface [polypeptide binding]; other site 579112000650 active site 579112000651 substrate binding site [chemical binding]; other site 579112000652 CoA binding site [chemical binding]; other site 579112000653 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 579112000654 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 579112000655 NADP binding site [chemical binding]; other site 579112000656 homopentamer interface [polypeptide binding]; other site 579112000657 substrate binding site [chemical binding]; other site 579112000658 active site 579112000659 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 579112000660 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 579112000661 Substrate binding site [chemical binding]; other site 579112000662 Cupin domain; Region: Cupin_2; cl09118 579112000663 phosphomannomutase CpsG; Provisional; Region: PRK15414 579112000664 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 579112000665 active site 579112000666 substrate binding site [chemical binding]; other site 579112000667 metal binding site [ion binding]; metal-binding site 579112000668 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 579112000669 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 579112000670 NADP-binding site; other site 579112000671 homotetramer interface [polypeptide binding]; other site 579112000672 substrate binding site [chemical binding]; other site 579112000673 homodimer interface [polypeptide binding]; other site 579112000674 active site 579112000675 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 579112000676 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 579112000677 inhibitor-cofactor binding pocket; inhibition site 579112000678 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112000679 catalytic residue [active] 579112000680 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 579112000681 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 579112000682 ABC-2 type transporter; Region: ABC2_membrane; cl11417 579112000683 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 579112000684 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides...; Region: ABC_KpsT_Wzt; cd03220 579112000685 Walker A/P-loop; other site 579112000686 ATP binding site [chemical binding]; other site 579112000687 Q-loop/lid; other site 579112000688 ABC transporter signature motif; other site 579112000689 Walker B; other site 579112000690 D-loop; other site 579112000691 H-loop/switch region; other site 579112000692 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 579112000693 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112000694 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 579112000695 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 579112000696 active site 579112000697 NAD binding site [chemical binding]; other site 579112000698 metal binding site [ion binding]; metal-binding site 579112000699 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112000700 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 579112000701 Acyl-CoA reductase (LuxC); Region: LuxC; pfam05893 579112000702 NAD(P) binding site [chemical binding]; other site 579112000703 catalytic residues [active] 579112000704 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 579112000705 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 6-...; Region: LbH_MAT_like; cd04647 579112000706 trimer interface [polypeptide binding]; other site 579112000707 active site 579112000708 substrate binding site [chemical binding]; other site 579112000709 CoA binding site [chemical binding]; other site 579112000710 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112000711 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 579112000712 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule...; Region: GT1_like_4; cd03795 579112000713 putative ADP-binding pocket [chemical binding]; other site 579112000714 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 579112000715 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 579112000716 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 579112000717 NAD(P) binding site [chemical binding]; other site 579112000718 homodimer interface [polypeptide binding]; other site 579112000719 substrate binding site [chemical binding]; other site 579112000720 active site 579112000721 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 579112000722 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 579112000723 putative NAD(P) binding site [chemical binding]; other site 579112000724 active site 579112000725 putative substrate binding site [chemical binding]; other site 579112000726 Bacterial sugar transferase; Region: Bac_transf; cl00939 579112000727 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 579112000728 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112000729 Beta-Casp domain; Region: Beta-Casp; cl12567 579112000730 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 579112000731 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 579112000732 Mechanosensitive ion channel; Region: MS_channel; pfam00924 579112000733 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 579112000734 putative uracil binding site [chemical binding]; other site 579112000735 putative active site [active] 579112000736 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 579112000737 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112000738 Protein of unknown function (DUF416); Region: DUF416; cl01166 579112000739 mannose-6-phosphate isomerase; Provisional; Region: PRK15131 579112000740 mannose-6-phosphate isomerase, class I; Region: manA; TIGR00218 579112000741 mannose-6-phosphate isomerase, class I; Region: manA; TIGR00218 579112000742 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 579112000743 fructokinase; Reviewed; Region: PRK09557 579112000744 Domain of unknown function DUF21; Region: DUF21; pfam01595 579112000745 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 579112000746 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 higher-...; Region: HU_IHF; cd00591 579112000747 IHF dimer interface [polypeptide binding]; other site 579112000748 IHF - DNA interface [nucleotide binding]; other site 579112000749 Protein of unknown function (DUF1481); Region: DUF1481; pfam07356 579112000750 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 579112000751 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 579112000752 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112000753 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 579112000754 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 579112000755 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 579112000756 purine monophosphate binding site [chemical binding]; other site 579112000757 dimer interface [polypeptide binding]; other site 579112000758 putative catalytic residues [active] 579112000759 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 579112000760 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 579112000761 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 579112000762 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 579112000763 DNA binding residues [nucleotide binding] 579112000764 dimer interface [polypeptide binding]; other site 579112000765 metal binding site [ion binding]; metal-binding site 579112000766 DNA-binding transcriptional activator CadC; Provisional; Region: PRK10153 579112000767 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...; Region: trans_reg_C; cd00383 579112000768 DNA binding site [nucleotide binding] 579112000769 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 579112000770 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 579112000771 lysine decarboxylase CadA; Provisional; Region: PRK15400 579112000772 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 579112000773 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and...; Region: Orn_deC_like; cd00615 579112000774 homodimer interface [polypeptide binding]; other site 579112000775 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112000776 catalytic residue [active] 579112000777 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 579112000778 Cache domain; Region: Cache_2; cl07034 579112000779 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112000780 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112000781 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112000782 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 579112000783 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 579112000784 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112000785 N-terminal plug; other site 579112000786 ligand-binding site [chemical binding]; other site 579112000787 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 579112000788 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 579112000789 active site 579112000790 intersubunit interface [polypeptide binding]; other site 579112000791 catalytic residue [active] 579112000792 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 579112000793 GntP family permease; Region: GntP_permease; cl15264 579112000794 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 579112000795 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 579112000796 ATP-binding site [chemical binding]; other site 579112000797 Gluconate-6-phosphate binding site [chemical binding]; other site 579112000798 Dehydratase family; Region: ILVD_EDD; cl00340 579112000799 6-phosphogluconate dehydratase; Region: edd; TIGR01196 579112000800 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 579112000801 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112000802 DNA binding site [nucleotide binding] 579112000803 domain linker motif; other site 579112000804 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 579112000805 putative ligand binding site [chemical binding]; other site 579112000806 putative dimerization interface [polypeptide binding]; other site 579112000807 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112000808 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 579112000809 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...; Region: DUS_like_FMN; cd02801 579112000810 FMN binding site [chemical binding]; other site 579112000811 active site 579112000812 catalytic residues [active] 579112000813 substrate binding site [chemical binding]; other site 579112000814 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 579112000815 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112000816 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 579112000817 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 579112000818 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112000819 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 579112000820 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 579112000821 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 579112000822 carboxyltransferase (CT) interaction site; other site 579112000823 biotinylation site [posttranslational modification]; other site 579112000824 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 579112000825 active site 579112000826 trimer interface [polypeptide binding]; other site 579112000827 dimer interface [polypeptide binding]; other site 579112000828 acetyl-CoA synthetase; Provisional; Region: PRK00174 579112000829 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 579112000830 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112000831 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 579112000832 active site 579112000833 substrate binding site [chemical binding]; other site 579112000834 catalytic site [active] 579112000835 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 579112000836 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 579112000837 ligand binding site [chemical binding]; other site 579112000838 flexible hinge region; other site 579112000839 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include...; Region: CBS_pair_CAP-ED_DUF294_assoc_bac; cd04589 579112000840 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 579112000841 metal binding triad; other site 579112000842 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 579112000843 MFS_1 like family; Region: MFS_1_like; pfam12832 579112000844 Sodium:solute symporter family; Region: SSF; cl00456 579112000845 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112000846 PAS fold; Region: PAS_7; pfam12860 579112000847 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 trans-...; Region: HisKA; cl00080 579112000848 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 579112000849 ATP binding site [chemical binding]; other site 579112000850 Mg2+ binding site [ion binding]; other site 579112000851 G-X-G motif; other site 579112000852 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 579112000853 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112000854 active site 579112000855 phosphorylation site [posttranslational modification] 579112000856 intermolecular recognition site; other site 579112000857 dimerization interface [polypeptide binding]; other site 579112000858 guanosine pentaphosphate phosphohydrolase; Provisional; Region: PRK11031 579112000859 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 579112000860 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 579112000861 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 579112000862 ATP binding site [chemical binding]; other site 579112000863 Mg++ binding site [ion binding]; other site 579112000864 motif III; other site 579112000865 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 579112000866 nucleotide binding region [chemical binding]; other site 579112000867 ATP-binding site [chemical binding]; other site 579112000868 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 579112000869 catalytic residues [active] 579112000870 transcription termination factor Rho; Provisional; Region: rho; PRK09376 579112000871 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 579112000872 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...; Region: Rho_CSD; cd04459 579112000873 RNA binding site [nucleotide binding]; other site 579112000874 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of...; Region: rho_factor; cd01128 579112000875 multimer interface [polypeptide binding]; other site 579112000876 Walker A motif; other site 579112000877 ATP binding site [chemical binding]; other site 579112000878 Walker B motif; other site 579112000879 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 579112000880 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 579112000881 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 579112000882 catalytic loop [active] 579112000883 iron binding site [ion binding]; other site 579112000884 FMN reductase; Validated; Region: fre; PRK08051 579112000885 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD...; Region: flavin_oxioreductase; cd06189 579112000886 FAD binding pocket [chemical binding]; other site 579112000887 FAD binding motif [chemical binding]; other site 579112000888 phosphate binding motif [ion binding]; other site 579112000889 beta-alpha-beta structure motif; other site 579112000890 NAD binding pocket [chemical binding]; other site 579112000891 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 579112000892 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 579112000893 domain interface [polypeptide binding]; other site 579112000894 putative active site [active] 579112000895 catalytic site [active] 579112000896 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 579112000897 domain interface [polypeptide binding]; other site 579112000898 putative active site [active] 579112000899 catalytic site [active] 579112000900 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112000901 Coenzyme A binding pocket [chemical binding]; other site 579112000902 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 579112000903 FAD binding domain; Region: FAD_binding_4; pfam01565 579112000904 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 579112000905 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112000906 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 579112000907 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 579112000908 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 579112000909 pantothenate kinase; Provisional; Region: PRK05439 579112000910 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in...; Region: PanK; cd02025 579112000911 ATP-binding site [chemical binding]; other site 579112000912 CoA-binding site [chemical binding]; other site 579112000913 Mg2+-binding site [ion binding]; other site 579112000914 elongation factor Tu; Reviewed; Region: PRK00049 579112000915 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 579112000916 G1 box; other site 579112000917 GEF interaction site [polypeptide binding]; other site 579112000918 GTP/Mg2+ binding site [chemical binding]; other site 579112000919 Switch I region; other site 579112000920 G2 box; other site 579112000921 G3 box; other site 579112000922 Switch II region; other site 579112000923 G4 box; other site 579112000924 G5 box; other site 579112000925 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 579112000926 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 579112000927 Antibiotic Binding Site [chemical binding]; other site 579112000928 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 579112000929 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 579112000930 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 579112000931 putative homodimer interface [polypeptide binding]; other site 579112000932 KOW motif; Region: KOW; cl00354 579112000933 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 579112000934 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 579112000935 23S rRNA interface [nucleotide binding]; other site 579112000936 L7/L12 interface [polypeptide binding]; other site 579112000937 putative thiostrepton binding site; other site 579112000938 L25 interface [polypeptide binding]; other site 579112000939 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...; Region: Ribosomal_L1; cd00403 579112000940 mRNA/rRNA interface [nucleotide binding]; other site 579112000941 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...; Region: Ribosomal_L10; cd05797 579112000942 23S rRNA interface [nucleotide binding]; other site 579112000943 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 579112000944 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 579112000945 core dimer interface [polypeptide binding]; other site 579112000946 peripheral dimer interface [polypeptide binding]; other site 579112000947 L10 interface [polypeptide binding]; other site 579112000948 L11 interface [polypeptide binding]; other site 579112000949 putative EF-Tu interaction site [polypeptide binding]; other site 579112000950 putative EF-G interaction site [polypeptide binding]; other site 579112000951 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 579112000952 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 579112000953 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 579112000954 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 579112000955 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 579112000956 RPB11 interaction site [polypeptide binding]; other site 579112000957 RPB12 interaction site [polypeptide binding]; other site 579112000958 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 579112000959 RPB3 interaction site [polypeptide binding]; other site 579112000960 RPB1 interaction site [polypeptide binding]; other site 579112000961 RPB11 interaction site [polypeptide binding]; other site 579112000962 RPB10 interaction site [polypeptide binding]; other site 579112000963 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 579112000964 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 579112000965 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 579112000966 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 579112000967 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 579112000968 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 579112000969 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 579112000970 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 579112000971 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 579112000972 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 579112000973 DNA binding site [nucleotide binding] 579112000974 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 579112000975 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; Region: Rsd_AlgQ; cl11478 579112000976 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 579112000977 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 579112000978 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 579112000979 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 579112000980 putative NADH binding site [chemical binding]; other site 579112000981 putative active site [active] 579112000982 nudix motif; other site 579112000983 putative metal binding site [ion binding]; other site 579112000984 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 579112000985 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This...; Region: URO-D; cd00717 579112000986 substrate binding site [chemical binding]; other site 579112000987 active site 579112000988 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112000989 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112000990 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 579112000991 Peptidase family M23; Region: Peptidase_M23; pfam01551 579112000992 Sulfatase; Region: Sulfatase; cl10460 579112000993 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 579112000994 EamA-like transporter family; Region: EamA; cl01037 579112000995 EamA-like transporter family; Region: EamA; cl01037 579112000996 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 579112000997 transmembrane helices; other site 579112000998 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 579112000999 GTPase RsgA; Reviewed; Region: PRK12288 579112001000 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence...; Region: YjeQ_engC; cd01854 579112001001 GTPase/OB domain interface [polypeptide binding]; other site 579112001002 GTPase/Zn-binding domain interface [polypeptide binding]; other site 579112001003 GTP/Mg2+ binding site [chemical binding]; other site 579112001004 G4 box; other site 579112001005 G5 box; other site 579112001006 G1 box; other site 579112001007 Switch I region; other site 579112001008 G2 box; other site 579112001009 G3 box; other site 579112001010 Switch II region; other site 579112001011 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 579112001012 putative active site [active] 579112001013 putative substrate binding site [chemical binding]; other site 579112001014 catalytic site [active] 579112001015 dimer interface [polypeptide binding]; other site 579112001016 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 579112001017 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 579112001018 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 579112001019 Localisation of periplasmic protein complexes; Region: AMIN; pfam11741 579112001020 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 579112001021 active site 579112001022 metal binding site [ion binding]; metal-binding site 579112001023 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 579112001024 putative peptidoglycan binding site; other site 579112001025 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 579112001026 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 579112001027 putative peptidoglycan binding site; other site 579112001028 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 579112001029 putative peptidoglycan binding site; other site 579112001030 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 579112001031 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 579112001032 ATP binding site [chemical binding]; other site 579112001033 Mg2+ binding site [ion binding]; other site 579112001034 G-X-G motif; other site 579112001035 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 579112001036 ATP binding site [chemical binding]; other site 579112001037 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 579112001038 IPP transferase; Region: IPPT; cl00403 579112001039 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 579112001040 Sm1 motif; other site 579112001041 intra - hexamer interaction site; other site 579112001042 inter - hexamer interaction site [polypeptide binding]; other site 579112001043 nucleotide binding pocket [chemical binding]; other site 579112001044 Sm2 motif; other site 579112001045 GTPase HflX; Provisional; Region: PRK11058 579112001046 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 579112001047 G1 box; other site 579112001048 GTP/Mg2+ binding site [chemical binding]; other site 579112001049 Switch I region; other site 579112001050 G2 box; other site 579112001051 G3 box; other site 579112001052 Switch II region; other site 579112001053 G4 box; other site 579112001054 G5 box; other site 579112001055 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 579112001056 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 579112001057 HflK protein; Region: hflK; TIGR01933 579112001058 FtsH protease regulator HflC; Provisional; Region: PRK11029 579112001059 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 579112001060 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 579112001061 SlyX; Region: SlyX; cl01090 579112001062 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues...; Region: WD40; cl02567 579112001063 structural tetrad; other site 579112001064 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10902 579112001065 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 579112001066 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 579112001067 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 579112001068 YheO-like PAS domain; Region: PAS_6; pfam08348 579112001069 DsrE/DsrF-like family; Region: DrsE; cl00672 579112001070 DsrE/DsrF-like family; Region: DrsE; cl00672 579112001071 DsrE/DsrF-like family; Region: DrsE; cl00672 579112001072 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 579112001073 S17 interaction site [polypeptide binding]; other site 579112001074 S8 interaction site; other site 579112001075 16S rRNA interaction site [nucleotide binding]; other site 579112001076 streptomycin interaction site [chemical binding]; other site 579112001077 23S rRNA interaction site [nucleotide binding]; other site 579112001078 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 579112001079 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 579112001080 elongation factor G; Reviewed; Region: PRK00007 579112001081 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 579112001082 G1 box; other site 579112001083 putative GEF interaction site [polypeptide binding]; other site 579112001084 GTP/Mg2+ binding site [chemical binding]; other site 579112001085 Switch I region; other site 579112001086 G2 box; other site 579112001087 G3 box; other site 579112001088 Switch II region; other site 579112001089 G4 box; other site 579112001090 G5 box; other site 579112001091 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...; Region: EFG_mtEFG_II; cd04088 579112001092 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...; Region: EFG_mtEFG1_IV; cd01434 579112001093 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...; Region: EFG_mtEFG_C; cd03713 579112001094 elongation factor Tu; Reviewed; Region: PRK00049 579112001095 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 579112001096 G1 box; other site 579112001097 GEF interaction site [polypeptide binding]; other site 579112001098 GTP/Mg2+ binding site [chemical binding]; other site 579112001099 Switch I region; other site 579112001100 G2 box; other site 579112001101 G3 box; other site 579112001102 Switch II region; other site 579112001103 G4 box; other site 579112001104 G5 box; other site 579112001105 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 579112001106 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 579112001107 Antibiotic Binding Site [chemical binding]; other site 579112001108 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 579112001109 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 579112001110 Ferritin-like domain; Region: Ferritin; pfam00210 579112001111 heme binding site [chemical binding]; other site 579112001112 ferroxidase pore; other site 579112001113 ferroxidase diiron center [ion binding]; other site 579112001114 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 579112001115 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 579112001116 dimer interface [polypeptide binding]; other site 579112001117 ssDNA binding site [nucleotide binding]; other site 579112001118 tetramer (dimer of dimers) interface [polypeptide binding]; other site 579112001119 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 579112001120 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 579112001121 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 579112001122 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 579112001123 Protein of unknown function, DUF481; Region: DUF481; cl01213 579112001124 replicative DNA helicase; Provisional; Region: PRK08840 579112001125 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 579112001126 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 579112001127 Walker A motif; other site 579112001128 ATP binding site [chemical binding]; other site 579112001129 Walker B motif; other site 579112001130 DNA binding loops [nucleotide binding] 579112001131 alanine racemase; Reviewed; Region: alr; PRK00053 579112001132 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 579112001133 active site 579112001134 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 579112001135 substrate binding site [chemical binding]; other site 579112001136 catalytic residues [active] 579112001137 dimer interface [polypeptide binding]; other site 579112001138 Uncharacterised protein family UPF0047; Region: UPF0047; cl00439 579112001139 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 579112001140 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 579112001141 active site 579112001142 dimer interface [polypeptide binding]; other site 579112001143 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 579112001144 dimer interface [polypeptide binding]; other site 579112001145 active site 579112001146 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112001147 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 579112001148 CheC-like family; Region: CheC; pfam04509 579112001149 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 579112001150 metal binding site 2 [ion binding]; metal-binding site 579112001151 putative DNA binding helix; other site 579112001152 metal binding site 1 [ion binding]; metal-binding site 579112001153 dimer interface [polypeptide binding]; other site 579112001154 structural Zn2+ binding site [ion binding]; other site 579112001155 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 579112001156 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...; Region: DUS_like_FMN; cd02801 579112001157 FMN binding site [chemical binding]; other site 579112001158 active site 579112001159 catalytic residues [active] 579112001160 substrate binding site [chemical binding]; other site 579112001161 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 579112001162 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 579112001163 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 579112001164 FAD binding pocket [chemical binding]; other site 579112001165 FAD binding motif [chemical binding]; other site 579112001166 catalytic residues [active] 579112001167 NAD binding pocket [chemical binding]; other site 579112001168 phosphate binding motif [ion binding]; other site 579112001169 beta-alpha-beta structure motif; other site 579112001170 sulfite reductase subunit beta; Provisional; Region: PRK13504 579112001171 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 579112001172 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 579112001173 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 579112001174 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 579112001175 Active Sites [active] 579112001176 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 579112001177 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 579112001178 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 579112001179 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 579112001180 substrate binding pocket [chemical binding]; other site 579112001181 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 579112001182 B12 binding site [chemical binding]; other site 579112001183 cobalt ligand [ion binding]; other site 579112001184 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 579112001185 aspartate kinase III; Validated; Region: PRK09084 579112001186 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 579112001187 nucleotide binding site [chemical binding]; other site 579112001188 substrate binding site [chemical binding]; other site 579112001189 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_1; cd04932 579112001190 lysine allosteric regulatory site; other site 579112001191 dimer interface [polypeptide binding]; other site 579112001192 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 579112001193 dimer interface [polypeptide binding]; other site 579112001194 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 579112001195 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT), serine-...; Region: AGAT_like; cd06451 579112001196 homodimer interface [polypeptide binding]; other site 579112001197 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112001198 catalytic residue [active] 579112001199 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 579112001200 O-Antigen ligase; Region: Wzy_C; cl04850 579112001201 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 579112001202 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 579112001203 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 579112001204 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 579112001205 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 579112001206 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 579112001207 active site 579112001208 tetramer interface [polypeptide binding]; other site 579112001209 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 579112001210 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...; Region: LuxR_C_like; cd06170 579112001211 DNA binding residues [nucleotide binding] 579112001212 dimerization interface [polypeptide binding]; other site 579112001213 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 579112001214 dimer interface [polypeptide binding]; other site 579112001215 ssDNA binding site [nucleotide binding]; other site 579112001216 tetramer (dimer of dimers) interface [polypeptide binding]; other site 579112001217 regulatory protein CsrD; Provisional; Region: PRK11059 579112001218 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112001219 metal binding site [ion binding]; metal-binding site 579112001220 active site 579112001221 I-site; other site 579112001222 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 579112001223 Pilus assembly protein, PilO; Region: PilO; cl01234 579112001224 Type II secretory pathway, component PulD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulD; COG1450 579112001225 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 579112001226 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 579112001227 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 579112001228 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112001229 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 579112001230 binding surface 579112001231 TPR motif; other site 579112001232 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 579112001233 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 579112001234 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112001235 Walker A motif; other site 579112001236 ATP binding site [chemical binding]; other site 579112001237 Walker B motif; other site 579112001238 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 579112001239 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 579112001240 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 579112001241 legume lectins; Region: lectin_L-type; cl14058 579112001242 homotetramer interaction site [polypeptide binding]; other site 579112001243 homodimer interaction site [polypeptide binding]; other site 579112001244 carbohydrate binding site [chemical binding]; other site 579112001245 metal binding site [ion binding]; metal-binding site 579112001246 rod shape-determining protein MreB; Provisional; Region: PRK13927 579112001247 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 579112001248 ATP binding site [chemical binding]; other site 579112001249 profilin binding site; other site 579112001250 rod shape-determining protein MreC; Provisional; Region: PRK13922 579112001251 rod shape-determining protein MreC; Region: MreC; pfam04085 579112001252 rod shape-determining protein MreD; Region: MreD; cl01087 579112001253 Maf-like protein; Region: Maf; pfam02545 579112001254 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 579112001255 active site 579112001256 dimer interface [polypeptide binding]; other site 579112001257 ribonuclease G; Provisional; Region: PRK11712 579112001258 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 579112001259 homodimer interface [polypeptide binding]; other site 579112001260 oligonucleotide binding site [chemical binding]; other site 579112001261 TIGR02099 family protein; Region: TIGR02099 579112001262 Predicted amidohydrolase [General function prediction only]; Region: COG0388 579112001263 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 579112001264 putative active site [active] 579112001265 catalytic triad [active] 579112001266 dimer interface [polypeptide binding]; other site 579112001267 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 579112001268 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 579112001269 Amidinotransferase; Region: Amidinotransf; cl12043 579112001270 Arginine deiminase [Amino acid transport and metabolism]; Region: ArcA; COG2235 579112001271 Protein of unknown function (DUF1260); Region: DUF1260; cl01170 579112001272 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 579112001273 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 579112001274 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 579112001275 Ligand Binding Site [chemical binding]; other site 579112001276 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; cl09110 579112001277 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 579112001278 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 579112001279 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 579112001280 arginine repressor; Provisional; Region: PRK05066 579112001281 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 579112001282 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 579112001283 malate dehydrogenase; Provisional; Region: PRK05086 579112001284 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 579112001285 NAD binding site [chemical binding]; other site 579112001286 dimerization interface [polypeptide binding]; other site 579112001287 Substrate binding site [chemical binding]; other site 579112001288 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 579112001289 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 579112001290 octaprenyl diphosphate synthase; Provisional; Region: PRK10888 579112001291 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 579112001292 substrate binding pocket [chemical binding]; other site 579112001293 chain length determination region; other site 579112001294 substrate-Mg2+ binding site; other site 579112001295 catalytic residues [active] 579112001296 aspartate-rich region 1; other site 579112001297 active site lid residues [active] 579112001298 aspartate-rich region 2; other site 579112001299 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 579112001300 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 579112001301 GTPase CgtA; Reviewed; Region: obgE; PRK12298 579112001302 GTP1/OBG; Region: GTP1_OBG; pfam01018 579112001303 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 579112001304 G1 box; other site 579112001305 GTP/Mg2+ binding site [chemical binding]; other site 579112001306 Switch I region; other site 579112001307 G2 box; other site 579112001308 G3 box; other site 579112001309 Switch II region; other site 579112001310 G4 box; other site 579112001311 G5 box; other site 579112001312 Uncharacterized conserved protein [Function unknown]; Region: COG2966 579112001313 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 579112001314 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 579112001315 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 5,10-...; Region: DHFR; cd00209 579112001316 folate binding site [chemical binding]; other site 579112001317 NADP+ binding site [chemical binding]; other site 579112001318 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 579112001319 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 579112001320 active site 579112001321 metal binding site [ion binding]; metal-binding site 579112001322 Protein of unknown function (DUF525); Region: DUF525; cl01119 579112001323 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112001324 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 579112001325 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 579112001326 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 579112001327 SurA N-terminal domain; Region: SurA_N; pfam09312 579112001328 PPIC-type PPIASE domain; Region: Rotamase; cl08278 579112001329 PPIC-type PPIASE domain; Region: Rotamase; cl08278 579112001330 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 579112001331 OstA-like protein; Region: OstA; cl00844 579112001332 Organic solvent tolerance protein; Region: OstA_C; pfam04453 579112001333 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 579112001334 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 579112001335 putative metal binding site [ion binding]; other site 579112001336 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...; Region: DnaJ; cd06257 579112001337 HSP70 interaction site [polypeptide binding]; other site 579112001338 Cache domain; Region: Cache_2; cl07034 579112001339 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112001340 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112001341 murein transglycosylase C; Provisional; Region: mltC; PRK11671 579112001342 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 579112001343 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 579112001344 N-acetyl-D-glucosamine binding site [chemical binding]; other site 579112001345 catalytic residue [active] 579112001346 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 579112001347 adenine DNA glycosylase; Provisional; Region: PRK10880 579112001348 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 579112001349 minor groove reading motif; other site 579112001350 helix-hairpin-helix signature motif; other site 579112001351 substrate binding pocket [chemical binding]; other site 579112001352 active site 579112001353 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 579112001354 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 579112001355 DNA binding and oxoG recognition site [nucleotide binding] 579112001356 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112001357 Glutaminase; Region: Glutaminase; cl00907 579112001358 HemN family oxidoreductase; Provisional; Region: PRK05660 579112001359 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 579112001360 FeS/SAM binding site; other site 579112001361 HemN C-terminal region; Region: HemN_C; pfam06969 579112001362 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 Ham1-...; Region: HAM1; cd00515 579112001363 active site 579112001364 dimerization interface [polypeptide binding]; other site 579112001365 Uncharacterised ACR, YggU family COG1872; Region: DUF167; cl00811 579112001366 YGGT family; Region: YGGT; cl00508 579112001367 YGGT family; Region: YGGT; cl00508 579112001368 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 579112001369 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112001370 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 579112001371 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 579112001372 catalytic residue [active] 579112001373 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 579112001374 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 579112001375 Walker A motif; other site 579112001376 ATP binding site [chemical binding]; other site 579112001377 Walker B motif; other site 579112001378 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 579112001379 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 579112001380 Walker A motif; other site 579112001381 ATP binding site [chemical binding]; other site 579112001382 Walker B motif; other site 579112001383 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...; Region: LuxR_C_like; cd06170 579112001384 DNA binding residues [nucleotide binding] 579112001385 dimerization interface [polypeptide binding]; other site 579112001386 tyrosyl-tRNA synthetase; Provisional; Region: PRK13354 579112001387 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 579112001388 active site 579112001389 HIGH motif; other site 579112001390 dimer interface [polypeptide binding]; other site 579112001391 KMSKS motif; other site 579112001392 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 579112001393 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 579112001394 glutathione synthetase; Provisional; Region: PRK05246 579112001395 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 579112001396 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112001397 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 579112001398 Endonuclease I; Region: Endonuclease_1; cl01003 579112001399 DNA-specific endonuclease I; Provisional; Region: PRK15137 579112001400 SprT homologues; Region: SprT; cl01182 579112001401 SprT-like family; Region: SprT-like; pfam10263 579112001402 S-adenosylmethionine synthetase; Validated; Region: PRK05250 579112001403 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 579112001404 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 579112001405 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 579112001406 transketolase; Reviewed; Region: PRK12753 579112001407 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 579112001408 TPP-binding site [chemical binding]; other site 579112001409 dimer interface [polypeptide binding]; other site 579112001410 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 579112001411 PYR/PP interface [polypeptide binding]; other site 579112001412 dimer interface [polypeptide binding]; other site 579112001413 TPP binding site [chemical binding]; other site 579112001414 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 579112001415 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112001416 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112001417 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 579112001418 dimerization interface [polypeptide binding]; other site 579112001419 enterobactin receptor protein; Provisional; Region: PRK13483 579112001420 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112001421 N-terminal plug; other site 579112001422 ligand-binding site [chemical binding]; other site 579112001423 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 579112001424 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 579112001425 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 579112001426 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 579112001427 substrate binding site [chemical binding]; other site 579112001428 hinge regions; other site 579112001429 ADP binding site [chemical binding]; other site 579112001430 catalytic site [active] 579112001431 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 579112001432 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 579112001433 active site 579112001434 intersubunit interface [polypeptide binding]; other site 579112001435 zinc binding site [ion binding]; other site 579112001436 Na+ binding site [ion binding]; other site 579112001437 mechanosensitive channel MscS; Provisional; Region: PRK10334 579112001438 Conserved TM helix; Region: TM_helix; pfam05552 579112001439 Mechanosensitive ion channel; Region: MS_channel; pfam00924 579112001440 LysE type translocator; Region: LysE; cl00565 579112001441 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 579112001442 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112001443 The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; Region: PBP2_IciA_ArgP; cd08428 579112001444 putative dimerization interface [polypeptide binding]; other site 579112001445 Protein of unknown function (DUF541); Region: SIMPL; cl01077 579112001446 pyruvate kinase; Provisional; Region: PRK09206 579112001447 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; cd00288 579112001448 domain interfaces; other site 579112001449 active site 579112001450 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 579112001451 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112001452 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 579112001453 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 579112001454 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...; Region: GFAT; cd00714 579112001455 glutaminase active site [active] 579112001456 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 579112001457 dimer interface [polypeptide binding]; other site 579112001458 active site 579112001459 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 579112001460 dimer interface [polypeptide binding]; other site 579112001461 active site 579112001462 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 579112001463 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924; Region: LPLAT_ACT14924-like; cd07986 579112001464 putative acyl-acceptor binding pocket; other site 579112001465 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112001466 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 579112001467 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 579112001468 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 579112001469 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 579112001470 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 579112001471 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 579112001472 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...; Region: Sigma70_r4; cd06171 579112001473 DNA binding residues [nucleotide binding] 579112001474 DNA primase; Validated; Region: dnaG; PRK05667 579112001475 CHC2 zinc finger; Region: zf-CHC2; cl02597 579112001476 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 579112001477 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 579112001478 active site 579112001479 metal binding site [ion binding]; metal-binding site 579112001480 interdomain interaction site; other site 579112001481 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 579112001482 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 579112001483 GatB domain; Region: GatB_Yqey; cl11497 579112001484 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 579112001485 UGMP family protein; Validated; Region: PRK09604 579112001486 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 579112001487 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 579112001488 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 579112001489 Domain of unknown function (DUF205); Region: DUF205; cl00410 579112001490 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines...; Region: DHNA_DHNTPE; cd00534 579112001491 homooctamer interface [polypeptide binding]; other site 579112001492 active site 579112001493 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 579112001494 catalytic center binding site [active] 579112001495 ATP binding site [chemical binding]; other site 579112001496 Bacitracin resistance protein BacA; Region: BacA; cl00858 579112001497 Septum formation initiator; Region: DivIC; cl11433 579112001498 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 579112001499 substrate binding site [chemical binding]; other site 579112001500 dimer interface [polypeptide binding]; other site 579112001501 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...; Region: MECDP_synthase; cd00554 579112001502 homotrimer interaction site [polypeptide binding]; other site 579112001503 zinc binding site [ion binding]; other site 579112001504 CDP-binding sites; other site 579112001505 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 579112001506 PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_EcTruD; cd02575 579112001507 Permutation of conserved domain; other site 579112001508 active site 579112001509 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 579112001510 Survival protein SurE; Region: SurE; cl00448 579112001511 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112001512 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 579112001513 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 579112001514 putative peptidoglycan binding site; other site 579112001515 Peptidase family M23; Region: Peptidase_M23; pfam01551 579112001516 RNA polymerase sigma factor RpoS; Validated; Region: PRK05657 579112001517 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 579112001518 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 579112001519 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 579112001520 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...; Region: Sigma70_r4; cd06171 579112001521 DNA binding residues [nucleotide binding] 579112001522 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 579112001523 MutS domain I; Region: MutS_I; pfam01624 579112001524 MutS domain II; Region: MutS_II; pfam05188 579112001525 MutS family domain IV; Region: MutS_IV; pfam05190 579112001526 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 579112001527 Walker A/P-loop; other site 579112001528 ATP binding site [chemical binding]; other site 579112001529 Q-loop/lid; other site 579112001530 ABC transporter signature motif; other site 579112001531 Walker B; other site 579112001532 D-loop; other site 579112001533 H-loop/switch region; other site 579112001534 cysteine synthases; Region: cysKM; TIGR01136 579112001535 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 579112001536 dimer interface [polypeptide binding]; other site 579112001537 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112001538 catalytic residue [active] 579112001539 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 579112001540 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 579112001541 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...; Region: TM_PBP2; cd06261 579112001542 dimer interface [polypeptide binding]; other site 579112001543 conserved gate region; other site 579112001544 putative PBP binding loops; other site 579112001545 ABC-ATPase subunit interface; other site 579112001546 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...; Region: TM_PBP2; cd06261 579112001547 dimer interface [polypeptide binding]; other site 579112001548 conserved gate region; other site 579112001549 putative PBP binding loops; other site 579112001550 ABC-ATPase subunit interface; other site 579112001551 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 579112001552 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-...; Region: ABC_CysA_sulfate_importer; cd03296 579112001553 Walker A/P-loop; other site 579112001554 ATP binding site [chemical binding]; other site 579112001555 Q-loop/lid; other site 579112001556 ABC transporter signature motif; other site 579112001557 Walker B; other site 579112001558 D-loop; other site 579112001559 H-loop/switch region; other site 579112001560 TOBE-like domain; Region: TOBE_3; pfam12857 579112001561 Competence-damaged protein; Region: CinA; cl00666 579112001562 recombinase A; Provisional; Region: recA; PRK09354 579112001563 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 579112001564 hexamer interface [polypeptide binding]; other site 579112001565 Walker A motif; other site 579112001566 ATP binding site [chemical binding]; other site 579112001567 Walker B motif; other site 579112001568 RecX family; Region: RecX; cl00936 579112001569 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 579112001570 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation...; Region: AlaRS_core; cd00673 579112001571 motif 1; other site 579112001572 active site 579112001573 motif 2; other site 579112001574 motif 3; other site 579112001575 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 579112001576 DHHA1 domain; Region: DHHA1; pfam02272 579112001577 aspartate kinase; Validated; Region: PRK08841 579112001578 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 579112001579 putative nucleotide binding site [chemical binding]; other site 579112001580 putative catalytic residues [active] 579112001581 putative Mg ion binding site [ion binding]; other site 579112001582 putative aspartate binding site [chemical binding]; other site 579112001583 Global regulator protein family; Region: CsrA; cl00670 579112001584 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; cl01458 579112001585 oxaloacetate decarboxylase; Provisional; Region: PRK14040 579112001586 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 579112001587 active site 579112001588 catalytic residues [active] 579112001589 metal binding site [ion binding]; metal-binding site 579112001590 homodimer binding site [polypeptide binding]; other site 579112001591 Conserved carboxylase domain; Region: PYC_OADA; pfam02436 579112001592 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 579112001593 carboxyltransferase (CT) interaction site; other site 579112001594 biotinylation site [posttranslational modification]; other site 579112001595 subunit; Region: OAD_beta; cl00816 579112001596 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 579112001597 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 579112001598 putative NAD(P) binding site [chemical binding]; other site 579112001599 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 579112001600 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 579112001601 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 579112001602 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 579112001603 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 579112001604 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 579112001605 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 579112001606 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl01099 579112001607 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 579112001608 hypothetical protein; Provisional; Region: PRK11573 579112001609 Domain of unknown function DUF21; Region: DUF21; pfam01595 579112001610 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 579112001611 Transporter associated domain; Region: CorC_HlyC; cl08393 579112001612 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 579112001613 signal recognition particle protein; Provisional; Region: PRK10867 579112001614 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 579112001615 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 579112001616 P loop; other site 579112001617 GTP binding site [chemical binding]; other site 579112001618 Signal peptide binding domain; Region: SRP_SPB; pfam02978 579112001619 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 579112001620 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 579112001621 RimM N-terminal domain; Region: RimM; pfam01782 579112001622 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 579112001623 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 579112001624 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 579112001625 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 579112001626 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 579112001627 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 C-...; Region: PDZ_serine_protease; cd00987 579112001628 protein binding site [polypeptide binding]; other site 579112001629 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 579112001630 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 579112001631 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 C-...; Region: PDZ_serine_protease; cd00987 579112001632 protein binding site [polypeptide binding]; other site 579112001633 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 C-...; Region: PDZ_serine_protease; cd00987 579112001634 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 579112001635 AFG1-like ATPase; Region: AFG1_ATPase; pfam03969 579112001636 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 579112001637 23S rRNA interface [nucleotide binding]; other site 579112001638 L3 interface [polypeptide binding]; other site 579112001639 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 579112001640 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 579112001641 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 579112001642 [2Fe-2S] cluster binding site [ion binding]; other site 579112001643 cytochrome b; Provisional; Region: CYTB; MTH00145 579112001644 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cd00284 579112001645 Qi binding site; other site 579112001646 intrachain domain interface; other site 579112001647 interchain domain interface [polypeptide binding]; other site 579112001648 heme bH binding site [chemical binding]; other site 579112001649 heme bL binding site [chemical binding]; other site 579112001650 Qo binding site; other site 579112001651 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: cytochrome_b_C; cd00290 579112001652 interchain domain interface [polypeptide binding]; other site 579112001653 intrachain domain interface; other site 579112001654 Qi binding site; other site 579112001655 Qo binding site; other site 579112001656 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 579112001657 stringent starvation protein A; Provisional; Region: sspA; PRK09481 579112001658 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 579112001659 C-terminal domain interface [polypeptide binding]; other site 579112001660 putative GSH binding site (G-site) [chemical binding]; other site 579112001661 dimer interface [polypeptide binding]; other site 579112001662 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 579112001663 dimer interface [polypeptide binding]; other site 579112001664 N-terminal domain interface [polypeptide binding]; other site 579112001665 Stringent starvation protein B; Region: SspB; cl01120 579112001666 BON domain; Region: BON; cl02771 579112001667 BON domain; Region: BON; cl02771 579112001668 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 579112001669 dimer interface [polypeptide binding]; other site 579112001670 active site 579112001671 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 579112001672 LppC putative lipoprotein; Region: LppC; pfam04348 579112001673 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 579112001674 putative ligand binding site [chemical binding]; other site 579112001675 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 579112001676 Predicted methyltransferases [General function prediction only]; Region: COG0313 579112001677 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112001678 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112001679 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 579112001680 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 579112001681 active site clefts [active] 579112001682 zinc binding site [ion binding]; other site 579112001683 dimer interface [polypeptide binding]; other site 579112001684 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 579112001685 Sulfate transporter family; Region: Sulfate_transp; cl00967 579112001686 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 579112001687 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 579112001688 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112001689 Walker A/P-loop; other site 579112001690 ATP binding site [chemical binding]; other site 579112001691 Q-loop/lid; other site 579112001692 ABC transporter signature motif; other site 579112001693 Walker B; other site 579112001694 D-loop; other site 579112001695 H-loop/switch region; other site 579112001696 ABC-2 type transporter; Region: ABC2_membrane; cl11417 579112001697 pantoate--beta-alanine ligase; Region: panC; TIGR00018 579112001698 Pantoate-beta-alanine ligase; Region: PanC; cd00560 579112001699 active site 579112001700 ATP-binding site [chemical binding]; other site 579112001701 pantoate-binding site; other site 579112001702 HXXH motif; other site 579112001703 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 579112001704 oligomerization interface [polypeptide binding]; other site 579112001705 active site 579112001706 metal binding site [ion binding]; metal-binding site 579112001707 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 579112001708 catalytic center binding site [active] 579112001709 ATP binding site [chemical binding]; other site 579112001710 poly(A) polymerase I; Provisional; Region: pcnB; PRK11623 579112001711 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 579112001712 active site 579112001713 NTP binding site [chemical binding]; other site 579112001714 metal binding triad [ion binding]; metal-binding site 579112001715 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 579112001716 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 579112001717 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 579112001718 active site 579112001719 nucleotide binding site [chemical binding]; other site 579112001720 HIGH motif; other site 579112001721 KMSKS motif; other site 579112001722 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 579112001723 Sugar fermentation stimulation protein; Region: SfsA; cl00647 579112001724 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 579112001725 Transglycosylase; Region: Transgly; cl07896 579112001726 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 579112001727 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 579112001728 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 579112001729 active site 579112001730 nucleophile elbow; other site 579112001731 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 579112001732 Surface antigen; Region: Bac_surface_Ag; cl03097 579112001733 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 579112001734 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change...; Region: AcnB_Swivel; cd01576 579112001735 substrate binding site [chemical binding]; other site 579112001736 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 579112001737 substrate binding site [chemical binding]; other site 579112001738 ligand binding site [chemical binding]; other site 579112001739 Uncharacterised protein family (UPF0231); Region: UPF0231; cl11474 579112001740 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 579112001741 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 579112001742 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 579112001743 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 579112001744 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...; Region: TM_PBP2; cd06261 579112001745 dimer interface [polypeptide binding]; other site 579112001746 conserved gate region; other site 579112001747 putative PBP binding loops; other site 579112001748 ABC-ATPase subunit interface; other site 579112001749 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...; Region: TM_PBP2; cl00427 579112001750 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 579112001751 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 579112001752 Walker A/P-loop; other site 579112001753 ATP binding site [chemical binding]; other site 579112001754 Q-loop/lid; other site 579112001755 ABC transporter signature motif; other site 579112001756 Walker B; other site 579112001757 D-loop; other site 579112001758 H-loop/switch region; other site 579112001759 TOBE domain; Region: TOBE_2; cl01440 579112001760 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 579112001761 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a...; Region: PGM_like2; cd05800 579112001762 active site 579112001763 substrate binding site [chemical binding]; other site 579112001764 metal binding site [ion binding]; metal-binding site 579112001765 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 579112001766 Putative carbohydrate binding domain; Region: CBM_X; cl05621 579112001767 Glycosyltransferase family 36; Region: Glyco_transf_36; pfam06165 579112001768 Glycosyltransferase 36 associated family; Region: GT36_AF; pfam06205 579112001769 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i); Region: GH20_chitobiase-like; cd06563 579112001770 active site 579112001771 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 579112001772 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 579112001773 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 579112001774 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 579112001775 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112001776 Walker A/P-loop; other site 579112001777 ATP binding site [chemical binding]; other site 579112001778 Q-loop/lid; other site 579112001779 ABC transporter signature motif; other site 579112001780 Walker B; other site 579112001781 D-loop; other site 579112001782 H-loop/switch region; other site 579112001783 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112001784 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 579112001785 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112001786 Walker A/P-loop; other site 579112001787 ATP binding site [chemical binding]; other site 579112001788 Q-loop/lid; other site 579112001789 ABC transporter signature motif; other site 579112001790 Walker B; other site 579112001791 D-loop; other site 579112001792 H-loop/switch region; other site 579112001793 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112001794 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...; Region: TM_PBP2; cd06261 579112001795 dimer interface [polypeptide binding]; other site 579112001796 conserved gate region; other site 579112001797 putative PBP binding loops; other site 579112001798 ABC-ATPase subunit interface; other site 579112001799 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 579112001800 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...; Region: TM_PBP2; cd06261 579112001801 dimer interface [polypeptide binding]; other site 579112001802 conserved gate region; other site 579112001803 putative PBP binding loops; other site 579112001804 ABC-ATPase subunit interface; other site 579112001805 The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold; Region: PBP2_TmCBP_oligosaccharides_like; cd08509 579112001806 substrate binding site [chemical binding]; other site 579112001807 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 579112001808 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 579112001809 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 connected by an extended linker. The...; Region: HAMP; cd06225 579112001810 dimerization interface [polypeptide binding]; other site 579112001811 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 trans-...; Region: HisKA; cd00082 579112001812 dimer interface [polypeptide binding]; other site 579112001813 phosphorylation site [posttranslational modification] 579112001814 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 579112001815 ATP binding site [chemical binding]; other site 579112001816 Mg2+ binding site [ion binding]; other site 579112001817 G-X-G motif; other site 579112001818 Response regulator receiver domain; Region: Response_reg; pfam00072 579112001819 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112001820 active site 579112001821 phosphorylation site [posttranslational modification] 579112001822 intermolecular recognition site; other site 579112001823 dimerization interface [polypeptide binding]; other site 579112001824 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112001825 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 579112001826 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 579112001827 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 579112001828 S-adenosylmethionine binding site [chemical binding]; other site 579112001829 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 579112001830 Domain of unknown function DUF20; Region: UPF0118; cl00465 579112001831 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 579112001832 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 579112001833 inhibitor-cofactor binding pocket; inhibition site 579112001834 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112001835 catalytic residue [active] 579112001836 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 579112001837 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 579112001838 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 579112001839 putative peptidase; Provisional; Region: PRK11649 579112001840 Peptidase family M23; Region: Peptidase_M23; pfam01551 579112001841 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 579112001842 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 579112001843 active site 579112001844 HIGH motif; other site 579112001845 dimer interface [polypeptide binding]; other site 579112001846 KMSKS motif; other site 579112001847 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 579112001848 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl15297 579112001849 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 579112001850 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface...; Region: gram_neg_porins; cd00342 579112001851 trimer interface [polypeptide binding]; other site 579112001852 eyelet of channel; other site 579112001853 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 579112001854 domain; Region: GreA_GreB_N; pfam03449 579112001855 C-term; Region: GreA_GreB; pfam01272 579112001856 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 579112001857 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 579112001858 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 579112001859 S-adenosylmethionine binding site [chemical binding]; other site 579112001860 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 579112001861 FtsH Extracellular; Region: FtsH_ext; pfam06480 579112001862 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...; Region: AAA; cd00009 579112001863 Walker A motif; other site 579112001864 ATP binding site [chemical binding]; other site 579112001865 Walker B motif; other site 579112001866 arginine finger; other site 579112001867 Peptidase family M41; Region: Peptidase_M41; pfam01434 579112001868 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 579112001869 dihydropteroate synthase; Region: DHPS; TIGR01496 579112001870 substrate binding pocket [chemical binding]; other site 579112001871 dimer interface [polypeptide binding]; other site 579112001872 inhibitor binding site; inhibition site 579112001873 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 579112001874 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 UDP-N-...; Region: GlmM; cd05802 579112001875 active site 579112001876 substrate binding site [chemical binding]; other site 579112001877 metal binding site [ion binding]; metal-binding site 579112001878 Preprotein translocase SecG subunit; Region: SecG; cl09123 579112001879 ribosome maturation protein RimP; Reviewed; Region: PRK00092 579112001880 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 579112001881 Sm1 motif; other site 579112001882 predicted subunit interaction site [polypeptide binding]; other site 579112001883 RNA binding pocket [nucleotide binding]; other site 579112001884 Sm2 motif; other site 579112001885 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 579112001886 NusA N-terminal domain; Region: NusA_N; pfam08529 579112001887 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...; Region: S1_NusA; cd04455 579112001888 RNA binding site [nucleotide binding]; other site 579112001889 homodimer interface [polypeptide binding]; other site 579112001890 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 579112001891 G-X-X-G motif; other site 579112001892 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 579112001893 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 579112001894 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 579112001895 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 579112001896 translation initiation factor IF-2; Region: IF-2; TIGR00487 579112001897 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 579112001898 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 579112001899 G1 box; other site 579112001900 putative GEF interaction site [polypeptide binding]; other site 579112001901 GTP/Mg2+ binding site [chemical binding]; other site 579112001902 Switch I region; other site 579112001903 G2 box; other site 579112001904 G3 box; other site 579112001905 Switch II region; other site 579112001906 G4 box; other site 579112001907 G5 box; other site 579112001908 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...; Region: IF2_mtIF2_II; cd03702 579112001909 Translation-initiation factor 2; Region: IF-2; pfam11987 579112001910 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...; Region: mtIF2_IVc; cd03692 579112001911 Ribosome-binding factor A; Region: RBFA; cl00542 579112001912 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 579112001913 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 579112001914 RNA binding site [nucleotide binding]; other site 579112001915 active site 579112001916 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...; Region: Ribosomal_S15p_S13e; cd00353 579112001917 16S/18S rRNA binding site [nucleotide binding]; other site 579112001918 S13e-L30e interaction site [polypeptide binding]; other site 579112001919 25S rRNA binding site [nucleotide binding]; other site 579112001920 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 579112001921 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 579112001922 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 579112001923 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 579112001924 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 579112001925 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 579112001926 putative nucleic acid binding region [nucleotide binding]; other site 579112001927 G-X-X-G motif; other site 579112001928 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 579112001929 RNA binding site [nucleotide binding]; other site 579112001930 domain interface; other site 579112001931 lipoprotein NlpI; Provisional; Region: PRK11189 579112001932 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 579112001933 binding surface 579112001934 TPR motif; other site 579112001935 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112001936 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 579112001937 MatE; Region: MatE; cl10513 579112001938 MatE; Region: MatE; cl10513 579112001939 Peptidase family U32; Region: Peptidase_U32; cl03113 579112001940 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 579112001941 Peptidase family U32; Region: Peptidase_U32; cl03113 579112001942 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112001943 PAS domain S-box; Region: sensory_box; TIGR00229 579112001944 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112001945 metal binding site [ion binding]; metal-binding site 579112001946 active site 579112001947 I-site; other site 579112001948 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 579112001949 SCP-2 sterol transfer family; Region: SCP2; cl01225 579112001950 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112001951 Coenzyme A binding pocket [chemical binding]; other site 579112001952 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 579112001953 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 579112001954 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112001955 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112001956 metal binding site [ion binding]; metal-binding site 579112001957 active site 579112001958 I-site; other site 579112001959 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 579112001960 