-- dump date 20111121_010133 -- class Genbank::misc_feature -- table misc_feature_note -- id note 643561000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 643561000002 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 643561000003 Walker A motif; other site 643561000004 ATP binding site [chemical binding]; other site 643561000005 Walker B motif; other site 643561000006 arginine finger; other site 643561000007 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 643561000008 DnaA box-binding interface [nucleotide binding]; other site 643561000009 DNA polymerase III subunit beta; Validated; Region: PRK05643 643561000010 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 643561000011 putative DNA binding surface [nucleotide binding]; other site 643561000012 dimer interface [polypeptide binding]; other site 643561000013 beta-clamp/clamp loader binding surface; other site 643561000014 beta-clamp/translesion DNA polymerase binding surface; other site 643561000015 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 643561000016 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 643561000017 ATP binding site [chemical binding]; other site 643561000018 Mg2+ binding site [ion binding]; other site 643561000019 G-X-G motif; other site 643561000020 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 643561000021 anchoring element; other site 643561000022 dimer interface [polypeptide binding]; other site 643561000023 ATP binding site [chemical binding]; other site 643561000024 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 643561000025 active site 643561000026 putative metal-binding site [ion binding]; other site 643561000027 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 643561000028 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 643561000029 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 643561000030 Abi-like protein; Region: Abi_2; cl01988 643561000031 HsdM N-terminal domain; Region: HsdM_N; pfam12161 643561000032 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 643561000033 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 643561000034 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 643561000035 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 643561000036 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 643561000037 LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; Region: LOTUS; cl14879 643561000038 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 643561000039 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 643561000040 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561000041 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561000042 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 643561000043 Protein of unknown function DUF45; Region: DUF45; cl00636 643561000044 Protein of unknown function DUF262; Region: DUF262; cl14890 643561000045 Protein of unknown function DUF262; Region: DUF262; cl14890 643561000046 Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: RtcR; COG4650 643561000047 Regulator of RNA terminal phosphate cyclase; Region: RtcR; pfam06956 643561000048 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 643561000049 Walker A motif; other site 643561000050 ATP binding site [chemical binding]; other site 643561000051 Walker B motif; other site 643561000052 arginine finger; other site 643561000053 TROVE domain; Region: TROVE; pfam05731 643561000054 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2425 643561000055 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 643561000056 hypothetical protein; Reviewed; Region: PRK09588 643561000057 Predicted nucleotidyltransferase; Region: Nuc-transf; cl01417 643561000058 RNA 3'-terminal-phosphate cyclase; Provisional; Region: PRK04204 643561000059 This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats with a...; Region: EPT_RTPC-like; cl00288 643561000060 putative active site [active] 643561000061 Flagellin N-methylase; Region: FliB; cl00497 643561000062 OsmC-like protein; Region: OsmC; cl00767 643561000063 hydrogenase, Fe-only; Region: Fe_only_hydrog; TIGR02512 643561000064 homoserine dehydrogenase; Provisional; Region: PRK06349 643561000065 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000066 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 643561000067 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 643561000068 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561000069 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561000070 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 643561000071 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 643561000072 active site 643561000073 catalytic site [active] 643561000074 substrate binding site [chemical binding]; other site 643561000075 transcriptional regulatory protein PtsJ; Provisional; Region: PRK15481 643561000076 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561000077 DNA-binding site [nucleotide binding]; DNA binding site 643561000078 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 643561000079 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561000080 catalytic residue [active] 643561000081 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 643561000082 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561000083 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000084 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 643561000085 dimerization interface [polypeptide binding]; other site 643561000086 2-isopropylmalate synthase; Validated; Region: PRK03739 643561000087 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 643561000088 active site 643561000089 catalytic residues [active] 643561000090 metal binding site [ion binding]; metal-binding site 643561000091 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 643561000092 outer membrane lipoprotein; Provisional; Region: spr; PRK10838 643561000093 NlpC/P60 family; Region: NLPC_P60; cl11438 643561000094 NeuB family; Region: NeuB; cl00496 643561000095 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 643561000096 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 643561000097 PAS fold; Region: PAS_3; pfam08447 643561000098 putative active site [active] 643561000099 heme pocket [chemical binding]; other site 643561000100 GAF domain; Region: GAF; cl00853 643561000101 PAS domain S-box; Region: sensory_box; TIGR00229 643561000102 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 643561000103 GAF domain; Region: GAF; cl00853 643561000104 PAS domain S-box; Region: sensory_box; TIGR00229 643561000105 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 643561000106 putative active site [active] 643561000107 heme pocket [chemical binding]; other site 643561000108 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561000109 metal binding site [ion binding]; metal-binding site 643561000110 active site 643561000111 I-site; other site 643561000112 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 643561000113 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 