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 579112001961 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 579112001962 G1 box; other site 579112001963 putative GEF interaction site [polypeptide binding]; other site 579112001964 GTP/Mg2+ binding site [chemical binding]; other site 579112001965 Switch I region; other site 579112001966 G2 box; other site 579112001967 G3 box; other site 579112001968 Switch II region; other site 579112001969 G4 box; other site 579112001970 G5 box; other site 579112001971 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 579112001972 helicase 45; Provisional; Region: PTZ00424 579112001973 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 579112001974 ATP binding site [chemical binding]; other site 579112001975 Mg++ binding site [ion binding]; other site 579112001976 motif III; other site 579112001977 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 579112001978 nucleotide binding region [chemical binding]; other site 579112001979 ATP-binding site [chemical binding]; other site 579112001980 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 579112001981 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 579112001982 S-adenosylmethionine binding site [chemical binding]; other site 579112001983 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 579112001984 peptide chain release factor 2; Provisional; Region: PRK08787 579112001985 RF-1 domain; Region: RF-1; cl02875 579112001986 RF-1 domain; Region: RF-1; cl02875 579112001987 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 579112001988 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-...; Region: LysRS_N; cd04322 579112001989 dimer interface [polypeptide binding]; other site 579112001990 putative anticodon binding site; other site 579112001991 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 579112001992 motif 1; other site 579112001993 active site 579112001994 motif 2; other site 579112001995 motif 3; other site 579112001996 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 579112001997 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...; Region: AAA; cd00009 579112001998 Walker A motif; other site 579112001999 ATP binding site [chemical binding]; other site 579112002000 Walker B motif; other site 579112002001 arginine finger; other site 579112002002 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112002003 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 579112002004 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...; Region: Aldo_ket_red; cd06660 579112002005 active site 579112002006 catalytic tetrad [active] 579112002007 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex; Region: MutH_Sau3AI; cd00583 579112002008 putative DNA-binding cleft [nucleotide binding]; other site 579112002009 putative DNA clevage site; other site 579112002010 molecular lever; other site 579112002011 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where...; Region: Ap4A_hydrolase_plant_like; cd03671 579112002012 putative active site [active] 579112002013 Ap4A binding site [chemical binding]; other site 579112002014 nudix motif; other site 579112002015 putative metal binding site [ion binding]; other site 579112002016 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 579112002017 GAF domain; Region: GAF; cl00853 579112002018 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 579112002019 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 579112002020 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 579112002021 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 579112002022 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 579112002023 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 579112002024 dimerization interface [polypeptide binding]; other site 579112002025 active site 579112002026 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 579112002027 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 579112002028 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 579112002029 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112002030 The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; Region: PBP2_NhaR; cd08429 579112002031 putative dimerization interface [polypeptide binding]; other site 579112002032 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 579112002033 dimerization interface [polypeptide binding]; other site 579112002034 putative DNA binding site [nucleotide binding]; other site 579112002035 putative Zn2+ binding site [ion binding]; other site 579112002036 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 579112002037 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 579112002038 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 579112002039 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 579112002040 active site 579112002041 Riboflavin kinase; Region: Flavokinase; cl03312 579112002042 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 579112002043 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 579112002044 active site 579112002045 HIGH motif; other site 579112002046 nucleotide binding site [chemical binding]; other site 579112002047 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 579112002048 active site 579112002049 KMSKS motif; other site 579112002050 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 579112002051 tRNA binding surface [nucleotide binding]; other site 579112002052 anticodon binding site; other site 579112002053 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 579112002054 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 579112002055 lipoprotein signal peptidase; Provisional; Region: PRK14787 579112002056 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 579112002057 LytB protein; Region: LYTB; cl00507 579112002058 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 579112002059 Carbon starvation protein CstA; Region: CstA; cl00856 579112002060 lipoprotein; Provisional; Region: PRK11443 579112002061 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 579112002062 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 579112002063 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112002064 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: PRK12570 579112002065 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 579112002066 putative active site [active] 579112002067 Uncharacterised protein family (UPF0075); Region: UPF0075; cl04217 579112002068 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 579112002069 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 579112002070 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112002071 active site 579112002072 phosphorylation site [posttranslational modification] 579112002073 intermolecular recognition site; other site 579112002074 dimerization interface [polypeptide binding]; other site 579112002075 LytTr DNA-binding domain; Region: LytTR; cl04498 579112002076 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 579112002077 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 579112002078 GAF domain; Region: GAF; cl00853 579112002079 Histidine kinase; Region: His_kinase; pfam06580 579112002080 NeuB family; Region: NeuB; cl00496 579112002081 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 579112002082 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 579112002083 Chorismate mutase type II; Region: CM_2; cl00693 579112002084 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112002085 PilZ domain; Region: PilZ; cl01260 579112002086 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 579112002087 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112002088 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112002089 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112002090 ABC transporter; Region: ABC_tran_2; pfam12848 579112002091 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112002092 Trp repressor protein; Region: Trp_repressor; cl01121 579112002093 Protein of unknown function DUF84; Region: NTPase_I-T; cl00866 579112002094 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112002095 metal binding site [ion binding]; metal-binding site 579112002096 active site 579112002097 I-site; other site 579112002098 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 579112002099 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 579112002100 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 579112002101 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 579112002102 Chorismate mutase type II; Region: CM_2; cl00693 579112002103 Prephenate dehydratase; Region: PDT; pfam00800 579112002104 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 579112002105 putative L-Phe binding site [chemical binding]; other site 579112002106 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site...; Region: RaiA; cd00552 579112002107 30S subunit binding site; other site 579112002108 outer membrane biogenesis protein BamD; Provisional; Region: PRK10866 579112002109 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 579112002110 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 579112002111 RNA binding surface [nucleotide binding]; other site 579112002112 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 579112002113 active site 579112002114 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 579112002115 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 579112002116 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 579112002117 Clp amino terminal domain; Region: Clp_N; pfam02861 579112002118 Clp amino terminal domain; Region: Clp_N; pfam02861 579112002119 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...; Region: AAA; cd00009 579112002120 Walker A motif; other site 579112002121 ATP binding site [chemical binding]; other site 579112002122 Walker B motif; other site 579112002123 arginine finger; other site 579112002124 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...; Region: AAA; cd00009 579112002125 Walker A motif; other site 579112002126 ATP binding site [chemical binding]; other site 579112002127 Walker B motif; other site 579112002128 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 579112002129 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 579112002130 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH...; Region: NfsA_FRP; cd02146 579112002131 dimer interface [polypeptide binding]; other site 579112002132 FMN binding site [chemical binding]; other site 579112002133 NADPH bind site [chemical binding]; other site 579112002134 hypothetical protein; Provisional; Region: PRK13795 579112002135 putative protease; Provisional; Region: PRK15452 579112002136 Peptidase family U32; Region: Peptidase_U32; cl03113 579112002137 Putative exonuclease, RdgC; Region: RdgC; cl01122 579112002138 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 579112002139 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112002140 active site 579112002141 phosphorylation site [posttranslational modification] 579112002142 intermolecular recognition site; other site 579112002143 dimerization interface [polypeptide binding]; other site 579112002144 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...; Region: trans_reg_C; cd00383 579112002145 DNA binding site [nucleotide binding] 579112002146 phosphate regulon sensor protein; Provisional; Region: phoR; PRK11006 579112002147 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 579112002148 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112002149 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 trans-...; Region: HisKA; cd00082 579112002150 dimer interface [polypeptide binding]; other site 579112002151 phosphorylation site [posttranslational modification] 579112002152 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 579112002153 ATP binding site [chemical binding]; other site 579112002154 Mg2+ binding site [ion binding]; other site 579112002155 G-X-G motif; other site 579112002156 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 579112002157 exopolyphosphatase; Provisional; Region: PRK10854 579112002158 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 579112002159 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 579112002160 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 579112002161 domain interface [polypeptide binding]; other site 579112002162 active site 579112002163 catalytic site [active] 579112002164 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 579112002165 domain interface [polypeptide binding]; other site 579112002166 active site 579112002167 catalytic site [active] 579112002168 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 579112002169 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...; Region: TM_PBP2; cd06261 579112002170 ABC-ATPase subunit interface; other site 579112002171 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 579112002172 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...; Region: TM_PBP2; cd06261 579112002173 dimer interface [polypeptide binding]; other site 579112002174 conserved gate region; other site 579112002175 putative PBP binding loops; other site 579112002176 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...; Region: TM_PBP2; cl00427 579112002177 ABC-ATPase subunit interface; other site 579112002178 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 579112002179 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 579112002180 Walker A/P-loop; other site 579112002181 ATP binding site [chemical binding]; other site 579112002182 Q-loop/lid; other site 579112002183 ABC transporter signature motif; other site 579112002184 Walker B; other site 579112002185 D-loop; other site 579112002186 H-loop/switch region; other site 579112002187 transcriptional regulator PhoU; Provisional; Region: PRK11115 579112002188 PhoU domain; Region: PhoU; pfam01895 579112002189 PhoU domain; Region: PhoU; pfam01895 579112002190 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 579112002191 CutC family; Region: CutC; cl01218 579112002192 peroxidase; Provisional; Region: PRK15000 579112002193 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic...; Region: PRX_Typ2cys; cd03015 579112002194 dimer interface [polypeptide binding]; other site 579112002195 decamer (pentamer of dimers) interface [polypeptide binding]; other site 579112002196 catalytic triad [active] 579112002197 peroxidatic and resolving cysteines [active] 579112002198 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 579112002199 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112002200 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 579112002201 dimerization interface [polypeptide binding]; other site 579112002202 malate synthase A; Region: malate_syn_A; TIGR01344 579112002203 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 579112002204 active site 579112002205 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 579112002206 tetramer interface [polypeptide binding]; other site 579112002207 active site 579112002208 Mg2+/Mn2+ binding site [ion binding]; other site 579112002209 FOG: CBS domain [General function prediction only]; Region: COG0517 579112002210 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-...; Region: CBS_pair; cl09141 579112002211 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 579112002212 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 579112002213 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 579112002214 Preprotein translocase subunit; Region: YajC; cl00806 579112002215 EnvZ/OmpR regulon moderator; Provisional; Region: PRK10629 579112002216 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 579112002217 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 579112002218 Protein export membrane protein; Region: SecD_SecF; cl14618 579112002219 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 579112002220 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 579112002221 Protein export membrane protein; Region: SecD_SecF; cl14618 579112002222 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 579112002223 active site 579112002224 dimerization interface [polypeptide binding]; other site 579112002225 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 579112002226 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 579112002227 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112002228 Rrf2 family protein; Region: rrf2_super; TIGR00738 579112002229 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 579112002230 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 579112002231 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112002232 catalytic residue [active] 579112002233 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 579112002234 trimerization site [polypeptide binding]; other site 579112002235 active site 579112002236 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 579112002237 co-chaperone HscB; Provisional; Region: hscB; PRK05014 579112002238 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...; Region: DnaJ; cd06257 579112002239 HSP70 interaction site [polypeptide binding]; other site 579112002240 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 579112002241 chaperone protein HscA; Provisional; Region: hscA; PRK05183 579112002242 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 579112002243 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 579112002244 catalytic loop [active] 579112002245 iron binding site [ion binding]; other site 579112002246 Protein of unknown function (DUF528); Region: DUF528; cl01123 579112002247 aminopeptidase B; Provisional; Region: PRK05015 579112002248 Peptidase; Region: DUF3663; pfam12404 579112002249 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 579112002250 interface (dimer of trimers) [polypeptide binding]; other site 579112002251 Substrate-binding/catalytic site; other site 579112002252 Zn-binding sites [ion binding]; other site 579112002253 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 579112002254 active site 579112002255 multimer interface [polypeptide binding]; other site 579112002256 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 579112002257 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; cl15259 579112002258 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 579112002259 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112002260 cytoskeletal protein RodZ; Provisional; Region: PRK10856 579112002261 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 579112002262 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 579112002263 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 579112002264 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 579112002265 dimer interface [polypeptide binding]; other site 579112002266 motif 1; other site 579112002267 active site 579112002268 motif 2; other site 579112002269 motif 3; other site 579112002270 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 579112002271 anticodon binding site; other site 579112002272 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 579112002273 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 579112002274 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 579112002275 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 579112002276 Trp docking motif; other site 579112002277 GTP-binding protein Der; Reviewed; Region: PRK00093 579112002278 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 579112002279 G1 box; other site 579112002280 GTP/Mg2+ binding site [chemical binding]; other site 579112002281 Switch I region; other site 579112002282 G2 box; other site 579112002283 Switch II region; other site 579112002284 G3 box; other site 579112002285 G4 box; other site 579112002286 G5 box; other site 579112002287 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 579112002288 G1 box; other site 579112002289 GTP/Mg2+ binding site [chemical binding]; other site 579112002290 Switch I region; other site 579112002291 G2 box; other site 579112002292 G3 box; other site 579112002293 Switch II region; other site 579112002294 G4 box; other site 579112002295 G5 box; other site 579112002296 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 579112002297 Protein of unknown function (DUF1407); Region: DUF1407; pfam07191 579112002298 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 579112002299 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 single-strand-...; Region: ExoVII_LU_OBF; cd04489 579112002300 generic binding surface II; other site 579112002301 generic binding surface I; other site 579112002302 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 579112002303 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 579112002304 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 579112002305 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the...; Region: IMPDH; cd00381 579112002306 active site 579112002307 GMP synthase; Reviewed; Region: guaA; PRK00074 579112002308 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 579112002309 AMP/PPi binding site [chemical binding]; other site 579112002310 candidate oxyanion hole; other site 579112002311 catalytic triad [active] 579112002312 potential glutamine specificity residues [chemical binding]; other site 579112002313 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 579112002314 ATP Binding subdomain [chemical binding]; other site 579112002315 Ligand Binding sites [chemical binding]; other site 579112002316 Dimerization subdomain; other site 579112002317 Glycoside hydrolase family 19 chitinase domain. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Family 19 chitinases are found primarily in plants (classes I, III, and IV), but...; Region: chitinase_glyco_hydro_19; cd00325 579112002318 putative sugar binding site [chemical binding]; other site 579112002319 catalytic residues [active] 579112002320 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 579112002321 chitin/cellulose binding site [chemical binding]; other site 579112002322 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 579112002323 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in...; Region: isochorismatase; cd01013 579112002324 hydrophobic substrate binding pocket; other site 579112002325 Isochorismatase family; Region: Isochorismatase; pfam00857 579112002326 active site 579112002327 conserved cis-peptide bond; other site 579112002328 Phosphopantetheine attachment site; Region: PP-binding; cl09936 579112002329 2,3-dihydroxybenzoate-AMP ligase; Region: DHB_AMP_lig; TIGR02275 579112002330 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112002331 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 579112002332 chorismate binding enzyme; Region: Chorismate_bind; cl10555 579112002333 2,3-dihydroxybenzoate-2,3-dehydrogenase; Validated; Region: PRK08220 579112002334 2,3 dihydro-2,3 dihydrozybenzoate dehydrogenases, classical (c) SDRs; Region: DH-DHB-DH_SDR_c; cd05331 579112002335 putative NAD(P) binding site [chemical binding]; other site 579112002336 active site 579112002337 Condensation domain; Region: Condensation; cl09290 579112002338 peptide synthase; Provisional; Region: PRK12316 579112002339 iron-enterobactin transporter periplasmic binding protein; Provisional; Region: PRK10957 579112002340 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor...; Region: FhuD; cd01146 579112002341 siderophore binding site; other site 579112002342 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112002343 ABC-ATPase subunit interface; other site 579112002344 dimer interface [polypeptide binding]; other site 579112002345 putative PBP binding regions; other site 579112002346 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 579112002347 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112002348 ABC-ATPase subunit interface; other site 579112002349 dimer interface [polypeptide binding]; other site 579112002350 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 579112002351 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 579112002352 Walker A/P-loop; other site 579112002353 ATP binding site [chemical binding]; other site 579112002354 Q-loop/lid; other site 579112002355 ABC transporter signature motif; other site 579112002356 Walker B; other site 579112002357 D-loop; other site 579112002358 H-loop/switch region; other site 579112002359 Phosphopantetheinyl transferase component of siderophore synthetase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntD; COG2977 579112002360 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 579112002361 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 579112002362 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112002363 The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; Region: PBP2_LeuO; cd08466 579112002364 putative substrate binding pocket [chemical binding]; other site 579112002365 putative dimerization interface [polypeptide binding]; other site 579112002366 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 579112002367 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112002368 SCP-2 sterol transfer family; Region: SCP2; cl01225 579112002369 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 579112002370 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 579112002371 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 579112002372 DNA-binding transcriptional regulator DsdC; Provisional; Region: PRK10086 579112002373 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112002374 HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 579112002375 dimerization interface [polypeptide binding]; other site 579112002376 substrate binding pocket [chemical binding]; other site 579112002377 Dopa 4,5-dioxygenase family; Region: DOPA_dioxygen; cl01562 579112002378 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 579112002379 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112002380 active site 579112002381 phosphorylation site [posttranslational modification] 579112002382 intermolecular recognition site; other site 579112002383 dimerization interface [polypeptide binding]; other site 579112002384 Transcriptional regulator; Region: CitT; pfam12431 579112002385 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 579112002386 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112002387 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 579112002388 ATP binding site [chemical binding]; other site 579112002389 Mg2+ binding site [ion binding]; other site 579112002390 G-X-G motif; other site 579112002391 subunit; Region: OAD_beta; cl00816 579112002392 oxaloacetate decarboxylase; Provisional; Region: PRK14040 579112002393 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 579112002394 active site 579112002395 catalytic residues [active] 579112002396 metal binding site [ion binding]; metal-binding site 579112002397 homodimer binding site [polypeptide binding]; other site 579112002398 Conserved carboxylase domain; Region: PYC_OADA; pfam02436 579112002399 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 579112002400 carboxyltransferase (CT) interaction site; other site 579112002401 biotinylation site [posttranslational modification]; other site 579112002402 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; cl01458 579112002403 2-hydroxycarboxylate transporter family; Region: 2HCT; cl01386 579112002404 Citrate lyase synthetase [Energy production and conversion]; Region: CitC; COG3053 579112002405 Citrate lyase ligase; Region: Citrate_lyase_ligase; cd02169 579112002406 putative active site [active] 579112002407 (T/H)XGH motif; other site 579112002408 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 579112002409 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 579112002410 Citrate lyase, alpha subunit (CitF); Region: CitF; pfam04223 579112002411 Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; Region: CitX; cl01498 579112002412 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 579112002413 ACT domain; Region: ACT_3; cl01447 579112002414 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 579112002415 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 579112002416 Ferredoxin [Energy production and conversion]; Region: COG1146 579112002417 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 579112002418 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 579112002419 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112002420 Uncharacterized conserved protein [Function unknown]; Region: COG4715 579112002421 SWIM zinc finger; Region: SWIM; cl11618 579112002422 Nuclease-related domain; Region: NERD; pfam08378 579112002423 Predicted HKD family nuclease [DNA replication, recombination, and repair]; Region: COG3886 579112002424 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 579112002425 putative homodimer interface [polypeptide binding]; other site 579112002426 putative active site [active] 579112002427 catalytic site [active] 579112002428 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 579112002429 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 579112002430 ATP binding site [chemical binding]; other site 579112002431 putative Mg++ binding site [ion binding]; other site 579112002432 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 579112002433 nucleotide binding region [chemical binding]; other site 579112002434 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112002435 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112002436 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 579112002437 HipA-like N-terminal domain; Region: HipA_N; pfam07805 579112002438 HipA-like C-terminal domain; Region: HipA_C; pfam07804 579112002439 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 579112002440 Integrase core domain; Region: rve; cl01316 579112002441 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II and Staphylococcus aureus AldA1 (SACOL0154)-like; Region: ALDH_ACDHII_AcoD-like; cd07559 579112002442 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 579112002443 NAD(P) binding site [chemical binding]; other site 579112002444 catalytic residues [active] 579112002445 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; cl00065 579112002446 Peptidase M66; Region: Peptidase_M66; pfam10462 579112002447 ToxR activated gene A lipoprotein; Region: TagA; pfam12561 579112002448 ToxR activated gene A lipoprotein; Region: TagA; pfam12561 579112002449 Beta/Gamma crystallin; Region: Crystall; cl02528 579112002450 Beta/Gamma crystallin; Region: Crystall; cl02528 579112002451 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 579112002452 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 579112002453 dimer interface [polypeptide binding]; other site 579112002454 catalytic triad [active] 579112002455 peroxidatic and resolving cysteines [active] 579112002456 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112002457 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112002458 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112002459 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112002460 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 579112002461 Toxin-coregulated pilus subunit TcpA; Region: TcpA; pfam05946 579112002462 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 579112002463 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 579112002464 Type II/IV secretion system protein; Region: GSPII_E; pfam00437 579112002465 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112002466 Walker A motif; other site 579112002467 ATP binding site [chemical binding]; other site 579112002468 Walker B motif; other site 579112002469 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 579112002470 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 579112002471 Vibrio cholerae toxin co-regulated pilus biosynthesis protein F; Region: TcpF; pfam06340 579112002472 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112002473 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112002474 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 579112002475 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 579112002476 Cache domain; Region: Cache_1; pfam02743 579112002477 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112002478 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112002479 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112002480 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 579112002481 RDD family; Region: RDD; cl00746 579112002482 Peptidase family M23; Region: Peptidase_M23; pfam01551 579112002483 Surface antigen; Region: Surface_Ag_2; cl01155 579112002484 integrase; Provisional; Region: PRK09692 579112002485 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 579112002486 active site 579112002487 Int/Topo IB signature motif; other site 579112002488 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 579112002489 SmpB-tmRNA interface; other site 579112002490 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 579112002491 putative coenzyme Q binding site [chemical binding]; other site 579112002492 Uncharacterised protein family (UPF0125); Region: UPF0125; cl01096 579112002493 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 579112002494 recombination and repair protein; Provisional; Region: PRK10869 579112002495 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 579112002496 Walker A/P-loop; other site 579112002497 ATP binding site [chemical binding]; other site 579112002498 Q-loop/lid; other site 579112002499 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 579112002500 ABC transporter signature motif; other site 579112002501 Walker B; other site 579112002502 D-loop; other site 579112002503 H-loop/switch region; other site 579112002504 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 579112002505 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 579112002506 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 579112002507 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 579112002508 dimer interface [polypeptide binding]; other site 579112002509 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 579112002510 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 579112002511 chaperone protein DnaJ; Provisional; Region: PRK10767 579112002512 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...; Region: DnaJ; cd06257 579112002513 HSP70 interaction site [polypeptide binding]; other site 579112002514 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 579112002515 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 579112002516 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 579112002517 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 579112002518 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 579112002519 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 579112002520 Type II transport protein GspH; Region: GspH; pfam12019 579112002521 hypothetical protein; Provisional; Region: PRK10557 579112002522 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 579112002523 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 579112002524 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; cl09110 579112002525 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 579112002526 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 579112002527 nucleoside/Zn binding site; other site 579112002528 dimer interface [polypeptide binding]; other site 579112002529 catalytic motif [active] 579112002530 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 579112002531 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...; Region: PBPb; cd00134 579112002532 substrate binding pocket [chemical binding]; other site 579112002533 membrane-bound complex binding site; other site 579112002534 hinge residues; other site 579112002535 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 579112002536 N-acetyl-D-glucosamine binding site [chemical binding]; other site 579112002537 catalytic residue [active] 579112002538 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 579112002539 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 579112002540 dimerization interface [polypeptide binding]; other site 579112002541 ATP binding site [chemical binding]; other site 579112002542 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...; Region: PurM-like; cl10019 579112002543 dimerization interface [polypeptide binding]; other site 579112002544 ATP binding site [chemical binding]; other site 579112002545 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 579112002546 putative active site [active] 579112002547 catalytic triad [active] 579112002548 Transposase IS200 like; Region: Y1_Tnp; cl00848 579112002549 Uncharacterised protein family (UPF0253); Region: UPF0253; cl11640 579112002550 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 579112002551 putative metal binding site [ion binding]; other site 579112002552 prolyl-tRNA synthetase; Provisional; Region: PRK09194 579112002553 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation...; Region: ProRS_core_prok; cd00779 579112002554 dimer interface [polypeptide binding]; other site 579112002555 motif 1; other site 579112002556 active site 579112002557 motif 2; other site 579112002558 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and single-...; Region: ProRS-INS; cd04334 579112002559 putative deacylase active site [active] 579112002560 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 579112002561 active site 579112002562 motif 3; other site 579112002563 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-...; Region: ProRS_anticodon_short; cd00861 579112002564 anticodon binding site; other site 579112002565 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 579112002566 homodimer interaction site [polypeptide binding]; other site 579112002567 cofactor binding site; other site 579112002568 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 579112002569 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 579112002570 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; cl09110 579112002571 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 579112002572 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 579112002573 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112002574 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 579112002575 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 579112002576 Domain of unknown function, DUF446; Region: DUF446; cl01187 579112002577 tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not...; Region: PseudoU_synth_TruC; cd02563 579112002578 probable active site [active] 579112002579 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 579112002580 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 with important pharmaceutical activity. DXS...; Region: TPP_DXS; cd02007 579112002581 TPP-binding site; other site 579112002582 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 579112002583 PYR/PP interface [polypeptide binding]; other site 579112002584 dimer interface [polypeptide binding]; other site 579112002585 TPP binding site [chemical binding]; other site 579112002586 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 579112002587 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 579112002588 substrate binding pocket [chemical binding]; other site 579112002589 chain length determination region; other site 579112002590 substrate-Mg2+ binding site; other site 579112002591 catalytic residues [active] 579112002592 aspartate-rich region 1; other site 579112002593 active site lid residues [active] 579112002594 aspartate-rich region 2; other site 579112002595 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 579112002596 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 579112002597 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 579112002598 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 579112002599 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 579112002600 ligand binding site [chemical binding]; other site 579112002601 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 579112002602 THUMP domain; Region: THUMP; cl12076 579112002603 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 579112002604 Ligand Binding Site [chemical binding]; other site 579112002605 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 579112002606 active site residue [active] 579112002607 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 579112002608 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112002609 HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 579112002610 dimerization interface [polypeptide binding]; other site 579112002611 substrate binding pocket [chemical binding]; other site 579112002612 Protein of unknown function (DUF423); Region: DUF423; cl01008 579112002613 flap endonuclease-like protein; Provisional; Region: PRK09482 579112002614 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 579112002615 active site 579112002616 metal binding site 1 [ion binding]; metal-binding site 579112002617 putative 5' ssDNA interaction site; other site 579112002618 metal binding site 3; metal-binding site 579112002619 metal binding site 2 [ion binding]; metal-binding site 579112002620 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 579112002621 putative DNA binding site [nucleotide binding]; other site 579112002622 putative metal binding site [ion binding]; other site 579112002623 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 579112002624 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 579112002625 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112002626 metal binding site [ion binding]; metal-binding site 579112002627 active site 579112002628 I-site; other site 579112002629 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 579112002630 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 579112002631 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 579112002632 Syd protein; Region: Syd; cl06405 579112002633 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 579112002634 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 579112002635 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...; Region: TM_PBP2; cd06261 579112002636 dimer interface [polypeptide binding]; other site 579112002637 conserved gate region; other site 579112002638 ABC-ATPase subunit interface; other site 579112002639 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 579112002640 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein; Region: ABC_MetN_methionine_transporter; cd03258 579112002641 Walker A/P-loop; other site 579112002642 ATP binding site [chemical binding]; other site 579112002643 Q-loop/lid; other site 579112002644 ABC transporter signature motif; other site 579112002645 Walker B; other site 579112002646 D-loop; other site 579112002647 H-loop/switch region; other site 579112002648 NIL domain; Region: NIL; cl09633 579112002649 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 579112002650 active site 579112002651 motif I; other site 579112002652 motif II; other site 579112002653 trehalose repressor; Provisional; Region: treR; PRK09492 579112002654 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112002655 DNA binding site [nucleotide binding] 579112002656 domain linker motif; other site 579112002657 Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_TreR_like; cd01542 579112002658 dimerization interface [polypeptide binding]; other site 579112002659 ligand binding site [chemical binding]; other site 579112002660 PTS system trehalose(maltose)-specific transporter subunits IIBC; Provisional; Region: PRK11007 579112002661 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...; Region: PTS_IIB_glc; cd00212 579112002662 active site turn [active] 579112002663 phosphorylation site [posttranslational modification] 579112002664 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112002665 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 579112002666 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 579112002667 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 579112002668 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 579112002669 Low molecular weight phosphatase family; Region: LMWPc; cd00115 579112002670 Active site [active] 579112002671 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 579112002672 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues...; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 579112002673 active site 579112002674 homodimer interface [polypeptide binding]; other site 579112002675 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 579112002676 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112002677 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 579112002678 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112002679 Serine acetyltransferase [Amino acid transport and metabolism]; Region: CysE; COG1045 579112002680 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 L-...; Region: LbH_SAT; cd03354 579112002681 trimer interface [polypeptide binding]; other site 579112002682 active site 579112002683 substrate binding site [chemical binding]; other site 579112002684 CoA binding site [chemical binding]; other site 579112002685 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 579112002686 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 579112002687 MatE; Region: MatE; cl10513 579112002688 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 579112002689 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 L-...; Region: LbH_SAT; cd03354 579112002690 trimer interface [polypeptide binding]; other site 579112002691 active site 579112002692 substrate binding site [chemical binding]; other site 579112002693 CoA binding site [chemical binding]; other site 579112002694 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112002695 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 579112002696 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 579112002697 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 579112002698 Jacalin-like lectin domain; Region: Jacalin_like; cl03205 579112002699 putative sugar binding site [chemical binding]; other site 579112002700 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 579112002701 O-Antigen ligase; Region: Wzy_C; cl04850 579112002702 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 579112002703 Bacterial sugar transferase; Region: Bac_transf; cl00939 579112002704 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 579112002705 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 579112002706 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 579112002707 SLBB domain; Region: SLBB; pfam10531 579112002708 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 579112002709 Chain length determinant protein; Region: Wzz; cl01623 579112002710 Chain length determinant protein; Region: Wzz; cl01623 579112002711 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 579112002712 VanZ like family; Region: VanZ; cl01971 579112002713 Uncharacterized conserved protein [Function unknown]; Region: COG1284 579112002714 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 579112002715 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...; Region: SHMT; cd00378 579112002716 dimer interface [polypeptide binding]; other site 579112002717 glycine-pyridoxal phosphate binding site [chemical binding]; other site 579112002718 active site 579112002719 folate binding site [chemical binding]; other site 579112002720 lipoyl synthase; Provisional; Region: PRK05481 579112002721 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; cl15259 579112002722 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 579112002723 Protein of unknown function (DUF493); Region: DUF493; cl01102 579112002724 Beta-lactamase; Region: Beta-lactamase; cl01009 579112002725 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 579112002726 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 579112002727 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 579112002728 rare lipoprotein A; Region: rlpA; TIGR00413 579112002729 Sporulation related domain; Region: SPOR; cl10051 579112002730 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 579112002731 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 579112002732 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 579112002733 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 579112002734 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 579112002735 Domain of unknown function DUF143; Region: DUF143; cl00519 579112002736 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 579112002737 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 579112002738 Lipopolysaccharide-assembly; Region: LptE; cl01125 579112002739 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 579112002740 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 579112002741 HIGH motif; other site 579112002742 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 579112002743 active site 579112002744 KMSKS motif; other site 579112002745 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 579112002746 tRNA binding surface [nucleotide binding]; other site 579112002747 hypothetical protein; Provisional; Region: PRK11032 579112002748 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 579112002749 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 579112002750 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 579112002751 putative active site [active] 579112002752 catalytic triad [active] 579112002753 putative dimer interface [polypeptide binding]; other site 579112002754 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 579112002755 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 579112002756 Transporter associated domain; Region: CorC_HlyC; cl08393 579112002757 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 579112002758 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 579112002759 PhoH-like protein; Region: PhoH; cl12134 579112002760 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 579112002761 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 579112002762 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 579112002763 FeS/SAM binding site; other site 579112002764 TRAM domain; Region: TRAM; cl01282 579112002765 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed; Region: ubiF; PRK08020 579112002766 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112002767 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_glc; cd00210 579112002768 HPr interaction site; other site 579112002769 glycerol kinase (GK) interaction site [polypeptide binding]; other site 579112002770 active site 579112002771 phosphorylation site [posttranslational modification] 579112002772 phosphoenolpyruvate-protein phosphotransferase; Provisional; Region: PRK11177 579112002773 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 579112002774 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 579112002775 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 579112002776 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 579112002777 dimerization domain swap beta strand [polypeptide binding]; other site 579112002778 regulatory protein interface [polypeptide binding]; other site 579112002779 active site 579112002780 regulatory phosphorylation site [posttranslational modification]; other site 579112002781 cysteine synthases; Region: cysKM; TIGR01136 579112002782 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 579112002783 dimer interface [polypeptide binding]; other site 579112002784 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112002785 catalytic residue [active] 579112002786 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 579112002787 cell division protein ZipA; Provisional; Region: PRK04335 579112002788 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cd00231 579112002789 FtsZ protein binding site [polypeptide binding]; other site 579112002790 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 579112002791 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 579112002792 nucleotide binding pocket [chemical binding]; other site 579112002793 K-X-D-G motif; other site 579112002794 catalytic site [active] 579112002795 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 579112002796 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 579112002797 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 579112002798 Dimer interface [polypeptide binding]; other site 579112002799 BRCT sequence motif; other site 579112002800 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface...; Region: gram_neg_porins; cd00342 579112002801 trimer interface [polypeptide binding]; other site 579112002802 eyelet of channel; other site 579112002803 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 579112002804 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 579112002805 DNA binding residues [nucleotide binding] 579112002806 dimer interface [polypeptide binding]; other site 579112002807 copper binding site [ion binding]; other site 579112002808 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 579112002809 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 579112002810 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 579112002811 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 579112002812 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 579112002813 Foie gras liver health family 1; Region: Foie-gras_1; pfam11817 579112002814 short chain dehydrogenase; Provisional; Region: PRK05693 579112002815 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 579112002816 NADP binding site [chemical binding]; other site 579112002817 active site 579112002818 steroid binding site; other site 579112002819 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 579112002820 TIGR01777 family protein; Region: yfcH 579112002821 putative NAD(P) binding site [chemical binding]; other site 579112002822 putative active site [active] 579112002823 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 579112002824 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 579112002825 active site 579112002826 metal binding site [ion binding]; metal-binding site 579112002827 homotetramer interface [polypeptide binding]; other site 579112002828 Rdx family; Region: Rdx; cl01407 579112002829 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...; Region: trans_reg_C; cd00383 579112002830 DNA binding site [nucleotide binding] 579112002831 heat shock protein 90; Provisional; Region: PRK05218 579112002832 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 579112002833 adenylate kinase; Reviewed; Region: adk; PRK00279 579112002834 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 579112002835 AMP-binding site [chemical binding]; other site 579112002836 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 579112002837 ferrochelatase; Reviewed; Region: hemH; PRK00035 579112002838 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 579112002839 C-terminal domain interface [polypeptide binding]; other site 579112002840 active site 579112002841 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 579112002842 active site 579112002843 N-terminal domain interface [polypeptide binding]; other site 579112002844 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; cl11420 579112002845 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 579112002846 transcriptional activator RfaH; Provisional; Region: rfaH; PRK09014 579112002847 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 579112002848 KOW motif; Region: KOW; cl00354 579112002849 asparagine synthetase B; Provisional; Region: asnB; PRK09431 579112002850 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 579112002851 active site 579112002852 dimer interface [polypeptide binding]; other site 579112002853 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...; Region: Asn_Synthase_B_C; cd01991 579112002854 Ligand Binding Site [chemical binding]; other site 579112002855 Molecular Tunnel; other site 579112002856 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 579112002857 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 579112002858 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112002859 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112002860 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 579112002861 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 579112002862 N-acetylglucosamine-6-phosphate deacetylase; Region: nagA; TIGR00221 579112002863 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 579112002864 active site 579112002865 dimer interface [polypeptide binding]; other site 579112002866 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 579112002867 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112002868 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...; Region: PTS_IIB_glc; cd00212 579112002869 active site turn [active] 579112002870 phosphorylation site [posttranslational modification] 579112002871 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 579112002872 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 579112002873 active site 579112002874 HIGH motif; other site 579112002875 nucleotide binding site [chemical binding]; other site 579112002876 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 579112002877 KMSKS motif; other site 579112002878 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 579112002879 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 579112002880 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 579112002881 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 579112002882 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 579112002883 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1)...; Region: PseudoU_synth_EcTruA; cd02570 579112002884 dimerization interface 3.5A [polypeptide binding]; other site 579112002885 active site 579112002886 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 579112002887 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 579112002888 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 579112002889 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 579112002890 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DedD; COG3147 579112002891 Sporulation related domain; Region: SPOR; cl10051 579112002892 Colicin V production protein; Region: Colicin_V; cl00567 579112002893 amidophosphoribosyltransferase; Provisional; Region: PRK09246 579112002894 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 579112002895 active site 579112002896 tetramer interface [polypeptide binding]; other site 579112002897 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 579112002898 Predicted permease [General function prediction only]; Region: COG2056 579112002899 GntP family permease; Region: GntP_permease; cl15264 579112002900 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; cl09110 579112002901 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 579112002902 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 579112002903 dimer interface [polypeptide binding]; other site 579112002904 putative active site [active] 579112002905 putative substrate binding site [chemical binding]; other site 579112002906 catalytic site [active] 579112002907 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 579112002908 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 579112002909 ligand binding site [chemical binding]; other site 579112002910 Protein of unknown function (DUF2753); Region: DUF2753; pfam10952 579112002911 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 579112002912 dimer interface [polypeptide binding]; other site 579112002913 active site 579112002914 metal binding site [ion binding]; metal-binding site 579112002915 glutathione binding site [chemical binding]; other site 579112002916 endonuclease III; Provisional; Region: PRK10702 579112002917 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 579112002918 minor groove reading motif; other site 579112002919 helix-hairpin-helix signature motif; other site 579112002920 substrate binding pocket [chemical binding]; other site 579112002921 active site 579112002922 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 579112002923 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 579112002924 FMN-binding domain; Region: FMN_bind; cl01081 579112002925 RnfE family; Region: NQR2_RnfD_RnfE; cl00779 579112002926 C subunit; Region: rnfC; TIGR01945 579112002927 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 579112002928 SLBB domain; Region: SLBB; pfam10531 579112002929 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 alpha-; Region: HCP_like; cl14655 579112002930 electron transport complex protein RnfC; Provisional; Region: PRK05035 579112002931 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]; Region: COG2878 579112002932 Putative Fe-S cluster; Region: FeS; pfam04060 579112002933 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 579112002934 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 579112002935 excinuclease ABC subunit B; Provisional; Region: PRK05298 579112002936 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 579112002937 ATP binding site [chemical binding]; other site 579112002938 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 579112002939 nucleotide binding region [chemical binding]; other site 579112002940 ATP-binding site [chemical binding]; other site 579112002941 Ultra-violet resistance protein B; Region: UvrB; pfam12344 579112002942 UvrB/uvrC motif; Region: UVR; pfam02151 579112002943 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 579112002944 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112002945 active site 579112002946 phosphorylation site [posttranslational modification] 579112002947 intermolecular recognition site; other site 579112002948 dimerization interface [polypeptide binding]; other site 579112002949 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...; Region: AAA; cd00009 579112002950 Walker A motif; other site 579112002951 ATP binding site [chemical binding]; other site 579112002952 Walker B motif; other site 579112002953 arginine finger; other site 579112002954 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112002955 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 579112002956 Uncharacterised protein family UPF0052; Region: UPF0052; pfam01933 579112002957 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 579112002958 phosphate binding site [ion binding]; other site 579112002959 putative substrate binding pocket [chemical binding]; other site 579112002960 dimer interface [polypeptide binding]; other site 579112002961 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 579112002962 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 579112002963 FeS/SAM binding site; other site 579112002964 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 579112002965 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 579112002966 MPT binding site; other site 579112002967 trimer interface [polypeptide binding]; other site 579112002968 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...; Region: MoaC_PE; cd01420 579112002969 trimer interface [polypeptide binding]; other site 579112002970 dimer interface [polypeptide binding]; other site 579112002971 putative active site [active] 579112002972 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 579112002973 MoaE interaction surface [polypeptide binding]; other site 579112002974 MoeB interaction surface [polypeptide binding]; other site 579112002975 thiocarboxylated glycine; other site 579112002976 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 579112002977 MoaE homodimer interface [polypeptide binding]; other site 579112002978 MoaD interaction [polypeptide binding]; other site 579112002979 active site residues [active] 579112002980 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112002981 metal binding site [ion binding]; metal-binding site 579112002982 active site 579112002983 I-site; other site 579112002984 FOG: CBS domain [General function prediction only]; Region: COG0517 579112002985 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-...; Region: CBS_pair_16; cd04629 579112002986 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 579112002987 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 579112002988 metal-binding site [ion binding] 579112002989 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 579112002990 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; cl11391 579112002991 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 579112002992 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 579112002993 Domain of unknown function (DUF3377); Region: DUF3377; pfam11857 579112002994 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 579112002995 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 579112002996 active site 579112002997 HIGH motif; other site 579112002998 KMSKS motif; other site 579112002999 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 579112003000 tRNA binding surface [nucleotide binding]; other site 579112003001 anticodon binding site; other site 579112003002 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 579112003003 dimer interface [polypeptide binding]; other site 579112003004 putative tRNA-binding site [nucleotide binding]; other site 579112003005 antiporter inner membrane protein; Provisional; Region: PRK11670 579112003006 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 579112003007 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 579112003008 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage...; Region: UMPK; cd02023 579112003009 ATP-binding site [chemical binding]; other site 579112003010 Sugar specificity; other site 579112003011 Pyrimidine base specificity; other site 579112003012 AsmA family; Region: AsmA; pfam05170 579112003013 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112003014 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 579112003015 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a...; Region: CobA_CobO_BtuR; cd00561 579112003016 homodimer interface [polypeptide binding]; other site 579112003017 Walker A motif; other site 579112003018 ATP binding site [chemical binding]; other site 579112003019 hydroxycobalamin binding site [chemical binding]; other site 579112003020 Walker B motif; other site 579112003021 Low molecular weight phosphatase family; Region: LMWPc; cd00115 579112003022 Active site [active] 579112003023 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 579112003024 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 579112003025 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 579112003026 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 579112003027 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 579112003028 RNA polymerase sigma factor; Provisional; Region: PRK12517 579112003029 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 579112003030 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112003031 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 579112003032 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 579112003033 dimer interface [polypeptide binding]; other site 579112003034 active site 579112003035 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 579112003036 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 579112003037 substrate binding site [chemical binding]; other site 579112003038 oxyanion hole (OAH) forming residues; other site 579112003039 trimer interface [polypeptide binding]; other site 579112003040 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 579112003041 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 579112003042 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a beta-...; Region: Arsenite_oxidase; cd02135 579112003043 putative FMN binding site [chemical binding]; other site 579112003044 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112003045 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112003046 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112003047 putative effector binding pocket; other site 579112003048 dimerization interface [polypeptide binding]; other site 579112003049 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003050 active site 579112003051 response regulator of RpoS; Provisional; Region: PRK10693 579112003052 phosphorylation site [posttranslational modification] 579112003053 intermolecular recognition site; other site 579112003054 dimerization interface [polypeptide binding]; other site 579112003055 Protein of unknown function (DUF454); Region: DUF454; cl01063 579112003056 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 579112003057 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 579112003058 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...; Region: AAA; cd00009 579112003059 Walker A motif; other site 579112003060 ATP binding site [chemical binding]; other site 579112003061 Walker B motif; other site 579112003062 arginine finger; other site 579112003063 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 579112003064 DNA polymerase III subunits tau domain IV DnaB-binding; Region: DNA_pol3_tau_4; pfam12168 579112003065 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 579112003066 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 579112003067 recombination protein RecR; Reviewed; Region: recR; PRK00076 579112003068 RecR protein; Region: RecR; pfam02132 579112003069 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 579112003070 putative active site [active] 579112003071 putative metal-binding site [ion binding]; other site 579112003072 tetramer interface [polypeptide binding]; other site 579112003073 Flagellin N-methylase; Region: FliB; cl00497 579112003074 Flagellin N-methylase; Region: FliB; cl00497 579112003075 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112003076 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 579112003077 NAD(P) binding site [chemical binding]; other site 579112003078 active site 579112003079 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 579112003080 putative inner membrane peptidase; Provisional; Region: PRK11778 579112003081 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 579112003082 tandem repeat interface [polypeptide binding]; other site 579112003083 oligomer interface [polypeptide binding]; other site 579112003084 active site residues [active] 579112003085 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 579112003086 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cl00342 579112003087 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112003088 catalytic residue [active] 579112003089 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 579112003090 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 579112003091 putative DNA binding site [nucleotide binding]; other site 579112003092 putative Zn2+ binding site [ion binding]; other site 579112003093 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112003094 acyl-CoA thioesterase II; Provisional; Region: PRK10526 579112003095 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 579112003096 active site 579112003097 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 579112003098 catalytic triad [active] 579112003099 dimer interface [polypeptide binding]; other site 579112003100 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3126 579112003101 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 579112003102 DNA binding site [nucleotide binding] 579112003103 active site 579112003104 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...; Region: PBPb; cd00134 579112003105 substrate binding pocket [chemical binding]; other site 579112003106 membrane-bound complex binding site; other site 579112003107 hinge residues; other site 579112003108 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...; Region: PBPb; cd00134 579112003109 substrate binding pocket [chemical binding]; other site 579112003110 membrane-bound complex binding site; other site 579112003111 hinge residues; other site 579112003112 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112003113 metal binding site [ion binding]; metal-binding site 579112003114 active site 579112003115 I-site; other site 579112003116 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 579112003117 dimerization interface [polypeptide binding]; other site 579112003118 putative DNA binding site [nucleotide binding]; other site 579112003119 putative Zn2+ binding site [ion binding]; other site 579112003120 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 579112003121 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 579112003122 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 579112003123 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (; Region: PTPc; cl00053 579112003124 active site 579112003125 catalytic residues [active] 579112003126 Major Facilitator Superfamily; Region: MFS_1; pfam07690 579112003127 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 579112003128 Cellulose binding domain; Region: CBM_2; cl02709 579112003129 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 579112003130 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is...; Region: GH18_chitinase; cd06548 579112003131 active site 579112003132 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 579112003133 Chitinase C; Region: ChiC; pfam06483 579112003134 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 579112003135 CAAX amino terminal protease self- immunity; Region: Abi; cl00558 579112003136 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 579112003137 substrate binding site [chemical binding]; other site 579112003138 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112003139 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 579112003140 SUA5 domain; Region: SUA5; pfam03481 579112003141 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 579112003142 putative binding surface; other site 579112003143 active site 579112003144 Response regulator receiver domain; Region: Response_reg; pfam00072 579112003145 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003146 active site 579112003147 phosphorylation site [posttranslational modification] 579112003148 intermolecular recognition site; other site 579112003149 dimerization interface [polypeptide binding]; other site 579112003150 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112003151 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003152 Response regulator receiver domain; Region: Response_reg; pfam00072 579112003153 active site 579112003154 phosphorylation site [posttranslational modification] 579112003155 intermolecular recognition site; other site 579112003156 dimerization interface [polypeptide binding]; other site 579112003157 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 579112003158 CheC-like family; Region: CheC; pfam04509 579112003159 sensory histidine kinase AtoS; Provisional; Region: PRK11360 579112003160 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 trans-...; Region: HisKA; cd00082 579112003161 dimer interface [polypeptide binding]; other site 579112003162 phosphorylation site [posttranslational modification] 579112003163 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 579112003164 ATP binding site [chemical binding]; other site 579112003165 Mg2+ binding site [ion binding]; other site 579112003166 G-X-G motif; other site 579112003167 Response regulator receiver domain; Region: Response_reg; pfam00072 579112003168 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003169 active site 579112003170 phosphorylation site [posttranslational modification] 579112003171 intermolecular recognition site; other site 579112003172 dimerization interface [polypeptide binding]; other site 579112003173 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 579112003174 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 579112003175 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003176 active site 579112003177 phosphorylation site [posttranslational modification] 579112003178 intermolecular recognition site; other site 579112003179 dimerization interface [polypeptide binding]; other site 579112003180 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112003181 Zn2+ binding site [ion binding]; other site 579112003182 Mg2+ binding site [ion binding]; other site 579112003183 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 579112003184 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 connected by an extended linker. The...; Region: HAMP; cd06225 579112003185 dimerization interface [polypeptide binding]; other site 579112003186 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 579112003187 ATP binding site [chemical binding]; other site 579112003188 Mg2+ binding site [ion binding]; other site 579112003189 G-X-G motif; other site 579112003190 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 579112003191 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 579112003192 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 579112003193 peptide binding site [polypeptide binding]; other site 579112003194 oligopeptide transporter permease; Reviewed; Region: oppB; PRK09471 579112003195 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...; Region: TM_PBP2; cd06261 579112003196 dimer interface [polypeptide binding]; other site 579112003197 conserved gate region; other site 579112003198 putative PBP binding loops; other site 579112003199 ABC-ATPase subunit interface; other site 579112003200 oligopeptide ABC transporter permease OppC; Provisional; Region: PRK15406 579112003201 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 579112003202 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...; Region: TM_PBP2; cd06261 579112003203 dimer interface [polypeptide binding]; other site 579112003204 conserved gate region; other site 579112003205 putative PBP binding loops; other site 579112003206 ABC-ATPase subunit interface; other site 579112003207 oligopeptide transporter ATP-binding component; Provisional; Region: oppD; PRK09473 579112003208 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112003209 Walker A/P-loop; other site 579112003210 ATP binding site [chemical binding]; other site 579112003211 Q-loop/lid; other site 579112003212 ABC transporter signature motif; other site 579112003213 Walker B; other site 579112003214 D-loop; other site 579112003215 H-loop/switch region; other site 579112003216 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112003217 oligopeptide ABC transporter ATP-binding protein OppF; Provisional; Region: PRK15079 579112003218 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112003219 Walker A/P-loop; other site 579112003220 ATP binding site [chemical binding]; other site 579112003221 Q-loop/lid; other site 579112003222 ABC transporter signature motif; other site 579112003223 Walker B; other site 579112003224 D-loop; other site 579112003225 H-loop/switch region; other site 579112003226 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112003227 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 579112003228 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 579112003229 putative dimer interface [polypeptide binding]; other site 579112003230 N-terminal domain interface [polypeptide binding]; other site 579112003231 putative substrate binding pocket (H-site) [chemical binding]; other site 579112003232 phosphate acetyltransferase; Reviewed; Region: PRK05632 579112003233 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112003234 DRTGG domain; Region: DRTGG; cl12147 579112003235 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 579112003236 Acetokinase family; Region: Acetate_kinase; cl01029 579112003237 Protein of unknown function, DUF412; Region: DUF412; cl01183 579112003238 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 579112003239 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 579112003240 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 579112003241 zinc binding site [ion binding]; other site 579112003242 putative ligand binding site [chemical binding]; other site 579112003243 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 579112003244 TM-ABC transporter signature motif; other site 579112003245 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 579112003246 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112003247 Walker A/P-loop; other site 579112003248 ATP binding site [chemical binding]; other site 579112003249 Q-loop/lid; other site 579112003250 ABC transporter signature motif; other site 579112003251 Walker B; other site 579112003252 D-loop; other site 579112003253 H-loop/switch region; other site 579112003254 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112003255 metal binding site [ion binding]; metal-binding site 579112003256 active site 579112003257 I-site; other site 579112003258 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 579112003259 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...; Region: DUS_like_FMN; cd02801 579112003260 FMN binding site [chemical binding]; other site 579112003261 active site 579112003262 catalytic residues [active] 579112003263 substrate binding site [chemical binding]; other site 579112003264 Predicted metal-binding protein related to the C-terminal domain of SecA [General function prediction only]; Region: COG3318 579112003265 Uncharacterised protein family (UPF0149); Region: UPF0149; cl01173 579112003266 SEC-C motif; Region: SEC-C; cl12132 579112003267 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 579112003268 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 579112003269 recombination factor protein RarA; Reviewed; Region: PRK13342 579112003270 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...; Region: AAA; cd00009 579112003271 Walker A motif; other site 579112003272 ATP binding site [chemical binding]; other site 579112003273 Walker B motif; other site 579112003274 arginine finger; other site 579112003275 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 579112003276 seryl-tRNA synthetase; Provisional; Region: PRK05431 579112003277 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 579112003278 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 579112003279 dimer interface [polypeptide binding]; other site 579112003280 active site 579112003281 motif 1; other site 579112003282 motif 2; other site 579112003283 motif 3; other site 579112003284 adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated; Region: PRK07986 579112003285 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 579112003286 inhibitor-cofactor binding pocket; inhibition site 579112003287 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112003288 catalytic residue [active] 579112003289 biotin synthase; Provisional; Region: PRK15108 579112003290 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 579112003291 FeS/SAM binding site; other site 579112003292 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 579112003293 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 579112003294 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 579112003295 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112003296 catalytic residue [active] 579112003297 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 579112003298 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 579112003299 S-adenosylmethionine binding site [chemical binding]; other site 579112003300 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 579112003301 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112003302 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112003303 Peptidase family M48; Region: Peptidase_M48; cl12018 579112003304 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 579112003305 short chain dehydrogenase; Provisional; Region: PRK06101 579112003306 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112003307 NAD(P) binding site [chemical binding]; other site 579112003308 active site 579112003309 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 579112003310 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112003311 Protein of unknown function (DUF1365); Region: DUF1365; cl01388 579112003312 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 579112003313 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 579112003314 S-adenosylmethionine binding site [chemical binding]; other site 579112003315 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 579112003316 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 579112003317 adenylosuccinate lyase; Provisional; Region: PRK09285 579112003318 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 579112003319 tetramer interface [polypeptide binding]; other site 579112003320 active site 579112003321 Protein of unknown function (DUF489); Region: DUF489; cl01097 579112003322 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 579112003323 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 579112003324 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 579112003325 substrate binding site [chemical binding]; other site 579112003326 ATP binding site [chemical binding]; other site 579112003327 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 579112003328 DNA binding protein, nucleoid-associated; Provisional; Region: PRK10328 579112003329 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 579112003330 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; cl09110 579112003331 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 579112003332 ATP phosphoribosyltransferase; Region: HisG; cl15266 579112003333 HisG, C-terminal domain; Region: HisG_C; cl06867 579112003334 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 579112003335 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 oxidation of L-histidinol to L-...; Region: Histidinol_dh; cd06572 579112003336 NAD binding site [chemical binding]; other site 579112003337 dimerization interface [polypeptide binding]; other site 579112003338 product binding site; other site 579112003339 substrate binding site [chemical binding]; other site 579112003340 zinc binding site [ion binding]; other site 579112003341 catalytic residues [active] 579112003342 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 579112003343 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 579112003344 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112003345 homodimer interface [polypeptide binding]; other site 579112003346 catalytic residue [active] 579112003347 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 579112003348 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 579112003349 active site 579112003350 motif I; other site 579112003351 motif II; other site 579112003352 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 579112003353 putative active site pocket [active] 579112003354 4-fold oligomerization interface [polypeptide binding]; other site 579112003355 metal binding residues [ion binding]; metal-binding site 579112003356 3-fold/trimer interface [polypeptide binding]; other site 579112003357 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 579112003358 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 579112003359 putative active site [active] 579112003360 oxyanion strand; other site 579112003361 catalytic triad [active] 579112003362 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 579112003363 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-...; Region: HisA; cd04732 579112003364 catalytic residues [active] 579112003365 Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]; Region: HisF; COG0107 579112003366 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)-formimino-5-; Region: HisF; cd04731 579112003367 substrate binding site [chemical binding]; other site 579112003368 glutamase interaction surface [polypeptide binding]; other site 579112003369 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 579112003370 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 579112003371 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 579112003372 23S rRNA pseudouridine synthase E; Provisional; Region: PRK11394 579112003373 PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-...; Region: PseudoU_synth_RluE; cd02566 579112003374 probable active site [active] 579112003375 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 579112003376 Monomeric isocitrate dehydrogenase; Region: IDH; pfam03971 579112003377 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 579112003378 DNA-binding site [nucleotide binding]; DNA binding site 579112003379 RNA-binding motif; other site 579112003380 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 579112003381 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 579112003382 Clp amino terminal domain; Region: Clp_N; pfam02861 579112003383 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...; Region: AAA; cd00009 579112003384 Walker A motif; other site 579112003385 ATP binding site [chemical binding]; other site 579112003386 Walker B motif; other site 579112003387 arginine finger; other site 579112003388 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...; Region: AAA; cd00009 579112003389 Walker A motif; other site 579112003390 ATP binding site [chemical binding]; other site 579112003391 Walker B motif; other site 579112003392 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 579112003393 putative transporter; Provisional; Region: PRK04972 579112003394 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 579112003395 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; cl09110 579112003396 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; cl09110 579112003397 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 579112003398 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 579112003399 GSH binding site [chemical binding]; other site 579112003400 catalytic residues [active] 579112003401 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 579112003402 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH2; cd08183 579112003403 putative active site [active] 579112003404 metal binding site [ion binding]; metal-binding site 579112003405 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 579112003406 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...; Region: SIS_RpiR; cd05013 579112003407 putative active site [active] 579112003408 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 579112003409 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 579112003410 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112003411 catalytic residue [active] 579112003412 Membrane protein of unknown function (DUF340); Region: DUF340; cl01028 579112003413 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 579112003414 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112003415 TfoX N-terminal domain; Region: TfoX_N; cl01167 579112003416 TfoX N-terminal domain; Region: TfoX_N; cl01167 579112003417 Response regulator receiver domain; Region: Response_reg; pfam00072 579112003418 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003419 active site 579112003420 phosphorylation site [posttranslational modification] 579112003421 intermolecular recognition site; other site 579112003422 dimerization interface [polypeptide binding]; other site 579112003423 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 579112003424 ligand binding site [chemical binding]; other site 579112003425 flexible hinge region; other site 579112003426 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 579112003427 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 579112003428 ATP binding site [chemical binding]; other site 579112003429 Mg2+ binding site [ion binding]; other site 579112003430 G-X-G motif; other site 579112003431 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 579112003432 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...; Region: PSAT_like; cd00611 579112003433 homodimer interface [polypeptide binding]; other site 579112003434 substrate-cofactor binding pocket; other site 579112003435 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112003436 catalytic residue [active] 579112003437 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112003438 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 579112003439 Protein of unknown function (DUF785); Region: DUF785; cl01682 579112003440 tRNA mo(5)U34 methyltransferase; Provisional; Region: PRK15068 579112003441 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 579112003442 S-adenosylmethionine binding site [chemical binding]; other site 579112003443 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 579112003444 S-adenosylmethionine binding site [chemical binding]; other site 579112003445 Protein of unknown function DUF72; Region: DUF72; cl00777 579112003446 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 579112003447 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 579112003448 dimer interface [polypeptide binding]; other site 579112003449 anticodon binding site; other site 579112003450 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 579112003451 homodimer interface [polypeptide binding]; other site 579112003452 motif 1; other site 579112003453 active site 579112003454 motif 2; other site 579112003455 GAD domain; Region: GAD; pfam02938 579112003456 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 579112003457 active site 579112003458 motif 3; other site 579112003459 Thymidine kinase; Region: TK; cl00631 579112003460 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 579112003461 tryptophan synthase; Region: PLN02591 579112003462 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...; Region: Tryptophan_synthase_alpha; cd04724 579112003463 substrate binding site [chemical binding]; other site 579112003464 active site 579112003465 catalytic residues [active] 579112003466 heterodimer interface [polypeptide binding]; other site 579112003467 tryptophan synthase, beta chain; Region: PLN02618 579112003468 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 579112003469 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112003470 catalytic residue [active] 579112003471 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 579112003472 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 579112003473 active site 579112003474 ribulose/triose binding site [chemical binding]; other site 579112003475 phosphate binding site [ion binding]; other site 579112003476 substrate (anthranilate) binding pocket [chemical binding]; other site 579112003477 product (indole) binding pocket [chemical binding]; other site 579112003478 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric...; Region: PRAI; cd00405 579112003479 active site 579112003480 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 579112003481 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 579112003482 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 579112003483 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 579112003484 Glutamine amidotransferase class-I; Region: GATase; pfam00117 579112003485 glutamine binding [chemical binding]; other site 579112003486 catalytic triad [active] 579112003487 anthranilate synthase component I; Provisional; Region: PRK13564 579112003488 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 579112003489 chorismate binding enzyme; Region: Chorismate_bind; cl10555 579112003490 Tryptophan operon leader peptide; Region: Trp_leader2; pfam08056 579112003491 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 579112003492 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 579112003493 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 579112003494 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 579112003495 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 579112003496 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 579112003497 probable active site [active] 579112003498 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 579112003499 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112003500 Walker A/P-loop; other site 579112003501 ATP binding site [chemical binding]; other site 579112003502 Q-loop/lid; other site 579112003503 ABC transporter signature motif; other site 579112003504 Walker B; other site 579112003505 D-loop; other site 579112003506 H-loop/switch region; other site 579112003507 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 579112003508 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 579112003509 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112003510 Walker A/P-loop; other site 579112003511 ATP binding site [chemical binding]; other site 579112003512 Q-loop/lid; other site 579112003513 ABC transporter signature motif; other site 579112003514 Walker B; other site 579112003515 D-loop; other site 579112003516 H-loop/switch region; other site 579112003517 thioredoxin reductase; Provisional; Region: PRK10262 579112003518 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112003519 Uncharacterized protein conserved in bacteria (DUF2257); Region: DUF2257; cl01794 579112003520 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 579112003521 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 579112003522 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112003523 catalytic residue [active] 579112003524 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112003525 metal binding site [ion binding]; metal-binding site 579112003526 active site 579112003527 I-site; other site 579112003528 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 579112003529 putative active site [active] 579112003530 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 579112003531 malate dehydrogenase; Provisional; Region: PRK13529 579112003532 Malic enzyme, N-terminal domain; Region: malic; pfam00390 579112003533 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 579112003534 NAD(P) binding site [chemical binding]; other site 579112003535 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 579112003536 ATP binding site [chemical binding]; other site 579112003537 active site 579112003538 substrate binding site [chemical binding]; other site 579112003539 Sel1 repeat; Region: Sel1; cl02723 579112003540 Sel1 repeat; Region: Sel1; cl02723 579112003541 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...; Region: DnaJ; cl02542 579112003542 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 579112003543 ligand binding site [chemical binding]; other site 579112003544 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 579112003545 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 579112003546 FAD binding domain; Region: FAD_binding_4; pfam01565 579112003547 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 579112003548 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 579112003549 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]; Region: COG5640 579112003550 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cd00190 579112003551 cleavage site 579112003552 active site 579112003553 substrate binding sites [chemical binding]; other site 579112003554 Protein of unknown function (DUF3581); Region: DUF3581; pfam12119 579112003555 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 579112003556 tyrosine 2,3-aminomutase; Region: Tyr_2_3_mutase; TIGR03832 579112003557 active sites [active] 579112003558 tetramer interface [polypeptide binding]; other site 579112003559 urocanate hydratase; Provisional; Region: PRK05414 579112003560 urocanate hydratase; Region: hutU; TIGR01228 579112003561 Arginase family; Region: Arginase; cl00306 579112003562 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 579112003563 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria...; Region: Imidazolone-5PH; cd01296 579112003564 active site 579112003565 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 579112003566 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 579112003567 DNA-binding site [nucleotide binding]; DNA binding site 579112003568 UTRA domain; Region: UTRA; cl01230 579112003569 Protein of unknown function (DUF3187); Region: DUF3187; pfam11383 579112003570 Protein of unknown function, DUF440; Region: DUF440; cl11472 579112003571 elongation factor P; Provisional; Region: PRK04542 579112003572 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 579112003573 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 579112003574 RNA binding site [nucleotide binding]; other site 579112003575 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 579112003576 RNA binding site [nucleotide binding]; other site 579112003577 Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; Region: NT_Pol-beta-like; cl11966 579112003578 metal binding triad [ion binding]; metal-binding site 579112003579 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112003580 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 579112003581 DNA polymerase II; Reviewed; Region: PRK05762 579112003582 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 579112003583 active site 579112003584 catalytic site [active] 579112003585 substrate binding site [chemical binding]; other site 579112003586 DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as...; Region: POLBc_Pol_II; cd05537 579112003587 active site 579112003588 metal-binding site 579112003589 response regulator; Provisional; Region: PRK09483 579112003590 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003591 active site 579112003592 phosphorylation site [posttranslational modification] 579112003593 intermolecular recognition site; other site 579112003594 dimerization interface [polypeptide binding]; other site 579112003595 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...; Region: LuxR_C_like; cd06170 579112003596 DNA binding residues [nucleotide binding] 579112003597 dimerization interface [polypeptide binding]; other site 579112003598 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 579112003599 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 579112003600 GIY-YIG motif/motif A; other site 579112003601 active site 579112003602 catalytic site [active] 579112003603 putative DNA binding site [nucleotide binding]; other site 579112003604 metal binding site [ion binding]; metal-binding site 579112003605 UvrB/uvrC motif; Region: UVR; pfam02151 579112003606 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 579112003607 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 579112003608 Hemerythrin [Inorganic ion transport and metabolism]; Region: COG2703 579112003609 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl11605 579112003610 octamerization interface [polypeptide binding]; other site 579112003611 diferric-oxygen binding site [ion binding]; other site 579112003612 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 579112003613 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112003614 metal binding site [ion binding]; metal-binding site 579112003615 active site 579112003616 I-site; other site 579112003617 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 579112003618 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112003619 Coenzyme A binding pocket [chemical binding]; other site 579112003620 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 579112003621 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 579112003622 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 579112003623 dimer interface [polypeptide binding]; other site 579112003624 motif 1; other site 579112003625 active site 579112003626 motif 2; other site 579112003627 motif 3; other site 579112003628 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 579112003629 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 579112003630 putative tRNA-binding site [nucleotide binding]; other site 579112003631 B3/4 domain; Region: B3_4; cl11458 579112003632 tRNA synthetase B5 domain; Region: B5; cl08394 579112003633 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 579112003634 dimer interface [polypeptide binding]; other site 579112003635 motif 1; other site 579112003636 motif 3; other site 579112003637 motif 2; other site 579112003638 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 579112003639 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 higher-...; Region: HU_IHF; cd00591 579112003640 IHF dimer interface [polypeptide binding]; other site 579112003641 IHF - DNA interface [nucleotide binding]; other site 579112003642 Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; Region: NT_Pol-beta-like; cl11966 579112003643 metal binding triad [ion binding]; metal-binding site 579112003644 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 579112003645 S-adenosylmethionine binding site [chemical binding]; other site 579112003646 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 579112003647 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112003648 NAD(P) binding site [chemical binding]; other site 579112003649 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112003650 Membrane transport protein; Region: Mem_trans; cl09117 579112003651 cytidine deaminase; Provisional; Region: PRK09027 579112003652 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 579112003653 active site 579112003654 catalytic motif [active] 579112003655 Zn binding site [ion binding]; other site 579112003656 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 579112003657 active site 579112003658 catalytic motif [active] 579112003659 Zn binding site [ion binding]; other site 579112003660 LrgB-like family; Region: LrgB; cl00596 579112003661 LrgA family; Region: LrgA; cl00608 579112003662 exonuclease I; Provisional; Region: sbcB; PRK11779 579112003663 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 579112003664 active site 579112003665 substrate binding site [chemical binding]; other site 579112003666 catalytic site [active] 579112003667 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 579112003668 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 579112003669 SelR domain; Region: SelR; cl00369 579112003670 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 579112003671 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 579112003672 putative dimer interface [polypeptide binding]; other site 579112003673 active site pocket [active] 579112003674 putative cataytic base [active] 579112003675 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 579112003676 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is...; Region: CobU; cd00544 579112003677 homotrimer interface [polypeptide binding]; other site 579112003678 Walker A motif; other site 579112003679 GTP binding site [chemical binding]; other site 579112003680 Walker B motif; other site 579112003681 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 579112003682 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 579112003683 catalytic core [active] 579112003684 Peptidase M14 Succinylglutamate desuccinylase (ASTE, also known as N-succinyl-L-glutamate amidohydrolase, N2-succinylglutamate desuccinylase, and SGDS; EC 3.5.1.96) belongs to the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily...; Region: M14_ASTE; cd03855 579112003685 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 579112003686 putative active site [active] 579112003687 Zn-binding site [ion binding]; other site 579112003688 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 579112003689 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112003690 ABC-ATPase subunit interface; other site 579112003691 dimer interface [polypeptide binding]; other site 579112003692 putative PBP binding regions; other site 579112003693 vitamin B12-transporter ATPase; Provisional; Region: PRK03695 579112003694 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 579112003695 Walker A/P-loop; other site 579112003696 ATP binding site [chemical binding]; other site 579112003697 Q-loop/lid; other site 579112003698 ABC transporter signature motif; other site 579112003699 Walker B; other site 579112003700 D-loop; other site 579112003701 H-loop/switch region; other site 579112003702 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 579112003703 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 579112003704 Cache domain; Region: Cache_2; cl07034 579112003705 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112003706 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112003707 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112003708 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 579112003709 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-...; Region: CBS_pair; cl09141 579112003710 hypothetical protein; Provisional; Region: PRK03673 579112003711 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 579112003712 putative MPT binding site; other site 579112003713 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 579112003714 catalytic loop [active] 579112003715 iron binding site [ion binding]; other site 579112003716 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 579112003717 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 579112003718 dimer interface [polypeptide binding]; other site 579112003719 putative radical transfer pathway; other site 579112003720 diiron center [ion binding]; other site 579112003721 tyrosyl radical; other site 579112003722 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 579112003723 ATP cone domain; Region: ATP-cone; pfam03477 579112003724 Class I ribonucleotide reductase; Region: RNR_I; cd01679 579112003725 active site 579112003726 dimer interface [polypeptide binding]; other site 579112003727 catalytic residues [active] 579112003728 effector binding site; other site 579112003729 R2 peptide binding site; other site 579112003730 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 579112003731 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 579112003732 S-adenosylmethionine binding site [chemical binding]; other site 579112003733 DNA gyrase subunit A; Validated; Region: PRK05560 579112003734 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in...; Region: TOP4c; cd00187 579112003735 CAP-like domain; other site 579112003736 Active site [active] 579112003737 primary dimer interface [polypeptide binding]; other site 579112003738 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 579112003739 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 579112003740 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 579112003741 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 579112003742 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 579112003743 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 579112003744 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 579112003745 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 579112003746 active site residue [active] 579112003747 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112003748 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112003749 sugar efflux transporter; Region: 2A0120; TIGR00899 579112003750 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 579112003751 putative substrate translocation pore; other site 579112003752 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 579112003753 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 579112003754 dimerization interface [polypeptide binding]; other site 579112003755 active site 579112003756 Imelysin; Region: Peptidase_M75; cl09159 579112003757 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 579112003758 Imelysin; Region: Peptidase_M75; cl09159 579112003759 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3490 579112003760 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 579112003761 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 579112003762 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 579112003763 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 579112003764 Peptidase M15; Region: Peptidase_M15_3; cl01194 579112003765 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112003766 Protein of unknown function (DUF2982); Region: DUF2982; pfam11201 579112003767 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 579112003768 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 579112003769 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 579112003770 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; cl09110 579112003771 DctM-like transporters; Region: DctM; pfam06808 579112003772 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 579112003773 Cache domain; Region: Cache_2; cl07034 579112003774 Histidine kinase; Region: HisKA_3; pfam07730 579112003775 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 579112003776 ATP binding site [chemical binding]; other site 579112003777 Mg2+ binding site [ion binding]; other site 579112003778 G-X-G motif; other site 579112003779 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 579112003780 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003781 active site 579112003782 phosphorylation site [posttranslational modification] 579112003783 intermolecular recognition site; other site 579112003784 dimerization interface [polypeptide binding]; other site 579112003785 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...; Region: LuxR_C_like; cd06170 579112003786 DNA binding residues [nucleotide binding] 579112003787 dimerization interface [polypeptide binding]; other site 579112003788 Transcriptional regulators [Transcription]; Region: MarR; COG1846 579112003789 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112003790 BCCT family transporter; Region: BCCT; cl00569 579112003791 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 579112003792 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 579112003793 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 579112003794 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,N-...; Region: PTS_IIB_chitobiose_lichenan; cd05564 579112003795 active site 579112003796 P-loop; other site 579112003797 phosphorylation site [posttranslational modification] 579112003798 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112003799 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 579112003800 active site 579112003801 methionine cluster; other site 579112003802 phosphorylation site [posttranslational modification] 579112003803 metal binding site [ion binding]; metal-binding site 579112003804 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 579112003805 Glycoside Hydrolases Family 4; Phospho-beta-glucosidase; Region: GH4_P_beta_glucosidase; cd05296 579112003806 NAD binding site [chemical binding]; other site 579112003807 sugar binding site [chemical binding]; other site 579112003808 divalent metal binding site [ion binding]; other site 579112003809 tetramer (dimer of dimers) interface [polypeptide binding]; other site 579112003810 dimer interface [polypeptide binding]; other site 579112003811 YdjC-like protein; Region: YdjC; cl01344 579112003812 Transcriptional regulators [Transcription]; Region: PurR; COG1609 579112003813 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112003814 DNA binding site [nucleotide binding] 579112003815 domain linker motif; other site 579112003816 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 579112003817 dimerization interface (closed form) [polypeptide binding]; other site 579112003818 ligand binding site [chemical binding]; other site 579112003819 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl01208 579112003820 Cache domain; Region: Cache_1; pfam02743 579112003821 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112003822 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112003823 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 579112003824 active site 579112003825 substrate binding site [chemical binding]; other site 579112003826 catalytic site [active] 579112003827 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 579112003828 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 579112003829 ligand binding site [chemical binding]; other site 579112003830 flexible hinge region; other site 579112003831 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain...; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 579112003832 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 579112003833 metal binding triad; other site 579112003834 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 579112003835 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112003836 homodimer interface [polypeptide binding]; other site 579112003837 catalytic residue [active] 579112003838 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112003839 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112003840 Zn2+ binding site [ion binding]; other site 579112003841 Mg2+ binding site [ion binding]; other site 579112003842 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed; Region: PRK06427 579112003843 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 579112003844 dimer interface [polypeptide binding]; other site 579112003845 substrate binding site [chemical binding]; other site 579112003846 ATP binding site [chemical binding]; other site 579112003847 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 579112003848 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 (...; Region: EcAsnRS_like_N; cd04318 579112003849 putative dimer interface [polypeptide binding]; other site 579112003850 putative anticodon binding site; other site 579112003851 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...; Region: AsxRS_core; cd00776 579112003852 homodimer interface [polypeptide binding]; other site 579112003853 motif 1; other site 579112003854 motif 2; other site 579112003855 active site 579112003856 motif 3; other site 579112003857 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 579112003858 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112003859 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112003860 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112003861 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 579112003862 active site 579112003863 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 579112003864 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 579112003865 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 579112003866 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 579112003867 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 579112003868 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 579112003869 putative active site [active] 579112003870 putative CoA binding site [chemical binding]; other site 579112003871 nudix motif; other site 579112003872 metal binding site [ion binding]; metal-binding site 579112003873 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 579112003874 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 579112003875 chorismate binding enzyme; Region: Chorismate_bind; cl10555 579112003876 fumarate hydratase FumA; Provisional; Region: PRK15390 579112003877 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 579112003878 Fumarase C-terminus; Region: Fumerase_C; cl00795 579112003879 YcjX-like family, DUF463; Region: DUF463; cl01193 579112003880 hypothetical protein; Provisional; Region: PRK05415 579112003881 Domain of unknown function (DUF697); Region: DUF697; cl12064 579112003882 Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]; Region: TyrR; COG3283 579112003883 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 579112003884 putative aromatic amino acid binding site; other site 579112003885 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112003886 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...; Region: AAA; cd00009 579112003887 Walker A motif; other site 579112003888 ATP binding site [chemical binding]; other site 579112003889 Walker B motif; other site 579112003890 arginine finger; other site 579112003891 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 579112003892 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112003893 Protein of unknown function (DUF2947); Region: DUF2947; pfam11163 579112003894 Threonine/homoserine efflux transporter [Amino acid transport and metabolism]; Region: rhtA; COG5006 579112003895 EamA-like transporter family; Region: EamA; cl01037 579112003896 alanine racemase; Reviewed; Region: PRK13340 579112003897 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2; Region: PLPDE_III_AR2; cd06826 579112003898 active site 579112003899 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 579112003900 dimer interface [polypeptide binding]; other site 579112003901 substrate binding site [chemical binding]; other site 579112003902 catalytic residues [active] 579112003903 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 579112003904 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112003905 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112003906 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112003907 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 579112003908 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 579112003909 transmembrane helices; other site 579112003910 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 579112003911 ligand binding site [chemical binding]; other site 579112003912 flexible hinge region; other site 579112003913 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 579112003914 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 579112003915 ATP binding site [chemical binding]; other site 579112003916 Mg2+ binding site [ion binding]; other site 579112003917 G-X-G motif; other site 579112003918 Response regulator receiver domain; Region: Response_reg; pfam00072 579112003919 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003920 active site 579112003921 phosphorylation site [posttranslational modification] 579112003922 intermolecular recognition site; other site 579112003923 dimerization interface [polypeptide binding]; other site 579112003924 Protein of unknown function (DUF535); Region: DUF535; cl01128 579112003925 MltA-interacting protein MipA; Region: MipA; cl01504 579112003926 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 579112003927 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112003928 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 trans-...; Region: HisKA; cl00080 579112003929 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 579112003930 ATP binding site [chemical binding]; other site 579112003931 Mg2+ binding site [ion binding]; other site 579112003932 G-X-G motif; other site 579112003933 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112003934 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 579112003935 active site 579112003936 phosphorylation site [posttranslational modification] 579112003937 intermolecular recognition site; other site 579112003938 dimerization interface [polypeptide binding]; other site 579112003939 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...; Region: trans_reg_C; cd00383 579112003940 DNA binding site [nucleotide binding] 579112003941 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 579112003942 Transglycosylase; Region: Transgly; cl07896 579112003943 Protein of unknown function (DUF539); Region: DUF539; cl01129 579112003944 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 579112003945 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 579112003946 Periplasmic binding proteins and sugar binding domain of LacI family; Region: Peripla_BP_1; pfam00532 579112003947 ligand binding site [chemical binding]; other site 579112003948 calcium binding site [ion binding]; other site 579112003949 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112003950 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional; Region: PRK10982 579112003951 Walker A/P-loop; other site 579112003952 ATP binding site [chemical binding]; other site 579112003953 Q-loop/lid; other site 579112003954 ABC transporter signature motif; other site 579112003955 Walker B; other site 579112003956 D-loop; other site 579112003957 H-loop/switch region; other site 579112003958 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 579112003959 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 579112003960 TM-ABC transporter signature motif; other site 579112003961 Protein of unknown function (DUF1460); Region: DUF1460; pfam07313 579112003962 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 579112003963 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 579112003964 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 579112003965 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 579112003966 Transcriptional regulators [Transcription]; Region: GntR; COG1802 579112003967 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 579112003968 DNA-binding site [nucleotide binding]; DNA binding site 579112003969 FCD domain; Region: FCD; cl11656 579112003970 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 579112003971 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 579112003972 tetramer interface [polypeptide binding]; other site 579112003973 active site 579112003974 Mg2+/Mn2+ binding site [ion binding]; other site 579112003975 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 579112003976 dimer interface [polypeptide binding]; other site 579112003977 Citrate synthase; Region: Citrate_synt; pfam00285 579112003978 active site 579112003979 citrylCoA binding site [chemical binding]; other site 579112003980 oxalacetate/citrate binding site [chemical binding]; other site 579112003981 coenzyme A binding site [chemical binding]; other site 579112003982 catalytic triad [active] 579112003983 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 579112003984 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 579112003985 substrate binding site [chemical binding]; other site 579112003986 ligand binding site [chemical binding]; other site 579112003987 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 579112003988 substrate binding site [chemical binding]; other site 579112003989 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 579112003990 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 579112003991 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 579112003992 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112003993 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112003994 Coenzyme A binding pocket [chemical binding]; other site 579112003995 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...; Region: Nudix_Hydrolase; cd02883 579112003996 nudix motif; other site 579112003997 M20 Peptidase T like enzymes specifically cleave tripeptides; Region: M20_peptT_like; cd05683 579112003998 peptidase T-like protein; Region: PepT-like; TIGR01883 579112003999 metal binding site [ion binding]; metal-binding site 579112004000 putative dimer interface [polypeptide binding]; other site 579112004001 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 579112004002 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 579112004003 dimer interface [polypeptide binding]; other site 579112004004 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 579112004005 active site 579112004006 Fe binding site [ion binding]; other site 579112004007 homogentisate 1,2-dioxygenase; Region: HgmA; cl10473 579112004008 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 579112004009 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 579112004010 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_N_Zeta; cd03042 579112004011 maleylacetoacetate isomerase; Region: maiA; TIGR01262 579112004012 C-terminal domain interface [polypeptide binding]; other site 579112004013 GSH binding site (G-site) [chemical binding]; other site 579112004014 putative dimer interface [polypeptide binding]; other site 579112004015 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 579112004016 dimer interface [polypeptide binding]; other site 579112004017 N-terminal domain interface [polypeptide binding]; other site 579112004018 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 579112004019 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 579112004020 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004021 active site 579112004022 phosphorylation site [posttranslational modification] 579112004023 intermolecular recognition site; other site 579112004024 dimerization interface [polypeptide binding]; other site 579112004025 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112004026 Zn2+ binding site [ion binding]; other site 579112004027 Mg2+ binding site [ion binding]; other site 579112004028 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 579112004029 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112004030 putative active site [active] 579112004031 heme pocket [chemical binding]; other site 579112004032 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 trans-...; Region: HisKA; cd00082 579112004033 dimer interface [polypeptide binding]; other site 579112004034 phosphorylation site [posttranslational modification] 579112004035 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 579112004036 ATP binding site [chemical binding]; other site 579112004037 Mg2+ binding site [ion binding]; other site 579112004038 G-X-G motif; other site 579112004039 Response regulator receiver domain; Region: Response_reg; pfam00072 579112004040 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004041 active site 579112004042 phosphorylation site [posttranslational modification] 579112004043 intermolecular recognition site; other site 579112004044 dimerization interface [polypeptide binding]; other site 579112004045 Response regulator receiver domain; Region: Response_reg; pfam00072 579112004046 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004047 active site 579112004048 phosphorylation site [posttranslational modification] 579112004049 intermolecular recognition site; other site 579112004050 dimerization interface [polypeptide binding]; other site 579112004051 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 579112004052 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 579112004053 catalytic triad [active] 579112004054 dimer interface [polypeptide binding]; other site 579112004055 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 579112004056 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 579112004057 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112004058 metal binding site [ion binding]; metal-binding site 579112004059 active site 579112004060 I-site; other site 579112004061 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 579112004062 PUA domain; Region: PUA; cl00607 579112004063 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 579112004064 S-adenosylmethionine binding site [chemical binding]; other site 579112004065 Acylphosphatase; Region: Acylphosphatase; cl00551 579112004066 DsrC like protein; Region: DsrC; cl01101 579112004067 YccA-like proteins; Region: YccA_like; cd10433 579112004068 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 579112004069 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 579112004070 Walker A/P-loop; other site 579112004071 ATP binding site [chemical binding]; other site 579112004072 Q-loop/lid; other site 579112004073 ABC transporter signature motif; other site 579112004074 Walker B; other site 579112004075 D-loop; other site 579112004076 H-loop/switch region; other site 579112004077 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...; Region: TM_PBP2; cd06261 579112004078 dimer interface [polypeptide binding]; other site 579112004079 conserved gate region; other site 579112004080 putative PBP binding loops; other site 579112004081 ABC-ATPase subunit interface; other site 579112004082 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 579112004083 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...; Region: TM_PBP2; cl00427 579112004084 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...; Region: TM_PBP2; cd06261 579112004085 dimer interface [polypeptide binding]; other site 579112004086 conserved gate region; other site 579112004087 putative PBP binding loops; other site 579112004088 ABC-ATPase subunit interface; other site 579112004089 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...; Region: PBPb; cd00134 579112004090 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 579112004091 substrate binding pocket [chemical binding]; other site 579112004092 membrane-bound complex binding site; other site 579112004093 hinge residues; other site 579112004094 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 579112004095 precorrin-2 dehydrogenase; Validated; Region: PRK06719 579112004096 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 579112004097 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 579112004098 sugar phosphate phosphatase; Provisional; Region: PRK10513 579112004099 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 579112004100 active site 579112004101 motif I; other site 579112004102 motif II; other site 579112004103 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; cl11391 579112004104 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 579112004105 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; cl15259 579112004106 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 579112004107 Ligand Binding Site [chemical binding]; other site 579112004108 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 579112004109 binding surface 579112004110 TPR motif; other site 579112004111 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 579112004112 binding surface 579112004113 TPR motif; other site 579112004114 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112004115 metal binding site [ion binding]; metal-binding site 579112004116 active site 579112004117 I-site; other site 579112004118 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...; Region: PBPb; cl15306 579112004119 substrate binding pocket [chemical binding]; other site 579112004120 NMT1/THI5 like; Region: NMT1; pfam09084 579112004121 membrane-bound complex binding site; other site 579112004122 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 579112004123 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112004124 metal binding site [ion binding]; metal-binding site 579112004125 active site 579112004126 I-site; other site 579112004127 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112004128 metal binding site [ion binding]; metal-binding site 579112004129 active site 579112004130 I-site; other site 579112004131 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 579112004132 DNA-K related protein; Region: DUF3731; pfam12531 579112004133 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 579112004134 Domain of unknown function (DUF2760); Region: DUF2760; pfam10816 579112004135 CHASE domain; Region: CHASE; cl01369 579112004136 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112004137 metal binding site [ion binding]; metal-binding site 579112004138 active site 579112004139 I-site; other site 579112004140 DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; Region: ERI-1_3'hExo_like; cd06133 579112004141 active site 579112004142 substrate binding site [chemical binding]; other site 579112004143 catalytic site [active] 579112004144 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 579112004145 putative metal binding site [ion binding]; other site 579112004146 ATP-dependent RNA helicase HrpA; Provisional; Region: PRK11131 579112004147 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 579112004148 ATP binding site [chemical binding]; other site 579112004149 putative Mg++ binding site [ion binding]; other site 579112004150 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 579112004151 nucleotide binding region [chemical binding]; other site 579112004152 ATP-binding site [chemical binding]; other site 579112004153 Helicase associated domain (HA2); Region: HA2; cl04503 579112004154 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 579112004155 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 579112004156 putative chaperone; Provisional; Region: PRK11678 579112004157 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 579112004158 lipoate-protein ligase A; Provisional; Region: lplA; PRK03822 579112004159 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 579112004160 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 579112004161 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; cl01792 579112004162 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112004163 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112004164 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112004165 putative effector binding pocket; other site 579112004166 dimerization interface [polypeptide binding]; other site 579112004167 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 579112004168 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 579112004169 putative substrate translocation pore; other site 579112004170 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 579112004171 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 579112004172 DNA photolyase; Region: DNA_photolyase; pfam00875 579112004173 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 579112004174 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 579112004175 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 579112004176 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004177 Response regulator receiver domain; Region: Response_reg; pfam00072 579112004178 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004179 active site 579112004180 phosphorylation site [posttranslational modification] 579112004181 intermolecular recognition site; other site 579112004182 dimerization interface [polypeptide binding]; other site 579112004183 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 579112004184 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 579112004185 putative binding surface; other site 579112004186 active site 579112004187 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 579112004188 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 579112004189 ATP binding site [chemical binding]; other site 579112004190 Mg2+ binding site [ion binding]; other site 579112004191 G-X-G motif; other site 579112004192 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112004193 Response regulator receiver domain; Region: Response_reg; pfam00072 579112004194 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004195 active site 579112004196 phosphorylation site [posttranslational modification] 579112004197 intermolecular recognition site; other site 579112004198 dimerization interface [polypeptide binding]; other site 579112004199 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 579112004200 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 579112004201 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112004202 conserved hypothetical protein; Region: TIGR02270 579112004203 Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]; Region: CheB; COG2201 579112004204 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004205 active site 579112004206 phosphorylation site [posttranslational modification] 579112004207 intermolecular recognition site; other site 579112004208 dimerization interface [polypeptide binding]; other site 579112004209 CheB methylesterase; Region: CheB_methylest; pfam01339 579112004210 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112004211 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112004212 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 579112004213 putative CheA interaction surface; other site 579112004214 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112004215 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004216 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112004217 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004218 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112004219 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004220 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 579112004221 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112004222 putative active site [active] 579112004223 heme pocket [chemical binding]; other site 579112004224 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112004225 putative active site [active] 579112004226 heme pocket [chemical binding]; other site 579112004227 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004228 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 579112004229 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 579112004230 ATP binding site [chemical binding]; other site 579112004231 Mg++ binding site [ion binding]; other site 579112004232 motif III; other site 579112004233 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 579112004234 nucleotide binding region [chemical binding]; other site 579112004235 ATP-binding site [chemical binding]; other site 579112004236 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112004237 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112004238 NodT family; Region: outer_NodT; TIGR01845 579112004239 Outer membrane efflux protein; Region: OEP; pfam02321 579112004240 Outer membrane efflux protein; Region: OEP; pfam02321 579112004241 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 579112004242 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 579112004243 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 579112004244 putative substrate translocation pore; other site 579112004245 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 579112004246 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 579112004247 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112004248 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004249 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 579112004250 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 579112004251 active site 579112004252 Zn binding site [ion binding]; other site 579112004253 Protein of unknown function (DUF796); Region: DUF796; cl01226 579112004254 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 579112004255 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 579112004256 Predicted lipase [Lipid metabolism]; Region: COG3675 579112004257 Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation,' the process of...; Region: Lipase_3; cd00519 579112004258 active site flap/lid [active] 579112004259 nucleophilic elbow; other site 579112004260 catalytic triad [active] 579112004261 Protein of unknown function (DUF2931); Region: DUF2931; pfam11153 579112004262 LysE type translocator; Region: LysE; cl00565 579112004263 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 579112004264 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 579112004265 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 579112004266 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 579112004267 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 579112004268 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...; Region: TM_PBP2; cd06261 579112004269 dimer interface [polypeptide binding]; other site 579112004270 conserved gate region; other site 579112004271 putative PBP binding loops; other site 579112004272 ABC-ATPase subunit interface; other site 579112004273 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 579112004274 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...; Region: TM_PBP2; cd06261 579112004275 dimer interface [polypeptide binding]; other site 579112004276 conserved gate region; other site 579112004277 putative PBP binding loops; other site 579112004278 ABC-ATPase subunit interface; other site 579112004279 putrescine/spermidine ABC transporter ATPase protein; Reviewed; Region: potA; PRK09452 579112004280 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues...; Region: ABC_PotA_N; cd03300 579112004281 Walker A/P-loop; other site 579112004282 ATP binding site [chemical binding]; other site 579112004283 Q-loop/lid; other site 579112004284 ABC transporter signature motif; other site 579112004285 Walker B; other site 579112004286 D-loop; other site 579112004287 H-loop/switch region; other site 579112004288 TOBE domain; Region: TOBE_2; cl01440 579112004289 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 579112004290 Uncharacterized FlgJ-related protein [General function prediction only]; Region: Bax; COG2992 579112004291 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 579112004292 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 579112004293 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 579112004294 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...; Region: Alpha_ANH_like_II; cd01993 579112004295 Ligand Binding Site [chemical binding]; other site 579112004296 universal stress protein UspE; Provisional; Region: PRK11175 579112004297 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 579112004298 Ligand Binding Site [chemical binding]; other site 579112004299 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 579112004300 Ligand Binding Site [chemical binding]; other site 579112004301 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 579112004302 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 579112004303 ligand binding site [chemical binding]; other site 579112004304 flexible hinge region; other site 579112004305 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 579112004306 putative switch regulator; other site 579112004307 non-specific DNA interactions [nucleotide binding]; other site 579112004308 DNA binding site [nucleotide binding] 579112004309 sequence specific DNA binding site [nucleotide binding]; other site 579112004310 putative cAMP binding site [chemical binding]; other site 579112004311 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 579112004312 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 579112004313 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 579112004314 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 579112004315 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 579112004316 metal-binding site [ion binding] 579112004317 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 579112004318 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; cl11391 579112004319 FixH; Region: FixH; cl01254 579112004320 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 579112004321 Cytochrome c; Region: Cytochrom_C; cl11414 579112004322 Cytochrome c; Region: Cytochrom_C; cl11414 579112004323 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of...; Region: cbb3_Oxidase_CcoQ; cd01324 579112004324 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 579112004325 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the...; Region: cbb3_Oxidase_I; cd01661 579112004326 Low-spin heme binding site [chemical binding]; other site 579112004327 Putative water exit pathway; other site 579112004328 Binuclear center (active site) [active] 579112004329 Putative proton exit pathway; other site 579112004330 Uncharacterized conserved protein [Function unknown]; Region: COG3287 579112004331 FIST N domain; Region: FIST; cl10701 579112004332 FIST C domain; Region: FIST_C; pfam10442 579112004333 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]; Region: COG4192 579112004334 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 trans-...; Region: HisKA; cd00082 579112004335 dimer interface [polypeptide binding]; other site 579112004336 phosphorylation site [posttranslational modification] 579112004337 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 579112004338 ATP binding site [chemical binding]; other site 579112004339 Mg2+ binding site [ion binding]; other site 579112004340 G-X-G motif; other site 579112004341 Response regulator receiver domain; Region: Response_reg; pfam00072 579112004342 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004343 active site 579112004344 phosphorylation site [posttranslational modification] 579112004345 intermolecular recognition site; other site 579112004346 dimerization interface [polypeptide binding]; other site 579112004347 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 579112004348 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 579112004349 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 579112004350 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112004351 Walker A/P-loop; other site 579112004352 ATP binding site [chemical binding]; other site 579112004353 Q-loop/lid; other site 579112004354 ABC transporter signature motif; other site 579112004355 Walker B; other site 579112004356 D-loop; other site 579112004357 H-loop/switch region; other site 579112004358 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 579112004359 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). The...; Region: Peptidase_C39_like; cd02259 579112004360 putative active site [active] 579112004361 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 579112004362 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 579112004363 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112004364 Walker A/P-loop; other site 579112004365 ATP binding site [chemical binding]; other site 579112004366 Q-loop/lid; other site 579112004367 ABC transporter signature motif; other site 579112004368 Walker B; other site 579112004369 D-loop; other site 579112004370 H-loop/switch region; other site 579112004371 RTX toxin acyltransferase family; Region: HlyC; cl01131 579112004372 hypothetical protein; Provisional; Region: PHA02515 579112004373 electron transport complex protein RnfC; Provisional; Region: PRK05035 579112004374 C-terminal region of Pasteurella multocida toxin residues 569-1285; Region: PMT_C; pfam11647 579112004375 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 579112004376 Peptidase C80 family; Region: Peptidase_C80; pfam11713 579112004377 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 579112004378 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112004379 Phage protein; Region: DUF3653; pfam12375 579112004380 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112004381 Phage replication protein CRI; Region: Phage_CRI; pfam05144 579112004382 phage/plasmid replication protein, gene II/X family; Region: rep_II_X; TIGR01629 579112004383 Phage X family; Region: Phage_X; cl11585 579112004384 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112004385 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112004386 Phage replication protein CRI; Region: Phage_CRI; pfam05144 579112004387 phage/plasmid replication protein, gene II/X family; Region: rep_II_X; TIGR01629 579112004388 Phage X family; Region: Phage_X; cl11585 579112004389 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112004390 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; cl01116 579112004391 putative transposase OrfB; Reviewed; Region: PHA02517 579112004392 Integrase core domain; Region: rve; cl01316 579112004393 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 579112004394 Organiser of macrodomain of Terminus of chromosome; Region: MatP; cl11476 579112004395 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 579112004396 Protein of unknown function (DUF1687); Region: DUF1687; pfam07955 579112004397 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 579112004398 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 579112004399 active site 1 [active] 579112004400 dimer interface [polypeptide binding]; other site 579112004401 active site 2 [active] 579112004402 Ribosome modulation factor; Region: RMF; cl01207 579112004403 Protein of unknown function (DUF3466); Region: DUF3466; pfam11949 579112004404 ABC transporter ATPase component; Reviewed; Region: PRK11147 579112004405 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112004406 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112004407 ABC transporter; Region: ABC_tran_2; pfam12848 579112004408 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112004409 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide...; Region: NrdH; cd02976 579112004410 catalytic residues [active] 579112004411 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 579112004412 THUMP domain; Region: THUMP; cl12076 579112004413 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112004414 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 579112004415 S-adenosylmethionine binding site [chemical binding]; other site 579112004416 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 579112004417 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD...; Region: DHOD_2_like; cd04738 579112004418 quinone interaction residues [chemical binding]; other site 579112004419 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 579112004420 active site 579112004421 catalytic residues [active] 579112004422 FMN binding site [chemical binding]; other site 579112004423 substrate binding site [chemical binding]; other site 579112004424 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 579112004425 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 579112004426 aminopeptidase N; Provisional; Region: pepN; PRK14015 579112004427 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 579112004428 active site 579112004429 Zn binding site [ion binding]; other site 579112004430 carboxy-terminal protease; Provisional; Region: PRK11186 579112004431 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 579112004432 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 579112004433 protein binding site [polypeptide binding]; other site 579112004434 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 579112004435 Catalytic dyad [active] 579112004436 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 579112004437 ProP expression regulator; Provisional; Region: PRK04950 579112004438 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 579112004439 GAF domain; Region: GAF; cl00853 579112004440 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 579112004441 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 579112004442 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112004443 Walker A/P-loop; other site 579112004444 ATP binding site [chemical binding]; other site 579112004445 Q-loop/lid; other site 579112004446 ABC transporter signature motif; other site 579112004447 Walker B; other site 579112004448 D-loop; other site 579112004449 H-loop/switch region; other site 579112004450 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 579112004451 Paraquat-inducible protein A; Region: PqiA; pfam04403 579112004452 Paraquat-inducible protein A; Region: PqiA; pfam04403 579112004453 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 579112004454 mce related protein; Region: MCE; pfam02470 579112004455 mce related protein; Region: MCE; pfam02470 579112004456 mce related protein; Region: MCE; pfam02470 579112004457 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 579112004458 mce related protein; Region: MCE; pfam02470 579112004459 mce related protein; Region: MCE; pfam02470 579112004460 mce related protein; Region: MCE; pfam02470 579112004461 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 579112004462 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112004463 Uncharacterized conserved protein [Function unknown]; Region: COG3270 579112004464 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 579112004465 NeuB family; Region: NeuB; cl00496 579112004466 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 579112004467 Protein of unknown function (DUF520); Region: DUF520; cl00723 579112004468 NAD-dependent deacetylase; Provisional; Region: PRK14138 579112004469 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes...; Region: SIRT5_Af1_CobB; cd01412 579112004470 NAD+ binding site [chemical binding]; other site 579112004471 substrate binding site [chemical binding]; other site 579112004472 Zn binding site [ion binding]; other site 579112004473 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 579112004474 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 579112004475 Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]; Region: FwdB; COG1029 579112004476 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 579112004477 [4Fe-4S] binding site [ion binding]; other site 579112004478 molybdopterin cofactor binding site; other site 579112004479 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 579112004480 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 579112004481 molybdopterin cofactor binding site; other site 579112004482 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 579112004483 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 579112004484 Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]; Region: HdrA; COG1148 579112004485 Ferredoxin [Energy production and conversion]; Region: COG1146 579112004486 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 alpha-; Region: HCP_like; cl14655 579112004487 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 579112004488 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 579112004489 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 579112004490 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 579112004491 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 579112004492 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112004493 Walker A/P-loop; other site 579112004494 ATP binding site [chemical binding]; other site 579112004495 Q-loop/lid; other site 579112004496 ABC transporter signature motif; other site 579112004497 Walker B; other site 579112004498 D-loop; other site 579112004499 H-loop/switch region; other site 579112004500 ABC transporter; Region: ABC_tran_2; pfam12848 579112004501 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112004502 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112004503 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 579112004504 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 trans-...; Region: HisKA; cd00082 579112004505 dimer interface [polypeptide binding]; other site 579112004506 phosphorylation site [posttranslational modification] 579112004507 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 579112004508 ATP binding site [chemical binding]; other site 579112004509 Mg2+ binding site [ion binding]; other site 579112004510 G-X-G motif; other site 579112004511 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 579112004512 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004513 active site 579112004514 phosphorylation site [posttranslational modification] 579112004515 intermolecular recognition site; other site 579112004516 dimerization interface [polypeptide binding]; other site 579112004517 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...; Region: AAA; cd00009 579112004518 Walker A motif; other site 579112004519 ATP binding site [chemical binding]; other site 579112004520 Walker B motif; other site 579112004521 arginine finger; other site 579112004522 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112004523 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 579112004524 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 579112004525 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...; Region: TM_PBP2; cd06261 579112004526 dimer interface [polypeptide binding]; other site 579112004527 conserved gate region; other site 579112004528 putative PBP binding loops; other site 579112004529 ABC-ATPase subunit interface; other site 579112004530 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 579112004531 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 579112004532 Walker A/P-loop; other site 579112004533 ATP binding site [chemical binding]; other site 579112004534 Q-loop/lid; other site 579112004535 ABC transporter signature motif; other site 579112004536 Walker B; other site 579112004537 D-loop; other site 579112004538 H-loop/switch region; other site 579112004539 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 579112004540 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 579112004541 GTP binding site [chemical binding]; other site 579112004542 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional; Region: PRK14491 579112004543 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa...; Region: MobB; cd03116 579112004544 Walker A motif; other site 579112004545 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 579112004546 dimer interface [polypeptide binding]; other site 579112004547 putative functional site; other site 579112004548 putative MPT binding site; other site 579112004549 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 579112004550 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 579112004551 fructokinase; Reviewed; Region: PRK09557 579112004552 DTW domain; Region: DTW; cl01221 579112004553 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 579112004554 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 579112004555 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004556 NlpC/P60 family; Region: NLPC_P60; cl11438 579112004557 Protein of unknown function (DUF3802); Region: DUF3802; pfam12290 579112004558 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 579112004559 Phosphotransferase enzyme family; Region: APH; pfam01636 579112004560 multidrug efflux protein; Reviewed; Region: PRK01766 579112004561 MatE; Region: MatE; cl10513 579112004562 MatE; Region: MatE; cl10513 579112004563 Protein of unknown function (DUF3080); Region: DUF3080; pfam11279 579112004564 DNA ligase; Provisional; Region: PRK09125 579112004565 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 579112004566 DNA binding site [nucleotide binding] 579112004567 active site 579112004568 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 579112004569 DNA binding site [nucleotide binding] 579112004570 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 579112004571 Gram-negative bacterial tonB protein; Region: TonB; cl10048 579112004572 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 579112004573 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 579112004574 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 579112004575 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 579112004576 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 579112004577 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 579112004578 