643561000114 Domain of Unknown Function (DUF1520); Region: DUF1520; pfam07480 643561000115 Putative exonuclease, RdgC; Region: RdgC; cl01122 643561000116 Nucleoside recognition; Region: Gate; cl00486 643561000117 Nucleoside recognition; Region: Gate; cl00486 643561000118 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 643561000119 beta-ketothiolase; Provisional; Region: PRK09051 643561000120 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 643561000121 dimer interface [polypeptide binding]; other site 643561000122 active site 643561000123 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 643561000124 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 643561000125 DNA binding residues [nucleotide binding] 643561000126 dimer interface [polypeptide binding]; other site 643561000127 copper binding site [ion binding]; other site 643561000128 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 643561000129 metal-binding site [ion binding] 643561000130 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 643561000131 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 643561000132 metal-binding site [ion binding] 643561000133 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 643561000134 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 643561000135 motif II; other site 643561000136 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 643561000137 dimerization interface [polypeptide binding]; other site 643561000138 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 643561000139 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 643561000140 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 643561000141 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 643561000142 Outer membrane efflux protein; Region: OEP; pfam02321 643561000143 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 643561000144 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561000145 active site 643561000146 phosphorylation site [posttranslational modification] 643561000147 intermolecular recognition site; other site 643561000148 dimerization interface [polypeptide binding]; other site 643561000149 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 643561000150 DNA binding site [nucleotide binding] 643561000151 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 643561000152 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 643561000153 dimer interface [polypeptide binding]; other site 643561000154 phosphorylation site [posttranslational modification] 643561000155 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 643561000156 ATP binding site [chemical binding]; other site 643561000157 Mg2+ binding site [ion binding]; other site 643561000158 G-X-G motif; other site 643561000159 NIPSNAP; Region: NIPSNAP; pfam07978 643561000160 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 643561000161 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 643561000162 FMN binding site [chemical binding]; other site 643561000163 active site 643561000164 substrate binding site [chemical binding]; other site 643561000165 catalytic residue [active] 643561000166 taurine ABC transporter, periplasmic binding protein; Region: taurine_ABC_bnd; TIGR01729 643561000167 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 643561000168 substrate binding pocket [chemical binding]; other site 643561000169 membrane-bound complex binding site; other site 643561000170 hinge residues; other site 643561000171 taurine transporter ATP-binding subunit; Provisional; Region: tauB; PRK11248 643561000172 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 643561000173 Walker A/P-loop; other site 643561000174 ATP binding site [chemical binding]; other site 643561000175 Q-loop/lid; other site 643561000176 ABC transporter signature motif; other site 643561000177 Walker B; other site 643561000178 D-loop; other site 643561000179 H-loop/switch region; other site 643561000180 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 643561000181 dimer interface [polypeptide binding]; other site 643561000182 conserved gate region; other site 643561000183 putative PBP binding loops; other site 643561000184 ABC-ATPase subunit interface; other site 643561000185 glutathionine S-transferase; Provisional; Region: PRK10542 643561000186 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_N_Beta; cd03057 643561000187 C-terminal domain interface [polypeptide binding]; other site 643561000188 GSH binding site (G-site) [chemical binding]; other site 643561000189 dimer interface [polypeptide binding]; other site 643561000190 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 643561000191 dimer interface [polypeptide binding]; other site 643561000192 N-terminal domain interface [polypeptide binding]; other site 643561000193 substrate binding pocket (H-site) [chemical binding]; other site 643561000194 Flagellin N-methylase; Region: FliB; cl00497 643561000195 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561000196 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 643561000197 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000198 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 643561000199 LysE type translocator; Region: LysE; cl00565 643561000200 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 643561000201 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 643561000202 P-loop; other site 643561000203 Magnesium ion binding site [ion binding]; other site 643561000204 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 643561000205 Magnesium ion binding site [ion binding]; other site 643561000206 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 643561000207 ParB-like nuclease domain; Region: ParBc; cl02129 643561000208 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 643561000209 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 643561000210 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561000211 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 643561000212 short chain dehydrogenase; Provisional; Region: PRK08278 643561000213 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000214 NAD(P) binding site [chemical binding]; other site 643561000215 active site 643561000216 enoyl-CoA hydratase; Provisional; Region: PRK05995 643561000217 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 643561000218 substrate binding site [chemical binding]; other site 643561000219 oxyanion hole (OAH) forming residues; other site 643561000220 trimer interface [polypeptide binding]; other site 643561000221 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 643561000222 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 643561000223 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561000224 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 643561000225 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 643561000226 carboxyltransferase (CT) interaction site; other site 643561000227 biotinylation site [posttranslational