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...; Region: TM_PBP2; cl00427 579112004579 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 579112004580 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...; Region: TM_PBP2; cd06261 579112004581 dimer interface [polypeptide binding]; other site 579112004582 conserved gate region; other site 579112004583 putative PBP binding loops; other site 579112004584 ABC-ATPase subunit interface; other site 579112004585 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 579112004586 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 579112004587 Walker A/P-loop; other site 579112004588 ATP binding site [chemical binding]; other site 579112004589 Q-loop/lid; other site 579112004590 ABC transporter signature motif; other site 579112004591 Walker B; other site 579112004592 D-loop; other site 579112004593 H-loop/switch region; other site 579112004594 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 579112004595 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112004596 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 579112004597 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 579112004598 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 579112004599 putative active site [active] 579112004600 catalytic site [active] 579112004601 putative metal binding site [ion binding]; other site 579112004602 Domain of unknown function (DUF386); Region: DUF386; cl01047 579112004603 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 579112004604 homotrimer interaction site [polypeptide binding]; other site 579112004605 putative active site [active] 579112004606 Transcriptional regulators [Transcription]; Region: PurR; COG1609 579112004607 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112004608 DNA binding site [nucleotide binding] 579112004609 domain linker motif; other site 579112004610 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 579112004611 dimerization interface (closed form) [polypeptide binding]; other site 579112004612 ligand binding site [chemical binding]; other site 579112004613 Beta-glucosidase/6-phospho-beta-glucosidase/beta- galactosidase [Carbohydrate transport and metabolism]; Region: BglB; cl01046 579112004614 6-phospho-beta-glucosidase; Reviewed; Region: arb; PRK09593 579112004615 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 579112004616 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 579112004617 dimer interface [polypeptide binding]; other site 579112004618 active site 579112004619 heme binding site [chemical binding]; other site 579112004620 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 579112004621 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112004622 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112004623 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 579112004624 substrate binding pocket [chemical binding]; other site 579112004625 dimerization interface [polypeptide binding]; other site 579112004626 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112004627 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...; Region: Biotinyl_lipoyl_domains; cl11404 579112004628 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 579112004629 Outer membrane efflux protein; Region: OEP; pfam02321 579112004630 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 579112004631 Outer membrane efflux protein; Region: OEP; pfam02321 579112004632 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 579112004633 FtsX-like permease family; Region: FtsX; pfam02687 579112004634 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 579112004635 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 579112004636 FtsX-like permease family; Region: FtsX; pfam02687 579112004637 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 579112004638 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 579112004639 Walker A/P-loop; other site 579112004640 ATP binding site [chemical binding]; other site 579112004641 Q-loop/lid; other site 579112004642 ABC transporter signature motif; other site 579112004643 Walker B; other site 579112004644 D-loop; other site 579112004645 H-loop/switch region; other site 579112004646 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 579112004647 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 579112004648 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 579112004649 fumarate hydratase; Reviewed; Region: fumC; PRK00485 579112004650 Class II fumarases; Region: Fumarase_classII; cd01362 579112004651 active site 579112004652 tetramer interface [polypeptide binding]; other site 579112004653 Protein of unknown function, DUF486; Region: DUF486; cl01236 579112004654 Predicted membrane protein (DUF2127); Region: DUF2127; cl01785 579112004655 ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function...; Region: ASCH_yqfb_like; cd06552 579112004656 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 579112004657 putative acyl-acceptor binding pocket; other site 579112004658 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 579112004659 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112004660 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 579112004661 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112004662 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 579112004663 dimerization interface [polypeptide binding]; other site 579112004664 NADH dehydrogenase subunit L; Provisional; Region: PRK08168 579112004665 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 579112004666 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3002 579112004667 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 579112004668 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 579112004669 E-class dimer interface [polypeptide binding]; other site 579112004670 P-class dimer interface [polypeptide binding]; other site 579112004671 active site 579112004672 Cu2+ binding site [ion binding]; other site 579112004673 Zn2+ binding site [ion binding]; other site 579112004674 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 579112004675 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 579112004676 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 579112004677 Clade 1 of the heme-binding enzyme catalase; Region: catalase_clade_1; cd08154 579112004678 tetramer interface [polypeptide binding]; other site 579112004679 heme binding pocket [chemical binding]; other site 579112004680 Protein of unknown function, DUF417; Region: DUF417; cl01162 579112004681 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112004682 The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; Region: PBP2_BudR; cd08451 579112004683 putative dimerization interface [polypeptide binding]; other site 579112004684 putative substrate binding pocket [chemical binding]; other site 579112004685 Alpha-acetolactate decarboxylase; Region: AAL_decarboxy; cl01408 579112004686 acetolactate synthase; Reviewed; Region: PRK08617 579112004687 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 579112004688 PYR/PP interface [polypeptide binding]; other site 579112004689 dimer interface [polypeptide binding]; other site 579112004690 TPP binding site [chemical binding]; other site 579112004691 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 579112004692 Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2...; Region: TPP_ALS; cd02010 579112004693 TPP-binding site [chemical binding]; other site 579112004694 dimer interface [polypeptide binding]; other site 579112004695 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 579112004696 classical (c) SDRs; Region: SDR_c; cd05233 579112004697 NAD(P) binding site [chemical binding]; other site 579112004698 active site 579112004699 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 579112004700 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112004701 metal binding site [ion binding]; metal-binding site 579112004702 active site 579112004703 I-site; other site 579112004704 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 579112004705 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 579112004706 active site 579112004707 catalytic residues [active] 579112004708 galactokinase; Provisional; Region: PRK05101 579112004709 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 579112004710 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 579112004711 galactose-1-phosphate uridylyltransferase; Provisional; Region: PRK11720 579112004712 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 579112004713 dimer interface [polypeptide binding]; other site 579112004714 active site 579112004715 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 579112004716 Major Facilitator Superfamily; Region: MFS_1; pfam07690 579112004717 putative substrate translocation pore; other site 579112004718 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 579112004719 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 579112004720 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...; Region: PBPb; cl15306 579112004721 substrate binding pocket [chemical binding]; other site 579112004722 membrane-bound complex binding site; other site 579112004723 hinge residues; other site 579112004724 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]; Region: COG5001 579112004725 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112004726 metal binding site [ion binding]; metal-binding site 579112004727 active site 579112004728 I-site; other site 579112004729 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 579112004730 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 579112004731 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112004732 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004733 active site 579112004734 phosphorylation site [posttranslational modification] 579112004735 intermolecular recognition site; other site 579112004736 dimerization interface [polypeptide binding]; other site 579112004737 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 579112004738 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...; Region: PBPb; cl15306 579112004739 substrate binding pocket [chemical binding]; other site 579112004740 membrane-bound complex binding site; other site 579112004741 hinge residues; other site 579112004742 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 579112004743 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004744 active site 579112004745 phosphorylation site [posttranslational modification] 579112004746 intermolecular recognition site; other site 579112004747 dimerization interface [polypeptide binding]; other site 579112004748 Transcriptional regulator; Region: CitT; pfam12431 579112004749 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 579112004750 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112004751 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 579112004752 ATP binding site [chemical binding]; other site 579112004753 Mg2+ binding site [ion binding]; other site 579112004754 G-X-G motif; other site 579112004755 Outer membrane efflux protein; Region: OEP; pfam02321 579112004756 Outer membrane efflux protein; Region: OEP; pfam02321 579112004757 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 579112004758 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...; Region: Biotinyl_lipoyl_domains; cl11404 579112004759 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 579112004760 Predicted membrane protein [Function unknown]; Region: COG1511 579112004761 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 579112004762 ABC-2 type transporter; Region: ABC2_membrane; cl11417 579112004763 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112004764 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 579112004765 proposed active site lysine [active] 579112004766 conserved cys residue [active] 579112004767 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 579112004768 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 579112004769 binding surface 579112004770 TPR motif; other site 579112004771 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 579112004772 binding surface 579112004773 TPR motif; other site 579112004774 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112004775 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 579112004776 Protein of unknown function DUF45; Region: DUF45; cl00636 579112004777 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide...; Region: NrdH; cd02976 579112004778 catalytic residues [active] 579112004779 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 579112004780 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112004781 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 579112004782 dimerization interface [polypeptide binding]; other site 579112004783 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 579112004784 Major Facilitator Superfamily; Region: MFS_1; pfam07690 579112004785 putative substrate translocation pore; other site 579112004786 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 579112004787 Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell...; Region: CA; cl02468 579112004788 Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell...; Region: CA; cd00031 579112004789 Ca2+ binding site [ion binding]; other site 579112004790 Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell...; Region: CA; cd00031 579112004791 Ca2+ binding site [ion binding]; other site 579112004792 Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell...; Region: CA; cd00031 579112004793 Ca2+ binding site [ion binding]; other site 579112004794 Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell...; Region: CA; cd00031 579112004795 Ca2+ binding site [ion binding]; other site 579112004796 Cadherin repeat domain; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion; these domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium; plays a role in cell...; Region: CA; cd00031 579112004797 Ca2+ binding site [ion binding]; other site 579112004798 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 579112004799 type 1 secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 579112004800 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 579112004801 Outer membrane efflux protein; Region: OEP; pfam02321 579112004802 Outer membrane efflux protein; Region: OEP; pfam02321 579112004803 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 579112004804 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 579112004805 ligand binding site [chemical binding]; other site 579112004806 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 579112004807 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 579112004808 dimer interface [polypeptide binding]; other site 579112004809 active site 579112004810 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 579112004811 catalytic residues [active] 579112004812 substrate binding site [chemical binding]; other site 579112004813 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 579112004814 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112004815 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional; Region: PRK06938 579112004816 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 579112004817 inhibitor-cofactor binding pocket; inhibition site 579112004818 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112004819 catalytic residue [active] 579112004820 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 579112004821 DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and...; Region: DOPA_deC_like; cd06450 579112004822 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112004823 catalytic residue [active] 579112004824 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 579112004825 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 579112004826 FtsX-like permease family; Region: FtsX; pfam02687 579112004827 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 579112004828 FtsX-like permease family; Region: FtsX; pfam02687 579112004829 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 579112004830 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 579112004831 Walker A/P-loop; other site 579112004832 ATP binding site [chemical binding]; other site 579112004833 Q-loop/lid; other site 579112004834 ABC transporter signature motif; other site 579112004835 Walker B; other site 579112004836 D-loop; other site 579112004837 H-loop/switch region; other site 579112004838 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 579112004839 MatE; Region: MatE; cl10513 579112004840 MatE; Region: MatE; cl10513 579112004841 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 579112004842 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112004843 NAD(P) binding site [chemical binding]; other site 579112004844 active site 579112004845 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 579112004846 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 579112004847 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 579112004848 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 579112004849 putative substrate translocation pore; other site 579112004850 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 579112004851 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 579112004852 RNA binding surface [nucleotide binding]; other site 579112004853 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 579112004854 active site 579112004855 uracil binding [chemical binding]; other site 579112004856 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 579112004857 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112004858 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 579112004859 nucleotide binding region [chemical binding]; other site 579112004860 ATP-binding site [chemical binding]; other site 579112004861 Predicted membrane protein [Function unknown]; Region: COG3212 579112004862 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 579112004863 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 579112004864 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004865 active site 579112004866 phosphorylation site [posttranslational modification] 579112004867 intermolecular recognition site; other site 579112004868 dimerization interface [polypeptide binding]; other site 579112004869 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...; Region: trans_reg_C; cd00383 579112004870 DNA binding site [nucleotide binding] 579112004871 sensor protein PhoQ; Provisional; Region: PRK10815 579112004872 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 579112004873 ATP binding site [chemical binding]; other site 579112004874 Mg2+ binding site [ion binding]; other site 579112004875 G-X-G motif; other site 579112004876 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 579112004877 5S rRNA interface [nucleotide binding]; other site 579112004878 CTC domain interface [polypeptide binding]; other site 579112004879 L16 interface [polypeptide binding]; other site 579112004880 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 579112004881 Ribosome recycling factor; Region: RRF_GI; pfam12614 579112004882 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004883 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112004884 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112004885 Protein of unknown function (DUF3103); Region: DUF3103; pfam11301 579112004886 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 579112004887 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 579112004888 motif II; other site 579112004889 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4533 579112004890 Sugar transport-related sRNA regulator N-term; Region: SgrR_N; pfam12793 579112004891 The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold; Region: PBP2_SgrR_like; cd08507 579112004892 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]; Region: COG5640 579112004893 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cd00190 579112004894 cleavage site 579112004895 active site 579112004896 substrate binding sites [chemical binding]; other site 579112004897 Peptidase family M9 N-terminal; Region: Peptidase_M9_N; pfam08453 579112004898 Collagenase; Region: Peptidase_M9; pfam01752 579112004899 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 579112004900 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 579112004901 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004902 active site 579112004903 phosphorylation site [posttranslational modification] 579112004904 intermolecular recognition site; other site 579112004905 dimerization interface [polypeptide binding]; other site 579112004906 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 579112004907 binding surface 579112004908 TPR motif; other site 579112004909 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 579112004910 Response regulator receiver domain; Region: Response_reg; pfam00072 579112004911 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004912 active site 579112004913 phosphorylation site [posttranslational modification] 579112004914 intermolecular recognition site; other site 579112004915 dimerization interface [polypeptide binding]; other site 579112004916 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 579112004917 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 579112004918 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...; Region: LuxR_C_like; cd06170 579112004919 DNA binding residues [nucleotide binding] 579112004920 dimerization interface [polypeptide binding]; other site 579112004921 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...; Region: PBPb; cd00134 579112004922 substrate binding pocket [chemical binding]; other site 579112004923 membrane-bound complex binding site; other site 579112004924 hinge residues; other site 579112004925 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 579112004926 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...; Region: PBPb; cl15306 579112004927 substrate binding pocket [chemical binding]; other site 579112004928 membrane-bound complex binding site; other site 579112004929 hinge residues; other site 579112004930 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 579112004931 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 trans-...; Region: HisKA; cd00082 579112004932 dimer interface [polypeptide binding]; other site 579112004933 phosphorylation site [posttranslational modification] 579112004934 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 579112004935 ATP binding site [chemical binding]; other site 579112004936 Mg2+ binding site [ion binding]; other site 579112004937 G-X-G motif; other site 579112004938 Response regulator receiver domain; Region: Response_reg; pfam00072 579112004939 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112004940 active site 579112004941 phosphorylation site [posttranslational modification] 579112004942 intermolecular recognition site; other site 579112004943 dimerization interface [polypeptide binding]; other site 579112004944 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 579112004945 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 579112004946 MgtE intracellular N domain; Region: MgtE_N; cl15244 579112004947 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 579112004948 Divalent cation transporter; Region: MgtE; cl00786 579112004949 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 579112004950 EamA-like transporter family; Region: EamA; cl01037 579112004951 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 579112004952 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 579112004953 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 579112004954 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 579112004955 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 579112004956 Walker A/P-loop; other site 579112004957 ATP binding site [chemical binding]; other site 579112004958 Q-loop/lid; other site 579112004959 ABC transporter signature motif; other site 579112004960 Walker B; other site 579112004961 D-loop; other site 579112004962 H-loop/switch region; other site 579112004963 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 579112004964 ABC-2 type transporter; Region: ABC2_membrane; cl11417 579112004965 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 579112004966 META domain; Region: META; cl01245 579112004967 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4134 579112004968 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 579112004969 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4135 579112004970 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...; Region: TM_PBP2; cd06261 579112004971 putative PBP binding loops; other site 579112004972 dimer interface [polypeptide binding]; other site 579112004973 ABC-ATPase subunit interface; other site 579112004974 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4136 579112004975 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112004976 Walker A/P-loop; other site 579112004977 ATP binding site [chemical binding]; other site 579112004978 Q-loop/lid; other site 579112004979 ABC transporter signature motif; other site 579112004980 Walker B; other site 579112004981 D-loop; other site 579112004982 H-loop/switch region; other site 579112004983 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 579112004984 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 579112004985 active site 579112004986 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 579112004987 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 579112004988 Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_1; cd09152 579112004989 putative active site [active] 579112004990 catalytic site [active] 579112004991 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_2; cd09158 579112004992 putative active site [active] 579112004993 catalytic site [active] 579112004994 cystathionine beta-lyase; Provisional; Region: PRK09028 579112004995 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 579112004996 homodimer interface [polypeptide binding]; other site 579112004997 substrate-cofactor binding pocket; other site 579112004998 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112004999 catalytic residue [active] 579112005000 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 579112005001 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 579112005002 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 579112005003 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 579112005004 E3 interaction surface; other site 579112005005 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 579112005006 PspC domain; Region: PspC; cl00864 579112005007 phage shock protein C; Region: phageshock_pspC; TIGR02978 579112005008 Phage shock protein B; Region: PspB; cl05946 579112005009 phage shock protein PspA; Provisional; Region: PRK10698 579112005010 phage shock protein A; Region: phageshock_pspA; TIGR02977 579112005011 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 579112005012 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...; Region: AAA; cd00009 579112005013 Walker A motif; other site 579112005014 ATP binding site [chemical binding]; other site 579112005015 Walker B motif; other site 579112005016 arginine finger; other site 579112005017 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112005018 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 579112005019 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 579112005020 peptide binding site [polypeptide binding]; other site 579112005021 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapB; COG4168 579112005022 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...; Region: TM_PBP2; cd06261 579112005023 dimer interface [polypeptide binding]; other site 579112005024 conserved gate region; other site 579112005025 putative PBP binding loops; other site 579112005026 ABC-ATPase subunit interface; other site 579112005027 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 579112005028 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 579112005029 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...; Region: TM_PBP2; cd06261 579112005030 dimer interface [polypeptide binding]; other site 579112005031 conserved gate region; other site 579112005032 putative PBP binding loops; other site 579112005033 ABC-ATPase subunit interface; other site 579112005034 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapD; COG4170 579112005035 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112005036 Walker A/P-loop; other site 579112005037 ATP binding site [chemical binding]; other site 579112005038 Q-loop/lid; other site 579112005039 ABC transporter signature motif; other site 579112005040 Walker B; other site 579112005041 D-loop; other site 579112005042 H-loop/switch region; other site 579112005043 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112005044 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 579112005045 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112005046 Walker A/P-loop; other site 579112005047 ATP binding site [chemical binding]; other site 579112005048 Q-loop/lid; other site 579112005049 ABC transporter signature motif; other site 579112005050 Walker B; other site 579112005051 D-loop; other site 579112005052 H-loop/switch region; other site 579112005053 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 579112005054 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 579112005055 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 579112005056 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-...; Region: CBS_pair; cl09141 579112005057 DHHA2 domain; Region: DHHA2; pfam02833 579112005058 Protein of unknown function (DUF2899); Region: DUF2899; pfam11449 579112005059 trimethylamine N-oxide reductase I catalytic subunit; Provisional; Region: PRK15102 579112005060 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 579112005061 molybdopterin cofactor binding site [chemical binding]; other site 579112005062 substrate binding site [chemical binding]; other site 579112005063 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 579112005064 molybdopterin cofactor binding site; other site 579112005065 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 579112005066 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 579112005067 Periplasmic nitrate reductase protein NapE; Region: NapE; cl01848 579112005068 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 579112005069 Phosphate-starvation-inducible E; Region: PsiE; cl01264 579112005070 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 579112005071 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005072 NAD(P) binding site [chemical binding]; other site 579112005073 active site 579112005074 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 579112005075 putative active site [active] 579112005076 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 579112005077 Intracellular septation protein A; Region: IspA; cl01098 579112005078 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain...; Region: BFIT_BACH; cd03442 579112005079 YCII-related domain; Region: YCII; cl00999 579112005080 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 579112005081 N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by...; Region: CIMS_N_terminal_like; cd03312 579112005082 THF binding site; other site 579112005083 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 catalyses the last step in the production of methionine by...; Region: CIMS_C_terminal_like; cd03311 579112005084 substrate binding site [chemical binding]; other site 579112005085 THF binding site; other site 579112005086 zinc-binding site [ion binding]; other site 579112005087 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 579112005088 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112005089 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 579112005090 putative dimerization interface [polypeptide binding]; other site 579112005091 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 579112005092 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 579112005093 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 579112005094 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 579112005095 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 579112005096 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112005097 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 579112005098 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-...; Region: CBS_pair; cl09141 579112005099 hypothetical protein; Provisional; Region: PRK01254 579112005100 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; cl15259 579112005101 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 579112005102 LysE type translocator; Region: LysE; cl00565 579112005103 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 579112005104 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112005105 cell division protein MukB; Provisional; Region: mukB; PRK04863 579112005106 MukB N-terminal; Region: MukB; pfam04310 579112005107 MukE-like family; Region: MukE; cl11471 579112005108 KicB killing factor; Region: KicB; cl11468 579112005109 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 579112005110 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 579112005111 S-adenosylmethionine binding site [chemical binding]; other site 579112005112 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 579112005113 putative active site [active] 579112005114 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 579112005115 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112005116 active site 579112005117 phosphorylation site [posttranslational modification] 579112005118 intermolecular recognition site; other site 579112005119 dimerization interface [polypeptide binding]; other site 579112005120 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...; Region: trans_reg_C; cd00383 579112005121 DNA binding site [nucleotide binding] 579112005122 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 579112005123 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 579112005124 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112005125 DNA binding site [nucleotide binding] 579112005126 domain linker motif; other site 579112005127 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 579112005128 dimerization interface [polypeptide binding]; other site 579112005129 ligand binding site [chemical binding]; other site 579112005130 TfoX N-terminal domain; Region: TfoX_N; cl01167 579112005131 TfoX N-terminal domain; Region: TfoX_N; cl01167 579112005132 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 579112005133 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 579112005134 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 579112005135 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 579112005136 glycogen synthase; Provisional; Region: glgA; PRK00654 579112005137 ADP-binding pocket [chemical binding]; other site 579112005138 homodimer interface [polypeptide binding]; other site 579112005139 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00844 579112005140 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 579112005141 ligand binding site [chemical binding]; other site 579112005142 oligomer interface [polypeptide binding]; other site 579112005143 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 rate-...; Region: LbH_G1P_AT_C; cd04651 579112005144 N-terminal domain interface [polypeptide binding]; other site 579112005145 sulfate 1 binding site; other site 579112005146 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 579112005147 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...; Region: TOPRIM_TopoIA_TopoI; cd03363 579112005148 active site 579112005149 interdomain interaction site; other site 579112005150 putative metal-binding site [ion binding]; other site 579112005151 nucleotide binding site [chemical binding]; other site 579112005152 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...; Region: TOP1Ac; cd00186 579112005153 domain I; other site 579112005154 DNA binding groove [nucleotide binding] 579112005155 phosphate binding site [ion binding]; other site 579112005156 domain II; other site 579112005157 domain III; other site 579112005158 nucleotide binding site [chemical binding]; other site 579112005159 catalytic site [active] 579112005160 domain IV; other site 579112005161 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 579112005162 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 579112005163 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 579112005164 Protein of unknown function (DUF2498); Region: DUF2498; cl11671 579112005165 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 579112005166 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 5-enolpyruvylshkimate-3-...; Region: EPSP_synthase; cd01556 579112005167 hinge; other site 579112005168 active site 579112005169 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 579112005170 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 579112005171 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 579112005172 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 579112005173 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 579112005174 rRNA binding site [nucleotide binding]; other site 579112005175 predicted 30S ribosome binding site; other site 579112005176 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 579112005177 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 579112005178 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005179 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 579112005180 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 579112005181 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 579112005182 active site 579112005183 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 579112005184 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112005185 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112005186 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 579112005187 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cl00342 579112005188 Protein of unknown function (DUF1496); Region: DUF1496; pfam07383 579112005189 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 579112005190 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 579112005191 tetramerization interface [polypeptide binding]; other site 579112005192 NAD(P) binding site [chemical binding]; other site 579112005193 catalytic residues [active] 579112005194 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112005195 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112005196 Surface antigen; Region: Bac_surface_Ag; cl03097 579112005197 Mechanosensitive ion channel; Region: MS_channel; pfam00924 579112005198 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 579112005199 Paraquat-inducible protein A; Region: PqiA; pfam04403 579112005200 Paraquat-inducible protein A; Region: PqiA; pfam04403 579112005201 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 579112005202 mce related protein; Region: MCE; pfam02470 579112005203 mce related protein; Region: MCE; pfam02470 579112005204 mce related protein; Region: MCE; pfam02470 579112005205 Protein of unknown function (DUF330); Region: DUF330; cl01135 579112005206 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 579112005207 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 579112005208 integrase; Provisional; Region: PRK09692 579112005209 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 579112005210 active site 579112005211 Int/Topo IB signature motif; other site 579112005212 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 579112005213 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005214 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 579112005215 ATP binding site [chemical binding]; other site 579112005216 putative Mg++ binding site [ion binding]; other site 579112005217 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112005218 Restriction endonuclease; Region: Mrr_cat; cl00747 579112005219 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 579112005220 ligand binding site [chemical binding]; other site 579112005221 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 579112005222 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 579112005223 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 579112005224 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 579112005225 ATP binding site [chemical binding]; other site 579112005226 putative Mg++ binding site [ion binding]; other site 579112005227 Protein of unknown function DUF262; Region: DUF262; cl14890 579112005228 Protein of unknown function DUF262; Region: DUF262; cl14890 579112005229 Protein of unknown function DUF262; Region: DUF262; cl14890 579112005230 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 579112005231 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 579112005232 HsdM N-terminal domain; Region: HsdM_N; pfam12161 579112005233 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 579112005234 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112005235 Predicted transcriptional regulator [Transcription]; Region: COG2378 579112005236 mutatrotase, YjhT family; Region: muta_rot_YjhT; TIGR03547 579112005237 Kelch motif; Region: Kelch_1; cl02701 579112005238 N-acetylneuraminic acid mutarotase; Provisional; Region: PRK14131 579112005239 Kelch motif; Region: Kelch_1; cl02701 579112005240 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 579112005241 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...; Region: SIS_RpiR; cd05013 579112005242 putative active site [active] 579112005243 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 579112005244 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 579112005245 catalytic residue [active] 579112005246 DctM-like transporters; Region: DctM; pfam06808 579112005247 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; cl09110 579112005248 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 579112005249 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 579112005250 Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]; Region: NanE; COG3010 579112005251 N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family...; Region: NanE; cd04729 579112005252 putative active site cavity [active] 579112005253 N-acetylmannosamine kinase; Provisional; Region: PRK05082 579112005254 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 579112005255 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 579112005256 N-acetylglucosamine-6-phosphate deacetylase; Region: nagA; TIGR00221 579112005257 active site 579112005258 dimer interface [polypeptide binding]; other site 579112005259 Neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: NanH; COG4409 579112005260 Vibrio cholerae sialidase, lectin insertion; Region: Sial-lect-inser; pfam09264 579112005261 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cd00260 579112005262 Vibrio cholerae sialidase, lectin insertion; Region: Sial-lect-inser; pfam09264 579112005263 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cd00260 579112005264 Asp-box motif; other site 579112005265 catalytic site [active] 579112005266 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 579112005267 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 579112005268 MPN+ (JAMM) motif; other site 579112005269 Zinc-binding site [ion binding]; other site 579112005270 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 579112005271 putative transposase OrfB; Reviewed; Region: PHA02517 579112005272 Integrase core domain; Region: rve; cl01316 579112005273 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; cl01116 579112005274 Predicted GTPase [General function prediction only]; Region: COG3596 579112005275 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 579112005276 Switch I region; other site 579112005277 Switch II region; other site 579112005278 G3 box; other site 579112005279 G4 box; other site 579112005280 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 579112005281 Protein of unknown function (DUF2986); Region: DUF2986; pfam11661 579112005282 LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback...; Region: LabA_like; cd06167 579112005283 putative metal binding site [ion binding]; other site 579112005284 Protein of unknown function, DUF393; Region: DUF393; cl01136 579112005285 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 579112005286 DNA photolyase; Region: DNA_photolyase; pfam00875 579112005287 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 579112005288 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005289 NAD(P) binding site [chemical binding]; other site 579112005290 active site 579112005291 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 579112005292 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 579112005293 GAF domain; Region: GAF; cl00853 579112005294 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...; Region: AAA; cd00009 579112005295 Walker A motif; other site 579112005296 ATP binding site [chemical binding]; other site 579112005297 Walker B motif; other site 579112005298 arginine finger; other site 579112005299 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112005300 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 579112005301 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 579112005302 NAD(P) binding site [chemical binding]; other site 579112005303 catalytic residues [active] 579112005304 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 579112005305 active site 579112005306 phosphorylation site [posttranslational modification] 579112005307 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112005308 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...; Region: PTS_IIB_fructose; cd05569 579112005309 P-loop; other site 579112005310 active site 579112005311 phosphorylation site [posttranslational modification] 579112005312 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 579112005313 active site 579112005314 phosphorylation site [posttranslational modification] 579112005315 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112005316 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...; Region: PTS_IIB_fructose; cd05569 579112005317 P-loop; other site 579112005318 active site 579112005319 phosphorylation site [posttranslational modification] 579112005320 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...; Region: PTS_IIB_fructose; cd05569 579112005321 P-loop; other site 579112005322 active site 579112005323 phosphorylation site [posttranslational modification] 579112005324 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 579112005325 regulatory protein interface [polypeptide binding]; other site 579112005326 active site 579112005327 regulatory phosphorylation site [posttranslational modification]; other site 579112005328 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 579112005329 active site 579112005330 phosphorylation site [posttranslational modification] 579112005331 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112005332 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112005333 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 579112005334 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 579112005335 active site 579112005336 phosphorylation site [posttranslational modification] 579112005337 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...; Region: PTS_IIB_fructose; cd05569 579112005338 P-loop; other site 579112005339 active site 579112005340 phosphorylation site [posttranslational modification] 579112005341 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112005342 mannose-6-phosphate isomerase; Provisional; Region: PRK15131 579112005343 mannose-6-phosphate isomerase, class I; Region: manA; TIGR00218 579112005344 mannose-6-phosphate isomerase, class I; Region: manA; TIGR00218 579112005345 Protein of unknown function (DUF1144); Region: DUF1144; pfam06610 579112005346 Cache domain; Region: Cache_1; pfam02743 579112005347 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 579112005348 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112005349 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 trans-...; Region: HisKA; cd00082 579112005350 dimer interface [polypeptide binding]; other site 579112005351 phosphorylation site [posttranslational modification] 579112005352 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 579112005353 ATP binding site [chemical binding]; other site 579112005354 Mg2+ binding site [ion binding]; other site 579112005355 G-X-G motif; other site 579112005356 Response regulator receiver domain; Region: Response_reg; pfam00072 579112005357 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112005358 active site 579112005359 phosphorylation site [posttranslational modification] 579112005360 intermolecular recognition site; other site 579112005361 dimerization interface [polypeptide binding]; other site 579112005362 Uncharacterised protein family (UPF0149); Region: UPF0149; cl01173 579112005363 Quinolinate synthetase A protein; Region: NadA; cl00420 579112005364 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 579112005365 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 579112005366 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 579112005367 ligand binding site [chemical binding]; other site 579112005368 translocation protein TolB; Provisional; Region: tolB; PRK04792 579112005369 TolB amino-terminal domain; Region: TolB_N; pfam04052 579112005370 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 579112005371 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 579112005372 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 579112005373 Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]; Region: TolA; COG3064 579112005374 Gram-negative bacterial tonB protein; Region: TonB; cl10048 579112005375 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 579112005376 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 579112005377 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 579112005378 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...; Region: 4HBT; cd00586 579112005379 active site 579112005380 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; cl11451 579112005381 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 579112005382 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 579112005383 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 579112005384 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 579112005385 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 579112005386 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 579112005387 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...; Region: AAA; cd00009 579112005388 Walker A motif; other site 579112005389 ATP binding site [chemical binding]; other site 579112005390 Walker B motif; other site 579112005391 arginine finger; other site 579112005392 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 579112005393 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 579112005394 RuvA N terminal domain; Region: RuvA_N; pfam01330 579112005395 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 579112005396 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 579112005397 active site 579112005398 putative DNA-binding cleft [nucleotide binding]; other site 579112005399 dimer interface [polypeptide binding]; other site 579112005400 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 579112005401 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 579112005402 active site 579112005403 HIGH motif; other site 579112005404 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 579112005405 KMSKS motif; other site 579112005406 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 579112005407 tRNA binding surface [nucleotide binding]; other site 579112005408 anticodon binding site; other site 579112005409 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 579112005410 substrate binding site [chemical binding]; other site 579112005411 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 579112005412 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 579112005413 putative active site [active] 579112005414 putative metal binding site [ion binding]; other site 579112005415 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 579112005416 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 579112005417 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112005418 hypothetical protein; Provisional; Region: PRK02250 579112005419 SEC-C motif; Region: SEC-C; cl12132 579112005420 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 579112005421 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface...; Region: gram_neg_porins; cd00342 579112005422 trimer interface [polypeptide binding]; other site 579112005423 eyelet of channel; other site 579112005424 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 579112005425 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112005426 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112005427 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 579112005428 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 579112005429 Primosomal replication protein priB and priC; Region: priB_priC; cl11483 579112005430 Protein of unknown function (DUF2496); Region: DUF2496; cl11670 579112005431 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 connected by an extended linker. The...; Region: HAMP; cd06225 579112005432 dimerization interface [polypeptide binding]; other site 579112005433 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112005434 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112005435 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 579112005436 putative phosphate binding site [ion binding]; other site 579112005437 putative catalytic site [active] 579112005438 active site 579112005439 metal binding site A [ion binding]; metal-binding site 579112005440 DNA binding site [nucleotide binding] 579112005441 putative AP binding site [nucleotide binding]; other site 579112005442 putative metal binding site B [ion binding]; other site 579112005443 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 579112005444 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...; Region: TM_PBP2; cd06261 579112005445 dimer interface [polypeptide binding]; other site 579112005446 conserved gate region; other site 579112005447 putative PBP binding loops; other site 579112005448 ABC-ATPase subunit interface; other site 579112005449 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 579112005450 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...; Region: TM_PBP2; cd06261 579112005451 dimer interface [polypeptide binding]; other site 579112005452 conserved gate region; other site 579112005453 putative PBP binding loops; other site 579112005454 ABC-ATPase subunit interface; other site 579112005455 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 579112005456 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...; Region: PBPb; cd00134 579112005457 substrate binding pocket [chemical binding]; other site 579112005458 membrane-bound complex binding site; other site 579112005459 hinge residues; other site 579112005460 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 579112005461 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 579112005462 Walker A/P-loop; other site 579112005463 ATP binding site [chemical binding]; other site 579112005464 Q-loop/lid; other site 579112005465 ABC transporter signature motif; other site 579112005466 Walker B; other site 579112005467 D-loop; other site 579112005468 H-loop/switch region; other site 579112005469 Protein of unknown function (DUF3360); Region: DUF3360; pfam11840 579112005470 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 579112005471 Pyruvate formate lyase 1; Region: PFL1; cd01678 579112005472 coenzyme A binding site [chemical binding]; other site 579112005473 active site 579112005474 catalytic residues [active] 579112005475 glycine loop; other site 579112005476 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; cl01409 579112005477 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112005478 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112005479 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112005480 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 579112005481 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 579112005482 FeS/SAM binding site; other site 579112005483 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 579112005484 YfbU domain; Region: YfbU; cl01137 579112005485 PrkA family serine protein kinase; Provisional; Region: PRK15455 579112005486 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112005487 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 579112005488 Protein of unknown function (DUF444); Region: DUF444; pfam04285 579112005489 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 579112005490 SpoVR family protein; Provisional; Region: PRK11767 579112005491 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 579112005492 Transposase IS200 like; Region: Y1_Tnp; cl00848 579112005493 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 579112005494 Ligand binding site [chemical binding]; other site 579112005495 oligomer interface [polypeptide binding]; other site 579112005496 Trm112p-like protein; Region: Trm112p; cl01066 579112005497 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 579112005498 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 579112005499 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 579112005500 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 579112005501 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 579112005502 Walker A/P-loop; other site 579112005503 ATP binding site [chemical binding]; other site 579112005504 Q-loop/lid; other site 579112005505 ABC transporter signature motif; other site 579112005506 Walker B; other site 579112005507 D-loop; other site 579112005508 H-loop/switch region; other site 579112005509 ComEC family competence protein; Provisional; Region: PRK11539 579112005510 Competence protein; Region: Competence; cl00471 579112005511 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112005512 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 579112005513 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 579112005514 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 579112005515 FtsX-like permease family; Region: FtsX; pfam02687 579112005516 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 579112005517 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 579112005518 Walker A/P-loop; other site 579112005519 ATP binding site [chemical binding]; other site 579112005520 Q-loop/lid; other site 579112005521 ABC transporter signature motif; other site 579112005522 Walker B; other site 579112005523 D-loop; other site 579112005524 H-loop/switch region; other site 579112005525 outer membrane-specific lipoprotein transporter subunit LolC; Provisional; Region: PRK10814 579112005526 FtsX-like permease family; Region: FtsX; pfam02687 579112005527 PilZ domain; Region: PilZ; cl01260 579112005528 transcription-repair coupling factor; Provisional; Region: PRK10689 579112005529 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 579112005530 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 579112005531 ATP binding site [chemical binding]; other site 579112005532 putative Mg++ binding site [ion binding]; other site 579112005533 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 579112005534 nucleotide binding region [chemical binding]; other site 579112005535 ATP-binding site [chemical binding]; other site 579112005536 TRCF domain; Region: TRCF; cl04088 579112005537 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 579112005538 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 579112005539 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112005540 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 579112005541 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005542 Uncharacterised protein family (UPF0227); Region: UPF0227; cl14886 579112005543 Phosphotransferase enzyme family; Region: APH; pfam01636 579112005544 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 579112005545 active site 579112005546 substrate binding site [chemical binding]; other site 579112005547 ATP binding site [chemical binding]; other site 579112005548 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 579112005549 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 579112005550 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG5633 579112005551 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 579112005552 putative dimer interface [polypeptide binding]; other site 579112005553 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 579112005554 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 579112005555 nucleotide binding site/active site [active] 579112005556 HIT family signature motif; other site 579112005557 catalytic residue [active] 579112005558 CHASE3 domain; Region: CHASE3; cl05000 579112005559 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112005560 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112005561 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112005562 Domain of unknown function (DUF1887); Region: DUF1887; pfam09002 579112005563 fatty acid metabolism regulator; Provisional; Region: PRK04984 579112005564 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 579112005565 DNA-binding site [nucleotide binding]; DNA binding site 579112005566 FCD domain; Region: FCD; cl11656 579112005567 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; cl09110 579112005568 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 579112005569 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 579112005570 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112005571 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 579112005572 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 579112005573 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112005574 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 579112005575 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; pfam05222 579112005576 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005577 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 579112005578 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112005579 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 579112005580 substrate binding site [chemical binding]; other site 579112005581 dimerization interface [polypeptide binding]; other site 579112005582 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 579112005583 active site 579112005584 dinuclear metal binding site [ion binding]; other site 579112005585 dimerization interface [polypeptide binding]; other site 579112005586 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 579112005587 active site 579112005588 dimer interface [polypeptide binding]; other site 579112005589 tetratricopeptide repeat protein; Provisional; Region: PRK11788 579112005590 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 579112005591 binding surface 579112005592 TPR motif; other site 579112005593 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 579112005594 binding surface 579112005595 TPR motif; other site 579112005596 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 579112005597 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 higher-...; Region: HU_IHF; cd00591 579112005598 IHF dimer interface [polypeptide binding]; other site 579112005599 IHF - DNA interface [nucleotide binding]; other site 579112005600 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 579112005601 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 579112005602 RNA binding site [nucleotide binding]; other site 579112005603 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 579112005604 RNA binding site [nucleotide binding]; other site 579112005605 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 579112005606 RNA binding site [nucleotide binding]; other site 579112005607 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec4; cd05689 579112005608 RNA binding site [nucleotide binding]; other site 579112005609 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 579112005610 RNA binding site [nucleotide binding]; other site 579112005611 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec6; cd05691 579112005612 RNA binding site [nucleotide binding]; other site 579112005613 cytidylate kinase; Provisional; Region: cmk; PRK00023 579112005614 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 579112005615 CMP-binding site; other site 579112005616 The sites determining sugar specificity; other site 579112005617 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 579112005618 periplasmic folding chaperone; Provisional; Region: PRK10788 579112005619 SurA N-terminal domain; Region: SurA_N; pfam09312 579112005620 PPIC-type PPIASE domain; Region: Rotamase; cl08278 579112005621 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 higher-...; Region: HU_IHF; cd00591 579112005622 IHF dimer interface [polypeptide binding]; other site 579112005623 IHF - DNA interface [nucleotide binding]; other site 579112005624 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 579112005625 Found in ATP-dependent protease La (LON); Region: LON; smart00464 579112005626 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...; Region: AAA; cd00009 579112005627 Walker A motif; other site 579112005628 ATP binding site [chemical binding]; other site 579112005629 Walker B motif; other site 579112005630 arginine finger; other site 579112005631 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 579112005632 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 579112005633 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 579112005634 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...; Region: AAA; cd00009 579112005635 Walker A motif; other site 579112005636 ATP binding site [chemical binding]; other site 579112005637 Walker B motif; other site 579112005638 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 579112005639 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 579112005640 oligomer interface [polypeptide binding]; other site 579112005641 active site residues [active] 579112005642 trigger factor; Provisional; Region: tig; PRK01490 579112005643 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 579112005644 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 579112005645 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 579112005646 EAL-domain associated signalling protein domain; Region: YkuI_C; pfam10388 579112005647 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 trans-...; Region: HisKA; cd00082 579112005648 dimer interface [polypeptide binding]; other site 579112005649 phosphorylation site [posttranslational modification] 579112005650 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 579112005651 ATP binding site [chemical binding]; other site 579112005652 Mg2+ binding site [ion binding]; other site 579112005653 G-X-G motif; other site 579112005654 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 579112005655 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112005656 active site 579112005657 phosphorylation site [posttranslational modification] 579112005658 intermolecular recognition site; other site 579112005659 dimerization interface [polypeptide binding]; other site 579112005660 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...; Region: AAA; cd00009 579112005661 Walker A motif; other site 579112005662 ATP binding site [chemical binding]; other site 579112005663 Walker B motif; other site 579112005664 arginine finger; other site 579112005665 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112005666 DctM-like transporters; Region: DctM; pfam06808 579112005667 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; cl09110 579112005668 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 579112005669 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 579112005670 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 579112005671 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 579112005672 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 579112005673 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112005674 metal binding site [ion binding]; metal-binding site 579112005675 active site 579112005676 I-site; other site 579112005677 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 579112005678 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 579112005679 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 579112005680 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 579112005681 putative acyl-acceptor binding pocket; other site 579112005682 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...; Region: 4HBT; cd00586 579112005683 active site 579112005684 LysE type translocator; Region: LysE; cl00565 579112005685 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 579112005686 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; cl11391 579112005687 OpgC protein; Region: OpgC_C; cl10497 579112005688 Acyltransferase family; Region: Acyl_transf_3; pfam01757 579112005689 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 579112005690 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 579112005691 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 579112005692 homodimer interface [polypeptide binding]; other site 579112005693 NADP binding site [chemical binding]; other site 579112005694 substrate binding site [chemical binding]; other site 579112005695 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 579112005696 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 579112005697 substrate binding pocket [chemical binding]; other site 579112005698 active site 579112005699 iron coordination sites [ion binding]; other site 579112005700 hypothetical protein; Provisional; Region: PRK07190 579112005701 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005702 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112005703 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112005704 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112005705 putative effector binding pocket; other site 579112005706 dimerization interface [polypeptide binding]; other site 579112005707 Pyoverdine/dityrosine biosynthesis protein [Secondary metabolites biosynthesis, transport, and catabolism]; Region: DIT1; COG3207 579112005708 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 579112005709 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG...; Region: CAS_like; cl00184 579112005710 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 579112005711 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 579112005712 molybdopterin cofactor binding site [chemical binding]; other site 579112005713 substrate binding site [chemical binding]; other site 579112005714 The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-like; cd02777 579112005715 molybdopterin cofactor binding site; other site 579112005716 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 579112005717 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 579112005718 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 579112005719 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 579112005720 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 579112005721 GH18 domain of Chitinase D (ChiD). ChiD, a chitinase found in Bacillus circulans, hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine in chitin and chitodextrins. The domain architecture of ChiD includes a catalytic glycosyl hydrolase family 18 (...; Region: GH18_chitinase_D-like; cd02871 579112005722 Glycosyl hydrolases family 18; Region: Glyco_hydro_18; pfam00704 579112005723 putative active site [active] 579112005724 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 579112005725 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 579112005726 Nucleoside recognition; Region: Gate; cl00486 579112005727 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 579112005728 transcriptional activator TtdR; Provisional; Region: PRK09801 579112005729 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112005730 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112005731 putative effector binding pocket; other site 579112005732 dimerization interface [polypeptide binding]; other site 579112005733 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 579112005734 lytic murein transglycosylase; Region: MltB_2; TIGR02283 579112005735 YcgL domain; Region: YcgL; cl01189 579112005736 septum formation inhibitor; Reviewed; Region: minC; PRK04804 579112005737 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 579112005738 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 579112005739 cell division inhibitor MinD; Provisional; Region: PRK10818 579112005740 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...; Region: MinD; cd02036 579112005741 Switch I; other site 579112005742 Switch II; other site 579112005743 Septum formation topological specificity factor MinE; Region: MinE; cl00538 579112005744 Uncharacterized lipoprotein NlpE involved in copper resistance; Region: NlpE; cl01138 579112005745 Protein of unknown function (DUF1244); Region: DUF1244; cl01385 579112005746 lysophospholipid transporter LplT; Provisional; Region: PRK11195 579112005747 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 579112005748 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 579112005749 putative acyl-acceptor binding pocket; other site 579112005750 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112005751 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112005752 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112005753 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 579112005754 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 579112005755 non-specific DNA binding site [nucleotide binding]; other site 579112005756 salt bridge; other site 579112005757 sequence-specific DNA binding site [nucleotide binding]; other site 579112005758 Cupin domain; Region: Cupin_2; cl09118 579112005759 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 579112005760 Sulfate transporter family; Region: Sulfate_transp; cl00967 579112005761 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 579112005762 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112005763 O-succinylbenzoate synthase; Provisional; Region: PRK05105 579112005764 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway...; Region: OSBS; cd03320 579112005765 active site 579112005766 dihydroxynaphthoic acid synthetase; Validated; Region: PRK07396 579112005767 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 579112005768 substrate binding site [chemical binding]; other site 579112005769 oxyanion hole (OAH) forming residues; other site 579112005770 trimer interface [polypeptide binding]; other site 579112005771 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Provisional; Region: PRK11126 579112005772 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 579112005773 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 579112005774 dimer interface [polypeptide binding]; other site 579112005775 tetramer interface [polypeptide binding]; other site 579112005776 PYR/PP interface [polypeptide binding]; other site 579112005777 TPP binding site [chemical binding]; other site 579112005778 TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key role in the menaquinone biosynthetic pathway, converting...; Region: TPP_SHCHC_synthase; cd02009 579112005779 TPP-binding site; other site 579112005780 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 579112005781 chorismate binding enzyme; Region: Chorismate_bind; cl10555 579112005782 tyrosine aminotransferase, eukaryotic; Region: tyr_amTase_E; TIGR01264 579112005783 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 579112005784 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112005785 homodimer interface [polypeptide binding]; other site 579112005786 catalytic residue [active] 579112005787 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112005788 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112005789 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 579112005790 DTW domain; Region: DTW; cl01221 579112005791 Rhomboid family; Region: Rhomboid; cl11446 579112005792 Oligoendopeptidase F [Amino acid transport and metabolism]; Region: COG1164 579112005793 Peptidase M3-like family, a zincin metallopeptidase, includes M3 and M32 families; Region: M3_like; cd06258 579112005794 active site 579112005795 Zn binding site [ion binding]; other site 579112005796 ribonuclease D; Region: rnd; TIGR01388 579112005797 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 579112005798 putative active site [active] 579112005799 catalytic site [active] 579112005800 putative substrate binding site [chemical binding]; other site 579112005801 HRDC domain; Region: HRDC; cl02578 579112005802 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 579112005803 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112005804 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 579112005805 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation', the process of becoming...; Region: Lipase; cl14883 579112005806 Outer membrane lipoprotein Slp family; Region: Slp; cl01164 579112005807 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 579112005808 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 579112005809 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112005810 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112005811 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 579112005812 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 579112005813 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 579112005814 putative substrate binding site [chemical binding]; other site 579112005815 putative active site [active] 579112005816 putative cosubstrate binding site; other site 579112005817 catalytic site [active] 579112005818 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 579112005819 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 579112005820 active site 579112005821 FMN binding site [chemical binding]; other site 579112005822 2,4-decadienoyl-CoA binding site; other site 579112005823 catalytic residue [active] 579112005824 4Fe-4S cluster binding site [ion binding]; other site 579112005825 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 579112005826 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005827 protease 4; Provisional; Region: PRK10949 579112005828 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 579112005829 tandem repeat interface [polypeptide binding]; other site 579112005830 oligomer interface [polypeptide binding]; other site 579112005831 active site residues [active] 579112005832 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 579112005833 tandem repeat interface [polypeptide binding]; other site 579112005834 oligomer interface [polypeptide binding]; other site 579112005835 active site residues [active] 579112005836 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cl00216 579112005837 active site/substrate binding site [active] 579112005838 tetramer interface [polypeptide binding]; other site 579112005839 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 579112005840 Protein of unknown function (DUF2989); Region: DUF2989; pfam11207 579112005841 SelR domain; Region: SelR; cl00369 579112005842 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 579112005843 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 579112005844 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 579112005845 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 579112005846 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 579112005847 active site 579112005848 phosphate binding residues; other site 579112005849 catalytic residues [active] 579112005850 Protein of unknown function (DUF2860); Region: DUF2860; pfam11059 579112005851 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 579112005852 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112005853 Protein of unknown function, DUF399; Region: DUF399; cl01139 579112005854 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112005855 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 579112005856 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112005857 active site 579112005858 phosphorylation site [posttranslational modification] 579112005859 intermolecular recognition site; other site 579112005860 dimerization interface [polypeptide binding]; other site 579112005861 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 579112005862 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 579112005863 pyruvate