modification]; other site 643561000228 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 643561000229 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561000230 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561000231 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 643561000232 TIGR03084 family protein; Region: TIGR03084 643561000233 DinB superfamily; Region: DinB_2; cl00986 643561000234 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561000235 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 643561000236 GtrA-like protein; Region: GtrA; cl00971 643561000237 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000238 hypothetical protein; Provisional; Region: PRK07233 643561000239 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000240 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000241 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 643561000242 NAD(P) binding site [chemical binding]; other site 643561000243 active site 643561000244 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 643561000245 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000246 FAD binding domain; Region: FAD_binding_4; pfam01565 643561000247 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 643561000248 hypothetical protein; Validated; Region: PRK08238 643561000249 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 643561000250 UbiA prenyltransferase family; Region: UbiA; cl00337 643561000251 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 643561000252 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 643561000253 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 643561000254 substrate binding pocket [chemical binding]; other site 643561000255 catalytic triad [active] 643561000256 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 643561000257 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 643561000258 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a...; Region: CbiX_SirB_N; cd03416 643561000259 putative active site [active] 643561000260 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a...; Region: CbiX_SirB_C; cd03414 643561000261 putative active site [active] 643561000262 Precorrin isomerase [Coenzyme metabolism]; Region: CobH; cl00913 643561000263 Precorrin-8X methylmutase; Region: CbiC; pfam02570 643561000264 CbiD; Region: CbiD; cl00828 643561000265 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 643561000266 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 643561000267 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 643561000268 S-adenosylmethionine binding site [chemical binding]; other site 643561000269 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 643561000270 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 643561000271 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 643561000272 Cobalamin synthesis G C-terminus; Region: CbiG_C; cl12133 643561000273 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 643561000274 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 643561000275 dimer interface [polypeptide binding]; other site 643561000276 [2Fe-2S] cluster binding site [ion binding]; other site 643561000277 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 643561000278 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561000279 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000280 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 643561000281 dimerization interface [polypeptide binding]; other site 643561000282 substrate binding pocket [chemical binding]; other site 643561000283 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 643561000284 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 643561000285 Flavin Reductases; Region: FlaRed; cl00801 643561000286 Cupin domain; Region: Cupin_2; cl09118 643561000287 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561000288 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 643561000289 putative substrate translocation pore; other site 643561000290 Yersinia/Haemophilus virulence surface antigen; Region: Peptidase_C58; cl04145 643561000291 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 643561000292 hns-dependent expression protein A (HdeA); Region: HdeA; cl05752 643561000293 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 643561000294 Protein of unknown function (DUF1010); Region: DUF1010; pfam06231 643561000295 YCII-related domain; Region: YCII; cl00999 643561000296 D-lactate dehydrogenase [cytochrome]; Region: PLN02805 643561000297 FAD binding domain; Region: FAD_binding_4; pfam01565 643561000298 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 643561000299 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 643561000300 active site 643561000301 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561000302 active site 643561000303 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 643561000304 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 643561000305 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 643561000306 CoenzymeA binding site [chemical binding]; other site 643561000307 subunit interaction site [polypeptide binding]; other site 643561000308 PHB binding site; other site 643561000309 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 643561000310 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 643561000311 Sulfate transporter family; Region: Sulfate_transp; cl00967 643561000312 Permease family; Region: Xan_ur_permease; pfam00860 643561000313 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561000314 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 643561000315 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561000316 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 643561000317 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 643561000318 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 643561000319 GAF domain; Region: GAF; cl00853 643561000320 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561000321 metal binding site [ion binding]; metal-binding site 643561000322 active site 643561000323 I-site; other site 643561000324 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 643561000325 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 643561000326 trimer interface [polypeptide binding]; other site 643561000327 putative metal binding site [ion binding]; other site 643561000328 Uncharacterized conserved protein [Function unknown]; Region: COG3603 643561000329 LysE type translocator; Region: LysE; cl00565 643561000330 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 643561000331 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000332 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 643561000333 putative dimerization interface [polypeptide binding]; other site 643561000334 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561000335 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561000336 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561000337 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 643561000338 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 643561000339 Walker A/P-loop; other site 643561000340 ATP binding site [chemical binding]; other site 643561000341 Q-loop/lid; other site 643561000342 ABC transporter signature motif; other site 643561000343 Walker B; other site 643561000344 D-loop; other site 643561000345 H-loop/switch region; other site 643561000346 Uncharacterized conserved protein [Function unknown]; Region: COG4754 643561000347 ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit; Region: ABC_transp; pfam09821 643561000348 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 643561000349 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 643561000350 dimer interface [polypeptide binding]; other site 643561000351 conserved gate region; other site 643561000352 putative PBP binding loops; other site 643561000353 ABC-ATPase subunit interface; other site 643561000354 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 643561000355 hypothetical protein; Provisional; Region: PRK09126 643561000356 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000357 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561000358 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000359 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 643561000360 dimerization interface [polypeptide binding]; other site 643561000361 substrate binding pocket [chemical binding]; other site 643561000362 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 643561000363 dimer interface [polypeptide binding]; other site 643561000364 NADP binding site [chemical binding]; other site 643561000365 catalytic residues [active] 643561000366 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561000367 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000368 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561000369 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 643561000370 Peptidase family M48; Region: Peptidase_M48; cl12018 643561000371 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 643561000372 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 643561000373 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561000374 Arginase family; Region: Arginase; cl00306 643561000375 ornithine cyclodeaminase; Validated; Region: PRK07589 643561000376 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000377 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561000378 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000379 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 643561000380 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 643561000381 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 643561000382 cell division inhibitor MinD; Provisional; Region: PRK10818 643561000383 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 643561000384 Switch I; other site 643561000385 Switch II; other site 643561000386 Septum formation topological specificity factor MinE; Region: MinE; cl00538 643561000387 Flavin Reductases; Region: FlaRed; cl00801 643561000388 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561000389 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 643561000390 Peptidase M14-like domain of Escherichia coli Murein Peptide Amidase A (MpaA) and related proteins. MpaA is a member of the M14 family of metallocarboxypeptidases (MCPs), however it has an exceptional type of activity, it hydrolyzes the gamma-D-...; Region: M14_MpaA_like; cd06904 643561000391 putative active site [active] 643561000392 Zn-binding site [ion binding]; other site 643561000393 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561000394 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561000395 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 643561000396 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 643561000397 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000398 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 643561000399 dimerization interface [polypeptide binding]; other site 643561000400 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561000401 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 643561000402 oligomeric interface; other site 643561000403 putative active site [active] 643561000404 homodimer interface [polypeptide binding]; other site 643561000405 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 643561000406 Ligand Binding Site [chemical binding]; other site 643561000407 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 643561000408 active site 643561000409 metal binding site [ion binding]; metal-binding site 643561000410 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 643561000411 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000412 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 643561000413 substrate binding pocket [chemical binding]; other site 643561000414 dimerization interface [polypeptide binding]; other site 643561000415 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_GTP; cd00819 643561000416 Phosphoenolpyruvate carboxykinase; Region: PEPCK; pfam00821 643561000417 active site 643561000418 substrate-binding site [chemical binding]; other site 643561000419 metal-binding site [ion binding] 643561000420 GTP binding site [chemical binding]; other site 643561000421 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561000422 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000423 NAD(P) binding site [chemical binding]; other site 643561000424 active site 643561000425 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 643561000426 Ligand Binding Site [chemical binding]; other site 643561000427 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl01208 643561000428 threonine dehydratase; Provisional; Region: PRK07334 643561000429 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 643561000430 tetramer interface [polypeptide binding]; other site 643561000431 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561000432 catalytic residue [active] 643561000433 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 643561000434 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561000435 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561000436 active site 643561000437 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000438 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 643561000439 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 643561000440 dimerization interface [polypeptide binding]; other site 643561000441 gentisate 1,2-dioxygenase; Region: gentisate_1_2; TIGR02272 643561000442 Cupin domain; Region: Cupin_2; cl09118 643561000443 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561000444 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 643561000445 maleylacetoacetate isomerase; Region: maiA; TIGR01262 643561000446 C-terminal domain interface [polypeptide binding]; other site 643561000447 GSH binding site (G-site) [chemical binding]; other site 643561000448 putative dimer interface [polypeptide binding]; other site 643561000449 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 643561000450 N-terminal domain interface [polypeptide binding]; other site 643561000451 dimer interface [polypeptide binding]; other site 643561000452 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 643561000453 benzoate transport; Region: 2A0115; TIGR00895 643561000454 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 643561000455 putative substrate translocation pore; other site 643561000456 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 643561000457 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561000458 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 643561000459 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000460 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 643561000461 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants...; Region: Thr-synth_1; cd01563 643561000462 homodimer interface [polypeptide binding]; other site 643561000463 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561000464 catalytic residue [active] 643561000465 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 643561000466 YheO-like PAS domain; Region: PAS_6; pfam08348 643561000467 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000468 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 643561000469 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561000470 Surface antigen; Region: Surface_Ag_2; cl01155 643561000471 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561000472 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000473 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 643561000474 substrate binding pocket [chemical binding]; other site 643561000475 dimerization interface [polypeptide binding]; other site 643561000476 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 643561000477 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 643561000478 catalytic loop [active] 643561000479 iron binding site [ion binding]; other site 643561000480 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S]...; Region: O2ase_reductase_like; cd06187 643561000481 FAD binding pocket [chemical binding]; other site 643561000482 FAD binding motif [chemical binding]; other site 643561000483 phosphate binding motif [ion binding]; other site 643561000484 beta-alpha-beta structure motif; other site 643561000485 NAD binding pocket [chemical binding]; other site 643561000486 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 643561000487 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1)...; Region: Rieske; cl00938 643561000488 iron-sulfur cluster [ion binding]; other site 643561000489 [2Fe-2S] cluster binding site [ion binding]; other site 643561000490 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 643561000491 putative alpha subunit interface [polypeptide binding]; other site 643561000492 putative active site [active] 643561000493 putative substrate binding site [chemical binding]; other site 643561000494 Fe binding site [ion binding]; other site 643561000495 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 643561000496 inter-subunit interface; other site 643561000497 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise...; Region: Rieske_RO_ferredoxin; cd03528 643561000498 [2Fe-2S] cluster binding site [ion binding]; other site 643561000499 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561000500 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 643561000501 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 643561000502 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 643561000503 Major Facilitator Superfamily; Region: MFS_1; pfam07690 643561000504 putative substrate translocation pore; other site 643561000505 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 643561000506 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561000507 active site 643561000508 phosphorylation site [posttranslational modification] 643561000509 intermolecular recognition site; other site 643561000510 dimerization interface [polypeptide binding]; other site 643561000511 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 643561000512 Walker A motif; other site 643561000513 ATP binding site [chemical binding]; other site 643561000514 Walker B motif; other site 643561000515 arginine finger; other site 643561000516 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561000517 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 643561000518 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 643561000519 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 643561000520 ATP binding site [chemical binding]; other site 643561000521 Mg2+ binding site [ion binding]; other site 643561000522 G-X-G motif; other site 643561000523 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 643561000524 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 643561000525 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 643561000526 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000527 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like_2; cd08448 643561000528 putative dimerization interface [polypeptide binding]; other site 643561000529 putative substrate binding pocket [chemical binding]; other site 643561000530 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561000531 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561000532 active site 643561000533 Cupin domain; Region: Cupin_2; cl09118 643561000534 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561000535 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561000536 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561000537 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 643561000538 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 643561000539 ATP binding site [chemical binding]; other site 643561000540 putative Mg++ binding site [ion binding]; other site 643561000541 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 643561000542 nucleotide binding region [chemical binding]; other site 643561000543 ATP-binding site [chemical binding]; other site 643561000544 RQC domain; Region: RQC; cl09632 643561000545 HRDC domain; Region: HRDC; cl02578 643561000546 Beta-lactamase; Region: Beta-lactamase; cl01009 643561000547 Beta-lactamase; Region: Beta-lactamase; cl01009 643561000548 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 643561000549 DEAD_2; Region: DEAD_2; cl14887 643561000550 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561000551 Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; Region: Adenylation_DNA_ligase_like; cl12015 643561000552 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 643561000553 Zn2+ binding site [ion binding]; other site 643561000554 Mg2+ binding site [ion binding]; other site 643561000555 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561000556 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561000557 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561000558 