kinase; Provisional; Region: PRK05826 579112005864 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 579112005865 domain interfaces; other site 579112005866 active site 579112005867 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 579112005868 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 579112005869 active site 579112005870 nucleophile elbow; other site 579112005871 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 579112005872 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 579112005873 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 579112005874 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112005875 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...; Region: PTS_IIB_glc; cd00212 579112005876 active site turn [active] 579112005877 phosphorylation site [posttranslational modification] 579112005878 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 579112005879 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 579112005880 active site 579112005881 DNA polymerase III subunit delta'; Validated; Region: PRK06090 579112005882 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112005883 C terminal; Region: DNApol3-delta_C; pfam09115 579112005884 thymidylate kinase; Validated; Region: tmk; PRK00698 579112005885 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting...; Region: TMPK; cd01672 579112005886 TMP-binding site; other site 579112005887 ATP-binding site [chemical binding]; other site 579112005888 YceG-like family; Region: YceG; pfam02618 579112005889 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 579112005890 dimerization interface [polypeptide binding]; other site 579112005891 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 579112005892 Aminotransferase class IV; Region: Aminotran_4; pfam01063 579112005893 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112005894 catalytic residue [active] 579112005895 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08722 579112005896 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 579112005897 dimer interface [polypeptide binding]; other site 579112005898 active site 579112005899 Phosphopantetheine attachment site; Region: PP-binding; cl09936 579112005900 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 579112005901 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 579112005902 NAD(P) binding site [chemical binding]; other site 579112005903 homotetramer interface [polypeptide binding]; other site 579112005904 homodimer interface [polypeptide binding]; other site 579112005905 active site 579112005906 Acyl transferase domain; Region: Acyl_transf_1; cl08282 579112005907 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 579112005908 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 579112005909 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 579112005910 dimer interface [polypeptide binding]; other site 579112005911 active site 579112005912 CoA binding pocket [chemical binding]; other site 579112005913 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 579112005914 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 579112005915 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 579112005916 Maf-like protein; Region: Maf; pfam02545 579112005917 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 579112005918 active site 579112005919 dimer interface [polypeptide binding]; other site 579112005920 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 579112005921 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 579112005922 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 579112005923 active site 579112005924 ribonuclease E; Reviewed; Region: rne; PRK10811 579112005925 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 579112005926 homodimer interface [polypeptide binding]; other site 579112005927 oligonucleotide binding site [chemical binding]; other site 579112005928 ribonuclease E; Reviewed; Region: rne; PRK10811 579112005929 ribonuclease E; Reviewed; Region: rne; PRK10811 579112005930 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 579112005931 Sulfate transporter family; Region: Sulfate_transp; cl00967 579112005932 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 579112005933 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 579112005934 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 579112005935 putative catalytic cysteine [active] 579112005936 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 579112005937 putative active site [active] 579112005938 metal binding site [ion binding]; metal-binding site 579112005939 MarC family integral membrane protein; Region: MarC; cl00919 579112005940 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 579112005941 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112005942 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 579112005943 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 579112005944 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; cl09110 579112005945 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 579112005946 Nucleoid-associated protein [General function prediction only]; Region: COG3081 579112005947 nucleoid-associated protein NdpA; Validated; Region: PRK00378 579112005948 Protein of unknown function (DUF1414); Region: DUF1414; cl01175 579112005949 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 579112005950 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 579112005951 Sulfatase; Region: Sulfatase; cl10460 579112005952 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 579112005953 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:...; Region: TOPRIM_TopoIA_TopoIII; cd03362 579112005954 DNA topoisomerase III; Provisional; Region: PRK07726 579112005955 active site 579112005956 putative interdomain interaction site [polypeptide binding]; other site 579112005957 putative metal-binding site [ion binding]; other site 579112005958 putative nucleotide binding site [chemical binding]; other site 579112005959 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...; Region: TOP1Ac; cd00186 579112005960 domain I; other site 579112005961 DNA binding groove [nucleotide binding] 579112005962 phosphate binding site [ion binding]; other site 579112005963 domain II; other site 579112005964 domain III; other site 579112005965 nucleotide binding site [chemical binding]; other site 579112005966 catalytic site [active] 579112005967 domain IV; other site 579112005968 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 579112005969 putative GSH binding site [chemical binding]; other site 579112005970 catalytic residues [active] 579112005971 superoxide dismutase; Provisional; Region: PRK10543 579112005972 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 579112005973 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 579112005974 Ribosomal S4P (gammaproteobacterial); Region: Ribosomal_S4Pg; pfam11993 579112005975 classical (c) SDRs; Region: SDR_c; cd05233 579112005976 NAD(P) binding site [chemical binding]; other site 579112005977 active site 579112005978 VacJ like lipoprotein; Region: VacJ; cl01073 579112005979 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 579112005980 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 579112005981 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 579112005982 binding surface 579112005983 TPR motif; other site 579112005984 Cytochrome C biogenesis protein; Region: CcmH; cl01179 579112005985 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 579112005986 catalytic residues [active] 579112005987 central insert; other site 579112005988 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 579112005989 CcmE; Region: CcmE; cl00994 579112005990 Heme exporter protein D (CcmD); Region: CcmD; cl11475 579112005991 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 579112005992 CcmB protein; Region: CcmB; cl01016 579112005993 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 579112005994 CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH); Region: ABC_CcmA_heme_exporter; cd03231 579112005995 Walker A/P-loop; other site 579112005996 ATP binding site [chemical binding]; other site 579112005997 Q-loop/lid; other site 579112005998 ABC transporter signature motif; other site 579112005999 Walker B; other site 579112006000 D-loop; other site 579112006001 H-loop/switch region; other site 579112006002 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 579112006003 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 579112006004 putative CheA interaction surface; other site 579112006005 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 579112006006 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 579112006007 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...; Region: ParA; cd02042 579112006008 Magnesium ion binding site [ion binding]; other site 579112006009 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 579112006010 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112006011 active site 579112006012 phosphorylation site [posttranslational modification] 579112006013 intermolecular recognition site; other site 579112006014 CheB methylesterase; Region: CheB_methylest; pfam01339 579112006015 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 579112006016 putative binding surface; other site 579112006017 active site 579112006018 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 579112006019 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 579112006020 ATP binding site [chemical binding]; other site 579112006021 Mg2+ binding site [ion binding]; other site 579112006022 G-X-G motif; other site 579112006023 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 579112006024 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 579112006025 Response regulator receiver domain; Region: Response_reg; pfam00072 579112006026 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112006027 active site 579112006028 phosphorylation site [posttranslational modification] 579112006029 intermolecular recognition site; other site 579112006030 dimerization interface [polypeptide binding]; other site 579112006031 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 579112006032 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 579112006033 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 579112006034 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...; Region: Sigma70_r4; cd06171 579112006035 DNA binding residues [nucleotide binding] 579112006036 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112006037 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 579112006038 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 579112006039 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 579112006040 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112006041 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 579112006042 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 579112006043 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 579112006044 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 579112006045 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 579112006046 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 579112006047 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_4; cd07268 579112006048 putative metal binding site [ion binding]; other site 579112006049 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 579112006050 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 579112006051 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 579112006052 active site 579112006053 HIGH motif; other site 579112006054 KMSK motif region; other site 579112006055 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 579112006056 tRNA binding surface [nucleotide binding]; other site 579112006057 anticodon binding site; other site 579112006058 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the...; Region: HIT_like; cl00228 579112006059 FeoC like transcriptional regulator; Region: FeoC; cl07573 579112006060 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 579112006061 Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this...; Region: FeoB; cd01879 579112006062 G1 box; other site 579112006063 GTP/Mg2+ binding site [chemical binding]; other site 579112006064 Switch I region; other site 579112006065 G2 box; other site 579112006066 G3 box; other site 579112006067 Switch II region; other site 579112006068 G4 box; other site 579112006069 G5 box; other site 579112006070 Nucleoside recognition; Region: Gate; cl00486 579112006071 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 579112006072 Nucleoside recognition; Region: Gate; cl00486 579112006073 FeoA domain; Region: FeoA; cl00838 579112006074 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 579112006075 Helix-turn-helix domain; Region: HTH_18; pfam12833 579112006076 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112006077 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 579112006078 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 579112006079 metal binding site [ion binding]; metal-binding site 579112006080 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 579112006081 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-...; Region: ABC_Metallic_Cations; cd03235 579112006082 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112006083 dimer interface [polypeptide binding]; other site 579112006084 putative PBP binding regions; other site 579112006085 ABC-ATPase subunit interface; other site 579112006086 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 579112006087 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112006088 CoA-ligase; Region: Ligase_CoA; pfam00549 579112006089 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 579112006090 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112006091 CoA-ligase; Region: Ligase_CoA; pfam00549 579112006092 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 579112006093 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 579112006094 E3 interaction surface; other site 579112006095 lipoyl attachment site [posttranslational modification]; other site 579112006096 e3 binding domain; Region: E3_binding; pfam02817 579112006097 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 579112006098 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 579112006099 TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of...; Region: TPP_E1_OGDC_like; cd02016 579112006100 TPP-binding site [chemical binding]; other site 579112006101 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 579112006102 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 579112006103 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 579112006104 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112006105 domain; Region: Succ_DH_flav_C; pfam02910 579112006106 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 579112006107 SdhC subunit interface [polypeptide binding]; other site 579112006108 proximal heme binding site [chemical binding]; other site 579112006109 cardiolipin binding site; other site 579112006110 Iron-sulfur protein interface; other site 579112006111 proximal quinone binding site [chemical binding]; other site 579112006112 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 579112006113 Iron-sulfur protein interface; other site 579112006114 proximal quinone binding site [chemical binding]; other site 579112006115 SdhD (CybS) interface [polypeptide binding]; other site 579112006116 proximal heme binding site [chemical binding]; other site 579112006117 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 579112006118 dimer interface [polypeptide binding]; other site 579112006119 Citrate synthase; Region: Citrate_synt; pfam00285 579112006120 active site 579112006121 citrylCoA binding site [chemical binding]; other site 579112006122 NADH binding [chemical binding]; other site 579112006123 cationic pore residues; other site 579112006124 oxalacetate/citrate binding site [chemical binding]; other site 579112006125 coenzyme A binding site [chemical binding]; other site 579112006126 catalytic triad [active] 579112006127 Uncharacterized conserved protein [Function unknown]; Region: COG0327 579112006128 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 579112006129 Domain of unknown function (DUF1853); Region: DUF1853; cl01545 579112006130 phosphoglucomutase, alpha-D-glucose phosphate-specific; Region: pgm; TIGR01132 579112006131 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl...; Region: PGM_like3; cd05801 579112006132 active site 579112006133 substrate binding site [chemical binding]; other site 579112006134 metal binding site [ion binding]; metal-binding site 579112006135 SeqA protein; Region: SeqA; cl11470 579112006136 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 579112006137 acyl-CoA esterase; Provisional; Region: PRK10673 579112006138 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 579112006139 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 579112006140 LrgB-like family; Region: LrgB; cl00596 579112006141 LrgA family; Region: LrgA; cl00608 579112006142 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112006143 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112006144 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 579112006145 putative dimerization interface [polypeptide binding]; other site 579112006146 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 579112006147 CoenzymeA binding site [chemical binding]; other site 579112006148 subunit interaction site [polypeptide binding]; other site 579112006149 PHB binding site; other site 579112006150 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 579112006151 metal binding site 2 [ion binding]; metal-binding site 579112006152 putative DNA binding helix; other site 579112006153 metal binding site 1 [ion binding]; metal-binding site 579112006154 dimer interface [polypeptide binding]; other site 579112006155 structural Zn2+ binding site [ion binding]; other site 579112006156 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 579112006157 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112006158 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 579112006159 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 579112006160 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112006161 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 579112006162 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 579112006163 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 579112006164 dimer interface [polypeptide binding]; other site 579112006165 active site 579112006166 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112006167 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 579112006168 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 579112006169 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 579112006170 YfcL protein; Region: YfcL; pfam08891 579112006171 Protein of unknown function, DUF462; Region: DUF462; cl01190 579112006172 Predicted membrane protein [Function unknown]; Region: COG2860 579112006173 UPF0126 domain; Region: UPF0126; pfam03458 579112006174 UPF0126 domain; Region: UPF0126; pfam03458 579112006175 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 579112006176 Tetramer interface [polypeptide binding]; other site 579112006177 Active site [active] 579112006178 FMN-binding site [chemical binding]; other site 579112006179 HemK family putative methylases; Region: hemK_fam; TIGR00536 579112006180 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 579112006181 S-adenosylmethionine binding site [chemical binding]; other site 579112006182 Smr domain; Region: Smr; cl02619 579112006183 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 579112006184 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 579112006185 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 579112006186 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 579112006187 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 579112006188 FliP family; Region: FliP; cl00593 579112006189 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 579112006190 flagellar motor switch protein; Validated; Region: fliN; PRK05698 579112006191 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 579112006192 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 579112006193 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 579112006194 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 579112006195 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 579112006196 Flagellar FliJ protein; Region: FliJ; cl09161 579112006197 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 579112006198 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08972 579112006199 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 579112006200 Walker A motif/ATP binding site; other site 579112006201 Walker B motif; other site 579112006202 flagellar assembly protein H; Validated; Region: fliH; PRK05687 579112006203 Flagellar assembly protein FliH; Region: FliH; pfam02108 579112006204 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 579112006205 MgtE intracellular N domain; Region: MgtE_N; cl15244 579112006206 FliG C-terminal domain; Region: FliG_C; pfam01706 579112006207 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 579112006208 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 579112006209 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 579112006210 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 579112006211 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 579112006212 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112006213 active site 579112006214 phosphorylation site [posttranslational modification] 579112006215 intermolecular recognition site; other site 579112006216 dimerization interface [polypeptide binding]; other site 579112006217 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...; Region: AAA; cd00009 579112006218 Walker A motif; other site 579112006219 ATP binding site [chemical binding]; other site 579112006220 Walker B motif; other site 579112006221 arginine finger; other site 579112006222 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112006223 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 579112006224 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112006225 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 trans-...; Region: HisKA; cl00080 579112006226 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 579112006227 ATP binding site [chemical binding]; other site 579112006228 G-X-G motif; other site 579112006229 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 579112006230 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 579112006231 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...; Region: AAA; cd00009 579112006232 Walker A motif; other site 579112006233 ATP binding site [chemical binding]; other site 579112006234 Walker B motif; other site 579112006235 arginine finger; other site 579112006236 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112006237 Flagellar protein FliS; Region: FliS; cl00654 579112006238 Flagellar protein FliT; Region: FliT; cl05125 579112006239 flagellar capping protein; Validated; Region: fliD; PRK08724 579112006240 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 579112006241 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 579112006242 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 579112006243 FlaG protein; Region: FlaG; cl00591 579112006244 flagellin; Reviewed; Region: PRK08869 579112006245 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 579112006246 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 579112006247 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 579112006248 flagellin; Reviewed; Region: PRK08869 579112006249 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 579112006250 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 579112006251 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 579112006252 flagellin; Reviewed; Region: PRK08869 579112006253 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 579112006254 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 579112006255 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 579112006256 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 579112006257 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 579112006258 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 579112006259 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; cl11547 579112006260 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 579112006261 putative catalytic residues [active] 579112006262 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 579112006263 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 579112006264 metal binding site [ion binding]; metal-binding site 579112006265 dimer interface [polypeptide binding]; other site 579112006266 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: VanY; COG1876 579112006267 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 579112006268 Protein of unknown function (DUF2897); Region: DUF2897; pfam11446 579112006269 lipoprotein; Provisional; Region: PRK11679 579112006270 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 579112006271 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 579112006272 dihydrodipicolinate synthase; Region: dapA; TIGR00674 579112006273 dimer interface [polypeptide binding]; other site 579112006274 active site 579112006275 catalytic residue [active] 579112006276 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 579112006277 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_1; cd04893 579112006278 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 579112006279 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...; Region: PRX_BCP; cd03017 579112006280 catalytic triad [active] 579112006281 Vibrio chemotaxis protein N terminus; Region: MCP_N; pfam05581 579112006282 Cache domain; Region: Cache_1; pfam02743 579112006283 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112006284 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112006285 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112006286 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 579112006287 Domain of unknown function DUF20; Region: UPF0118; cl00465 579112006288 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 two-...; Region: SirA_YedF_YeeD; cd00291 579112006289 CPxP motif; other site 579112006290 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 579112006291 Peptidase family M48; Region: Peptidase_M48; cl12018 579112006292 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 579112006293 binding surface 579112006294 TPR motif; other site 579112006295 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 579112006296 catalytic residues [active] 579112006297 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 579112006298 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 579112006299 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; cl01278 579112006300 Permease family; Region: Xan_ur_permease; pfam00860 579112006301 Sulfate transporter family; Region: Sulfate_transp; cl00967 579112006302 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 579112006303 putative deacylase active site [active] 579112006304 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 579112006305 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 579112006306 active site 579112006307 metal binding site [ion binding]; metal-binding site 579112006308 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 579112006309 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 579112006310 NeuB family; Region: NeuB; cl00496 579112006311 Uncharacterized conserved protein [Function unknown]; Region: COG2912 579112006312 hypothetical protein; Provisional; Region: PRK10941 579112006313 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 579112006314 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 579112006315 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112006316 peptide chain release factor 1; Validated; Region: prfA; PRK00591 579112006317 RF-1 domain; Region: RF-1; cl02875 579112006318 RF-1 domain; Region: RF-1; cl02875 579112006319 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 579112006320 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 579112006321 tRNA; other site 579112006322 putative tRNA binding site [nucleotide binding]; other site 579112006323 putative NADP binding site [chemical binding]; other site 579112006324 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 579112006325 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 579112006326 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 579112006327 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 579112006328 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 579112006329 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 579112006330 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 579112006331 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 579112006332 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 579112006333 putative active site [active] 579112006334 catalytic residue [active] 579112006335 GTP-binding protein YchF; Reviewed; Region: PRK09601 579112006336 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 579112006337 G1 box; other site 579112006338 GTP/Mg2+ binding site [chemical binding]; other site 579112006339 Switch I region; other site 579112006340 G2 box; other site 579112006341 Switch II region; other site 579112006342 G3 box; other site 579112006343 G4 box; other site 579112006344 G5 box; other site 579112006345 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 579112006346 flagellin; Reviewed; Region: PRK08869 579112006347 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 579112006348 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 579112006349 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 579112006350 flagellin; Reviewed; Region: PRK08869 579112006351 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 579112006352 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 579112006353 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 579112006354 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 579112006355 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08871 579112006356 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 579112006357 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 579112006358 Rod binding protein; Region: Rod-binding; cl01626 579112006359 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 579112006360 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 579112006361 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 579112006362 Flagellar L-ring protein; Region: FlgH; cl00905 579112006363 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 579112006364 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 579112006365 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 579112006366 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 579112006367 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 579112006368 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 579112006369 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 579112006370 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 579112006371 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 579112006372 Flagellar hook capping protein; Region: FlgD; cl04347 579112006373 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12631 579112006374 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 579112006375 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 579112006376 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 579112006377 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 579112006378 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 579112006379 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112006380 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112006381 Response regulator receiver domain; Region: Response_reg; pfam00072 579112006382 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112006383 active site 579112006384 phosphorylation site [posttranslational modification] 579112006385 intermolecular recognition site; other site 579112006386 dimerization interface [polypeptide binding]; other site 579112006387 SAF domain; Region: SAF; cl00555 579112006388 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 579112006389 FlgN protein; Region: FlgN; cl09176 579112006390 Protein of unknown function, DUF400; Region: DUF400; cl01141 579112006391 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 579112006392 Condensation domain; Region: Condensation; cl09290 579112006393 Nonribosomal peptide synthase; Region: NRPS; pfam08415 579112006394 Condensation domain; Region: Condensation; cl09290 579112006395 Nonribosomal peptide synthase; Region: NRPS; pfam08415 579112006396 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05605 579112006397 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 579112006398 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112006399 Condensation domain; Region: Condensation; cl09290 579112006400 Phosphopantetheine attachment site; Region: PP-binding; cl09936 579112006401 Condensation domain; Region: Condensation; cl09290 579112006402 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 579112006403 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 579112006404 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 579112006405 FAD binding pocket [chemical binding]; other site 579112006406 FAD binding motif [chemical binding]; other site 579112006407 phosphate binding motif [ion binding]; other site 579112006408 NAD binding pocket [chemical binding]; other site 579112006409 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 579112006410 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112006411 N-terminal plug; other site 579112006412 ligand-binding site [chemical binding]; other site 579112006413 outer membrane protein A; Reviewed; Region: PRK10808 579112006414 Surface antigen; Region: Surface_Ag_2; cl01155 579112006415 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 579112006416 ligand binding site [chemical binding]; other site 579112006417 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 579112006418 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 579112006419 active site 579112006420 HIGH motif; other site 579112006421 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 579112006422 active site 579112006423 KMSKS motif; other site 579112006424 copper exporting ATPase; Provisional; Region: copA; PRK10671 579112006425 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 579112006426 metal-binding site [ion binding] 579112006427 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 579112006428 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; cl11391 579112006429 Protein of unknown function, DUF; Region: DUF411; cl01142 579112006430 Putative carbohydrate binding domain; Region: CHB_HEX; cl03918 579112006431 N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism]; Region: Chb; COG3525 579112006432 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 579112006433 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_Sm-chitobiase-like; cd06569 579112006434 active site 579112006435 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 579112006436 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3735 579112006437 TraB family; Region: TraB; cl12050 579112006438 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 579112006439 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 579112006440 Smr domain; Region: Smr; cl02619 579112006441 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 579112006442 23S rRNA pseudouridine synthase F; Provisional; Region: PRK10475 579112006443 RNA binding surface [nucleotide binding]; other site 579112006444 PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluF; cd02554 579112006445 probable active site [active] 579112006446 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112006447 metal binding site [ion binding]; metal-binding site 579112006448 active site 579112006449 I-site; other site 579112006450 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 579112006451 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 579112006452 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...; Region: PurM; cd02196 579112006453 dimerization interface [polypeptide binding]; other site 579112006454 putative ATP binding site [chemical binding]; other site 579112006455 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 579112006456 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 579112006457 active site 579112006458 substrate binding site [chemical binding]; other site 579112006459 cosubstrate binding site; other site 579112006460 catalytic site [active] 579112006461 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 579112006462 putative active site [active] 579112006463 putative dimer interface [polypeptide binding]; other site 579112006464 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 579112006465 dimer interface [polypeptide binding]; other site 579112006466 active site 579112006467 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 579112006468 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 579112006469 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 579112006470 active site 579112006471 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 579112006472 TIGR03503 family protein; Region: TIGR03503 579112006473 Proteobacterial; Region: dnaQ_proteo; TIGR01406 579112006474 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 579112006475 active site 579112006476 substrate binding site [chemical binding]; other site 579112006477 catalytic site [active] 579112006478 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 579112006479 RNA/DNA hybrid binding site [nucleotide binding]; other site 579112006480 active site 579112006481 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 579112006482 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112006483 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112006484 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 579112006485 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 579112006486 N-acetyl-D-glucosamine binding site [chemical binding]; other site 579112006487 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 579112006488 putative peptidoglycan binding site; other site 579112006489 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 579112006490 putative peptidoglycan binding site; other site 579112006491 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 579112006492 putative peptidoglycan binding site; other site 579112006493 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 579112006494 putative catalytic site [active] 579112006495 putative phosphate binding site [ion binding]; other site 579112006496 putative metal binding site [ion binding]; other site 579112006497 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 579112006498 Phenolic acid decarboxylase (PAD); Region: PA_decarbox; cl01382 579112006499 Cytochrome c; Region: Cytochrom_C; cl11414 579112006500 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 579112006501 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 579112006502 Ligand Binding Site [chemical binding]; other site 579112006503 TilS substrate binding domain; Region: TilS; pfam09179 579112006504 B3/4 domain; Region: B3_4; cl11458 579112006505 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 579112006506 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 579112006507 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 579112006508 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 579112006509 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...; Region: DnaE_OBF; cd04485 579112006510 generic binding surface II; other site 579112006511 generic binding surface I; other site 579112006512 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 579112006513 RNA/DNA hybrid binding site [nucleotide binding]; other site 579112006514 active site 579112006515 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 579112006516 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 579112006517 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 579112006518 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A...; Region: LbH_UDP-GlcNAc_AT; cd03351 579112006519 active site 579112006520 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 579112006521 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 579112006522 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 579112006523 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2,3-...; Region: LbH_LpxD; cd03352 579112006524 trimer interface [polypeptide binding]; other site 579112006525 active site 579112006526 UDP-GlcNAc binding site [chemical binding]; other site 579112006527 lipid binding site [chemical binding]; lipid-binding site 579112006528 periplasmic chaperone; Provisional; Region: PRK10780 579112006529 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 579112006530 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 579112006531 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 579112006532 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 579112006533 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 579112006534 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 579112006535 Surface antigen; Region: Bac_surface_Ag; cl03097 579112006536 zinc metallopeptidase RseP; Provisional; Region: PRK10779 579112006537 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 579112006538 active site 579112006539 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...; Region: PDZ_metalloprotease; cd00989 579112006540 protein binding site [polypeptide binding]; other site 579112006541 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...; Region: PDZ_metalloprotease; cd00989 579112006542 protein binding site [polypeptide binding]; other site 579112006543 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 579112006544 putative substrate binding region [chemical binding]; other site 579112006545 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 579112006546 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 579112006547 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 579112006548 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 579112006549 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 579112006550 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 579112006551 catalytic residue [active] 579112006552 putative FPP diphosphate binding site; other site 579112006553 putative FPP binding hydrophobic cleft; other site 579112006554 dimer interface [polypeptide binding]; other site 579112006555 putative IPP diphosphate binding site; other site 579112006556 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 579112006557 hinge region; other site 579112006558 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...; Region: AAK_UMPK-PyrH-Ec; cd04254 579112006559 putative nucleotide binding site [chemical binding]; other site 579112006560 uridine monophosphate binding site [chemical binding]; other site 579112006561 homohexameric interface [polypeptide binding]; other site 579112006562 elongation factor Ts; Provisional; Region: tsf; PRK09377 579112006563 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 579112006564 Elongation factor TS; Region: EF_TS; pfam00889 579112006565 Elongation factor TS; Region: EF_TS; pfam00889 579112006566 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 579112006567 rRNA interaction site [nucleotide binding]; other site 579112006568 S8 interaction site; other site 579112006569 putative laminin-1 binding site; other site 579112006570 methionine aminopeptidase; Reviewed; Region: PRK07281 579112006571 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 579112006572 active site 579112006573 PII uridylyl-transferase; Provisional; Region: PRK05007 579112006574 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 579112006575 metal binding triad; other site 579112006576 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 579112006577 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112006578 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 579112006579 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 579112006580 Protein of unknown function (DUF3461); Region: DUF3461; cl10125 579112006581 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 579112006582 tetramer interfaces [polypeptide binding]; other site 579112006583 binuclear metal-binding site [ion binding]; other site 579112006584 thiamine monophosphate kinase; Provisional; Region: PRK05731 579112006585 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 579112006586 ATP binding site [chemical binding]; other site 579112006587 dimerization interface [polypeptide binding]; other site 579112006588 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-...; Region: NusB_Sun; cl00223 579112006589 putative RNA binding site [nucleotide binding]; other site 579112006590 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 579112006591 homopentamer interface [polypeptide binding]; other site 579112006592 active site 579112006593 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 579112006594 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 579112006595 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 579112006596 dimerization interface [polypeptide binding]; other site 579112006597 active site 579112006598 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 579112006599 Lumazine binding domain; Region: Lum_binding; pfam00677 579112006600 Lumazine binding domain; Region: Lum_binding; pfam00677 579112006601 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 579112006602 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 579112006603 catalytic motif [active] 579112006604 Zn binding site [ion binding]; other site 579112006605 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 5,10-...; Region: DHFR; cl00161 579112006606 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 579112006607 ATP cone domain; Region: ATP-cone; pfam03477 579112006608 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 579112006609 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 579112006610 putative catalytic cysteine [active] 579112006611 gamma-glutamyl kinase; Provisional; Region: PRK05429 579112006612 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 579112006613 nucleotide binding site [chemical binding]; other site 579112006614 homotetrameric interface [polypeptide binding]; other site 579112006615 putative phosphate binding site [ion binding]; other site 579112006616 putative allosteric binding site; other site 579112006617 PUA domain; Region: PUA; cl00607 579112006618 Transcriptional regulator Crl; Region: Crl; cl11653 579112006619 Alpha/beta hydrolase of unknown function (DUF1100); Region: DUF1100; pfam06500 579112006620 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 579112006621 Sulfate transporter family; Region: Sulfate_transp; cl00967 579112006622 Permease family; Region: Xan_ur_permease; pfam00860 579112006623 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 579112006624 aminoacyl-histidine dipeptidase; Region: aa-his-dipept; TIGR01893 579112006625 metal binding site [ion binding]; metal-binding site 579112006626 dimer interface [polypeptide binding]; other site 579112006627 Protein of unknown function (DUF785); Region: DUF785; cl01682 579112006628 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 579112006629 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112006630 Predicted deacylase [General function prediction only]; Region: COG3608 579112006631 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the...; Region: M14_ASTE_ASPA_like_1; cd06251 579112006632 putative active site [active] 579112006633 Zn-binding site [ion binding]; other site 579112006634 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 579112006635 CHASE4 domain; Region: CHASE4; cl01308 579112006636 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112006637 metal binding site [ion binding]; metal-binding site 579112006638 active site 579112006639 I-site; other site 579112006640 Protein of unknown function (DUF2884); Region: DUF2884; cl08135 579112006641 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 579112006642 active site 579112006643 DNA polymerase IV; Validated; Region: PRK02406 579112006644 DNA binding site [nucleotide binding] 579112006645 Protein of unknown function (DUF539); Region: DUF539; cl01129 579112006646 ApbE family; Region: ApbE; cl00643 579112006647 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 579112006648 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+...; Region: NADH_quinone_reductase; cd06188 579112006649 FAD binding pocket [chemical binding]; other site 579112006650 FAD binding motif [chemical binding]; other site 579112006651 phosphate binding motif [ion binding]; other site 579112006652 beta-alpha-beta structure motif; other site 579112006653 NAD binding pocket [chemical binding]; other site 579112006654 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 579112006655 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 579112006656 FMN-binding domain; Region: FMN_bind; cl01081 579112006657 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 579112006658 RnfE family; Region: NQR2_RnfD_RnfE; cl00779 579112006659 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 579112006660 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 579112006661 BolA-like protein; Region: BolA; cl00386 579112006662 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 579112006663 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 579112006664 S-adenosylmethionine binding site [chemical binding]; other site 579112006665 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG3056 579112006666 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 579112006667 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 579112006668 substrate binding site [chemical binding]; other site 579112006669 muropeptide transporter; Reviewed; Region: ampG; PRK11902 579112006670 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; cl11420 579112006671 Transcriptional activator [Transcription]; Region: ChrR; COG3806 579112006672 Cupin domain; Region: Cupin_2; cl09118 579112006673 RNA polymerase sigma factor; Provisional; Region: PRK12531 579112006674 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 579112006675 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...; Region: Sigma70_r4; cd06171 579112006676 DNA binding residues [nucleotide binding] 579112006677 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 579112006678 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 579112006679 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 579112006680 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112006681 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 579112006682 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 579112006683 conserved cys residue [active] 579112006684 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 579112006685 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 579112006686 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112006687 catalytic residue [active] 579112006688 Fe-S metabolism associated domain; Region: SufE; cl00951 579112006689 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 579112006690 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-...; Region: YgdL_like; cd00755 579112006691 putative ATP binding site [chemical binding]; other site 579112006692 putative substrate interface [chemical binding]; other site 579112006693 murein transglycosylase A; Provisional; Region: mltA; PRK11162 579112006694 MltA specific insert domain; Region: MltA; cl08398 579112006695 3D domain; Region: 3D; cl01439 579112006696 Protein of unknown function (DUF2850); Region: DUF2850; pfam11012 579112006697 N-acetylglutamate synthase; Validated; Region: PRK05279 579112006698 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an N-...; Region: AAK_NAGS-ABP; cd04237 579112006699 putative feedback inhibition sensing region; other site 579112006700 putative nucleotide binding site [chemical binding]; other site 579112006701 putative substrate binding site [chemical binding]; other site 579112006702 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112006703 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 579112006704 Putative ATPase (DUF699); Region: DUF699; pfam05127 579112006705 UvrD/REP helicase; Region: UvrD-helicase; cl14126 579112006706 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 579112006707 UvrD/REP helicase; Region: UvrD-helicase; cl14126 579112006708 UvrD/REP helicase; Region: UvrD-helicase; cl14126 579112006709 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 579112006710 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 579112006711 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 579112006712 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 579112006713 C4-dicarboxylate transporter/malic acid transport protein; Region: C4dic_mal_tran; pfam03595 579112006714 gating phenylalanine in ion channel; other site 579112006715 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 579112006716 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112006717 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 579112006718 putative dimerization interface [polypeptide binding]; other site 579112006719 YebG protein; Region: YebG; cl01217 579112006720 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Region: DapD_gpp; TIGR03536 579112006721 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 579112006722 putative trimer interface [polypeptide binding]; other site 579112006723 putative CoA binding site [chemical binding]; other site 579112006724 NnrS protein; Region: NnrS; cl01258 579112006725 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112006726 Coenzyme A binding pocket [chemical binding]; other site 579112006727 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). The...; Region: Peptidase_C39_like; cl00296 579112006728 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 579112006729 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112006730 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 579112006731 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 579112006732 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 579112006733 putative active site pocket [active] 579112006734 dimerization interface [polypeptide binding]; other site 579112006735 putative catalytic residue [active] 579112006736 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 579112006737 dimer interface [polypeptide binding]; other site 579112006738 putative tRNA-binding site [nucleotide binding]; other site 579112006739 DNA-binding transcriptional regulator GalR; Provisional; Region: PRK10727 579112006740 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112006741 DNA binding site [nucleotide binding] 579112006742 domain linker motif; other site 579112006743 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 579112006744 dimerization interface (closed form) [polypeptide binding]; other site 579112006745 ligand binding site [chemical binding]; other site 579112006746 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 579112006747 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 579112006748 domain; Region: Glyco_hydro_2; pfam00703 579112006749 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; cl14895 579112006750 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 579112006751 Chromate transporter; Region: Chromate_transp; pfam02417 579112006752 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 579112006753 Chromate transporter; Region: Chromate_transp; pfam02417 579112006754 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 579112006755 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112006756 Zn2+ binding site [ion binding]; other site 579112006757 Mg2+ binding site [ion binding]; other site 579112006758 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 579112006759 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112006760 elongation factor G; Reviewed; Region: PRK00007 579112006761 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 579112006762 G1 box; other site 579112006763 putative GEF interaction site [polypeptide binding]; other site 579112006764 GTP/Mg2+ binding site [chemical binding]; other site 579112006765 Switch I region; other site 579112006766 G2 box; other site 579112006767 G3 box; other site 579112006768 Switch II region; other site 579112006769 G4 box; other site 579112006770 G5 box; other site 579112006771 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...; Region: EFG_mtEFG_II; cd04088 579112006772 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...; Region: EFG_mtEFG1_IV; cd01434 579112006773 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...; Region: EFG_mtEFG_C; cd03713 579112006774 DNA repair protein RadA; Provisional; Region: PRK11823 579112006775 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 579112006776 Walker A motif/ATP binding site; other site 579112006777 ATP binding site [chemical binding]; other site 579112006778 Walker B motif; other site 579112006779 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 579112006780 PilZ domain; Region: PilZ; cl01260 579112006781 PilZ domain; Region: PilZ; cl01260 579112006782 phosphoserine phosphatase; Provisional; Region: serB; PRK11133 579112006783 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; cl11391 579112006784 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 579112006785 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 579112006786 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 579112006787 Sulfatase; Region: Sulfatase; cl10460 579112006788 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 579112006789 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 579112006790 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 579112006791 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 579112006792 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; cl06734 579112006793 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 579112006794 intersubunit interface [polypeptide binding]; other site 579112006795 active site 579112006796 catalytic residue [active] 579112006797 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 579112006798 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 579112006799 Nucleoside recognition; Region: Gate; cl00486 579112006800 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 579112006801 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 579112006802 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 579112006803 active site 579112006804 Protein of unknown function (DUF328); Region: DUF328; cl01143 579112006805 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 579112006806 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 579112006807 Uncharacterized conserved protein [Function unknown]; Region: COG3945 579112006808 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 579112006809 ligand binding site [chemical binding]; other site 579112006810 active site 579112006811 UGI interface [polypeptide binding]; other site 579112006812 catalytic site [active] 579112006813 endonuclease IV; Provisional; Region: PRK01060 579112006814 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 D-arabino-6-...; Region: AP2Ec; cd00019 579112006815 AP (apurinic/apyrimidinic) site pocket; other site 579112006816 DNA interaction; other site 579112006817 Metal-binding active site; metal-binding site 579112006818 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 579112006819 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 579112006820 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD)...; Region: Trp-synth-beta_II; cl00342 579112006821 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112006822 catalytic residue [active] 579112006823 homoserine kinase; Provisional; Region: PRK01212 579112006824 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 579112006825 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 579112006826 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 579112006827 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli AKI-...; Region: AAK_AK-HSDH; cd04257 579112006828 putative catalytic residues [active] 579112006829 putative nucleotide binding site [chemical binding]; other site 579112006830 putative aspartate binding site [chemical binding]; other site 579112006831 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 579112006832 dimer interface [polypeptide binding]; other site 579112006833 putative threonine allosteric regulatory site; other site 579112006834 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 579112006835 putative threonine allosteric regulatory site; other site 579112006836 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112006837 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 579112006838 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 579112006839 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 579112006840 two-component response regulator; Provisional; Region: PRK11173 579112006841 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112006842 active site 579112006843 phosphorylation site [posttranslational modification] 579112006844 intermolecular recognition site; other site 579112006845 dimerization interface [polypeptide binding]; other site 579112006846 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...; Region: trans_reg_C; cd00383 579112006847 DNA binding site [nucleotide binding] 579112006848 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 579112006849 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112006850 putative active site [active] 579112006851 heme pocket [chemical binding]; other site 579112006852 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 trans-...; Region: HisKA; cd00082 579112006853 dimer interface [polypeptide binding]; other site 579112006854 phosphorylation site [posttranslational modification] 579112006855 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 579112006856 ATP binding site [chemical binding]; other site 579112006857 Mg2+ binding site [ion binding]; other site 579112006858 G-X-G motif; other site 579112006859 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112006860 active site 579112006861 phosphorylation site [posttranslational modification] 579112006862 intermolecular recognition site; other site 579112006863 dimerization interface [polypeptide binding]; other site 579112006864 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 579112006865 putative binding surface; other site 579112006866 active site 579112006867 PAS fold; Region: PAS_4; pfam08448 579112006868 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112006869 PAS fold; Region: PAS_4; pfam08448 579112006870 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 579112006871 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112006872 metal binding site [ion binding]; metal-binding site 579112006873 active site 579112006874 I-site; other site 579112006875 radical SAM protein, TIGR01212 family; Region: TIGR01212 579112006876 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 579112006877 FeS/SAM binding site; other site 579112006878 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 579112006879 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 N-...; Region: GltS; cd00713 579112006880 active site 579112006881 dimer interface [polypeptide binding]; other site 579112006882 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 579112006883 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...; Region: GltS_FMN; cd02808 579112006884 active site 579112006885 FMN binding site [chemical binding]; other site 579112006886 substrate binding site [chemical binding]; other site 579112006887 3Fe-4S cluster binding site [ion binding]; other site 579112006888 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 579112006889 domain interface; other site 579112006890 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 579112006891 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 579112006892 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 N-...; Region: GltS; cd00713 579112006893 active site 579112006894 dimer interface [polypeptide binding]; other site 579112006895 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 579112006896 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...; Region: GltS_FMN; cd02808 579112006897 active site 579112006898 FMN binding site [chemical binding]; other site 579112006899 substrate binding site [chemical binding]; other site 579112006900 3Fe-4S cluster binding site [ion binding]; other site 579112006901 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 579112006902 domain interface; other site 579112006903 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 579112006904 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 alpha-; Region: HCP_like; cl14655 579112006905 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 579112006906 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 579112006907 5'-methylthioadenosine nucleosidase; Region: PLN02584 579112006908 CobD/Cbib protein; Region: CobD_Cbib; cl00561 579112006909 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 579112006910 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal...; Region: BtuF; cd01144 579112006911 cobalamin binding residues [chemical binding]; other site 579112006912 putative BtuC binding residues; other site 579112006913 dimer interface [polypeptide binding]; other site 579112006914 hypothetical protein; Provisional; Region: PRK10578 579112006915 UPF0126 domain; Region: UPF0126; pfam03458 579112006916 UPF0126 domain; Region: UPF0126; pfam03458 579112006917 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112006918 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112006919 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 579112006920 dimerization interface [polypeptide binding]; other site 579112006921 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 579112006922 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 579112006923 RT_Bac_retron_II: 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_II; cd03487 579112006924 putative active site [active] 579112006925 putative NTP binding site [chemical binding]; other site 579112006926 putative nucleic acid binding site [nucleotide binding]; other site 579112006927 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...; Region: HNHc; cl00083 579112006928 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 579112006929 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 579112006930 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112006931 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 579112006932 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 579112006933 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112006934 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 579112006935 IMP binding site; other site 579112006936 dimer interface [polypeptide binding]; other site 579112006937 interdomain contacts; other site 579112006938 partial ornithine binding site; other site 579112006939 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 579112006940 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 579112006941 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 579112006942 catalytic site [active] 579112006943 subunit interface [polypeptide binding]; other site 579112006944 dihydrodipicolinate reductase; Provisional; Region: PRK00048 579112006945 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112006946 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 579112006947 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 579112006948 active site 579112006949 8-oxo-dGMP binding site [chemical binding]; other site 579112006950 nudix motif; other site 579112006951 metal binding site [ion binding]; metal-binding site 579112006952 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 579112006953 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 579112006954 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 579112006955 nucleotide binding region [chemical binding]; other site 579112006956 ATP-binding site [chemical binding]; other site 579112006957 SEC-C motif; Region: SEC-C; cl12132 579112006958 Protein of unknown function (DUF721); Region: DUF721; cl02324 579112006959 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 579112006960 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 579112006961 cell division protein FtsZ; Validated; Region: PRK09330 579112006962 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...; Region: FtsZ_type1; cd02201 579112006963 nucleotide binding site [chemical binding]; other site 579112006964 SulA interaction site; other site 579112006965 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 579112006966 Cell division protein FtsA; Region: FtsA; cl11496 579112006967 Cell division protein FtsA; Region: FtsA; cl11496 579112006968 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 579112006969 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 579112006970 Cell division protein FtsQ; Region: FtsQ; pfam03799 579112006971 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 579112006972 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 579112006973 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 579112006974 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 579112006975 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 579112006976 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...; Region: GT1_MurG; cd03785 579112006977 active site 579112006978 homodimer interface [polypeptide binding]; other site 579112006979 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 579112006980 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK04663 579112006981 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112006982 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 579112006983 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 579112006984 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 579112006985 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 undecaprenyl-pyrophosphoryl-N-...; Region: GT_MraY; cd06852 579112006986 Mg++ binding site [ion binding]; other site 579112006987 putative catalytic motif [active] 579112006988 putative substrate binding site [chemical binding]; other site 579112006989 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 579112006990 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 579112006991 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 579112006992 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 579112006993 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 579112006994 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 579112006995 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 579112006996 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 579112006997 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 579112006998 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 579112006999 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 579112007000 Septum formation initiator; Region: DivIC; cl11433 579112007001 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 579112007002 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112007003 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 579112007004 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007005 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007006 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 579112007007 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 579112007008 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 579112007009 E3 interaction surface; other site 579112007010 lipoyl attachment site [posttranslational modification]; other site 579112007011 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 579112007012 E3 interaction surface; other site 579112007013 lipoyl attachment site [posttranslational modification]; other site 579112007014 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 579112007015 E3 interaction surface; other site 579112007016 lipoyl attachment site [posttranslational modification]; other site 579112007017 e3 binding domain; Region: E3_binding; pfam02817 579112007018 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 579112007019 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 579112007020 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 579112007021 dimer interface [polypeptide binding]; other site 579112007022 TPP-binding site [chemical binding]; other site 579112007023 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 579112007024 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 579112007025 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 579112007026 DNA-binding site [nucleotide binding]; DNA binding site 579112007027 FCD domain; Region: FCD; cl11656 579112007028 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 579112007029 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 579112007030 active site 579112007031 metal binding site [ion binding]; metal-binding site 579112007032 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 579112007033 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 579112007034 DHH family; Region: DHH; pfam01368 579112007035 DHHA1 domain; Region: DHHA1; pfam02272 579112007036 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 579112007037 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide...; Region: DsbA_DsbC_DsbG; cd03020 579112007038 dimerization domain [polypeptide binding]; other site 579112007039 dimer interface [polypeptide binding]; other site 579112007040 catalytic residues [active] 579112007041 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 579112007042 N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid...; Region: INT_XerDC; cd00798 579112007043 Int/Topo IB signature motif; other site 579112007044 active site 579112007045 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 579112007046 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 579112007047 substrate binding site [chemical binding]; other site 579112007048 amidase catalytic site [active] 579112007049 Zn binding residues [ion binding]; other site 579112007050 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 579112007051 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 5-...; Region: QPRTase; cd01572 579112007052 dimerization interface [polypeptide binding]; other site 579112007053 active site 579112007054 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 579112007055 Pilin (bacterial filament); Region: Pilin; pfam00114 579112007056 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 579112007057 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 579112007058 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 579112007059 Walker A motif; other site 579112007060 ATP binding site [chemical binding]; other site 579112007061 Walker B motif; other site 579112007062 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 579112007063 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 579112007064 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 579112007065 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 579112007066 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 579112007067 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 579112007068 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 579112007069 CoA-binding site [chemical binding]; other site 579112007070 ATP-binding [chemical binding]; other site 579112007071 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 579112007072 Domain of unknown function (DUF329); Region: DUF329; cl01144 579112007073 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 579112007074 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in...; Region: TOP4c; cd00187 579112007075 CAP-like domain; other site 579112007076 Active site [active] 579112007077 primary dimer interface [polypeptide binding]; other site 579112007078 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 579112007079 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 579112007080 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 579112007081 ATP binding site [chemical binding]; other site 579112007082 Mg2+ binding site [ion binding]; other site 579112007083 G-X-G motif; other site 579112007084 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 579112007085 anchoring element; other site 579112007086 dimer interface [polypeptide binding]; other site 579112007087 ATP binding site [chemical binding]; other site 579112007088 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 579112007089 active site 579112007090 metal binding site [ion binding]; metal-binding site 579112007091 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 579112007092 Uncharacterised protein family (UPF0227); Region: UPF0227; cl14886 579112007093 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 579112007094 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 579112007095 active site 579112007096 metal binding site [ion binding]; metal-binding site 579112007097 hexamer interface [polypeptide binding]; other site 579112007098 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 579112007099 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 579112007100 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...; Region: ADPRase_NUDT5; cd03424 579112007101 dimer interface [polypeptide binding]; other site 579112007102 ADP-ribose binding site [chemical binding]; other site 579112007103 active site 579112007104 nudix motif; other site 579112007105 metal binding site [ion binding]; metal-binding site 579112007106 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 579112007107 Outer membrane efflux protein; Region: OEP; pfam02321 579112007108 Outer membrane efflux protein; Region: OEP; pfam02321 579112007109 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 579112007110 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 579112007111 putative ribose interaction site [chemical binding]; other site 579112007112 putative ADP binding site [chemical binding]; other site 579112007113 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 579112007114 active site 579112007115 HIGH motif; other site 579112007116 nucleotide binding site [chemical binding]; other site 579112007117 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 579112007118 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 579112007119 metal binding triad; other site 579112007120 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 579112007121 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 579112007122 metal binding triad; other site 579112007123 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112007124 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112007125 Uncharacterized conserved protein [Function unknown]; Region: COG3025 579112007126 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 579112007127 putative active site [active] 579112007128 putative metal binding residues [ion binding]; other site 579112007129 signature motif; other site 579112007130 putative triphosphate binding site [ion binding]; other site 579112007131 CHAD domain; Region: CHAD; cl10506 579112007132 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 579112007133 Phosphate transporter family; Region: PHO4; cl00396 579112007134 Phosphate transporter family; Region: PHO4; cl00396 579112007135 SH3 domain protein [Signal transduction mechanisms]; Region: COG3103 579112007136 Bacterial SH3 domain; Region: SH3_3; cl02551 579112007137 type III secretion apparatus protein, YscD/HrpQ family; Region: type_III_yscD; TIGR02500 579112007138 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 579112007139 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...; Region: AAA; cd00009 579112007140 Walker A motif; other site 579112007141 ATP binding site [chemical binding]; other site 579112007142 Walker B motif; other site 579112007143 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 579112007144 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 579112007145 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 579112007146 active site 579112007147 NTP binding site [chemical binding]; other site 579112007148 metal binding triad [ion binding]; metal-binding site 579112007149 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 579112007150 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112007151 Zn2+ binding site [ion binding]; other site 579112007152 Mg2+ binding site [ion binding]; other site 579112007153 enolase; Provisional; Region: eno; PRK00077 579112007154 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 579112007155 dimer interface [polypeptide binding]; other site 579112007156 metal binding site [ion binding]; metal-binding site 579112007157 substrate binding pocket [chemical binding]; other site 579112007158 CTP synthetase; Validated; Region: pyrG; PRK05380 579112007159 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...; Region: CTGs; cd03113 579112007160 Catalytic site [active] 579112007161 Active site [active] 579112007162 UTP binding site [chemical binding]; other site 579112007163 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 579112007164 active site 579112007165 putative oxyanion hole; other site 579112007166 catalytic triad [active] 579112007167 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 579112007168 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 579112007169 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 579112007170 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 579112007171 synthetase active site [active] 579112007172 NTP binding site [chemical binding]; other site 579112007173 metal binding site [ion binding]; metal-binding site 579112007174 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...; Region: TGS_RelA_SpoT; cd01668 579112007175 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 579112007176 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 579112007177 TRAM domain; Region: TRAM; cl01282 579112007178 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112007179 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 579112007180 S-adenosylmethionine binding site [chemical binding]; other site 579112007181 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 579112007182 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 579112007183 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112007184 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 trans-...; Region: HisKA; cd00082 579112007185 dimer interface [polypeptide binding]; other site 579112007186 phosphorylation site [posttranslational modification] 579112007187 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 579112007188 ATP binding site [chemical binding]; other site 579112007189 Mg2+ binding site [ion binding]; other site 579112007190 G-X-G motif; other site 579112007191 Uncharacterized domain of BarA-like signal transduction histidine kinases [Signal transduction mechanisms]; Region: COG4999 579112007192 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112007193 active site 579112007194 phosphorylation site [posttranslational modification] 579112007195 intermolecular recognition site; other site 579112007196 dimerization interface [polypeptide binding]; other site 579112007197 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 579112007198 putative binding surface; other site 579112007199 active site 579112007200 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112007201 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112007202 metal binding site [ion binding]; metal-binding site 579112007203 active site 579112007204 I-site; other site 579112007205 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 579112007206 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 579112007207 active site 579112007208 hydrophilic channel; other site 579112007209 dimerization interface [polypeptide binding]; other site 579112007210 catalytic residues [active] 579112007211 active site lid [active] 579112007212 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 579112007213 Recombination protein O N terminal; Region: RecO_N; pfam11967 579112007214 Recombination protein O C terminal; Region: RecO_C; pfam02565 579112007215 GTPase Era; Reviewed; Region: era; PRK00089 579112007216 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 579112007217 G1 box; other site 579112007218 GTP/Mg2+ binding site [chemical binding]; other site 579112007219 Switch I region; other site 579112007220 G2 box; other site 579112007221 Switch II region; other site 579112007222 G3 box; other site 579112007223 G4 box; other site 579112007224 G5 box; other site 579112007225 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains...; Region: KH-I; cl00098 579112007226 ribonuclease III; Reviewed; Region: rnc; PRK00102 579112007227 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 post-...; Region: RIBOc; cd00593 579112007228 dimerization interface [polypeptide binding]; other site 579112007229 active site 579112007230 metal binding site [ion binding]; metal-binding site 579112007231 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...; Region: DSRM; cd00048 579112007232 dsRNA binding site [nucleotide binding]; other site 579112007233 signal peptidase I; Provisional; Region: PRK10861 579112007234 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 579112007235 Catalytic site [active] 579112007236 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 579112007237 GTP-binding protein LepA; Provisional; Region: PRK05433 579112007238 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 579112007239 G1 box; other site 579112007240 putative GEF interaction site [polypeptide binding]; other site 579112007241 GTP/Mg2+ binding site [chemical binding]; other site 579112007242 Switch I region; other site 579112007243 G2 box; other site 579112007244 G3 box; other site 579112007245 Switch II region; other site 579112007246 G4 box; other site 579112007247 G5 box; other site 579112007248 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-...; Region: lepA_II; cd03699 579112007249 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 579112007250 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 579112007251 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 579112007252 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 579112007253 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseA; COG3073 579112007254 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 579112007255 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 579112007256 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 579112007257 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 579112007258 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...; Region: Sigma70_r4; cd06171 579112007259 DNA binding residues [nucleotide binding] 579112007260 L-aspartate oxidase; Provisional; Region: PRK09077 579112007261 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007262 domain; Region: Succ_DH_flav_C; pfam02910 579112007263 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 579112007264 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 579112007265 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 579112007266 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 579112007267 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 579112007268 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007269 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 579112007270 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007271 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 579112007272 Uncharacterised protein family (UPF0149); Region: UPF0149; cl01173 579112007273 Cell division protein ZapA; Region: ZapA; cl01146 579112007274 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 579112007275 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 579112007276 tetramer (dimer of dimers) interface [polypeptide binding]; other site 579112007277 active site 579112007278 dimer interface [polypeptide binding]; other site 579112007279 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 579112007280 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007281 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 579112007282 L-serine binding site [chemical binding]; other site 579112007283 ACT domain interface; other site 579112007284 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 579112007285 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 579112007286 putative valine binding site [chemical binding]; other site 579112007287 dimer interface [polypeptide binding]; other site 579112007288 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 579112007289 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK08979 579112007290 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 579112007291 PYR/PP interface [polypeptide binding]; other site 579112007292 dimer interface [polypeptide binding]; other site 579112007293 TPP binding site [chemical binding]; other site 579112007294 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 579112007295 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 579112007296 TPP-binding site [chemical binding]; other site 579112007297 dimer interface [polypeptide binding]; other site 579112007298 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 579112007299 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112007300 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112007301 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 579112007302 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112007303 The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; Region: PBP2_LeuO; cd08466 579112007304 putative substrate binding pocket [chemical binding]; other site 579112007305 putative dimerization interface [polypeptide binding]; other site 579112007306 conserved hypothetical protein; Region: MJ1255; TIGR00661 579112007307 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 579112007308 active site 579112007309 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112007310 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112007311 2-isopropylmalate synthase; Validated; Region: PRK00915 579112007312 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 579112007313 active site 579112007314 catalytic residues [active] 579112007315 metal binding site [ion binding]; metal-binding site 579112007316 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 579112007317 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 579112007318 isocitrate dehydrogenase; Validated; Region: PRK06451 579112007319 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 579112007320 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 579112007321 substrate binding site [chemical binding]; other site 579112007322 ligand binding site [chemical binding]; other site 579112007323 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 3-...; Region: IPMI_Swivel; cd01577 579112007324 substrate binding site [chemical binding]; other site 579112007325 Protein of unknown function, DUF547; Region: DUF547; pfam04784 579112007326 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 579112007327 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 579112007328 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112007329 Zn2+ binding site [ion binding]; other site 579112007330 Mg2+ binding site [ion binding]; other site 579112007331 RDD family; Region: RDD; cl00746 579112007332 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 579112007333 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 579112007334 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 579112007335 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 579112007336 multifunctional aminopeptidase A; Provisional; Region: PRK00913 579112007337 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 579112007338 interface (dimer of trimers) [polypeptide binding]; other site 579112007339 Substrate-binding/catalytic site; other site 579112007340 Zn-binding sites [ion binding]; other site 579112007341 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 579112007342 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 579112007343 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 579112007344 HIGH motif; other site 579112007345 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 579112007346 active site 579112007347 KMSKS motif; other site 579112007348 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 579112007349 tRNA binding surface [nucleotide binding]; other site 579112007350 anticodon binding site; other site 579112007351 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 579112007352 glycerate dehydrogenase; Provisional; Region: PRK06932 579112007353 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007354 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 579112007355 active site 579112007356 ATP-dependent helicase HepA; Validated; Region: PRK04914 579112007357 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 579112007358 ATP binding site [chemical binding]; other site 579112007359 putative Mg++ binding site [ion binding]; other site 579112007360 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 579112007361 nucleotide binding region [chemical binding]; other site 579112007362 ATP-binding site [chemical binding]; other site 579112007363 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 579112007364 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 579112007365 putative active site [active] 579112007366 PhoH-like protein; Region: PhoH; cl12134 579112007367 ornithine carbamoyltransferase; Validated; Region: PRK02102 579112007368 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 579112007369 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007370 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 579112007371 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 579112007372 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007373 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 579112007374 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 579112007375 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 579112007376 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 579112007377 homotrimer interaction site [polypeptide binding]; other site 579112007378 putative active site [active] 579112007379 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 579112007380 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 579112007381 putative acyl-acceptor binding pocket; other site 579112007382 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated; Region: PRK09369 579112007383 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 579112007384 hinge; other site 579112007385 active site 579112007386 BolA-like protein; Region: BolA; cl00386 579112007387 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 579112007388 anti sigma factor interaction site; other site 579112007389 regulatory phosphorylation site [posttranslational modification]; other site 579112007390 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 579112007391 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 579112007392 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 579112007393 mce related protein; Region: MCE; pfam02470 579112007394 Domain of unknown function DUF140; Region: DUF140; cl00510 579112007395 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 579112007396 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 579112007397 Walker A/P-loop; other site 579112007398 ATP binding site [chemical binding]; other site 579112007399 Q-loop/lid; other site 579112007400 ABC transporter signature motif; other site 579112007401 Walker B; other site 579112007402 D-loop; other site 579112007403 H-loop/switch region; other site 579112007404 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 579112007405 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 579112007406 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 579112007407 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 579112007408 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-...; Region: SIS_Kpsf; cd05014 579112007409 putative active site [active] 579112007410 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 579112007411 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; cl11391 579112007412 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 579112007413 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 579112007414 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 579112007415 OstA-like protein; Region: OstA; cl00844 579112007416 lipopolysaccharide ABC transporter ATP-binding protein; Provisional; Region: PRK10895 579112007417 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 579112007418 Walker A/P-loop; other site 579112007419 ATP binding site [chemical binding]; other site 579112007420 Q-loop/lid; other site 579112007421 ABC transporter signature motif; other site 579112007422 Walker B; other site 579112007423 D-loop; other site 579112007424 H-loop/switch region; other site 579112007425 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 579112007426 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 579112007427 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 579112007428 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 579112007429 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site...; Region: RaiA; cd00552 579112007430 30S subunit binding site; other site 579112007431 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 579112007432 active site 579112007433 phosphorylation site [posttranslational modification] 579112007434 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112007435 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 579112007436 dimerization domain swap beta strand [polypeptide binding]; other site 579112007437 regulatory protein interface [polypeptide binding]; other site 579112007438 active site 579112007439 regulatory phosphorylation site [posttranslational modification]; other site 579112007440 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 579112007441 MgtE intracellular N domain; Region: MgtE_N; cl15244 579112007442 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 579112007443 Divalent cation transporter; Region: MgtE; cl00786 579112007444 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 579112007445 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 579112007446 Protein of unknown function (DUF615); Region: DUF615; cl01147 579112007447 thiamine ABC transporter, ATP-binding protein; Region: thiQ; TIGR01277 579112007448 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112007449 Walker A/P-loop; other site 579112007450 ATP binding site [chemical binding]; other site 579112007451 Q-loop/lid; other site 579112007452 ABC transporter signature motif; other site 579112007453 Walker B; other site 579112007454 D-loop; other site 579112007455 H-loop/switch region; other site 579112007456 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 579112007457 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...; Region: TM_PBP2; cd06261 579112007458 dimer interface [polypeptide binding]; other site 579112007459 conserved gate region; other site 579112007460 putative PBP binding loops; other site 579112007461 ABC-ATPase subunit interface; other site 579112007462 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...; Region: TM_PBP2; cd06261 579112007463 dimer interface [polypeptide binding]; other site 579112007464 conserved gate region; other site 579112007465 putative PBP binding loops; other site 579112007466 ABC-ATPase subunit interface; other site 579112007467 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 579112007468 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 579112007469 aromatic acid decarboxylase; Validated; Region: PRK05920 579112007470 Flavoprotein; Region: Flavoprotein; cl08021 579112007471 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 579112007472 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 579112007473 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 579112007474 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 579112007475 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1,7-...; Region: FBPase; cd00354 579112007476 metal binding site [ion binding]; metal-binding site 579112007477 active site 579112007478 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 579112007479 dimer interface [polypeptide binding]; other site 579112007480 substrate binding site [chemical binding]; other site 579112007481 metal binding sites [ion binding]; metal-binding site 579112007482 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 579112007483 putative active site pocket [active] 579112007484 dimerization interface [polypeptide binding]; other site 579112007485 putative catalytic residue [active] 579112007486 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 579112007487 Family of unknown function (DUF490); Region: DUF490; pfam04357 579112007488 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 579112007489 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 579112007490 Surface antigen; Region: Bac_surface_Ag; cl03097 579112007491 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 579112007492 Bacterial protein of unknown function (YtfJ_HI0045); Region: YtfJ_HI0045; cl01158 579112007493 Protein of unknown function (DUF2607); Region: DUF2607; pfam10795 579112007494 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 579112007495 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 579112007496 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 579112007497 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 579112007498 Walker A/P-loop; other site 579112007499 ATP binding site [chemical binding]; other site 579112007500 Q-loop/lid; other site 579112007501 ABC transporter signature motif; other site 579112007502 Walker B; other site 579112007503 D-loop; other site 579112007504 H-loop/switch region; other site 579112007505 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 579112007506 FtsX-like permease family; Region: FtsX; pfam02687 579112007507 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 579112007508 Protein of unknown function (DUF2806); Region: DUF2806; cl12560 579112007509 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically 'activated' sulfate form important for the assimilation...; Region: APSK; cd02027 579112007510 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 579112007511 ligand-binding site [chemical binding]; other site 579112007512 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 579112007513 CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which...; Region: CysN_ATPS; cd04166 579112007514 CysD dimerization site [polypeptide binding]; other site 579112007515 G1 box; other site 579112007516 putative GEF interaction site [polypeptide binding]; other site 579112007517 GTP/Mg2+ binding site [chemical binding]; other site 579112007518 Switch I region; other site 579112007519 G2 box; other site 579112007520 G3 box; other site 579112007521 Switch II region; other site 579112007522 G4 box; other site 579112007523 G5 box; other site 579112007524 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...; Region: CysN_NodQ_II; cd03695 579112007525 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...; Region: CysN_NoDQ_III; cd04095 579112007526 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 579112007527 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 579112007528 Active Sites [active] 579112007529 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 579112007530 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 579112007531 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 579112007532 active site 579112007533 metal binding site [ion binding]; metal-binding site 579112007534 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 579112007535 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 579112007536 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cl00047 579112007537 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 579112007538 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 579112007539 ATP binding site [chemical binding]; other site 579112007540 Mg++ binding site [ion binding]; other site 579112007541 motif III; other site 579112007542 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 579112007543 nucleotide binding region [chemical binding]; other site 579112007544 ATP-binding site [chemical binding]; other site 579112007545 DbpA RNA binding domain; Region: DbpA; pfam03880 579112007546 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112007547 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112007548 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 579112007549 Coenzyme A binding pocket [chemical binding]; other site 579112007550 Integral membrane protein DUF6; Region: DUF6; cl01037 579112007551 Opacity-associated protein A N-terminal motif; Region: OapA_N; pfam08525 579112007552 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 579112007553 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 579112007554 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 579112007555 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 579112007556 Protein of unknown function VcgC/VcgE (DUF2780); Region: DUF2780; pfam11075 579112007557 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 579112007558 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 579112007559 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 579112007560 alphaNTD homodimer interface [polypeptide binding]; other site 579112007561 alphaNTD - beta interaction site [polypeptide binding]; other site 579112007562 alphaNTD - beta' interaction site [polypeptide binding]; other site 579112007563 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 579112007564 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 579112007565 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 579112007566 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 579112007567 RNA binding surface [nucleotide binding]; other site 579112007568 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 579112007569 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 579112007570 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 579112007571 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 579112007572 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 579112007573 SecY translocase; Region: SecY; pfam00344 579112007574 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 579112007575 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...; Region: Ribosomal_L30; cd01658 579112007576 23S rRNA binding site [nucleotide binding]; other site 579112007577 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 579112007578 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 579112007579 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 579112007580 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 579112007581 5S rRNA interface [nucleotide binding]; other site 579112007582 23S rRNA interface [nucleotide binding]; other site 579112007583 L5 interface [polypeptide binding]; other site 579112007584 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 579112007585 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 579112007586 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 579112007587 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 579112007588 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 579112007589 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 579112007590 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 579112007591 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 579112007592 KOW motif; Region: KOW; cl00354 579112007593 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 579112007594 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 579112007595 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...; Region: Ribosomal_L29_HIP; cd00427 579112007596 L23 interface [polypeptide binding]; other site 579112007597 signal recognition particle (SRP54) interaction site; other site 579112007598 trigger factor interaction site; other site 579112007599 23S rRNA interface [nucleotide binding]; other site 579112007600 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 579112007601 23S rRNA interface [nucleotide binding]; other site 579112007602 5S rRNA interface [nucleotide binding]; other site 579112007603 putative antibiotic binding site [chemical binding]; other site 579112007604 L25 interface [polypeptide binding]; other site 579112007605 L27 interface [polypeptide binding]; other site 579112007606 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 579112007607 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...; Region: 30S_S3_KH; cd02412 579112007608 G-X-X-G motif; other site 579112007609 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 579112007610 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 579112007611 putative translocon binding site; other site 579112007612 protein-rRNA interface [nucleotide binding]; other site 579112007613 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 579112007614 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 579112007615 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 579112007616 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 579112007617 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 579112007618 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 579112007619 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 579112007620 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 579112007621 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 579112007622 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 579112007623 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 579112007624 exoribonuclease R; Provisional; Region: PRK11642 579112007625 Ribonuclease R winged-helix domain; Region: HTH_12; pfam08461 579112007626 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 579112007627 RNB domain; Region: RNB; pfam00773 579112007628 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an...; Region: S1_RNase_R; cd04471 579112007629 RNA binding site [nucleotide binding]; other site 579112007630 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 579112007631 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 579112007632 Sulfatase; Region: Sulfatase; cl10460 579112007633 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 579112007634 Sel1 repeat; Region: Sel1; cl02723 579112007635 Sel1 repeat; Region: Sel1; cl02723 579112007636 adenylosuccinate synthetase; Provisional; Region: PRK01117 579112007637 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 r-...; Region: AdSS; cd03108 579112007638 GDP-binding site [chemical binding]; other site 579112007639 ACT binding site; other site 579112007640 IMP binding site; other site 579112007641 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 579112007642 catalytic nucleophile [active] 579112007643 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 579112007644 Probable metal-binding protein (DUF2387); Region: DUF2387; cl01410 579112007645 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 579112007646 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 579112007647 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007648 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 579112007649 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 579112007650 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112007651 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112007652 ABC transporter; Region: ABC_tran_2; pfam12848 579112007653 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 579112007654 Protein of unknown function (DUF2390); Region: DUF2390; cl02376 579112007655 putative hydrolase; Provisional; Region: PRK10985 579112007656 Uncharacterised protein family (UPF0270); Region: UPF0270; cl01180 579112007657 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112007658 Active site [active] 579112007659 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 579112007660 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 579112007661 ligand binding site [chemical binding]; other site 579112007662 flexible hinge region; other site 579112007663 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 579112007664 putative switch regulator; other site 579112007665 non-specific DNA interactions [nucleotide binding]; other site 579112007666 DNA binding site [nucleotide binding] 579112007667 sequence specific DNA binding site [nucleotide binding]; other site 579112007668 putative cAMP binding site [chemical binding]; other site 579112007669 Domain of unknown function (DUF1338); Region: DUF1338; cl02226 579112007670 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 579112007671 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 579112007672 NAD(P) binding site [chemical binding]; other site 579112007673 catalytic residues [active] 579112007674 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 579112007675 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 579112007676 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 579112007677 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 579112007678 inhibitor-cofactor binding pocket; inhibition site 579112007679 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112007680 catalytic residue [active] 579112007681 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 579112007682 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 579112007683 glutamine binding [chemical binding]; other site 579112007684 catalytic triad [active] 579112007685 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 579112007686 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 579112007687 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 579112007688 FeS/SAM binding site; other site 579112007689 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 579112007690 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 579112007691 generic binding surface I; other site 579112007692 generic binding surface II; other site 579112007693 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 579112007694 putative catalytic site [active] 579112007695 putative metal binding site [ion binding]; other site 579112007696 putative phosphate binding site [ion binding]; other site 579112007697 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 579112007698 conserved hypothetical protein; Region: TIGR02285 579112007699 tryptophanyl-tRNA synthetase; Region: trpS; TIGR00233 579112007700 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 579112007701 active site 579112007702 HIGH motif; other site 579112007703 dimer interface [polypeptide binding]; other site 579112007704 KMSKS motif; other site 579112007705 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 579112007706 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 579112007707 motif II; other site 579112007708 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...; Region: RPE; cd00429 579112007709 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 579112007710 substrate binding site [chemical binding]; other site 579112007711 hexamer interface [polypeptide binding]; other site 579112007712 metal binding site [ion binding]; metal-binding site 579112007713 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 579112007714 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 579112007715 Sporulation related domain; Region: SPOR; cl10051 579112007716 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 579112007717 active site 579112007718 dimer interface [polypeptide binding]; other site 579112007719 metal binding site [ion binding]; metal-binding site 579112007720 shikimate kinase; Reviewed; Region: aroK; PRK00131 579112007721 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...; Region: SK; cd00464 579112007722 ADP binding site [chemical binding]; other site 579112007723 magnesium binding site [ion binding]; other site 579112007724 putative shikimate binding site; other site 579112007725 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 579112007726 Secretin and TonB N terminus short domain; Region: STN; cl06624 579112007727 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 579112007728 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 579112007729 Pilus assembly protein, PilP; Region: PilP; cl01235 579112007730 Pilus assembly protein, PilO; Region: PilO; cl01234 579112007731 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 579112007732 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 579112007733 type IV pilus assembly protein PilM; Region: pilM; TIGR01175 579112007734 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 579112007735 Transglycosylase; Region: Transgly; cl07896 579112007736 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 579112007737 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 579112007738 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112007739 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 579112007740 dimerization interface [polypeptide binding]; other site 579112007741 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 579112007742 catalytic triad [active] 579112007743 dimer interface [polypeptide binding]; other site 579112007744 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 579112007745 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 579112007746 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 579112007747 Protein of unknown function (DUF3624); Region: DUF3624; pfam12292 579112007748 argininosuccinate lyase; Provisional; Region: PRK04833 579112007749 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 579112007750 active sites [active] 579112007751 tetramer interface [polypeptide binding]; other site 579112007752 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 579112007753 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 579112007754 ANP binding site [chemical binding]; other site 579112007755 Substrate Binding Site II [chemical binding]; other site 579112007756 Substrate Binding Site I [chemical binding]; other site 579112007757 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 579112007758 nucleotide binding site [chemical binding]; other site 579112007759 substrate binding site [chemical binding]; other site 579112007760 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 579112007761 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007762 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 579112007763 acetylornithine deacetylase; Provisional; Region: PRK05111 579112007764 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 579112007765 metal binding site [ion binding]; metal-binding site 579112007766 putative dimer interface [polypeptide binding]; other site 579112007767 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 579112007768 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 579112007769 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112007770 Virulence activator alpha C-term; Region: Vir_act_alpha_C; pfam10400 579112007771 serine acetyltransferase; Provisional; Region: cysE; PRK11132 579112007772 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 579112007773 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 L-...; Region: LbH_SAT; cd03354 579112007774 trimer interface [polypeptide binding]; other site 579112007775 active site 579112007776 substrate binding site [chemical binding]; other site 579112007777 CoA binding site [chemical binding]; other site 579112007778 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 579112007779 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007780 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 579112007781 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 579112007782 SecA binding site; other site 579112007783 Preprotein binding site; other site 579112007784 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 579112007785 active site residue [active] 579112007786 poxB regulator PoxA; Provisional; Region: PRK09350 579112007787 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 579112007788 motif 1; other site 579112007789 dimer interface [polypeptide binding]; other site 579112007790 active site 579112007791 motif 2; other site 579112007792 motif 3; other site 579112007793 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 579112007794 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007795 domain; Region: Succ_DH_flav_C; pfam02910 579112007796 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 579112007797 Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitC; cd00546 579112007798 D-subunit interface [polypeptide binding]; other site 579112007799 Iron-sulfur protein interface; other site 579112007800 proximal quinone binding site [chemical binding]; other site 579112007801 distal quinone binding site [chemical binding]; other site 579112007802 Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitD; cd00547 579112007803 Iron-sulfur protein interface; other site 579112007804 proximal quinone binding site [chemical binding]; other site 579112007805 C-subunit interface; other site 579112007806 distal quinone binding site; other site 579112007807 elongation factor P; Validated; Region: PRK00529 579112007808 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 579112007809 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 579112007810 RNA binding site [nucleotide binding]; other site 579112007811 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 579112007812 RNA binding site [nucleotide binding]; other site 579112007813 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 579112007814 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 579112007815 FeS/SAM binding site; other site 579112007816 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 579112007817 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 579112007818 ring oligomerisation interface [polypeptide binding]; other site 579112007819 ATP/Mg binding site [chemical binding]; other site 579112007820 stacking interactions; other site 579112007821 hinge regions; other site 579112007822 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...; Region: cpn10; cd00320 579112007823 oligomerisation interface [polypeptide binding]; other site 579112007824 mobile loop; other site 579112007825 roof hairpin; other site 579112007826 Predicted transcriptional regulator [Transcription]; Region: COG2345 579112007827 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112007828 Protein of unknown function (DUF3135); Region: DUF3135; pfam11333 579112007829 Protein of unknown function (DUF805); Region: DUF805; cl01224 579112007830 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 579112007831 putative substrate binding pocket [chemical binding]; other site 579112007832 trimer interface [polypeptide binding]; other site 579112007833 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 579112007834 substrate binding site [chemical binding]; other site 579112007835 dimer interface [polypeptide binding]; other site 579112007836 catalytic triad [active] 579112007837 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 579112007838 MatE; Region: MatE; cl10513 579112007839 MatE; Region: MatE; cl10513 579112007840 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 579112007841 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]; Region: MenA; COG1575 579112007842 UbiA prenyltransferase family; Region: UbiA; cl00337 579112007843 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 579112007844 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...; Region: AAA; cd00009 579112007845 Walker A motif; other site 579112007846 ATP binding site [chemical binding]; other site 579112007847 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112007848 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 579112007849 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 579112007850 active site 579112007851 HslU subunit interaction site [polypeptide binding]; other site 579112007852 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 579112007853 Sporulation related domain; Region: SPOR; cl10051 579112007854 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112007855 DNA binding site [nucleotide binding] 579112007856 DNA-binding transcriptional regulator CytR; Provisional; Region: PRK11041 579112007857 domain linker motif; other site 579112007858 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; Region: PBP1_LacI_like_6; cd06284 579112007859 dimerization interface [polypeptide binding]; other site 579112007860 ligand binding site [chemical binding]; other site 579112007861 primosome assembly protein PriA; Validated; Region: PRK05580 579112007862 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 579112007863 ATP binding site [chemical binding]; other site 579112007864 putative Mg++ binding site [ion binding]; other site 579112007865 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112007866 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 579112007867 Malic enzyme, N-terminal domain; Region: malic; pfam00390 579112007868 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 579112007869 putative NAD(P) binding site [chemical binding]; other site 579112007870 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence; Region: Met_repressor_MetJ; cd00490 579112007871 dimerization interface [polypeptide binding]; other site 579112007872 DNA binding site [nucleotide binding] 579112007873 corepressor binding sites; other site 579112007874 cystathionine gamma-synthase; Provisional; Region: PRK08861 579112007875 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 579112007876 homodimer interface [polypeptide binding]; other site 579112007877 substrate-cofactor binding pocket; other site 579112007878 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112007879 catalytic residue [active] 579112007880 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 579112007881 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 579112007882 nucleotide binding site [chemical binding]; other site 579112007883 substrate binding site [chemical binding]; other site 579112007884 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112007885 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 579112007886 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 579112007887 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...; Region: MTHFR; cd00537 579112007888 FAD binding site [chemical binding]; other site 579112007889 Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism]; Region: GlpX; COG1494 579112007890 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 579112007891 putative active site [active] 579112007892 6-phosphofructokinase; Provisional; Region: PRK03202 579112007893 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent...; Region: Bacterial_PFK; cd00763 579112007894 active site 579112007895 ADP/pyrophosphate binding site [chemical binding]; other site 579112007896 dimerization interface [polypeptide binding]; other site 579112007897 allosteric effector site; other site 579112007898 fructose-1,6-bisphosphate binding site; other site 579112007899 Cation efflux family; Region: Cation_efflux; cl00316 579112007900 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 579112007901 dimer interface [polypeptide binding]; other site 579112007902 DNA-binding transcriptional regulator CpxR; Provisional; Region: PRK10955 579112007903 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112007904 active site 579112007905 phosphorylation site [posttranslational modification] 579112007906 intermolecular recognition site; other site 579112007907 dimerization interface [polypeptide binding]; other site 579112007908 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...; Region: trans_reg_C; cd00383 579112007909 DNA binding site [nucleotide binding] 579112007910 two-component sensor protein; Provisional; Region: cpxA; PRK09470 579112007911 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112007912 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 trans-...; Region: HisKA; cd00082 579112007913 dimer interface [polypeptide binding]; other site 579112007914 phosphorylation site [posttranslational modification] 579112007915 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 579112007916 ATP binding site [chemical binding]; other site 579112007917 Mg2+ binding site [ion binding]; other site 579112007918 G-X-G motif; other site 579112007919 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 579112007920 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 579112007921 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 579112007922 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 579112007923 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 579112007924 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112007925 metal binding site [ion binding]; metal-binding site 579112007926 active site 579112007927 I-site; other site 579112007928 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 579112007929 Aspartase; Region: Aspartase; cd01357 579112007930 active sites [active] 579112007931 tetramer interface [polypeptide binding]; other site 579112007932 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 579112007933 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 579112007934 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 579112007935 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 579112007936 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 579112007937 DsbD alpha interface [polypeptide binding]; other site 579112007938 catalytic residues [active] 579112007939 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 579112007940 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112007941 active site 579112007942 phosphorylation site [posttranslational modification] 579112007943 intermolecular recognition site; other site 579112007944 dimerization interface [polypeptide binding]; other site 579112007945 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...; Region: LuxR_C_like; cd06170 579112007946 DNA binding residues [nucleotide binding] 579112007947 dimerization interface [polypeptide binding]; other site 579112007948 NhaP-type Na+/H+ and K+/H+ antiporters with a unique C-terminal domain [Inorganic ion transport and metabolism]; Region: COG3263 579112007949 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 579112007950 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; cl09110 579112007951 Transporter associated domain; Region: CorC_HlyC; cl08393 579112007952 Predicted membrane protein [Function unknown]; Region: COG4327; cl01781 579112007953 Sodium:solute symporter family; Region: SSF; cl00456 579112007954 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 579112007955 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...; Region: GMPK; cd00071 579112007956 catalytic site [active] 579112007957 G-X2-G-X-G-K; other site 579112007958 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 579112007959 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 579112007960 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112007961 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 579112007962 synthetase active site [active] 579112007963 NTP binding site [chemical binding]; other site 579112007964 metal binding site [ion binding]; metal-binding site 579112007965 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...; Region: TGS_RelA_SpoT; cd01668 579112007966 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 579112007967 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 579112007968 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 four-...; Region: RecG_wedge_OBF; cd04488 579112007969 ssDNA binding site; other site 579112007970 generic binding surface II; other site 579112007971 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 579112007972 ATP binding site [chemical binding]; other site 579112007973 putative Mg++ binding site [ion binding]; other site 579112007974 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 579112007975 nucleotide binding region [chemical binding]; other site 579112007976 ATP-binding site [chemical binding]; other site 579112007977 Permease family; Region: Xan_ur_permease; pfam00860 579112007978 Sulfate transporter family; Region: Sulfate_transp; cl00967 579112007979 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 579112007980 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112007981 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 trans-...; Region: HisKA; cd00082 579112007982 dimer interface [polypeptide binding]; other site 579112007983 phosphorylation site [posttranslational modification] 579112007984 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 579112007985 ATP binding site [chemical binding]; other site 579112007986 Mg2+ binding site [ion binding]; other site 579112007987 G-X-G motif; other site 579112007988 osmolarity response regulator; Provisional; Region: ompR; PRK09468 579112007989 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112007990 active site 579112007991 phosphorylation site [posttranslational modification] 579112007992 intermolecular recognition site; other site 579112007993 dimerization interface [polypeptide binding]; other site 579112007994 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...; Region: trans_reg_C; cd00383 579112007995 DNA binding site [nucleotide binding] 579112007996 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 579112007997 domain; Region: GreA_GreB_N; pfam03449 579112007998 C-term; Region: GreA_GreB; pfam01272 579112007999 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 579112008000 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 579112008001 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 579112008002 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...; Region: S1_Tex; cd05685 579112008003 RNA binding site [nucleotide binding]; other site 579112008004 putative pimeloyl-BioC--CoA transferase BioH; Region: bioH; TIGR01738 579112008005 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 579112008006 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 579112008007 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 579112008008 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 579112008009 NifU-like domain; Region: NifU; cl00484 579112008010 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 579112008011 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...; Region: ADPRase_NUDT5; cd03424 579112008012 dimer interface [polypeptide binding]; other site 579112008013 ADP-ribose binding site [chemical binding]; other site 579112008014 active site 579112008015 nudix motif; other site 579112008016 metal binding site [ion binding]; metal-binding site 579112008017 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 579112008018 active site 579112008019 Bacterial type II secretion system protein N; Region: GSPII_N; pfam01203 579112008020 General secretion pathway, M protein; Region: GspM; cl01222 579112008021 Type II secretory pathway, component PulL [Intracellular trafficking and secretion]; Region: PulL; COG3297 579112008022 GspL cytoplasmic actin-ATPase-like region; Region: GspL; pfam05134 579112008023 GspL periplasmic domain; Region: GspL_C; cl14909 579112008024 General secretion pathway protein K; Region: GspK; pfam03934 579112008025 general secretion pathway protein J; Region: gspJ; TIGR01711 579112008026 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 579112008027 Pseudopilin GspJ; Region: GspJ; pfam11612 579112008028 general secretion pathway protein I; Region: gspI; TIGR01707 579112008029 Bacterial type II secretion system protein I/J; Region: GSPII_IJ; pfam02501 579112008030 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 579112008031 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 579112008032 general secretion pathway protein F; Region: GspF; TIGR02120 579112008033 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 579112008034 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 579112008035 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 579112008036 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 579112008037 Walker A motif; other site 579112008038 ATP binding site [chemical binding]; other site 579112008039 Walker B motif; other site 579112008040 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 579112008041 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 579112008042 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 579112008043 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 579112008044 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 579112008045 general secretion pathway protein C; Region: typeII_sec_gspC; TIGR01713 579112008046 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 579112008047 RNA binding surface [nucleotide binding]; other site 579112008048 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 579112008049 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 579112008050 dimerization interface [polypeptide binding]; other site 579112008051 domain crossover interface; other site 579112008052 redox-dependent activation switch; other site 579112008053 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 579112008054 active site 579112008055 substrate-binding site [chemical binding]; other site 579112008056 metal-binding site [ion binding] 579112008057 ATP binding site [chemical binding]; other site 579112008058 AsmA family; Region: AsmA; pfam05170 579112008059 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112008060 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 579112008061 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...; Region: Dtyr_deacylase; cd00563 579112008062 putative active site [active] 579112008063 dimerization interface [polypeptide binding]; other site 579112008064 putative tRNAtyr binding site [nucleotide binding]; other site 579112008065 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 579112008066 Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]; Region: NadR; cl01238 579112008067 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 579112008068 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 579112008069 G1 box; other site 579112008070 putative GEF interaction site [polypeptide binding]; other site 579112008071 GTP/Mg2+ binding site [chemical binding]; other site 579112008072 Switch I region; other site 579112008073 G2 box; other site 579112008074 G3 box; other site 579112008075 Switch II region; other site 579112008076 G4 box; other site 579112008077 G5 box; other site 579112008078 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 579112008079 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...; Region: BipA_TypA_C; cd03710 579112008080 glutamine synthetase; Provisional; Region: glnA; PRK09469 579112008081 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 579112008082 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 579112008083 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 579112008084 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112008085 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 trans-...; Region: HisKA; cl00080 579112008086 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 579112008087 ATP binding site [chemical binding]; other site 579112008088 Mg2+ binding site [ion binding]; other site 579112008089 G-X-G motif; other site 579112008090 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 579112008091 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112008092 active site 579112008093 phosphorylation site [posttranslational modification] 579112008094 intermolecular recognition site; other site 579112008095 dimerization interface [polypeptide binding]; other site 579112008096 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...; Region: AAA; cd00009 579112008097 Walker A motif; other site 579112008098 ATP binding site [chemical binding]; other site 579112008099 Walker B motif; other site 579112008100 arginine finger; other site 579112008101 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112008102 Cache domain; Region: Cache_1; pfam02743 579112008103 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112008104 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112008105 metal binding site [ion binding]; metal-binding site 579112008106 active site 579112008107 I-site; other site 579112008108 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 579112008109 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...; Region: metallo-dependent_hydrolases; cl00281 579112008110 active site 579112008111 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 579112008112 Cation transport protein; Region: TrkH; cl10514 579112008113 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 579112008114 hypothetical protein; Provisional; Region: PRK11568 579112008115 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 579112008116 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 579112008117 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 579112008118 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 579112008119 substrate binding site [chemical binding]; other site 579112008120 oxyanion hole (OAH) forming residues; other site 579112008121 trimer interface [polypeptide binding]; other site 579112008122 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 579112008123 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 579112008124 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 579112008125 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 579112008126 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 579112008127 dimer interface [polypeptide binding]; other site 579112008128 active site 579112008129 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 579112008130 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112008131 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 579112008132 dimerization interface [polypeptide binding]; other site 579112008133 putative transporter; Provisional; Region: PRK11043 579112008134 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 579112008135 putative substrate translocation pore; other site 579112008136 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 579112008137 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 579112008138 Substrate binding site [chemical binding]; other site 579112008139 Mg++ binding site [ion binding]; other site 579112008140 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 579112008141 active site 579112008142 substrate binding site [chemical binding]; other site 579112008143 CoA binding site [chemical binding]; other site 579112008144 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 579112008145 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 579112008146 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 579112008147 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 579112008148 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 579112008149 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 579112008150 alpha subunit interaction interface [polypeptide binding]; other site 579112008151 Walker A motif; other site 579112008152 ATP binding site [chemical binding]; other site 579112008153 Walker B motif; other site 579112008154 inhibitor binding site; inhibition site 579112008155 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 579112008156 ATP synthase; Region: ATP-synt; cl00365 579112008157 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 579112008158 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 579112008159 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 579112008160 beta subunit interaction interface [polypeptide binding]; other site 579112008161 Walker A motif; other site 579112008162 ATP binding site [chemical binding]; other site 579112008163 Walker B motif; other site 579112008164 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 579112008165 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 579112008166 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 579112008167 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 579112008168 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 579112008169 ATP synthase subunit C; Region: ATP-synt_C; cl00466 579112008170 ATP synthase A chain; Region: ATP-synt_A; cl00413 579112008171 ATP synthase I chain; Region: ATP_synt_I; cl09170 579112008172 ParB-like partition proteins; Region: parB_part; TIGR00180 579112008173 ParB-like nuclease domain; Region: ParBc; cl02129 579112008174 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 579112008175 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112008176 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 579112008177 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 579112008178 S-adenosylmethionine binding site [chemical binding]; other site 579112008179 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112008180 glucose-inhibited division protein A; Region: gidA; TIGR00136 579112008181 Protein of unknown function (DUF3346); Region: DUF3346; pfam11826 579112008182 Protein of unknown function (DUF3283); Region: DUF3283; pfam11686 579112008183 Domain of unknown function DUF28; Region: DUF28; cl00361 579112008184 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 579112008185 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112008186 NAD(P) binding pocket [chemical binding]; other site 579112008187 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 579112008188 Cache domain; Region: Cache_2; cl07034 579112008189 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112008190 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112008191 Protein of unknown function (DUF2810); Region: DUF2810; cl08159 579112008192 transcriptional regulator MalT; Provisional; Region: PRK04841 579112008193 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...; Region: LuxR_C_like; cd06170 579112008194 DNA binding residues [nucleotide binding] 579112008195 dimerization interface [polypeptide binding]; other site 579112008196 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 579112008197 homodimer interface [polypeptide binding]; other site 579112008198 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 579112008199 active site pocket [active] 579112008200 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 579112008201 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 579112008202 glycogen branching enzyme; Provisional; Region: PRK05402 579112008203 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 579112008204 Glycogen branching enzyme N-terminus domain. Glycogen branching enzyme (AKA 1,4 alpha glucan branching enzyme) catalyzes the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage yielding a...; Region: Glycogen_branching_enzyme_N_term; cd02855 579112008205 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 579112008206 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 579112008207 Protein of unknown function (DUF796); Region: DUF796; cl01226 579112008208 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 579112008209 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 579112008210 MAPEG family; Region: MAPEG; cl09190 579112008211 Predicted O-acyltransferase [General function prediction only]; Region: COG3274; cl00792 579112008212 Acyltransferase family; Region: Acyl_transf_3; pfam01757 579112008213 Membrane transport protein; Region: Mem_trans; cl09117 579112008214 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 579112008215 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 579112008216 transmembrane helices; other site 579112008217 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 579112008218 Chitinase N-terminus domain. Chitinases hydrolyze the abundant natural biopolymer chitin, producing smaller chito-oligosaccharides. Chitin consists of multiple N-acetyl-D-glucosamine (NAG) residues connected via beta-1,4-glycosidic linkages and is an...; Region: Chitinase_N_term; cd02848 579112008219 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 579112008220 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is...; Region: GH18_chitinase; cd06548 579112008221 active site 579112008222 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 579112008223 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 579112008224 chitin/cellulose binding site [chemical binding]; other site 579112008225 Transcriptional regulator [Transcription]; Region: IclR; COG1414 579112008226 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112008227 Bacterial transcriptional regulator; Region: IclR; pfam01614 579112008228 Arginase family; Region: Arginase; cl00306 579112008229 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112008230 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112008231 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 579112008232 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 579112008233 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112008234 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 579112008235 active site 579112008236 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 579112008237 Protein of unknown function (DUF461); Region: DUF461; cl01071 579112008238 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 579112008239 Cu(I) binding site [ion binding]; other site 579112008240 Domain of unknown function (DUF368); Region: DUF368; cl00893 579112008241 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 579112008242 Flagellar protein YcgR; Region: YcgR_2; pfam12945 579112008243 PilZ domain; Region: PilZ; cl01260 579112008244 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112008245 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 579112008246 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 579112008247 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 579112008248 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 579112008249 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 579112008250 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 579112008251 protein binding site [polypeptide binding]; other site 579112008252 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 579112008253 Domain interface; other site 579112008254 Peptide binding site; other site 579112008255 Active site tetrad [active] 579112008256 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 579112008257 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...; Region: Biotinyl_lipoyl_domains; cl11404 579112008258 Protein of unknown function (DUF3302); Region: DUF3302; pfam11742 579112008259 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112008260 metal binding site [ion binding]; metal-binding site 579112008261 active site 579112008262 I-site; other site 579112008263 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 579112008264 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112008265 DNA binding residues [nucleotide binding] 579112008266 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 579112008267 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 579112008268 Protein of unknown function (DUF523); Region: DUF523; cl00733 579112008269 Protein of unknown function (DUF1722); Region: DUF1722; cl01284 579112008270 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 579112008271 DNA binding residues [nucleotide binding] 579112008272 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 579112008273 DNA photolyase; Region: DNA_photolyase; pfam00875 579112008274 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 579112008275 L,D-transpeptidase; Provisional; Region: PRK10190 579112008276 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 579112008277 putative peptidoglycan binding site; other site 579112008278 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 579112008279 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 579112008280 helicase 45; Provisional; Region: PTZ00424 579112008281 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 579112008282 ATP binding site [chemical binding]; other site 579112008283 Mg++ binding site [ion binding]; other site 579112008284 motif III; other site 579112008285 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 579112008286 nucleotide binding region [chemical binding]; other site 579112008287 ATP-binding site [chemical binding]; other site 579112008288 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 579112008289 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 579112008290 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 579112008291 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112008292 N-terminal plug; other site 579112008293 ligand-binding site [chemical binding]; other site 579112008294 Peptidase M36 family also known as fungalysin family; Region: M36; cd09596 579112008295 Zn binding site [ion binding]; other site 579112008296 Regulatory P domain of the subtilisin-like proprotein convertases and other proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG4935 579112008297 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 579112008298 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 579112008299 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112008300 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112008301 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112008302 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 579112008303 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 579112008304 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...; Region: TM_PBP2; cd06261 579112008305 dimer interface [polypeptide binding]; other site 579112008306 conserved gate region; other site 579112008307 putative PBP binding loops; other site 579112008308 ABC-ATPase subunit interface; other site 579112008309 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 579112008310 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...; Region: TM_PBP2; cd06261 579112008311 dimer interface [polypeptide binding]; other site 579112008312 conserved gate region; other site 579112008313 putative PBP binding loops; other site 579112008314 ABC-ATPase subunit interface; other site 579112008315 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14253 579112008316 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 579112008317 Walker A/P-loop; other site 579112008318 ATP binding site [chemical binding]; other site 579112008319 Q-loop/lid; other site 579112008320 ABC transporter signature motif; other site 579112008321 Walker B; other site 579112008322 D-loop; other site 579112008323 H-loop/switch region; other site 579112008324 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 579112008325 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 579112008326 Nucleoside recognition; Region: Gate; cl00486 579112008327 putative transporter; Provisional; Region: PRK11660 579112008328 Sulfate transporter family; Region: Sulfate_transp; cl00967 579112008329 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 579112008330 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 579112008331 putative peptidase; Provisional; Region: PRK11649 579112008332 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 579112008333 Peptidase family M23; Region: Peptidase_M23; pfam01551 579112008334 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 579112008335 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112008336 metal binding site [ion binding]; metal-binding site 579112008337 active site 579112008338 I-site; other site 579112008339 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 579112008340 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112008341 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112008342 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112008343 putative effector binding pocket; other site 579112008344 dimerization interface [polypeptide binding]; other site 579112008345 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 579112008346 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 579112008347 putative substrate translocation pore; other site 579112008348 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 579112008349 Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Region: HTH_SoxR; cd01110 579112008350 DNA binding residues [nucleotide binding] 579112008351 dimer interface [polypeptide binding]; other site 579112008352 [2Fe-2S] cluster binding site [ion binding]; other site 579112008353 H+ Antiporter protein; Region: 2A0121; TIGR00900 579112008354 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 579112008355 putative substrate translocation pore; other site 579112008356 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 579112008357 EamA-like transporter family; Region: EamA; cl01037 579112008358 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 579112008359 EamA-like transporter family; Region: EamA; cl01037 579112008360 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112008361 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 579112008362 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112008363 Peptidase M66; Region: Peptidase_M66; pfam10462 579112008364 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 579112008365 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...; Region: Nudix_Hydrolase; cl00447 579112008366 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 579112008367 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting...; Region: PncB_like; cd01401 579112008368 active site 579112008369 putative oxidoreductase; Provisional; Region: PRK11579 579112008370 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112008371 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 579112008372 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 579112008373 active site residue [active] 579112008374 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 579112008375 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 579112008376 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 579112008377 motif II; other site 579112008378 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 579112008379 Sulfate transporter family; Region: Sulfate_transp; cl00967 579112008380 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 579112008381 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 579112008382 phosphodiesterase; Provisional; Region: PRK12704 579112008383 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 579112008384 active site 579112008385 Uncharacterized conserved protein [Function unknown]; Region: COG4104 579112008386 PAAR motif; Region: PAAR_motif; pfam05488 579112008387 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 579112008388 Protein of unknown function (DUF770); Region: DUF770; cl01402 579112008389 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 579112008390 Protein of unknown function (DUF877); Region: DUF877; pfam05943 579112008391 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 579112008392 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 579112008393 type VI secretion protein, VC_A0110 family; Region: VI_chp_6; TIGR03359 579112008394 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 579112008395 Predicted component of the type VI protein secretion system, contains a FHA domain [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]; Region: COG3456 579112008396 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 579112008397 Bacterial protein of unknown function (DUF876); Region: DUF876; cl01406 579112008398 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 579112008399 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 579112008400 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...; Region: AAA; cd00009 579112008401 Walker A motif; other site 579112008402 ATP binding site [chemical binding]; other site 579112008403 Walker B motif; other site 579112008404 arginine finger; other site 579112008405 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...; Region: AAA; cd00009 579112008406 Walker A motif; other site 579112008407 ATP binding site [chemical binding]; other site 579112008408 Walker B motif; other site 579112008409 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 579112008410 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 579112008411 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...; Region: AAA; cd00009 579112008412 Walker A motif; other site 579112008413 ATP binding site [chemical binding]; other site 579112008414 Walker B motif; other site 579112008415 arginine finger; other site 579112008416 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112008417 Protein of unknown function (DUF3121); Region: DUF3121; cl11879 579112008418 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 579112008419 type VI secretion-associated protein, VC_A0119 family; Region: VI_chp_7; TIGR03362 579112008420 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 579112008421 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 579112008422 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 579112008423 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3515 579112008424 