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 643561000559 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 643561000560 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 643561000561 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 643561000562 NAD(P) binding site [chemical binding]; other site 643561000563 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 643561000564 amidase; Provisional; Region: PRK07869 643561000565 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 643561000566 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561000567 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 643561000568 N-terminal plug; other site 643561000569 ligand-binding site [chemical binding]; other site 643561000570 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561000571 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000572 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 643561000573 dimerization interface [polypeptide binding]; other site 643561000574 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 643561000575 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 643561000576 Response regulator receiver domain; Region: Response_reg; pfam00072 643561000577 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561000578 active site 643561000579 phosphorylation site [posttranslational modification] 643561000580 intermolecular recognition site; other site 643561000581 dimerization interface [polypeptide binding]; other site 643561000582 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 643561000583 DNA binding residues [nucleotide binding] 643561000584 dimerization interface [polypeptide binding]; other site 643561000585 Sodium:solute symporter family; Region: SSF; cl00456 643561000586 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 643561000587 dimer interface [polypeptide binding]; other site 643561000588 phosphorylation site [posttranslational modification] 643561000589 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 643561000590 ATP binding site [chemical binding]; other site 643561000591 Mg2+ binding site [ion binding]; other site 643561000592 G-X-G motif; other site 643561000593 Response regulator receiver domain; Region: Response_reg; pfam00072 643561000594 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561000595 active site 643561000596 phosphorylation site [posttranslational modification] 643561000597 intermolecular recognition site; other site 643561000598 dimerization interface [polypeptide binding]; other site 643561000599 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561000600 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 643561000601 putative ligand binding site [chemical binding]; other site 643561000602 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561000603 TM-ABC transporter signature motif; other site 643561000604 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561000605 TM-ABC transporter signature motif; other site 643561000606 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 643561000607 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561000608 Walker A/P-loop; other site 643561000609 ATP binding site [chemical binding]; other site 643561000610 Q-loop/lid; other site 643561000611 ABC transporter signature motif; other site 643561000612 Walker B; other site 643561000613 D-loop; other site 643561000614 H-loop/switch region; other site 643561000615 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 643561000616 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561000617 Walker A/P-loop; other site 643561000618 ATP binding site [chemical binding]; other site 643561000619 Q-loop/lid; other site 643561000620 ABC transporter signature motif; other site 643561000621 Walker B; other site 643561000622 D-loop; other site 643561000623 H-loop/switch region; other site 643561000624 Acetamidase/Formamidase family; Region: FmdA_AmdA; cl01023 643561000625 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 643561000626 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 643561000627 Predicted amidohydrolase [General function prediction only]; Region: COG0388 643561000628 multimer interface [polypeptide binding]; other site 643561000629 active site 643561000630 catalytic triad [active] 643561000631 dimer interface [polypeptide binding]; other site 643561000632 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 643561000633 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000634 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 643561000635 dimerization interface [polypeptide binding]; other site 643561000636 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 643561000637 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-...; Region: MLE; cd03318 643561000638 octamer interface [polypeptide binding]; other site 643561000639 active site 643561000640 Papain-like cysteine protease AvrRpt2; Region: Peptidase_C70; pfam12385 643561000641 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 643561000642 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561000643 DNA-binding site [nucleotide binding]; DNA binding site 643561000644 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 643561000645 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561000646 homodimer interface [polypeptide binding]; other site 643561000647 catalytic residue [active] 643561000648 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_1; cd08460 643561000649 putative substrate binding pocket [chemical binding]; other site 643561000650 putative dimerization interface [polypeptide binding]; other site 643561000651 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 643561000652 Predicted NTPase (NACHT family) [Signal transduction mechanisms]; Region: COG5635 643561000653 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 643561000654 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561000655 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000656 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 643561000657 dimerization interface [polypeptide binding]; other site 643561000658 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561000659 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 643561000660 substrate binding pocket [chemical binding]; other site 643561000661 membrane-bound complex binding site; other site 643561000662 hinge residues; other site 643561000663 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 643561000664 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 643561000665 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 643561000666 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 643561000667 Ureidoglycolate hydrolase; Region: Ureidogly_hydro; cl01250 643561000668 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 643561000669 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 643561000670 Walker A/P-loop; other site 643561000671 ATP binding site [chemical binding]; other site 643561000672 Q-loop/lid; other