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 579112008425 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 579112008426 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 579112008427 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 579112008428 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 579112008429 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 579112008430 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 579112008431 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 579112008432 D-ribose transporter ATP binding protein; Provisional; Region: PRK10762 579112008433 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 579112008434 Walker A/P-loop; other site 579112008435 ATP binding site [chemical binding]; other site 579112008436 Q-loop/lid; other site 579112008437 ABC transporter signature motif; other site 579112008438 Walker B; other site 579112008439 D-loop; other site 579112008440 H-loop/switch region; other site 579112008441 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 579112008442 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 579112008443 TM-ABC transporter signature motif; other site 579112008444 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 579112008445 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 579112008446 ligand binding site [chemical binding]; other site 579112008447 dimerization interface [polypeptide binding]; other site 579112008448 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 579112008449 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of...; Region: ribokinase; cd01174 579112008450 substrate binding site [chemical binding]; other site 579112008451 dimer interface [polypeptide binding]; other site 579112008452 ATP binding site [chemical binding]; other site 579112008453 transcriptional repressor RbsR; Provisional; Region: PRK10423 579112008454 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112008455 DNA binding site [nucleotide binding] 579112008456 domain linker motif; other site 579112008457 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 579112008458 dimerization interface [polypeptide binding]; other site 579112008459 ligand binding site [chemical binding]; other site 579112008460 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 579112008461 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 579112008462 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 579112008463 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 579112008464 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 579112008465 ligand binding site [chemical binding]; other site 579112008466 flexible hinge region; other site 579112008467 Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins; Region: GDPD_EcGlpQ_like; cd08600 579112008468 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 579112008469 active site 579112008470 catalytic site [active] 579112008471 metal binding site [ion binding]; metal-binding site 579112008472 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 579112008473 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 579112008474 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 579112008475 Protein of unknown function (DUF3316); Region: DUF3316; pfam11777 579112008476 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3397 579112008477 Chitin binding domain; Region: Chitin_bind_3; cl03871 579112008478 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 579112008479 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cd00036 579112008480 chitin/cellulose binding site [chemical binding]; other site 579112008481 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 579112008482 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112008483 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 579112008484 ATP binding site [chemical binding]; other site 579112008485 Mg2+ binding site [ion binding]; other site 579112008486 G-X-G motif; other site 579112008487 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 579112008488 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112008489 active site 579112008490 phosphorylation site [posttranslational modification] 579112008491 intermolecular recognition site; other site 579112008492 dimerization interface [polypeptide binding]; other site 579112008493 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...; Region: AAA; cd00009 579112008494 Walker A motif; other site 579112008495 ATP binding site [chemical binding]; other site 579112008496 Walker B motif; other site 579112008497 arginine finger; other site 579112008498 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112008499 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 579112008500 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 579112008501 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; cl09110 579112008502 Predicted dehydrogenase [General function prediction only]; Region: COG0579 579112008503 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 579112008504 Peptidase M66; Region: Peptidase_M66; pfam10462 579112008505 ToxR activated gene A lipoprotein; Region: TagA; pfam12561 579112008506 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(...; Region: Pep_deformylase; cd00487 579112008507 active site 579112008508 catalytic residues [active] 579112008509 metal binding site [ion binding]; metal-binding site 579112008510 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 579112008511 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 579112008512 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 579112008513 FAD binding pocket [chemical binding]; other site 579112008514 FAD binding motif [chemical binding]; other site 579112008515 phosphate binding motif [ion binding]; other site 579112008516 beta-alpha-beta structure motif; other site 579112008517 NAD binding pocket [chemical binding]; other site 579112008518 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 579112008519 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 579112008520 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 579112008521 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12663 579112008522 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 579112008523 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 579112008524 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12647 579112008525 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 579112008526 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 579112008527 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 579112008528 universal stress protein UspE; Provisional; Region: PRK11175 579112008529 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 579112008530 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 579112008531 Ligand Binding Site [chemical binding]; other site 579112008532 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 579112008533 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 579112008534 tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional; Region: tnaA; PRK13238 579112008535 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 579112008536 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112008537 catalytic residue [active] 579112008538 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 579112008539 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 579112008540 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112008541 metal binding site [ion binding]; metal-binding site 579112008542 active site 579112008543 I-site; other site 579112008544 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 579112008545 DNA-binding site [nucleotide binding]; DNA binding site 579112008546 RNA-binding motif; other site 579112008547 Protein of unknown function (DUF541); Region: SIMPL; cl01077 579112008548 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 579112008549 metal ion-dependent adhesion site (MIDAS); other site 579112008550 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 579112008551 VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-...; Region: vWA_BatA_type; cd01467 579112008552 metal ion-dependent adhesion site (MIDAS); other site 579112008553 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 579112008554 Protein of unknown function DUF58; Region: DUF58; pfam01882 579112008555 MoxR-like ATPases [General function prediction only]; Region: COG0714 579112008556 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...; Region: AAA; cd00009 579112008557 Walker A motif; other site 579112008558 ATP binding site [chemical binding]; other site 579112008559 Walker B motif; other site 579112008560 arginine finger; other site 579112008561 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112008562 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112008563 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112008564 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112008565 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 579112008566 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 579112008567 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 579112008568 catalytic residues [active] 579112008569 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 579112008570 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 579112008571 Nucleoside recognition; Region: Gate; cl00486 579112008572 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 579112008573 peptidase T; Region: peptidase-T; TIGR01882 579112008574 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 579112008575 metal binding site [ion binding]; metal-binding site 579112008576 dimer interface [polypeptide binding]; other site 579112008577 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 579112008578 Mechanosensitive ion channel; Region: MS_channel; pfam00924 579112008579 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 579112008580 GAF domain; Region: GAF; cl00853 579112008581 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...; Region: AAA; cd00009 579112008582 Walker A motif; other site 579112008583 ATP binding site [chemical binding]; other site 579112008584 Walker B motif; other site 579112008585 arginine finger; other site 579112008586 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 579112008587 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 579112008588 heme-binding site [chemical binding]; other site 579112008589 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 579112008590 FAD binding pocket [chemical binding]; other site 579112008591 FAD binding motif [chemical binding]; other site 579112008592 phosphate binding motif [ion binding]; other site 579112008593 beta-alpha-beta structure motif; other site 579112008594 NAD binding pocket [chemical binding]; other site 579112008595 Heme binding pocket [chemical binding]; other site 579112008596 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 579112008597 DNA-binding site [nucleotide binding]; DNA binding site 579112008598 RNA-binding motif; other site 579112008599 Domain of unknown function; Region: DUF331; cl01149 579112008600 Response regulator receiver domain; Region: Response_reg; pfam00072 579112008601 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112008602 active site 579112008603 phosphorylation site [posttranslational modification] 579112008604 intermolecular recognition site; other site 579112008605 dimerization interface [polypeptide binding]; other site 579112008606 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 579112008607 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112008608 putative carbohydrate kinase; Provisional; Region: PRK10565 579112008609 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 579112008610 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 579112008611 putative substrate binding site [chemical binding]; other site 579112008612 putative ATP binding site [chemical binding]; other site 579112008613 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 579112008614 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112008615 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; cl09110 579112008616 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; cl09110 579112008617 Ion channel; Region: Ion_trans_2; cl11596 579112008618 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05096 579112008619 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the...; Region: IMPDH; cd00381 579112008620 active site 579112008621 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 579112008622 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112008623 cofactor binding site; other site 579112008624 DNA binding site [nucleotide binding] 579112008625 substrate interaction site [chemical binding]; other site 579112008626 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112008627 Protein of unknown function DUF262; Region: DUF262; cl14890 579112008628 Uncharacterized conserved protein [Function unknown]; Region: COG4938 579112008629 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112008630 Walker A/P-loop; other site 579112008631 ATP binding site [chemical binding]; other site 579112008632 Q-loop/lid; other site 579112008633 Protein of unknown function (DUF3696); Region: DUF3696; pfam12476 579112008634 Transposase IS200 like; Region: Y1_Tnp; cl00848 579112008635 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 579112008636 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 579112008637 ATP binding site [chemical binding]; other site 579112008638 Mg++ binding site [ion binding]; other site 579112008639 motif III; other site 579112008640 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 579112008641 nucleotide binding region [chemical binding]; other site 579112008642 ATP-binding site [chemical binding]; other site 579112008643 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 579112008644 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 579112008645 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...; Region: NAD_synthase; cd00553 579112008646 homodimer interface [polypeptide binding]; other site 579112008647 NAD binding pocket [chemical binding]; other site 579112008648 ATP binding pocket [chemical binding]; other site 579112008649 Mg binding site [ion binding]; other site 579112008650 active-site loop [active] 579112008651 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 579112008652 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 579112008653 active site 579112008654 (T/H)XGH motif; other site 579112008655 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 579112008656 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 579112008657 active site 579112008658 phosphorylation site [posttranslational modification] 579112008659 intermolecular recognition site; other site 579112008660 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 579112008661 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 579112008662 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112008663 Zn2+ binding site [ion binding]; other site 579112008664 Mg2+ binding site [ion binding]; other site 579112008665 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 579112008666 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 579112008667 ATP binding site [chemical binding]; other site 579112008668 Mg2+ binding site [ion binding]; other site 579112008669 G-X-G motif; other site 579112008670 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 579112008671 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; cl09110 579112008672 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 579112008673 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 579112008674 putative substrate translocation pore; other site 579112008675 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112008676 metal binding site [ion binding]; metal-binding site 579112008677 active site 579112008678 I-site; other site 579112008679 Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: fatty_acyltransferase_like; cd01846 579112008680 active site 579112008681 catalytic triad [active] 579112008682 oxyanion hole [active] 579112008683 Hemolytic toxin N terminal; Region: Hemolysin_N; pfam12563 579112008684 Leukocidin/Hemolysin toxin family; Region: Leukocidin; cl08468 579112008685 Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly...; Region: RICIN; cl00126 579112008686 Jacalin-like lectin domain; Region: Jacalin_like; cd09302 579112008687 putative sugar binding site [chemical binding]; other site 579112008688 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 579112008689 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112008690 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112008691 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112008692 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 579112008693 lipase chaperone; Provisional; Region: PRK01294 579112008694 Proteobacterial lipase chaperone protein; Region: Lipase_chap; cl02224 579112008695 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4412 579112008696 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 579112008697 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 579112008698 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cl14635 579112008699 TIGR03442 family protein; Region: TIGR03442 579112008700 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 579112008701 putative active site [active] 579112008702 putative dimer interface [polypeptide binding]; other site 579112008703 ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CeuA; COG4607 579112008704 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 579112008705 putative ligand binding residues [chemical binding]; other site 579112008706 ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]; Region: CeuC; COG4605 579112008707 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112008708 ABC-ATPase subunit interface; other site 579112008709 dimer interface [polypeptide binding]; other site 579112008710 putative PBP binding regions; other site 579112008711 ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]; Region: CeuC; COG4605 579112008712 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112008713 ABC-ATPase subunit interface; other site 579112008714 dimer interface [polypeptide binding]; other site 579112008715 putative PBP binding regions; other site 579112008716 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 579112008717 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 579112008718 Walker A/P-loop; other site 579112008719 ATP binding site [chemical binding]; other site 579112008720 Q-loop/lid; other site 579112008721 ABC transporter signature motif; other site 579112008722 Walker B; other site 579112008723 D-loop; other site 579112008724 H-loop/switch region; other site 579112008725 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112008726 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112008727 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 579112008728 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112008729 N-terminal plug; other site 579112008730 ligand-binding site [chemical binding]; other site 579112008731 Uncharacterized protein conserved in bacteria (DUF2218); Region: DUF2218; cl01424 579112008732 Acetokinase family; Region: Acetate_kinase; cl01029 579112008733 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 579112008734 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4337 579112008735 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 579112008736 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 connected by an extended linker. The...; Region: HAMP; cd06225 579112008737 dimerization interface [polypeptide binding]; other site 579112008738 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 trans-...; Region: HisKA; cd00082 579112008739 dimer interface [polypeptide binding]; other site 579112008740 phosphorylation site [posttranslational modification] 579112008741 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 579112008742 ATP binding site [chemical binding]; other site 579112008743 Mg2+ binding site [ion binding]; other site 579112008744 G-X-G motif; other site 579112008745 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 579112008746 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112008747 active site 579112008748 phosphorylation site [posttranslational modification] 579112008749 intermolecular recognition site; other site 579112008750 dimerization interface [polypeptide binding]; other site 579112008751 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...; Region: trans_reg_C; cd00383 579112008752 DNA binding site [nucleotide binding] 579112008753 putative L-xylulose 5-phosphate 3-epimerase; Reviewed; Region: PRK13210 579112008754 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 D-arabino-6-...; Region: AP2Ec; cd00019 579112008755 AP (apurinic/apyrimidinic) site pocket; other site 579112008756 DNA interaction; other site 579112008757 Metal-binding active site; metal-binding site 579112008758 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 579112008759 active site 579112008760 dimer interface [polypeptide binding]; other site 579112008761 magnesium binding site [ion binding]; other site 579112008762 pyridoxal phosphate (PLP) phosphatase; Provisional; Region: PRK10530 579112008763 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 579112008764 active site 579112008765 motif I; other site 579112008766 motif II; other site 579112008767 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; cl11391 579112008768 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 579112008769 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 579112008770 intersubunit interface [polypeptide binding]; other site 579112008771 active site 579112008772 Zn2+ binding site [ion binding]; other site 579112008773 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 579112008774 active site 579112008775 phosphorylation site [posttranslational modification] 579112008776 PTS system ascorbate-specific transporter subunits IICB; Provisional; Region: PRK09548 579112008777 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 579112008778 PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a...; Region: PTS_IIB_ascorbate; cd05563 579112008779 P-loop; other site 579112008780 active site 579112008781 phosphorylation site [posttranslational modification] 579112008782 transcriptional repressor UlaR; Provisional; Region: PRK13509 579112008783 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112008784 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 579112008785 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112008786 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 579112008787 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 579112008788 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 579112008789 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 579112008790 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 579112008791 trimer interface [polypeptide binding]; other site 579112008792 active site 579112008793 substrate binding site [chemical binding]; other site 579112008794 CoA binding site [chemical binding]; other site 579112008795 Protein of unknown function (DUF3111); Region: DUF3111; pfam11308 579112008796 Protein of unknown function (DUF3111); Region: DUF3111; pfam11308 579112008797 Protein of unknown function (DUF2861); Region: DUF2861; pfam11060 579112008798 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 579112008799 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112008800 active site 579112008801 phosphorylation site [posttranslational modification] 579112008802 intermolecular recognition site; other site 579112008803 dimerization interface [polypeptide binding]; other site 579112008804 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...; Region: trans_reg_C; cd00383 579112008805 DNA binding site [nucleotide binding] 579112008806 Domain of unknown function (DUF3404); Region: DUF3404; pfam11884 579112008807 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 579112008808 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 trans-...; Region: HisKA; cl00080 579112008809 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 579112008810 ATP binding site [chemical binding]; other site 579112008811 Mg2+ binding site [ion binding]; other site 579112008812 G-X-G motif; other site 579112008813 Cupin domain; Region: Cupin_2; cl09118 579112008814 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 579112008815 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112008816 Coenzyme A binding pocket [chemical binding]; other site 579112008817 Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Region: HTH_Cfa; cd04789 579112008818 DNA binding residues [nucleotide binding] 579112008819 putative dimer interface [polypeptide binding]; other site 579112008820 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 579112008821 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 579112008822 S-adenosylmethionine binding site [chemical binding]; other site 579112008823 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 579112008824 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112008825 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 579112008826 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 579112008827 putative substrate translocation pore; other site 579112008828 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112008829 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112008830 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112008831 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 579112008832 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 579112008833 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112008834 catalytic residue [active] 579112008835 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 579112008836 Beta-lactamase; Region: Beta-lactamase; cl01009 579112008837 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 579112008838 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112008839 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 579112008840 active site 579112008841 zinc binding site [ion binding]; other site 579112008842 putative transposase OrfB; Reviewed; Region: PHA02517 579112008843 Integrase core domain; Region: rve; cl01316 579112008844 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; cl01116 579112008845 glycine dehydrogenase; Provisional; Region: PRK05367 579112008846 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2...; Region: GDC-P; cd00613 579112008847 tetramer interface [polypeptide binding]; other site 579112008848 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112008849 catalytic residue [active] 579112008850 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2...; Region: GDC-P; cd00613 579112008851 tetramer interface [polypeptide binding]; other site 579112008852 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112008853 catalytic residue [active] 579112008854 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-...; Region: GCS_H; cd06848 579112008855 lipoyl attachment site [posttranslational modification]; other site 579112008856 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 579112008857 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...; Region: SHMT; cd00378 579112008858 dimer interface [polypeptide binding]; other site 579112008859 glycine-pyridoxal phosphate binding site [chemical binding]; other site 579112008860 active site 579112008861 folate binding site [chemical binding]; other site 579112008862 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 579112008863 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 579112008864 non-specific DNA binding site [nucleotide binding]; other site 579112008865 salt bridge; other site 579112008866 sequence-specific DNA binding site [nucleotide binding]; other site 579112008867 Cupin domain; Region: Cupin_2; cl09118 579112008868 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 579112008869 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 579112008870 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 579112008871 Phage integrase family; Region: Phage_integrase; pfam00589 579112008872 active site 579112008873 Int/Topo IB signature motif; other site 579112008874 Transposase domain (DUF772); Region: DUF772; cl12084 579112008875 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 579112008876 Uncharacterized conserved protein [Function unknown]; Region: COG4104 579112008877 PAAR motif; Region: PAAR_motif; pfam05488 579112008878 PAAR motif; Region: PAAR_motif; pfam05488 579112008879 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 579112008880 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...; Region: TGS_ThrRS_N; cd01667 579112008881 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 579112008882 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 579112008883 active site 579112008884 dimer interface [polypeptide binding]; other site 579112008885 motif 1; other site 579112008886 motif 2; other site 579112008887 motif 3; other site 579112008888 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 579112008889 anticodon binding site; other site 579112008890 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 579112008891 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 579112008892 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 579112008893 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 579112008894 23S rRNA binding site [nucleotide binding]; other site 579112008895 L21 binding site [polypeptide binding]; other site 579112008896 L13 binding site [polypeptide binding]; other site 579112008897 integron integrase; Region: integrase_gron; TIGR02249 579112008898 DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element)...; Region: INT_IntI; cd01193 579112008899 Int/Topo IB signature motif; other site 579112008900 VCR001,attC site or 59 base element in super integron 579112008901 VCR002,attC site or 59 base element in super integron 579112008902 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112008903 VCR003,attC site or 59 base element in super integron 579112008904 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 579112008905 VCR004,attC site or 59 base element in super integron 579112008906 OsmC-like protein; Region: OsmC; cl00767 579112008907 VCR005,attC site or 59 base element in super integron 579112008908 VCR006,attC site or 59 base element in super integron 579112008909 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112008910 VCR007,attC site or 59 base element in super integron 579112008911 DNA polymerase II large subunit; Provisional; Region: PRK14715 579112008912 VCR008,attC site or 59 base element in super integron 579112008913 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112008914 VCR009,attC site or 59 base element in super integron 579112008915 Protein of unknown function (DUF2988); Region: DUF2988; pfam11206 579112008916 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112008917 VCR010,attC site or 59 base element in super integron 579112008918 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 579112008919 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112008920 VCR011,attC site or 59 base element in super integron 579112008921 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 579112008922 VCR012,attC site or 59 base element in super integron 579112008923 Bacterial protein of unknown function (DUF925); Region: DUF925; cl01435 579112008924 VCR013,attC site or 59 base element in super integron 579112008925 VCR014,attC site or 59 base element in super integron 579112008926 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112008927 VCR015,attC site or 59 base element in super integron 579112008928 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112008929 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 579112008930 VCR016,attC site or 59 base element in super integron 579112008931 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112008932 VCR017,attC site or 59 base element in super integron 579112008933 VCR018,attC site or 59 base element in super integron 579112008934 VCR019,attC site or 59 base element in super integron 579112008935 VCR020,attC site or 59 base element in super integron 579112008936 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112008937 Coenzyme A binding pocket [chemical binding]; other site 579112008938 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112008939 VCR021,attC site or 59 base element in super integron 579112008940 VCR022,attC site or 59 base element in super integron 579112008941 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112008942 VCR023,attC site or 59 base element in super integron 579112008943 VCR024,attC site or 59 base element in super integron 579112008944 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 579112008945 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112008946 VCR025,attC site or 59 base element in super integron 579112008947 VCR026,attC site or 59 base element in super integron 579112008948 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112008949 VCR027,attC site or 59 base element in super integron 579112008950 Protein of unknown function (DUF3709); Region: DUF3709; pfam12493 579112008951 VCR028,attC site or 59 base element in super integron 579112008952 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 579112008953 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112008954 VCR029,attC site or 59 base element in super integron 579112008955 Protein of unknown function (DUF3709); Region: DUF3709; pfam12493 579112008956 VCR030,attC site or 59 base element in super integron 579112008957 Protein of unknown function (DUF3709); Region: DUF3709; pfam12493 579112008958 VCR031,attC site or 59 base element in super integron 579112008959 VCR032,attC site or 59 base element in super integron 579112008960 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_19; cd07262 579112008961 VCR033,attC site or 59 base element in super integron 579112008962 VCR034,attC site or 59 base element in super integron 579112008963 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_7; cd04664 579112008964 nudix motif; other site 579112008965 VCR035,attC site or 59 base element in super integron 579112008966 VCR036,attC site or 59 base element in super integron 579112008967 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 579112008968 putative active site [active] 579112008969 putative NTP binding site [chemical binding]; other site 579112008970 putative nucleic acid binding site [nucleotide binding]; other site 579112008971 VCR037,attC site or 59 base element in super integron 579112008972 VCR038,attC site or 59 base element in super integron 579112008973 VCR039,attC site or 59 base element in super integron 579112008974 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112008975 VCR040,attC site or 59 base element in super integron 579112008976 short chain dehydrogenase; Provisional; Region: PRK06123 579112008977 classical (c) SDRs; Region: SDR_c; cd05233 579112008978 NAD(P) binding site [chemical binding]; other site 579112008979 active site 579112008980 VCR041,attC site or 59 base element in super integron 579112008981 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112008982 VCR042,attC site or 59 base element in super integron 579112008983 VCR043,attC site or 59 base element in super integron 579112008984 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112008985 VCR044,attC site or 59 base element in super integron 579112008986 Protein of unknown function (DUF2988); Region: DUF2988; pfam11206 579112008987 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112008988 VCR045,attC site or 59 base element in super integron 579112008989 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...; Region: HNHc; cd00085 579112008990 active site 579112008991 VCR046,attC site or 59 base element in super integron 579112008992 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 579112008993 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 579112008994 VCR047,attC site or 59 base element in super integron 579112008995 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3183 579112008996 VCR048,attC site or 59 base element in super integron 579112008997 VCR049,attC site or 59 base element in super integron 579112008998 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112008999 Phd_YefM; Region: PhdYeFM; cl09153 579112009000 VCR050,attC site or 59 base element in super integron 579112009001 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...; Region: Nudix_Hydrolase; cd02883 579112009002 nudix motif; other site 579112009003 VCR051,attC site or 59 base element in super integron 579112009004 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 579112009005 Protein of unknown function (DUF1196); Region: DUF1196; pfam06709 579112009006 VCR052,attC site or 59 base element in super integron 579112009007 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 579112009008 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009009 VCR053,attC site or 59 base element in super integron 579112009010 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 579112009011 VCR054,attC site or 59 base element in super integron 579112009012 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009013 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 579112009014 VCR055,attC site or 59 base element in super integron 579112009015 VCR056,attC site or 59 base element in super integron 579112009016 VCR057,attC site or 59 base element in super integron 579112009017 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112009018 RelB antitoxin; Region: RelB; cl01171 579112009019 VCR058,attC site or 59 base element in super integron 579112009020 Phd_YefM; Region: PhdYeFM; cl09153 579112009021 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112009022 VCR059,attC site or 59 base element in super integron 579112009023 Protein of unknown function (DUF3709); Region: DUF3709; pfam12493 579112009024 VCR060,attC site or 59 base element in super integron 579112009025 VCR061,attC site or 59 base element in super integron 579112009026 VCR062,attC site or 59 base element in super integron 579112009027 Microcin C7 self-immunity protein determines resistance to exogenous microcin C7; Region: Peptidase_S66_mccF_like; cd07062 579112009028 putative dimer interface [polypeptide binding]; other site 579112009029 catalytic triad [active] 579112009030 VCR063,attC site or 59 base element in super integron 579112009031 VCR064,attC site or 59 base element in super integron 579112009032 VCR065,attC site or 59 base element in super integron 579112009033 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 579112009034 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112009035 VCR066,attC site or 59 base element in super integron 579112009036 Protein of unknown function (DUF3709); Region: DUF3709; pfam12493 579112009037 VCR067,attC site or 59 base element in super integron 579112009038 VCR068,attC site or 59 base element in super integron 579112009039 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 579112009040 dimer interface [polypeptide binding]; other site 579112009041 metal binding site [ion binding]; metal-binding site 579112009042 VCR069,attC site or 59 base element in super integron 579112009043 Protein of unknown function (DUF2805); Region: DUF2805; cl11923 579112009044 VCR070,attC site or 59 base element in super integron 579112009045 VCR071,attC site or 59 base element in super integron 579112009046 VCR072,attC site or 59 base element in super integron 579112009047 Protein of unknown function (DUF3709); Region: DUF3709; pfam12493 579112009048 VCR073,attC site or 59 base element in super integron 579112009049 VCR074,attC site or 59 base element in super integron 579112009050 OsmC-like protein; Region: OsmC; cl00767 579112009051 VCR075,attC site or 59 base element in super integron 579112009052 VCR076,attC site or 59 base element in super integron 579112009053 Protein of unknown function (DUF497); Region: DUF497; cl01108 579112009054 VCR077,attC site or 59 base element in super integron 579112009055 VCR078,attC site or 59 base element in super integron 579112009056 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112009057 VCR079,attC site or 59 base element in super integron 579112009058 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112009059 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009060 Coenzyme A binding pocket [chemical binding]; other site 579112009061 VCR080,attC site or 59 base element in super integron 579112009062 VCR081,attC site or 59 base element in super integron 579112009063 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 579112009064 VCR082,attC site or 59 base element in super integron 579112009065 VCR083,attC site or 59 base element in super integron 579112009066 VCR084,attC site or 59 base element in super integron 579112009067 Stress responsive A/B Barrel Domain; Region: Dabb; cl06768 579112009068 VCR085,attC site or 59 base element in super integron 579112009069 VCR086,attC site or 59 base element in super integron 579112009070 VCR087,attC site or 59 base element in super integron 579112009071 putative transposase OrfB; Reviewed; Region: PHA02517 579112009072 Integrase core domain; Region: rve; cl01316 579112009073 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; cl01116 579112009074 VCR088,attC site or 59 base element in super integron 579112009075 Domain of unknown function (DUF1817); Region: DUF1817; cl02292 579112009076 VCR089,attC site or 59 base element in super integron 579112009077 VCR090,attC site or 59 base element in super integron 579112009078 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 579112009079 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112009080 VCR091,attC site or 59 base element in super integron 579112009081 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009082 VCR092,attC site or 59 base element in super integron 579112009083 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 579112009084 VCR093,attC site or 59 base element in super integron 579112009085 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112009086 Phd_YefM; Region: PhdYeFM; cl09153 579112009087 VCR094,attC site or 59 base element in super integron 579112009088 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112009089 VCR095,attC site or 59 base element in super integron 579112009090 VCR096,attC site or 59 base element in super integron 579112009091 Protein of unknown function (DUF3465); Region: DUF3465; pfam11948 579112009092 VCR097,attC site or 59 base element in super integron 579112009093 HEPN domain; Region: HEPN; cl00824 579112009094 VCR098,attC site or 59 base element in super integron 579112009095 VCR099,attC site or 59 base element in super integron 579112009096 VCR100,attC site or 59 base element in super integron 579112009097 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 579112009098 VCR101,attC site or 59 base element in super integron 579112009099 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 579112009100 conserved cys residue [active] 579112009101 VCR102,attC site or 59 base element in super integron 579112009102 VCR103,attC site or 59 base element in super integron 579112009103 VCR104,attC site or 59 base element in super integron 579112009104 Protein of unknown function (DUF2806); Region: DUF2806; cl12560 579112009105 VCR105,attC site or 59 base element in super integron 579112009106 VCR106,attC site or 59 base element in super integron 579112009107 VCR107,attC site or 59 base element in super integron 579112009108 VCR108,attC site or 59 base element in super integron 579112009109 VCR109,attC site or 59 base element in super integron 579112009110 VCR110,attC site or 59 base element in super integron 579112009111 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 579112009112 dimer interface [polypeptide binding]; other site 579112009113 metal binding site [ion binding]; metal-binding site 579112009114 VCR111,attC site or 59 base element in super integron 579112009115 VCR112,attC site or 59 base element in super integron 579112009116 VCR113,attC site or 59 base element in super integron 579112009117 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 579112009118 Protein of unknown function (DUF1196); Region: DUF1196; pfam06709 579112009119 VCR114,attC site or 59 base element in super integron 579112009120 Protein of unknown function (DUF1196); Region: DUF1196; pfam06709 579112009121 VCR115,attC site or 59 base element in super integron 579112009122 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112009123 VCR116,attC site or 59 base element in super integron 579112009124 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 579112009125 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112009126 Coenzyme A binding pocket [chemical binding]; other site 579112009127 VCR117,attC site or 59 base element in super integron 579112009128 Transposase domain (DUF772); Region: DUF772; cl12084 579112009129 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 579112009130 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 579112009131 CoA binding site [chemical binding]; other site 579112009132 active site 579112009133 VCR118,attC site or 59 base element in super integron 579112009134 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009135 VCR119,attC site or 59 base element in super integron 579112009136 Fic/DOC family; Region: Fic; cl00960 579112009137 VCR120,attC site or 59 base element in super integron 579112009138 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_16; cd07263 579112009139 VCR121,attC site or 59 base element in super integron 579112009140 Phd_YefM; Region: PhdYeFM; cl09153 579112009141 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112009142 VCR122,attC site or 59 base element in super integron 579112009143 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009144 VCR123,attC site or 59 base element in super integron 579112009145 Protein of unknown function, DUF645; Region: DUF645; pfam04875 579112009146 VCR124,attC site or 59 base element in super integron 579112009147 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009148 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 579112009149 VCR125,attC site or 59 base element in super integron 579112009150 VCR126,attC site or 59 base element in super integron 579112009151 VCR127,attC site or 59 base element in super integron 579112009152 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 579112009153 VCR128,attC site or 59 base element in super integron 579112009154 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 579112009155 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009156 VCR129,attC site or 59 base element in super integron 579112009157 Phd_YefM; Region: PhdYeFM; cl09153 579112009158 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112009159 VCR130,attC site or 59 base element in super integron 579112009160 Transposase IS200 like; Region: Y1_Tnp; cl00848 579112009161 VCR131,attC site or 59 base element in super integron 579112009162 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 579112009163 VCR132,attC site or 59 base element in super integron 579112009164 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 579112009165 C-terminal domain interface [polypeptide binding]; other site 579112009166 GSH binding site (G-site) [chemical binding]; other site 579112009167 dimer interface [polypeptide binding]; other site 579112009168 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 579112009169 N-terminal domain interface [polypeptide binding]; other site 579112009170 dimer interface [polypeptide binding]; other site 579112009171 substrate binding pocket (H-site) [chemical binding]; other site 579112009172 VCR133,attC site or 59 base element in super integron 579112009173 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 579112009174 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 579112009175 VCR134,attC site or 59 base element in super integron 579112009176 VCR135,attC site or 59 base element in super integron 579112009177 VCR136,attC site or 59 base element in super integron 579112009178 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 579112009179 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 579112009180 VCR137,attC site or 59 base element in super integron 579112009181 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 579112009182 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009183 VCR138,attC site or 59 base element in super integron 579112009184 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_16; cd07263 579112009185 VCR139,attC site or 59 base element in super integron 579112009186 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; cl01116 579112009187 putative transposase OrfB; Reviewed; Region: PHA02517 579112009188 Integrase core domain; Region: rve; cl01316 579112009189 Sulfatase; Region: Sulfatase; cl10460 579112009190 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 579112009191 ATP cone domain; Region: ATP-cone; pfam03477 579112009192 Class III ribonucleotide reductase; Region: RNR_III; cd01675 579112009193 effector binding site; other site 579112009194 active site 579112009195 Zn binding site [ion binding]; other site 579112009196 glycine loop; other site 579112009197 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; cl15259 579112009198 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 579112009199 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 579112009200 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112009201 homodimer interface [polypeptide binding]; other site 579112009202 catalytic residue [active] 579112009203 Protein of unknown function (DUF785); Region: DUF785; cl01682 579112009204 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...; Region: PTS_IIB_fructose; cd05569 579112009205 P-loop; other site 579112009206 active site 579112009207 phosphorylation site [posttranslational modification] 579112009208 PTS system fructose-specific transporter subunits IIBC; Provisional; Region: PRK10712 579112009209 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...; Region: PTS_IIB_fructose; cd05569 579112009210 P-loop; other site 579112009211 active site 579112009212 phosphorylation site [posttranslational modification] 579112009213 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112009214 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 579112009215 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 579112009216 putative substrate binding site [chemical binding]; other site 579112009217 putative ATP binding site [chemical binding]; other site 579112009218 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional; Region: PRK11109 579112009219 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 579112009220 active site 579112009221 phosphorylation site [posttranslational modification] 579112009222 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; cl00163 579112009223 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 579112009224 dimerization domain swap beta strand [polypeptide binding]; other site 579112009225 regulatory protein interface [polypeptide binding]; other site 579112009226 active site 579112009227 regulatory phosphorylation site [posttranslational modification]; other site 579112009228 DNA-binding transcriptional regulator FruR; Provisional; Region: PRK11303 579112009229 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112009230 DNA binding site [nucleotide binding] 579112009231 domain linker motif; other site 579112009232 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 579112009233 dimerization interface [polypeptide binding]; other site 579112009234 ligand binding site [chemical binding]; other site 579112009235 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 579112009236 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 579112009237 active site 579112009238 metal binding site [ion binding]; metal-binding site 579112009239 DNA binding site [nucleotide binding] 579112009240 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 579112009241 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 579112009242 SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini; Region: ABC_sbcCD; cd03279 579112009243 Walker A/P-loop; other site 579112009244 ATP binding site [chemical binding]; other site 579112009245 Q-loop/lid; other site 579112009246 SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini; Region: ABC_sbcCD; cd03279 579112009247 ABC transporter signature motif; other site 579112009248 Walker B; other site 579112009249 D-loop; other site 579112009250 H-loop/switch region; other site 579112009251 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 579112009252 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 trans-...; Region: HisKA; cl00080 579112009253 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 579112009254 ATP binding site [chemical binding]; other site 579112009255 Mg2+ binding site [ion binding]; other site 579112009256 G-X-G motif; other site 579112009257 Response regulator receiver domain; Region: Response_reg; pfam00072 579112009258 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112009259 active site 579112009260 phosphorylation site [posttranslational modification] 579112009261 intermolecular recognition site; other site 579112009262 dimerization interface [polypeptide binding]; other site 579112009263 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 579112009264 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 579112009265 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112009266 catalytic residue [active] 579112009267 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 579112009268 C4-dicarboxylate transporter/malic acid transport protein; Region: C4dic_mal_tran; pfam03595 579112009269 gating phenylalanine in ion channel; other site 579112009270 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 579112009271 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-...; Region: EriC; cd01031 579112009272 Cl- selectivity filter; other site 579112009273 Cl- binding residues [ion binding]; other site 579112009274 pore gating glutamate residue; other site 579112009275 dimer interface [polypeptide binding]; other site 579112009276 H+/Cl- coupling transport residue; other site 579112009277 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 579112009278 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112009279 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 579112009280 YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases...; Region: YlqF; cd01856 579112009281 GTP/Mg2+ binding site [chemical binding]; other site 579112009282 G4 box; other site 579112009283 G5 box; other site 579112009284 G1 box; other site 579112009285 Switch I region; other site 579112009286 G2 box; other site 579112009287 G3 box; other site 579112009288 Switch II region; other site 579112009289 K+ potassium transporter; Region: K_trans; cl01227 579112009290 potassium uptake protein; Region: kup; TIGR00794 579112009291 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 579112009292 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 579112009293 dimer interface [polypeptide binding]; other site 579112009294 PYR/PP interface [polypeptide binding]; other site 579112009295 TPP binding site [chemical binding]; other site 579112009296 substrate binding site [chemical binding]; other site 579112009297 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 579112009298 Domain of unknown function; Region: EKR; cl11037 579112009299 4Fe-4S binding domain; Region: Fer4; cl02805 579112009300 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin...; Region: TPP_enzymes; cl01629 579112009301 TPP-binding site [chemical binding]; other site 579112009302 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 579112009303 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 trans-...; Region: HisKA; cd00082 579112009304 dimer interface [polypeptide binding]; other site 579112009305 phosphorylation site [posttranslational modification] 579112009306 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 579112009307 ATP binding site [chemical binding]; other site 579112009308 Mg2+ binding site [ion binding]; other site 579112009309 G-X-G motif; other site 579112009310 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 579112009311 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112009312 active site 579112009313 phosphorylation site [posttranslational modification] 579112009314 intermolecular recognition site; other site 579112009315 dimerization interface [polypeptide binding]; other site 579112009316 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...; Region: trans_reg_C; cd00383 579112009317 DNA binding site [nucleotide binding] 579112009318 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 579112009319 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 579112009320 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 579112009321 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 579112009322 YceI-like domain; Region: YceI; cl01001 579112009323 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 579112009324 FOG: CBS domain [General function prediction only]; Region: COG0517 579112009325 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-...; Region: CBS_pair; cl09141 579112009326 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-...; Region: CBS_pair; cl09141 579112009327 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 579112009328 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112009329 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 579112009330 putative dimerization interface [polypeptide binding]; other site 579112009331 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 579112009332 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 579112009333 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 579112009334 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 579112009335 putative active site [active] 579112009336 putative metal-binding site [ion binding]; other site 579112009337 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 579112009338 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 579112009339 active site 579112009340 metal binding site [ion binding]; metal-binding site 579112009341 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 579112009342 Integral membrane protein TerC family; Region: TerC; cl10468 579112009343 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 579112009344 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 579112009345 PhnA protein; Region: PhnA; pfam03831 579112009346 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_2; cd06160 579112009347 active site 579112009348 putative substrate binding region [chemical binding]; other site 579112009349 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 579112009350 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 579112009351 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 579112009352 putative substrate translocation pore; other site 579112009353 Domain of unknown function (DUF3332); Region: DUF3332; pfam11810 579112009354 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...; Region: PBPb; cd00134 579112009355 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 579112009356 substrate binding pocket [chemical binding]; other site 579112009357 membrane-bound complex binding site; other site 579112009358 hinge residues; other site 579112009359 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112009360 metal binding site [ion binding]; metal-binding site 579112009361 active site 579112009362 I-site; other site 579112009363 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 579112009364 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 579112009365 Protein of unknown function (DUF3233); Region: DUF3233; pfam11557 579112009366 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112009367 metal binding site [ion binding]; metal-binding site 579112009368 active site 579112009369 I-site; other site 579112009370 Late competence development protein ComFB; Region: ComFB; pfam10719 579112009371 Transcriptional activator HlyU; Region: HlyU; cl02273 579112009372 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 579112009373 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; pfam05222 579112009374 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112009375 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 579112009376 NAD(P) transhydrogenase beta subunit; Region: PNTB; cl00566 579112009377 Domain of unknown function (DUF3404); Region: DUF3404; pfam11884 579112009378 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 trans-...; Region: HisKA; cl00080 579112009379 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 579112009380 ATP binding site [chemical binding]; other site 579112009381 Mg2+ binding site [ion binding]; other site 579112009382 G-X-G motif; other site 579112009383 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 579112009384 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112009385 active site 579112009386 phosphorylation site [posttranslational modification] 579112009387 intermolecular recognition site; other site 579112009388 dimerization interface [polypeptide binding]; other site 579112009389 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...; Region: trans_reg_C; cd00383 579112009390 DNA binding site [nucleotide binding] 579112009391 Protein of unknown function (DUF2861); Region: DUF2861; pfam11060 579112009392 Uncharacterised protein family (UPF0181); Region: UPF0181; cl11477 579112009393 translation initiation factor Sui1; Validated; Region: PRK06824 579112009394 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two...; Region: SUI1_eIF1; cl00229 579112009395 Predicted RNA interaction site [nucleotide binding]; other site 579112009396 putative binding site; other site 579112009397 Mutations affecting start-site selection; other site 579112009398 Protein of unknown function (DUF3319); Region: DUF3319; pfam11782 579112009399 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 579112009400 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 579112009401 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 579112009402 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 579112009403 Sporulation related domain; Region: SPOR; cl10051 579112009404 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 579112009405 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112009406 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009407 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 579112009408 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112009409 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 579112009410 dimerization interface [polypeptide binding]; other site 579112009411 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 579112009412 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112009413 N-terminal plug; other site 579112009414 ligand-binding site [chemical binding]; other site 579112009415 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4533 579112009416 Sugar transport-related sRNA regulator N-term; Region: SgrR_N; pfam12793 579112009417 The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold; Region: PBP2_SgrR_like; cd08507 579112009418 Protein of unknown function (DUF3389); Region: DUF3389; pfam11869 579112009419 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 579112009420 CoenzymeA binding site [chemical binding]; other site 579112009421 subunit interaction site [polypeptide binding]; other site 579112009422 PHB binding site; other site 579112009423 Peptidase family M48; Region: Peptidase_M48; cl12018 579112009424 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 579112009425 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...; Region: PBPb; cd00134 579112009426 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 579112009427 substrate binding pocket [chemical binding]; other site 579112009428 membrane-bound complex binding site; other site 579112009429 hinge residues; other site 579112009430 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 579112009431 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen...; Region: GST_N_Ure2p_like; cd03048 579112009432 C-terminal domain interface [polypeptide binding]; other site 579112009433 GSH binding site (G-site) [chemical binding]; other site 579112009434 dimer interface [polypeptide binding]; other site 579112009435 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 579112009436 N-terminal domain interface [polypeptide binding]; other site 579112009437 putative dimer interface [polypeptide binding]; other site 579112009438 active site 579112009439 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 579112009440 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 579112009441 putative C-terminal domain interface [polypeptide binding]; other site 579112009442 putative GSH binding site (G-site) [chemical binding]; other site 579112009443 putative dimer interface [polypeptide binding]; other site 579112009444 C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases; Region: GST_C_GTT2_like; cd03182 579112009445 putative N-terminal domain interface [polypeptide binding]; other site 579112009446 putative dimer interface [polypeptide binding]; other site 579112009447 putative substrate binding pocket (H-site) [chemical binding]; other site 579112009448 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112009449 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112009450 Domain of unknown function (DUF296); Region: DUF296; cl00720 579112009451 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 579112009452 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112009453 Walker A/P-loop; other site 579112009454 ATP binding site [chemical binding]; other site 579112009455 Q-loop/lid; other site 579112009456 ABC transporter signature motif; other site 579112009457 Walker B; other site 579112009458 D-loop; other site 579112009459 H-loop/switch region; other site 579112009460 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112009461 Walker A/P-loop; other site 579112009462 ATP binding site [chemical binding]; other site 579112009463 Q-loop/lid; other site 579112009464 ABC transporter signature motif; other site 579112009465 Walker B; other site 579112009466 D-loop; other site 579112009467 H-loop/switch region; other site 579112009468 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112009469 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 579112009470 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 579112009471 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...; Region: TM_PBP2; cd06261 579112009472 dimer interface [polypeptide binding]; other site 579112009473 conserved gate region; other site 579112009474 putative PBP binding loops; other site 579112009475 ABC-ATPase subunit interface; other site 579112009476 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 579112009477 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...; Region: TM_PBP2; cd06261 579112009478 dimer interface [polypeptide binding]; other site 579112009479 conserved gate region; other site 579112009480 putative PBP binding loops; other site 579112009481 ABC-ATPase subunit interface; other site 579112009482 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 579112009483 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 579112009484 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_27; cd04686 579112009485 nudix motif; other site 579112009486 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 579112009487 Domain of unknown function (DUF333); Region: DUF333; pfam03891 579112009488 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 579112009489 putative active site [active] 579112009490 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; cl11420 579112009491 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 579112009492 transcriptional regulator protein; Region: phnR; TIGR03337 579112009493 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 579112009494 DNA-binding site [nucleotide binding]; DNA binding site 579112009495 UTRA domain; Region: UTRA; cl01230 579112009496 putative 2-aminoethylphosphonate ABC transporter, permease protein; Region: PhnU2; TIGR03262 579112009497 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...; Region: TM_PBP2; cd06261 579112009498 dimer interface [polypeptide binding]; other site 579112009499 conserved gate region; other site 579112009500 putative PBP binding loops; other site 579112009501 ABC-ATPase subunit interface; other site 579112009502 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...; Region: TM_PBP2; cd06261 579112009503 dimer interface [polypeptide binding]; other site 579112009504 conserved gate region; other site 579112009505 putative PBP binding loops; other site 579112009506 ABC-ATPase subunit interface; other site 579112009507 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein; Region: PhnT2; TIGR03265 579112009508 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112009509 Walker A/P-loop; other site 579112009510 ATP binding site [chemical binding]; other site 579112009511 Q-loop/lid; other site 579112009512 ABC transporter signature motif; other site 579112009513 Walker B; other site 579112009514 D-loop; other site 579112009515 H-loop/switch region; other site 579112009516 TOBE domain; Region: TOBE_2; cl01440 579112009517 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 579112009518 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate binding protein; Region: PhnS; TIGR03227 579112009519 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 579112009520 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 579112009521 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112009522 catalytic residue [active] 579112009523 4-aminobutyrate aminotransferase; Provisional; Region: PRK06082 579112009524 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 579112009525 inhibitor-cofactor binding pocket; inhibition site 579112009526 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112009527 catalytic residue [active] 579112009528 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; cl11391 579112009529 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 579112009530 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 579112009531 C-term; Region: GreA_GreB; pfam01272 579112009532 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 579112009533 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 579112009534 motif II; other site 579112009535 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 579112009536 conserved cys residue [active] 579112009537 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 579112009538 formate--tetrahydrofolate ligase; Provisional; Region: PRK13506 579112009539 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 579112009540 Potassium binding sites [ion binding]; other site 579112009541 Cesium cation binding sites [ion binding]; other site 579112009542 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 579112009543 SelR domain; Region: SelR; cl00369 579112009544 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 579112009545 homodecamer interface [polypeptide binding]; other site 579112009546 GTP cyclohydrolase I; Provisional; Region: PLN03044 579112009547 active site 579112009548 putative catalytic site residues [active] 579112009549 zinc binding site [ion binding]; other site 579112009550 GTP-CH-I/GFRP interaction surface; other site 579112009551 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 579112009552 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 579112009553 dimer interface [polypeptide binding]; other site 579112009554 putative functional site; other site 579112009555 putative MPT binding site; other site 579112009556 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 579112009557 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...; Region: ThiF_MoeB_HesA_family; cd00757 579112009558 ATP binding site [chemical binding]; other site 579112009559 substrate interface [chemical binding]; other site 579112009560 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_17; cd08356 579112009561 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 579112009562 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but...; Region: TST_Repeat_1; cd01448 579112009563 active site residue [active] 579112009564 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 579112009565 active site residue [active] 579112009566 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 579112009567 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 579112009568 transaldolase-like protein; Provisional; Region: PTZ00411 579112009569 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 579112009570 active site 579112009571 dimer interface [polypeptide binding]; other site 579112009572 catalytic residue [active] 579112009573 transketolase; Reviewed; Region: PRK12753 579112009574 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 579112009575 TPP-binding site [chemical binding]; other site 579112009576 dimer interface [polypeptide binding]; other site 579112009577 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 579112009578 PYR/PP interface [polypeptide binding]; other site 579112009579 dimer interface [polypeptide binding]; other site 579112009580 TPP binding site [chemical binding]; other site 579112009581 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 579112009582 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 579112009583 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 579112009584 N-terminal plug; other site 579112009585 ligand-binding site [chemical binding]; other site 579112009586 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 579112009587 Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]; Region: SecA; COG0653 579112009588 Nuclease-related domain; Region: NERD; pfam08378 579112009589 SEC-C motif; Region: SEC-C; cl12132 579112009590 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 579112009591 Putative ammonia monooxygenase; Region: AmoA; pfam05145 579112009592 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 579112009593 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 579112009594 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112009595 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009596 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_32; cd04691 579112009597 nudix motif; other site 579112009598 GlpM protein; Region: GlpM; cl01212 579112009599 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112009600 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112009601 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112009602 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112009603 putative effector binding pocket; other site 579112009604 dimerization interface [polypeptide binding]; other site 579112009605 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 579112009606 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 579112009607 dimer interface [polypeptide binding]; other site 579112009608 FMN binding site [chemical binding]; other site 579112009609 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 579112009610 Protein export membrane protein; Region: SecD_SecF; cl14618 579112009611 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 579112009612 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 579112009613 YeeE/YedE family (DUF395); Region: DUF395; cl01018 579112009614 YeeE/YedE family (DUF395); Region: DUF395; cl01018 579112009615 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 579112009616 dimerization interface [polypeptide binding]; other site 579112009617 putative DNA binding site [nucleotide binding]; other site 579112009618 putative Zn2+ binding site [ion binding]; other site 579112009619 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 579112009620 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 579112009621 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112009622 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 579112009623 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 rhodanese-...; Region: RHOD_Pyr_redox; cd01524 579112009624 active site residue [active] 579112009625 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 579112009626 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924; Region: LPLAT_ACT14924-like; cd07986 579112009627 putative acyl-acceptor binding pocket; other site 579112009628 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112009629 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 579112009630 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 579112009631 Protein of unknown function (DUF3069); Region: DUF3069; pfam11269 579112009632 PTS system, sucrose-specific IIBC component; Region: PTS-II-BC-sucr; TIGR01996 579112009633 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...; Region: PTS_IIB_glc; cd00212 579112009634 active site turn [active] 579112009635 phosphorylation site [posttranslational modification] 579112009636 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112009637 Transcriptional regulators [Transcription]; Region: PurR; COG1609 579112009638 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112009639 DNA binding site [nucleotide binding] 579112009640 domain linker motif; other site 579112009641 Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_TreR_like; cd01542 579112009642 dimerization interface [polypeptide binding]; other site 579112009643 ligand binding site [chemical binding]; other site 579112009644 Beta-fructosidases (levanase/invertase) [Carbohydrate transport and metabolism]; Region: SacC; COG1621 579112009645 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 579112009646 substrate binding [chemical binding]; other site 579112009647 active site 579112009648 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 579112009649 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 579112009650 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 579112009651 putative substrate binding site [chemical binding]; other site 579112009652 putative ATP binding site [chemical binding]; other site 579112009653 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 579112009654 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 579112009655 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112009656 PAS fold; Region: PAS_3; pfam08447 579112009657 putative active site [active] 579112009658 heme pocket [chemical binding]; other site 579112009659 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112009660 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112009661 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 579112009662 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 579112009663 ligand binding site [chemical binding]; other site 579112009664 peptidyl-prolyl isomerase, gliding motility-associated; Region: ppisom_GldI; TIGR03516 579112009665 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 579112009666 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 579112009667 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 579112009668 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; cl11391 579112009669 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 579112009670 motif II; other site 579112009671 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112009672 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112009673 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112009674 C4-dicarboxylate transporter DcuC; Provisional; Region: dcuC; cl15274 579112009675 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; COG3069 579112009676 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 579112009677 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 579112009678 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 579112009679 Sodium:solute symporter family; Region: SSF; cl00456 579112009680 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 579112009681 benzoate transport; Region: 2A0115; TIGR00895 579112009682 putative substrate translocation pore; other site 579112009683 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 579112009684 Transcriptional regulators [Transcription]; Region: PurR; COG1609 579112009685 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 579112009686 DNA binding site [nucleotide binding] 579112009687 domain linker motif; other site 579112009688 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_2; cd06278 579112009689 putative dimerization interface [polypeptide binding]; other site 579112009690 putative ligand binding site [chemical binding]; other site 579112009691 transcriptional regulator NarP; Provisional; Region: PRK10403 579112009692 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112009693 active site 579112009694 phosphorylation site [posttranslational modification] 579112009695 intermolecular recognition site; other site 579112009696 dimerization interface [polypeptide binding]; other site 579112009697 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...; Region: LuxR_C_like; cd06170 579112009698 DNA binding residues [nucleotide binding] 579112009699 dimerization interface [polypeptide binding]; other site 579112009700 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 579112009701 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112009702 Histidine kinase; Region: HisKA_3; pfam07730 579112009703 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 579112009704 ATP binding site [chemical binding]; other site 579112009705 Mg2+ binding site [ion binding]; other site 579112009706 G-X-G motif; other site 579112009707 ferredoxin-type protein; Provisional; Region: PRK10194 579112009708 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 alpha-; Region: HCP_like; cl14655 579112009709 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 alpha-; Region: HCP_like; cl14655 579112009710 NapD protein; Region: NapD; cl01163 579112009711 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 579112009712 NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored...; Region: MopB_Nitrate-R-NapA-like; cd02754 579112009713 [4Fe-4S] binding site [ion binding]; other site 579112009714 molybdopterin cofactor binding site; other site 579112009715 NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 579112009716 molybdopterin cofactor binding site; other site 579112009717 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 579112009718 Nitrate/TMAO reductases, membrane-bound tetraheme cytochrome c subunit [Energy production and conversion]; Region: TorC; COG3005 579112009719 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl09485 579112009720 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112009721 Zn2+ binding site [ion binding]; other site 579112009722 Mg2+ binding site [ion binding]; other site 579112009723 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112009724 Zn2+ binding site [ion binding]; other site 579112009725 Mg2+ binding site [ion binding]; other site 579112009726 DNA-binding transcriptional activator UhpA; Provisional; Region: PRK10360 579112009727 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112009728 active site 579112009729 phosphorylation site [posttranslational modification] 579112009730 intermolecular recognition site; other site 579112009731 dimerization interface [polypeptide binding]; other site 579112009732 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...; Region: LuxR_C_like; cd06170 579112009733 DNA binding residues [nucleotide binding] 579112009734 dimerization interface [polypeptide binding]; other site 579112009735 Signal transduction histidine kinase, glucose-6-phosphate specific [Signal transduction mechanisms]; Region: UhpB; COG3851 579112009736 MASE1; Region: MASE1; pfam05231 579112009737 Histidine kinase; Region: HisKA_3; pfam07730 579112009738 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 579112009739 ATP binding site [chemical binding]; other site 579112009740 Mg2+ binding site [ion binding]; other site 579112009741 G-X-G motif; other site 579112009742 regulatory protein UhpC; Provisional; Region: PRK11663 579112009743 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 579112009744 putative substrate translocation pore; other site 579112009745 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 579112009746 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 579112009747 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 579112009748 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...; Region: TM_PBP2; cd06261 579112009749 dimer interface [polypeptide binding]; other site 579112009750 conserved gate region; other site 579112009751 putative PBP binding loops; other site 579112009752 ABC-ATPase subunit interface; other site 579112009753 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...; Region: TM_PBP2; cd06261 579112009754 dimer interface [polypeptide binding]; other site 579112009755 conserved gate region; other site 579112009756 putative PBP binding loops; other site 579112009757 ABC-ATPase subunit interface; other site 579112009758 ferric transporter ATP-binding subunit; Provisional; Region: fbpC; PRK11432 579112009759 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112009760 Walker A/P-loop; other site 579112009761 ATP binding site [chemical binding]; other site 579112009762 Q-loop/lid; other site 579112009763 ABC transporter signature motif; other site 579112009764 Walker B; other site 579112009765 D-loop; other site 579112009766 H-loop/switch region; other site 579112009767 TOBE domain; Region: TOBE_2; cl01440 579112009768 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 579112009769 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 579112009770 Phasin protein; Region: Phasin_2; cl11491 579112009771 putative acyltransferase; Provisional; Region: PRK05790 579112009772 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 579112009773 dimer interface [polypeptide binding]; other site 579112009774 active site 579112009775 acetoacetyl-CoA reductase; Provisional; Region: PRK12824 579112009776 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 579112009777 NAD(P) binding site [chemical binding]; other site 579112009778 homotetramer interface [polypeptide binding]; other site 579112009779 homodimer interface [polypeptide binding]; other site 579112009780 active site 579112009781 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13021 579112009782 Protein export membrane protein; Region: SecD_SecF; cl14618 579112009783 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 579112009784 Protein export membrane protein; Region: SecD_SecF; cl14618 579112009785 PAS fold; Region: PAS; pfam00989 579112009786 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112009787 putative active site [active] 579112009788 heme pocket [chemical binding]; other site 579112009789 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112009790 metal binding site [ion binding]; metal-binding site 579112009791 active site 579112009792 I-site; other site 579112009793 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 579112009794 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 579112009795 ligand binding site [chemical binding]; other site 579112009796 oligomer interface [polypeptide binding]; other site 579112009797 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 rate-...; Region: LbH_G1P_AT_C; cd04651 579112009798 dimer interface [polypeptide binding]; other site 579112009799 N-terminal domain interface [polypeptide binding]; other site 579112009800 sulfate 1 binding site; other site 579112009801 Uncharacterized protein contain chitin-binding domain type 3 [General function prediction only]; Region: COG3979 579112009802 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 579112009803 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 579112009804 Chitinase [Carbohydrate transport and metabolism]; Region: ChiA; COG3325 579112009805 The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is...; Region: GH18_chitinase; cd06548 579112009806 active site 579112009807 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 579112009808 Chitinase C; Region: ChiC; pfam06483 579112009809 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 579112009810 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 579112009811 dimer interface [polypeptide binding]; other site 579112009812 active site 579112009813 metal binding site [ion binding]; metal-binding site 579112009814 YhhN-like protein; Region: YhhN; cl01505 579112009815 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 579112009816 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112009817 active site 579112009818 phosphorylation site [posttranslational modification] 579112009819 intermolecular recognition site; other site 579112009820 dimerization interface [polypeptide binding]; other site 579112009821 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112009822 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 579112009823 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]; Region: COG4192 579112009824 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112009825 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 trans-...; Region: HisKA; cl00080 579112009826 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 579112009827 ATP binding site [chemical binding]; other site 579112009828 Mg2+ binding site [ion binding]; other site 579112009829 G-X-G motif; other site 579112009830 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 579112009831 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 579112009832 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 579112009833 putative substrate translocation pore; other site 579112009834 pyruvate kinase; Provisional; Region: PRK05826 579112009835 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 579112009836 domain interfaces; other site 579112009837 active site 579112009838 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 579112009839 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112009840 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 trans-...; Region: HisKA; cd00082 579112009841 dimer interface [polypeptide binding]; other site 579112009842 phosphorylation site [posttranslational modification] 579112009843 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 579112009844 ATP binding site [chemical binding]; other site 579112009845 Mg2+ binding site [ion binding]; other site 579112009846 G-X-G motif; other site 579112009847 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112009848 active site 579112009849 phosphorylation site [posttranslational modification] 579112009850 intermolecular recognition site; other site 579112009851 dimerization interface [polypeptide binding]; other site 579112009852 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 579112009853 TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria; Region: PBP1_TorT-like; cd06306 579112009854 putative ligand binding site [chemical binding]; other site 579112009855 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 579112009856 active site 579112009857 dimer interfaces [polypeptide binding]; other site 579112009858 catalytic residues [active] 579112009859 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 579112009860 Isochorismatase family; Region: Isochorismatase; pfam00857 579112009861 catalytic triad [active] 579112009862 metal binding site [ion binding]; metal-binding site 579112009863 conserved cis-peptide bond; other site 579112009864 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 579112009865 Uncharacterized conserved protein [Function unknown]; Region: COG5591 579112009866 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 579112009867 DNA helicase IV; Provisional; Region: helD; PRK11054 579112009868 DNA helicase IV / RNA helicase N terminal; Region: Nucleolin_N; pfam12462 579112009869 UvrD/REP helicase; Region: UvrD-helicase; cl14126 579112009870 hypothetical membrane protein, TIGR01666; Region: YCCS 579112009871 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 579112009872 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 579112009873 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 trans-...; Region: HisKA; cd00082 579112009874 dimer interface [polypeptide binding]; other site 579112009875 phosphorylation site [posttranslational modification] 579112009876 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 579112009877 ATP binding site [chemical binding]; other site 579112009878 Mg2+ binding site [ion binding]; other site 579112009879 G-X-G motif; other site 579112009880 Heme NO binding; Region: HNOB; cl15268 579112009881 Class I hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classI; cd00643 579112009882 tetramerization interface [polypeptide binding]; other site 579112009883 substrate binding pocket [chemical binding]; other site 579112009884 catalytic residues [active] 579112009885 inhibitor binding sites; inhibition site 579112009886 NADP(H) binding site [chemical binding]; other site 579112009887 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112009888 molybdate transporter ATP-binding protein; Provisional; Region: modC; PRK11144 579112009889 Walker A/P-loop; other site 579112009890 ATP binding site [chemical binding]; other site 579112009891 Q-loop/lid; other site 579112009892 ABC transporter signature motif; other site 579112009893 Walker B; other site 579112009894 D-loop; other site 579112009895 H-loop/switch region; other site 579112009896 TOBE domain; Region: TOBE_2; cl01440 579112009897 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...; Region: TM_PBP2; cd06261 579112009898 dimer interface [polypeptide binding]; other site 579112009899 conserved gate region; other site 579112009900 putative PBP binding loops; other site 579112009901 ABC-ATPase subunit interface; other site 579112009902 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 579112009903 cobyric acid synthase; Provisional; Region: PRK00784 579112009904 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112009905 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 579112009906 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 579112009907 catalytic triad [active] 579112009908 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 579112009909 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 579112009910 Walker A/P-loop; other site 579112009911 ATP binding site [chemical binding]; other site 579112009912 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 579112009913 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 579112009914 Flagellar protein YcgR; Region: YcgR_2; pfam12945 579112009915 PilZ domain; Region: PilZ; cl01260 579112009916 LuxQ, periplasmic; Region: LuxQ-periplasm; pfam09308 579112009917 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 579112009918 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 trans-...; Region: HisKA; cd00082 579112009919 dimer interface [polypeptide binding]; other site 579112009920 phosphorylation site [posttranslational modification] 579112009921 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 579112009922 ATP binding site [chemical binding]; other site 579112009923 Mg2+ binding site [ion binding]; other site 579112009924 G-X-G motif; other site 579112009925 Response regulator receiver domain; Region: Response_reg; pfam00072 579112009926 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112009927 active site 579112009928 phosphorylation site [posttranslational modification] 579112009929 intermolecular recognition site; other site 579112009930 dimerization interface [polypeptide binding]; other site 579112009931 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 579112009932 Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs; Region: PBP1_LuxPQ_Quorum_Sensing; cd06303 579112009933 ligand binding site [chemical binding]; other site 579112009934 subunit interaction site [polypeptide binding]; other site 579112009935 calcium binding site [ion binding]; other site 579112009936 Uncharacterized conserved protein [Function unknown]; Region: COG5613 579112009937 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 579112009938 GIY-YIG motif/motif A; other site 579112009939 putative active site [active] 579112009940 putative metal binding site [ion binding]; other site 579112009941 Protein of unknown function, DUF480; Region: DUF480; cl01209 579112009942 Protein of unknown function (DUF496); Region: DUF496; cl09955 579112009943 glycerol kinase; Provisional; Region: glpK; PRK00047 579112009944 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 579112009945 N- and C-terminal domain interface [polypeptide binding]; other site 579112009946 active site 579112009947 MgATP binding site [chemical binding]; other site 579112009948 catalytic site [active] 579112009949 metal binding site [ion binding]; metal-binding site 579112009950 glycerol binding site [chemical binding]; other site 579112009951 homotetramer interface [polypeptide binding]; other site 579112009952 homodimer interface [polypeptide binding]; other site 579112009953 FBP binding site [chemical binding]; other site 579112009954 protein IIAGlc interface [polypeptide binding]; other site 579112009955 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-...; Region: MIP; cd00333 579112009956 amphipathic channel; other site 579112009957 Asn-Pro-Ala signature motifs; other site 579112009958 sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional; Region: glpA; PRK11101 579112009959 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 579112009960 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 579112009961 anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated; Region: PRK05329 579112009962 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl10040 579112009963 C subunit; Region: glycerol3P_GlpC; TIGR03379 579112009964 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 alpha-; Region: HCP_like; cl14655 579112009965 Cysteine-rich domain; Region: CCG; pfam02754 579112009966 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 579112009967 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 579112009968 dimer interface [polypeptide binding]; other site 579112009969 active site 579112009970 CoA binding pocket [chemical binding]; other site 579112009971 thioredoxin 2; Provisional; Region: PRK10996 579112009972 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 579112009973 catalytic residues [active] 579112009974 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 579112009975 Major Facilitator Superfamily; Region: MFS_1; pfam07690 579112009976 putative substrate translocation pore; other site 579112009977 Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation,' the process of...; Region: Lipase_3; cd00519 579112009978 active site flap/lid [active] 579112009979 nucleophilic elbow; other site 579112009980 catalytic triad [active] 579112009981 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 579112009982 active site 579112009983 metal binding site [ion binding]; metal-binding site 579112009984 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112009985 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112009986 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 579112009987 dimerization interface [polypeptide binding]; other site 579112009988 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 579112009989 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...; Region: TM_PBP2; cd06261 579112009990 dimer interface [polypeptide binding]; other site 579112009991 conserved gate region; other site 579112009992 putative PBP binding loops; other site 579112009993 ABC-ATPase subunit interface; other site 579112009994 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 579112009995 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...; Region: TM_PBP2; cd06261 579112009996 dimer interface [polypeptide binding]; other site 579112009997 conserved gate region; other site 579112009998 putative PBP binding loops; other site 579112009999 ABC-ATPase subunit interface; other site 579112010000 putative ABC transporter arginine-biding protein; Provisional; Region: PRK15007 579112010001 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...; Region: PBPb; cd00134 579112010002 substrate binding pocket [chemical binding]; other site 579112010003 membrane-bound complex binding site; other site 579112010004 hinge residues; other site 579112010005 arginine transporter ATP-binding subunit; Provisional; Region: artP; PRK11124 579112010006 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 579112010007 Walker A/P-loop; other site 579112010008 ATP binding site [chemical binding]; other site 579112010009 Q-loop/lid; other site 579112010010 ABC transporter signature motif; other site 579112010011 Walker B; other site 579112010012 D-loop; other site 579112010013 H-loop/switch region; other site 579112010014 hypothetical protein; Provisional; Region: yieM; PRK10997 579112010015 VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-...; Region: VWA_YIEM_type; cd01462 579112010016 metal ion-dependent adhesion site (MIDAS); other site 579112010017 regulatory ATPase RavA; Provisional; Region: PRK13531 579112010018 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...; Region: AAA; cd00009 579112010019 Walker A motif; other site 579112010020 ATP binding site [chemical binding]; other site 579112010021 Walker B motif; other site 579112010022 arginine finger; other site 579112010023 Protein of unknown function (DUF3763); Region: DUF3763; pfam12592 579112010024 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...; Region: ADPRase_NUDT5; cd03424 579112010025 dimer interface [polypeptide binding]; other site 579112010026 ADP-ribose binding site [chemical binding]; other site 579112010027 active site 579112010028 nudix motif; other site 579112010029 metal binding site [ion binding]; metal-binding site 579112010030 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 579112010031 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 579112010032 tetramer interface [polypeptide binding]; other site 579112010033 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112010034 catalytic residue [active] 579112010035 Cytochrome c; Region: Cytochrom_C; cl11414 579112010036 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112010037 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112010038 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 579112010039 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 579112010040 ATP binding site [chemical binding]; other site 579112010041 Mg++ binding site [ion binding]; other site 579112010042 motif III; other site 579112010043 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 579112010044 nucleotide binding region [chemical binding]; other site 579112010045 ATP-binding site [chemical binding]; other site 579112010046 Protein of unknown function, DUF479; Region: DUF479; cl01203 579112010047 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 579112010048 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010049 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010050 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010051 UDP-galactose-4-epimerase; Provisional; Region: PRK10675 579112010052 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 579112010053 NAD binding site [chemical binding]; other site 579112010054 homodimer interface [polypeptide binding]; other site 579112010055 active site 579112010056 substrate binding site [chemical binding]; other site 579112010057 LamB/YcsF family; Region: LamB_YcsF; cl00664 579112010058 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 579112010059 Allophanate hydrolase subunit 1; Region: AHS1; smart00796 579112010060 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 579112010061 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 579112010062 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 579112010063 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112010064 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 579112010065 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112010066 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 579112010067 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 579112010068 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 579112010069 Walker A/P-loop; other site 579112010070 ATP binding site [chemical binding]; other site 579112010071 Q-loop/lid; other site 579112010072 ABC transporter signature motif; other site 579112010073 Walker B; other site 579112010074 D-loop; other site 579112010075 H-loop/switch region; other site 579112010076 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 579112010077 active site 579112010078 catalytic triad [active] 579112010079 oxyanion hole [active] 579112010080 switch loop; other site 579112010081 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 579112010082 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 579112010083 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112010084 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 579112010085 GAF domain; Region: GAF; cl00853 579112010086 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 579112010087 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 579112010088 Predicted ATPase of the ABC class [General function prediction only]; Region: COG3044 579112010089 DNA-J related protein; Region: DNAJ_related; pfam12339 579112010090 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...; Region: DnaJ; cd06257 579112010091 HSP70 interaction site [polypeptide binding]; other site 579112010092 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 579112010093 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 579112010094 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 579112010095 putative transposase OrfB; Reviewed; Region: PHA02517 579112010096 Integrase core domain; Region: rve; cl01316 579112010097 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; cl01116 579112010098 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 579112010099 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 579112010100 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 579112010101 catalytic residues [active] 579112010102 catalytic nucleophile [active] 579112010103 Presynaptic Site I dimer interface [polypeptide binding]; other site 579112010104 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 579112010105 Synaptic Flat tetramer interface [polypeptide binding]; other site 579112010106 Synaptic Site I dimer interface [polypeptide binding]; other site 579112010107 DNA binding site [nucleotide binding] 579112010108 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 579112010109 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 579112010110 active site 579112010111 motif I; other site 579112010112 motif II; other site 579112010113 CreA protein; Region: CreA; cl01154 579112010114 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, 2-...; Region: ribokinase_pfkB_like; cl00192 579112010115 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 579112010116 substrate binding site [chemical binding]; other site 579112010117 ATP binding site [chemical binding]; other site 579112010118 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 579112010119 Sulfatase; Region: Sulfatase; cl10460 579112010120 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cd00190 579112010121 cleavage site 579112010122 active site 579112010123 substrate binding sites [chemical binding]; other site 579112010124 helicase 45; Provisional; Region: PTZ00424 579112010125 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 579112010126 ATP binding site [chemical binding]; other site 579112010127 Mg++ binding site [ion binding]; other site 579112010128 motif III; other site 579112010129 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 579112010130 nucleotide binding region [chemical binding]; other site 579112010131 ATP-binding site [chemical binding]; other site 579112010132 DbpA RNA binding domain; Region: DbpA; pfam03880 579112010133 exoribonuclease II; Provisional; Region: PRK05054 579112010134 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 579112010135 RNB domain; Region: RNB; pfam00773 579112010136 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 579112010137 Protein of unknown function (DUF3024); Region: DUF3024; pfam11225 579112010138 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 579112010139 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 579112010140 putative active site [active] 579112010141 putative catalytic site [active] 579112010142 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 579112010143 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 579112010144 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 579112010145 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 579112010146 Chitin binding domain; Region: Chitin_bind_3; cl03871 579112010147 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 579112010148 M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica aminopeptidase; Region: M28_AAP; cd03879 579112010149 active site 579112010150 metal binding site [ion binding]; metal-binding site 579112010151 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 579112010152 Arginase family; Region: Arginase; cl00306 579112010153 arginine decarboxylase; Provisional; Region: PRK05354 579112010154 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 579112010155 dimer interface [polypeptide binding]; other site 579112010156 active site 579112010157 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 579112010158 catalytic residues [active] 579112010159 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 579112010160 Mechanosensitive ion channel; Region: MS_channel; pfam00924 579112010161 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 579112010162 MgtE intracellular N domain; Region: MgtE_N; cl15244 579112010163 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 579112010164 Divalent cation transporter; Region: MgtE; cl00786 579112010165 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...; Region: cpn10; cd00320 579112010166 oligomerisation interface [polypeptide binding]; other site 579112010167 mobile loop; other site 579112010168 roof hairpin; other site 579112010169 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 579112010170 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 579112010171 ring oligomerisation interface [polypeptide binding]; other site 579112010172 ATP/Mg binding site [chemical binding]; other site 579112010173 stacking interactions; other site 579112010174 hinge regions; other site 579112010175 aspartate kinase; Validated; Region: PRK09181 579112010176 AAK_AK-Ectoine: Amino Acid Kinase Superfamily (AAK), AK-Ectoine; this CD includes the N-terminal catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium...; Region: AAK_AK-Ectoine; cd04248 579112010177 putative catalytic residues [active] 579112010178 putative nucleotide binding site [chemical binding]; other site 579112010179 putative aspartate binding site [chemical binding]; other site 579112010180 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-...; Region: CBS_pair; cl09141 579112010181 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway; Region: ACT_AK-Ectoine_2; cd04915 579112010182 Cupin domain; Region: Cupin_2; cl09118 579112010183 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 579112010184 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 579112010185 inhibitor-cofactor binding pocket; inhibition site 579112010186 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112010187 catalytic residue [active] 579112010188 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112010189 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 579112010190 Coenzyme A binding pocket [chemical binding]; other site 579112010191 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 579112010192 aromatic arch; other site 579112010193 DCoH dimer interaction site [polypeptide binding]; other site 579112010194 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 579112010195 DCoH tetramer interaction site [polypeptide binding]; other site 579112010196 substrate binding site [chemical binding]; other site 579112010197 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH)...; Region: pro_PheOH; cd03348 579112010198 cofactor binding site; other site 579112010199 metal binding site [ion binding]; metal-binding site 579112010200 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 579112010201 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112010202 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112010203 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010204 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 579112010205 substrate binding pocket [chemical binding]; other site 579112010206 dimerization interface [polypeptide binding]; other site 579112010207 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 579112010208 S-adenosylmethionine binding site [chemical binding]; other site 579112010209 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112010210 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010211 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 579112010212 dimerization interface [polypeptide binding]; other site 579112010213 Cation efflux family; Region: Cation_efflux; cl00316 579112010214 aromatic amino acid exporter; Provisional; Region: PRK11689 579112010215 maltose O-acetyltransferase; Provisional; Region: PRK10092 579112010216 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 579112010217 active site 579112010218 substrate binding site [chemical binding]; other site 579112010219 trimer interface [polypeptide binding]; other site 579112010220 CoA binding site [chemical binding]; other site 579112010221 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 579112010222 Domain of unknown function DUF21; Region: DUF21; pfam01595 579112010223 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 579112010224 Transporter associated domain; Region: CorC_HlyC; cl08393 579112010225 OsmC-like protein; Region: OsmC; cl00767 579112010226 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 579112010227 catalytic motif [active] 579112010228 Zn binding site [ion binding]; other site 579112010229 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 579112010230 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 579112010231 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 579112010232 LysE type translocator; Region: LysE; cl00565 579112010233 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 579112010234 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112010235 metal binding site [ion binding]; metal-binding site 579112010236 active site 579112010237 I-site; other site 579112010238 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 579112010239 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 579112010240 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 579112010241 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 579112010242 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 579112010243 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 579112010244 type 1 secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 579112010245 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 579112010246 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112010247 active site 579112010248 phosphorylation site [posttranslational modification] 579112010249 intermolecular recognition site; other site 579112010250 dimerization interface [polypeptide binding]; other site 579112010251 LytTr DNA-binding domain; Region: LytTR; cl04498 579112010252 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 579112010253 Histidine kinase; Region: His_kinase; pfam06580 579112010254 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 579112010255 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 579112010256 FtsX-like permease family; Region: FtsX; pfam02687 579112010257 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 579112010258 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 579112010259 Walker A/P-loop; other site 579112010260 ATP binding site [chemical binding]; other site 579112010261 Q-loop/lid; other site 579112010262 ABC transporter signature motif; other site 579112010263 Walker B; other site 579112010264 D-loop; other site 579112010265 H-loop/switch region; other site 579112010266 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...; Region: Aldo_ket_red; cd06660 579112010267 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 579112010268 active site 579112010269 catalytic tetrad [active] 579112010270 alpha-amylase; Reviewed; Region: malS; PRK09505 579112010271 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 579112010272 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 579112010273 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 579112010274 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 579112010275 Bacterial virulence factor lipase N-terminal; Region: Lipase_bact_N; pfam12262 579112010276 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112010277 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 579112010278 putative active site [active] 579112010279 heme pocket [chemical binding]; other site 579112010280 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112010281 putative active site [active] 579112010282 heme pocket [chemical binding]; other site 579112010283 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010284 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 579112010285 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 579112010286 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 579112010287 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 579112010288 active site 579112010289 Zn binding site [ion binding]; other site 579112010290 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 579112010291 Surface antigen; Region: Surface_Ag_2; cl01155 579112010292 Beta-lactamase; Region: Beta-lactamase; cl01009 579112010293 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 579112010294 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 579112010295 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 579112010296 DNA-binding site [nucleotide binding]; DNA binding site 579112010297 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 579112010298 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112010299 homodimer interface [polypeptide binding]; other site 579112010300 catalytic residue [active] 579112010301 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 579112010302 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 579112010303 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 579112010304 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 579112010305 D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive...; Region: D-Ser-dehyd; cd06447 579112010306 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 579112010307 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 579112010308 catalytic residue [active] 579112010309 D-serine deaminase transcriptional activator; Region: dsdC; TIGR02036 579112010310 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010311 HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 579112010312 dimerization interface [polypeptide binding]; other site 579112010313 substrate binding pocket [chemical binding]; other site 579112010314 Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile. CGH is present in a number of probiotic microbial organisms that...; Region: Ntn_CGH; cd01902 579112010315 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 579112010316 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 579112010317 Bacillus haemolytic enterotoxin (HBL); Region: Bacillus_HBL; pfam05791 579112010318 Apolipoprotein L; Region: ApoL; pfam05461 579112010319 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 579112010320 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 579112010321 NAD(P) binding site [chemical binding]; other site 579112010322 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 579112010323 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-...; Region: KBL_like; cd06454 579112010324 substrate-cofactor binding pocket; other site 579112010325 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112010326 catalytic residue [active] 579112010327 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 579112010328 Autoinducer binding domain; Region: Autoind_bind; pfam03472 579112010329 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...; Region: LuxR_C_like; cd06170 579112010330 DNA binding residues [nucleotide binding] 579112010331 dimerization interface [polypeptide binding]; other site 579112010332 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112010333 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010334 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112010335 putative effector binding pocket; other site 579112010336 dimerization interface [polypeptide binding]; other site 579112010337 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 579112010338 putative metal binding site [ion binding]; other site 579112010339 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 579112010340 Cytochrome b562; Region: Cytochrom_B562; cl01546 579112010341 putative hydrolase; Validated; Region: PRK09248 579112010342 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 579112010343 RNase P subunit p30; Region: RNase_P_p30; cl03389 579112010344 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 579112010345 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010346 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 579112010347 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112010348 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 579112010349 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 579112010350 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 579112010351 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 579112010352 putative active site [active] 579112010353 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112010354 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 579112010355 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 579112010356 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112010357 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 579112010358 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 579112010359 catalytic residues [active] 579112010360 Glycerate kinase family; Region: Gly_kinase; cl00841 579112010361 GntP family permease; Region: GntP_permease; cl15264 579112010362 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 579112010363 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 579112010364 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010365 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010366 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 579112010367 ChuX-like family; Region: DUF1008; cl01509 579112010368 coproporphyrinogen III oxidase; Provisional; Region: PRK09058 579112010369 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 579112010370 FeS/SAM binding site; other site 579112010371 HemN C-terminal region; Region: HemN_C; pfam06969 579112010372 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 579112010373 Gram-negative bacterial tonB protein; Region: TonB; cl10048 579112010374 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 579112010375 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 579112010376 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 579112010377 ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ChuT; COG4558 579112010378 Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a...; Region: HutB; cd01149 579112010379 putative hemin binding site; other site 579112010380 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 579112010381 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...; Region: TM_ABC_iron-siderophores_like; cd06550 579112010382 ABC-ATPase subunit interface; other site 579112010383 dimer interface [polypeptide binding]; other site 579112010384 putative PBP binding regions; other site 579112010385 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 579112010386 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 579112010387 Walker A/P-loop; other site 579112010388 ATP binding site [chemical binding]; other site 579112010389 Q-loop/lid; other site 579112010390 ABC transporter signature motif; other site 579112010391 Walker B; other site 579112010392 D-loop; other site 579112010393 H-loop/switch region; other site 579112010394 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112010395 Protein of unknown function (DUF406); Region: DUF406; cl11449 579112010396 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112010397 Glycerol-3-phosphate O-acyltransferase [Lipid metabolism]; Region: PlsB; COG2937 579112010398 Vibrio chemotaxis protein N terminus; Region: MCP_N; pfam05581 579112010399 Cache domain; Region: Cache_1; pfam02743 579112010400 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010401 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010402 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010403 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 579112010404 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 579112010405 MOSC domain; Region: MOSC; pfam03473 579112010406 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 579112010407 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 579112010408 FAD binding pocket [chemical binding]; other site 579112010409 FAD binding motif [chemical binding]; other site 579112010410 phosphate binding motif [ion binding]; other site 579112010411 beta-alpha-beta structure motif; other site 579112010412 NAD binding pocket [chemical binding]; other site 579112010413 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 579112010414 catalytic loop [active] 579112010415 iron binding site [ion binding]; other site 579112010416 Dihydroorotase [Nucleotide transport and metabolism]; Region: PyrC; COG0418 579112010417 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 579112010418 active site 579112010419 substrate binding pocket [chemical binding]; other site 579112010420 dimer interface [polypeptide binding]; other site 579112010421 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112010422 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112010423 Protein of unknown function (DUF805); Region: DUF805; cl01224 579112010424 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112010425 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 579112010426 Protein of unknown function (DUF808); Region: DUF808; cl01002 579112010427 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 579112010428 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 579112010429 Zn2+ binding site [ion binding]; other site 579112010430 Mg2+ binding site [ion binding]; other site 579112010431 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 579112010432 DNA-binding site [nucleotide binding]; DNA binding site 579112010433 RNA-binding motif; other site 579112010434 A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site...; Region: Peptidase_M14-like_4; cd06231 579112010435 putative active site [active] 579112010436 Zn-binding site [ion binding]; other site 579112010437 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112010438 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 579112010439 EamA-like transporter family; Region: EamA; cl01037 579112010440 EamA-like transporter family; Region: EamA; cl01037 579112010441 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112010442 PAS fold; Region: PAS_4; pfam08448 579112010443 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112010444 metal binding site [ion binding]; metal-binding site 579112010445 active site 579112010446 I-site; other site 579112010447 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 579112010448 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010449 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 579112010450 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain...; Region: BFIT_BACH; cd03442 579112010451 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 579112010452 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...; Region: TM_PBP2; cd06261 579112010453 dimer interface [polypeptide binding]; other site 579112010454 conserved gate region; other site 579112010455 putative PBP binding loops; other site 579112010456 ABC-ATPase subunit interface; other site 579112010457 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...; Region: TM_PBP2; cd06261 579112010458 dimer interface [polypeptide binding]; other site 579112010459 conserved gate region; other site 579112010460 putative PBP binding loops; other site 579112010461 ABC-ATPase subunit interface; other site 579112010462 Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]; Region: MalE; COG2182 579112010463 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 579112010464 maltose/maltodextrin transporter ATP-binding protein; Provisional; Region: PRK11000 579112010465 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 579112010466 Walker A/P-loop; other site 579112010467 ATP binding site [chemical binding]; other site 579112010468 Q-loop/lid; other site 579112010469 ABC transporter signature motif; other site 579112010470 Walker B; other site 579112010471 D-loop; other site 579112010472 H-loop/switch region; other site 579112010473 TOBE domain; Region: TOBE_2; cl01440 579112010474 spermidine N1-acetyltransferase; Provisional; Region: PRK15130 579112010475 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 579112010476 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; cl09210 579112010477 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 579112010478 Domain of unknown function (DUF74); Region: DUF74; cl00426 579112010479 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 579112010480 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...; Region: LuxR_C_like; cd06170 579112010481 DNA binding residues [nucleotide binding] 579112010482 dimerization interface [polypeptide binding]; other site 579112010483 PPIC-type PPIASE domain; Region: Rotamase; cl08278 579112010484 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112010485 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 579112010486 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112010487 active site 579112010488 phosphorylation site [posttranslational modification] 579112010489 intermolecular recognition site; other site 579112010490 dimerization interface [polypeptide binding]; other site 579112010491 Transcriptional regulators [Transcription]; Region: MarR; COG1846 579112010492 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010493 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112010494 metal binding site [ion binding]; metal-binding site 579112010495 active site 579112010496 I-site; other site 579112010497 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 579112010498 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 579112010499 non-specific DNA binding site [nucleotide binding]; other site 579112010500 salt bridge; other site 579112010501 sequence-specific DNA binding site [nucleotide binding]; other site 579112010502 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 579112010503 CHASE domain; Region: CHASE; cl01369 579112010504 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112010505 metal binding site [ion binding]; metal-binding site 579112010506 active site 579112010507 I-site; other site 579112010508 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 579112010509 Domain of unknown function (DUF3541); Region: DUF3541; pfam12060 579112010510 EamA-like transporter family; Region: EamA; cl01037 579112010511 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 579112010512 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010513 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 579112010514 dimerization interface [polypeptide binding]; other site 579112010515 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112010516 metal binding site [ion binding]; metal-binding site 579112010517 active site 579112010518 I-site; other site 579112010519 Pirin-related protein [General function prediction only]; Region: COG1741 579112010520 Cupin domain; Region: Cupin_2; cl09118 579112010521 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 579112010522 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 579112010523 Protein of unknown function (DUF2850); Region: DUF2850; pfam11012 579112010524 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 579112010525 Major Facilitator Superfamily; Region: MFS_1; pfam07690 579112010526 putative substrate translocation pore; other site 579112010527 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010528 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010529 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010530 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 579112010531 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 579112010532 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 579112010533 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112010534 Walker A/P-loop; other site 579112010535 ATP binding site [chemical binding]; other site 579112010536 Q-loop/lid; other site 579112010537 ABC transporter signature motif; other site 579112010538 Walker B; other site 579112010539 D-loop; other site 579112010540 H-loop/switch region; other site 579112010541 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112010542 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112010543 Walker A/P-loop; other site 579112010544 ATP binding site [chemical binding]; other site 579112010545 Q-loop/lid; other site 579112010546 ABC transporter signature motif; other site 579112010547 Walker B; other site 579112010548 D-loop; other site 579112010549 H-loop/switch region; other site 579112010550 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112010551 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...; Region: PBPb; cd00134 579112010552 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 579112010553 substrate binding pocket [chemical binding]; other site 579112010554 membrane-bound complex binding site; other site 579112010555 hinge residues; other site 579112010556 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 579112010557 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010558 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010559 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...; Region: PBPb; cl15306 579112010560 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 579112010561 substrate binding pocket [chemical binding]; other site 579112010562 membrane-bound complex binding site; other site 579112010563 hinge residues; other site 579112010564 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112010565 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010566 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112010567 putative effector binding pocket; other site 579112010568 dimerization interface [polypeptide binding]; other site 579112010569 L-lactate permease; Region: Lactate_perm; cl00701 579112010570 glycolate transporter; Provisional; Region: PRK09695 579112010571 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 579112010572 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 579112010573 active site 579112010574 substrate binding site [chemical binding]; other site 579112010575 FMN binding site [chemical binding]; other site 579112010576 putative catalytic residues [active] 579112010577 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 579112010578 FAD binding domain; Region: FAD_binding_4; pfam01565 579112010579 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 579112010580 Domain of unknown function (DUF299); Region: DUF299; cl00780 579112010581 phosphoenolpyruvate synthase; Validated; Region: PRK06464 579112010582 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 579112010583 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 579112010584 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 579112010585 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112010586 PAS fold; Region: PAS_3; pfam08447 579112010587 putative active site [active] 579112010588 heme pocket [chemical binding]; other site 579112010589 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010590 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010591 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 579112010592 MatE; Region: MatE; cl10513 579112010593 MatE; Region: MatE; cl10513 579112010594 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 579112010595 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 579112010596 ATP binding site [chemical binding]; other site 579112010597 Mg++ binding site [ion binding]; other site 579112010598 motif III; other site 579112010599 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 579112010600 nucleotide binding region [chemical binding]; other site 579112010601 ATP-binding site [chemical binding]; other site 579112010602 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010603 transcriptional activator TtdR; Provisional; Region: PRK09801 579112010604 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112010605 putative effector binding pocket; other site 579112010606 dimerization interface [polypeptide binding]; other site 579112010607 Glutaredoxin 2 [Posttranslational modification, protein turnover, chaperones]; Region: GrxB; COG2999 579112010608 GST_N family, Glutaredoxin 2 (GRX2) subfamily; composed of bacterial proteins similar to E. coli GRX2, an atypical GRX with a molecular mass of about 24kD, compared with other GRXs which are 9-12kD in size. GRX2 adopts a GST fold containing an N-...; Region: GST_N_GRX2; cd03037 579112010609 C-terminal domain interface [polypeptide binding]; other site 579112010610 GSH binding site (G-site) [chemical binding]; other site 579112010611 catalytic residues [active] 579112010612 putative dimer interface [polypeptide binding]; other site 579112010613 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 579112010614 dimer interface [polypeptide binding]; other site 579112010615 substrate binding pocket (H-site) [chemical binding]; other site 579112010616 N-terminal domain interface [polypeptide binding]; other site 579112010617 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 579112010618 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 579112010619 FMN binding site [chemical binding]; other site 579112010620 active site 579112010621 substrate binding site [chemical binding]; other site 579112010622 catalytic residue [active] 579112010623 Amidinotransferase; Region: Amidinotransf; cl12043 579112010624 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 579112010625 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 579112010626 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 579112010627 Walker A/P-loop; other site 579112010628 ATP binding site [chemical binding]; other site 579112010629 Q-loop/lid; other site 579112010630 ABC transporter signature motif; other site 579112010631 Walker B; other site 579112010632 D-loop; other site 579112010633 H-loop/switch region; other site 579112010634 Protein of unknown function (DUF445); Region: DUF445; pfam04286 579112010635 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 579112010636 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 579112010637 FMN binding site [chemical binding]; other site 579112010638 active site 579112010639 substrate binding site [chemical binding]; other site 579112010640 catalytic residue [active] 579112010641 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 579112010642 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 579112010643 LysE type translocator; Region: LysE; cl00565 579112010644 Cupin domain; Region: Cupin_2; cl09118 579112010645 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 579112010646 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112010647 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112010648 AzlC protein; Region: AzlC; cl00570 579112010649 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 579112010650 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 579112010651 Transcriptional regulators [Transcription]; Region: MarR; COG1846 579112010652 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010653 OsmC-like protein; Region: OsmC; cl00767 579112010654 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface...; Region: gram_neg_porins; cd00342 579112010655 trimer interface [polypeptide binding]; other site 579112010656 eyelet of channel; other site 579112010657 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 579112010658 EamA-like transporter family; Region: EamA; cl01037 579112010659 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 579112010660 GSH binding site [chemical binding]; other site 579112010661 catalytic residues [active] 579112010662 Nucleoside recognition; Region: Gate; cl00486 579112010663 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 579112010664 Nucleoside recognition; Region: Gate; cl00486 579112010665 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; cl09110 579112010666 transmembrane helices; other site 579112010667 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 579112010668 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 579112010669 DNA binding site [nucleotide binding] 579112010670 active site 579112010671 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 579112010672 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 579112010673 AlkA N-terminal domain; Region: AlkA_N; cl05528 579112010674 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 579112010675 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 579112010676 DoxX; Region: DoxX; cl00976 579112010677 transcriptional regulator HdfR; Provisional; Region: PRK03601 579112010678 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010679 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 579112010680 Protein of unknown function, DUF; Region: DUF413; cl10479 579112010681 N-formylglutamate amidohydrolase; Region: FGase; cl01522 579112010682 Domain of unknown function (DUF1704); Region: DUF1704; cl06858 579112010683 conserved hypothetical protein; Region: QEGLA; TIGR02421 579112010684 Protein of unknown function (DUF3081); Region: DUF3081; pfam11280 579112010685 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...; Region: GlcN6P_deaminase; cd01399 579112010686 active site 579112010687 trimer interface [polypeptide binding]; other site 579112010688 allosteric site; other site 579112010689 active site lid [active] 579112010690 hexamer (dimer of trimers) interface [polypeptide binding]; other site 579112010691 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 579112010692 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 579112010693 Sel1 repeat; Region: Sel1; cl02723 579112010694 Maltose operon periplasmic protein precursor (MalM); Region: MalM; cl11647 579112010695 The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel beta-...; Region: Maltoporin-like; cd01346 579112010696 trimer interface; other site 579112010697 sugar binding site [chemical binding]; other site 579112010698 Type II secretory pathway, pullulanase PulA and related glycosidases [Carbohydrate transport and metabolism]; Region: PulA; COG1523 579112010699 Glycogen_debranching_enzyme N-terminal domain. Glycogen debranching enzymes have both 4-alpha-glucanotransferase and amylo-1,6-glucosidase activities. As a transferase it transfers a segment of a 1,4-alpha-D-glucan to a new 4-position in an acceptor...; Region: Glycogen_debranching_enzyme_N_term; cd02856 579112010700 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 579112010701 Protein of unknown function (DUF2999); Region: DUF2999; pfam11212 579112010702 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 579112010703 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010704 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010705 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010706 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 579112010707 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 579112010708 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 579112010709 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010710 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010711 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 579112010712 NeuB family; Region: NeuB; cl00496 579112010713 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 579112010714 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 579112010715 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 579112010716 Walker A/P-loop; other site 579112010717 ATP binding site [chemical binding]; other site 579112010718 Q-loop/lid; other site 579112010719 ABC transporter signature motif; other site 579112010720 Walker B; other site 579112010721 D-loop; other site 579112010722 H-loop/switch region; other site 579112010723 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...; Region: TM_PBP2; cd06261 579112010724 dimer interface [polypeptide binding]; other site 579112010725 conserved gate region; other site 579112010726 putative PBP binding loops; other site 579112010727 ABC-ATPase subunit interface; other site 579112010728 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 579112010729 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...; Region: PBPb; cd00134 579112010730 substrate binding pocket [chemical binding]; other site 579112010731 membrane-bound complex binding site; other site 579112010732 hinge residues; other site 579112010733 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 579112010734 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...; Region: TM_PBP2; cd06261 579112010735 dimer interface [polypeptide binding]; other site 579112010736 conserved gate region; other site 579112010737 putative PBP binding loops; other site 579112010738 ABC-ATPase subunit interface; other site 579112010739 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 579112010740 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 deoxyribose-1-...; Region: PGM2; cd05799 579112010741 active site 579112010742 substrate binding site [chemical binding]; other site 579112010743 metal binding site [ion binding]; metal-binding site 579112010744 Polymer-forming cytoskeletal; Region: Bactofilin; cl09137 579112010745 Peptidase family M23; Region: Peptidase_M23; pfam01551 579112010746 PTS system mannitol-specific transporter subunit IICBA; Provisional; Region: PRK15083 579112010747 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 579112010748 PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a...; Region: PTS_IIB_mannitol; cd05567 579112010749 active site 579112010750 P-loop; other site 579112010751 phosphorylation site [posttranslational modification] 579112010752 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 579112010753 active site 579112010754 phosphorylation site [posttranslational modification] 579112010755 mannitol-1-phosphate 5-dehydrogenase; Provisional; Region: PRK02318 579112010756 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 579112010757 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 579112010758 Mannitol repressor; Region: MtlR; cl11450 579112010759 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 579112010760 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112010761 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 579112010762 hypothetical protein; Provisional; Region: PRK11770 579112010763 Domain of unknown function (DUF307); Region: DUF307; pfam03733 579112010764 Domain of unknown function (DUF307); Region: DUF307; pfam03733 579112010765 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 579112010766 Member of the Rhodanese Homology Domain superfamily. This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins; Region: RHOD_PspE2; cd01521 579112010767 active site residue [active] 579112010768 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 579112010769 NAD binding site [chemical binding]; other site 579112010770 substrate binding site [chemical binding]; other site 579112010771 putative active site [active] 579112010772 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112010773 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010774 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112010775 putative effector binding pocket; other site 579112010776 dimerization interface [polypeptide binding]; other site 579112010777 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 connected by an extended linker. The...; Region: HAMP; cd06225 579112010778 dimerization interface [polypeptide binding]; other site 579112010779 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010780 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010781 classical (c) SDRs; Region: SDR_c; cd05233 579112010782 NAD(P) binding site [chemical binding]; other site 579112010783 active site 579112010784 Transcriptional regulator [Transcription]; Region: LysR; COG0583 579112010785 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010786 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 579112010787 putative effector binding pocket; other site 579112010788 dimerization interface [polypeptide binding]; other site 579112010789 Protein of unknown function (DUF358); Region: DUF358; cl00827 579112010790 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 579112010791 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 579112010792 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 579112010793 ornithine decarboxylase; Provisional; Region: PRK13578 579112010794 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 579112010795 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and...; Region: Orn_deC_like; cd00615 579112010796 homodimer interface [polypeptide binding]; other site 579112010797 pyridoxal 5'-phosphate binding site [chemical binding]; other site 579112010798 catalytic residue [active] 579112010799 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 579112010800 Protein of unknown function (DUF2618); Region: DUF2618; pfam10940 579112010801 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 579112010802 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 579112010803 NAD(P) binding site [chemical binding]; other site 579112010804 catalytic residues [active] 579112010805 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 579112010806 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 579112010807 Cache domain; Region: Cache_1; pfam02743 579112010808 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010809 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010810 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010811 Sodium:solute symporter family; Region: SSF; cl00456 579112010812 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 579112010813 NAD(P) binding site [chemical binding]; other site 579112010814 catalytic residues [active] 579112010815 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 579112010816 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 579112010817 Proline dehydrogenase; Region: Pro_dh; cl03282 579112010818 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 579112010819 Glutamate binding site [chemical binding]; other site 579112010820 NAD binding site [chemical binding]; other site 579112010821 catalytic residues [active] 579112010822 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112010823 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 579112010824 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 579112010825 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 579112010826 PEGA domain; Region: PEGA; pfam08308 579112010827 PEGA domain; Region: PEGA; pfam08308 579112010828 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl00556 579112010829 PAS fold; Region: PAS_4; pfam08448 579112010830 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 579112010831 putative active site [active] 579112010832 heme pocket [chemical binding]; other site 579112010833 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...; Region: LuxR_C_like; cd06170 579112010834 DNA binding residues [nucleotide binding] 579112010835 dimerization interface [polypeptide binding]; other site 579112010836 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 579112010837 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 579112010838 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 579112010839 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 579112010840 Outer membrane efflux protein; Region: OEP; pfam02321 579112010841 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 579112010842 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010843 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 579112010844 active site 579112010845 I-site; other site 579112010846 metal binding site [ion binding]; metal-binding site 579112010847 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 579112010848 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 579112010849 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 579112010850 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 579112010851 ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two...; Region: ABCC_bacteriocin_exporters; cd03245 579112010852 Walker A/P-loop; other site 579112010853 ATP binding site [chemical binding]; other site 579112010854 Q-loop/lid; other site 579112010855 ABC transporter signature motif; other site 579112010856 Walker B; other site 579112010857 D-loop; other site 579112010858 H-loop/switch region; other site 579112010859 Uncharacterized conserved protein [Function unknown]; Region: COG1315 579112010860 Response regulator receiver domain; Region: Response_reg; pfam00072 579112010861 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112010862 active site 579112010863 phosphorylation site [posttranslational modification] 579112010864 intermolecular recognition site; other site 579112010865 dimerization interface [polypeptide binding]; other site 579112010866 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 579112010867 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 579112010868 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 579112010869 anti sigma factor interaction site; other site 579112010870 regulatory phosphorylation site [posttranslational modification]; other site 579112010871 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 579112010872 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112010873 active site 579112010874 phosphorylation site [posttranslational modification] 579112010875 intermolecular recognition site; other site 579112010876 dimerization interface [polypeptide binding]; other site 579112010877 CheB methylesterase; Region: CheB_methylest; pfam01339 579112010878 CheD chemotactic sensory transduction; Region: CheD; cl00810 579112010879 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 579112010880 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 579112010881 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 579112010882 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 579112010883 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010884 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 connected by an extended linker. The...; Region: HAMP; cl01054 579112010885 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 579112010886 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 579112010887 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112010888 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 579112010889 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 579112010890 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 579112010891 putative binding surface; other site 579112010892 active site 579112010893 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 579112010894 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 579112010895 ATP binding site [chemical binding]; other site 579112010896 Mg2+ binding site [ion binding]; other site 579112010897 G-X-G motif; other site 579112010898 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 579112010899 Response regulator receiver domain; Region: Response_reg; pfam00072 579112010900 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112010901 active site 579112010902 phosphorylation site [posttranslational modification] 579112010903 intermolecular recognition site; other site 579112010904 dimerization interface [polypeptide binding]; other site 579112010905 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 579112010906 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_3; cd08490 579112010907 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 579112010908 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 579112010909 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...; Region: TM_PBP2; cd06261 579112010910 dimer interface [polypeptide binding]; other site 579112010911 conserved gate region; other site 579112010912 putative PBP binding loops; other site 579112010913 ABC-ATPase subunit interface; other site 579112010914 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...; Region: TM_PBP2; cd06261 579112010915 dimer interface [polypeptide binding]; other site 579112010916 conserved gate region; other site 579112010917 putative PBP binding loops; other site 579112010918 ABC-ATPase subunit interface; other site 579112010919 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 579112010920 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112010921 Walker A/P-loop; other site 579112010922 ATP binding site [chemical binding]; other site 579112010923 Q-loop/lid; other site 579112010924 ABC transporter signature motif; other site 579112010925 Walker B; other site 579112010926 D-loop; other site 579112010927 H-loop/switch region; other site 579112010928 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 579112010929 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 579112010930 Walker A/P-loop; other site 579112010931 ATP binding site [chemical binding]; other site 579112010932 Q-loop/lid; other site 579112010933 ABC transporter signature motif; other site 579112010934 Walker B; other site 579112010935 D-loop; other site 579112010936 H-loop/switch region; other site 579112010937 putative metal dependent hydrolase; Provisional; Region: PRK11598 579112010938 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 579112010939 Sulfatase; Region: Sulfatase; cl10460 579112010940 sensor protein QseC; Provisional; Region: PRK10337 579112010941 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 trans-...; Region: HisKA; cd00082 579112010942 dimer interface [polypeptide binding]; other site 579112010943 phosphorylation site [posttranslational modification] 579112010944 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 579112010945 ATP binding site [chemical binding]; other site 579112010946 Mg2+ binding site [ion binding]; other site 579112010947 G-X-G motif; other site 579112010948 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 579112010949 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 579112010950 active site 579112010951 phosphorylation site [posttranslational modification] 579112010952 intermolecular recognition site; other site 579112010953 dimerization interface [polypeptide binding]; other site 579112010954 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...; Region: trans_reg_C; cd00383 579112010955 DNA binding site [nucleotide binding] 579112010956 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 579112010957 TPR motif; other site 579112010958 binding surface 579112010959 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 579112010960 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 579112010961 NAD(P) binding site [chemical binding]; other site 579112010962 active site 579112010963 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 579112010964 heme binding pocket [chemical binding]; other site 579112010965 heme ligand [chemical binding]; other site 579112010966 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 579112010967 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 579112010968 Thermostable hemolysin; Region: T_hemolysin; pfam12261 579112010969 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]; Region: COG1444 579112010970 Putative ATPase (DUF699); Region: DUF699; pfam05127 579112010971 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 579112010972 Coenzyme A binding pocket [chemical binding]; other site 579112010973 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 579112010974 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 579112010975 plasmid-partitioning protein; Provisional; Region: PRK13698 579112010976 ParB-like nuclease domain; Region: ParBc; cl02129 579112010977 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 579112010978 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...; Region: ParA; cd02042 579112010979 P-loop; other site 579112010980 Magnesium ion binding site [ion binding]; other site 579112010981 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...; Region: ParA; cd02042 579112010982 Magnesium ion binding site [ion binding]; other site