site 643561000673 ABC transporter signature motif; other site 643561000674 Walker B; other site 643561000675 D-loop; other site 643561000676 H-loop/switch region; other site 643561000677 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 643561000678 dimer interface [polypeptide binding]; other site 643561000679 conserved gate region; other site 643561000680 putative PBP binding loops; other site 643561000681 ABC-ATPase subunit interface; other site 643561000682 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 643561000683 dimer interface [polypeptide binding]; other site 643561000684 conserved gate region; other site 643561000685 putative PBP binding loops; other site 643561000686 ABC-ATPase subunit interface; other site 643561000687 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 643561000688 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 643561000689 substrate binding pocket [chemical binding]; other site 643561000690 membrane-bound complex binding site; other site 643561000691 hinge residues; other site 643561000692 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561000693 DNA-binding site [nucleotide binding]; DNA binding site 643561000694 FCD domain; Region: FCD; cl11656 643561000695 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 643561000696 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 643561000697 substrate binding pocket [chemical binding]; other site 643561000698 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 643561000699 B12 binding site [chemical binding]; other site 643561000700 cobalt ligand [ion binding]; other site 643561000701 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 643561000702 CRISPR-associated protein Cas9/Csn1, subtype II/NMEMI; Region: cas_Csn1; TIGR01865 643561000703 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 643561000704 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 643561000705 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cl11442 643561000706 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561000707 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561000708 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561000709 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561000710 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561000711 Pseudomonas-type; Region: PC_PLC; TIGR03396 643561000712 Sulfatase; Region: Sulfatase; cl10460 643561000713 Domain of unknown function (DUF756); Region: DUF756; pfam05506 643561000714 Domain of unknown function (DUF756); Region: DUF756; pfam05506 643561000715 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561000716 metal binding site [ion binding]; metal-binding site 643561000717 active site 643561000718 I-site; other site 643561000719 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 643561000720 Protein of unknown function DUF72; Region: DUF72; cl00777 643561000721 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 643561000722 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 643561000723 FAD binding pocket [chemical binding]; other site 643561000724 FAD binding motif [chemical binding]; other site 643561000725 phosphate binding motif [ion binding]; other site 643561000726 beta-alpha-beta structure motif; other site 643561000727 NAD binding pocket [chemical binding]; other site 643561000728 transcriptional regulator; Provisional; Region: PRK10632 643561000729 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000730 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 643561000731 putative effector binding pocket; other site 643561000732 putative dimerization interface [polypeptide binding]; other site 643561000733 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 643561000734 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000735 NAD(P) binding site [chemical binding]; other site 643561000736 active site 643561000737 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 643561000738 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561000739 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561000740 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 643561000741 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561000742 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 643561000743 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561000744 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561000745 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 643561000746 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 643561000747 dimer interface [polypeptide binding]; other site 643561000748 phosphorylation site [posttranslational modification] 643561000749 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 643561000750 ATP binding site [chemical binding]; other site 643561000751 Mg2+ binding site [ion binding]; other site 643561000752 G-X-G motif; other site 643561000753 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 643561000754 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561000755 active site 643561000756 phosphorylation site [posttranslational modification] 643561000757 intermolecular recognition site; other site 643561000758 dimerization interface [polypeptide binding]; other site 643561000759 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 643561000760 Walker A motif; other site 643561000761 ATP binding site [chemical binding]; other site 643561000762 Walker B motif; other site 643561000763 arginine finger; other site 643561000764 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561000765 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 643561000766 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561000767 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 643561000768 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 643561000769 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 643561000770 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 643561000771 Uncharacterized conserved protein [Function unknown]; Region: COG4104 643561000772 PAAR motif; Region: PAAR_motif; pfam05488 643561000773 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 643561000774 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 643561000775 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 643561000776 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 643561000777 FAD binding domain; Region: FAD_binding_4; pfam01565 643561000778 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 643561000779 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 643561000780 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 643561000781 Cysteine-rich domain; Region: CCG; pfam02754 643561000782 Cysteine-rich domain; Region: CCG; pfam02754 643561000783 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 643561000784 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue...; Region: GSH_Peroxidase; cd00340 643561000785 catalytic residues [active] 643561000786 dimer interface [polypeptide binding]; other site 643561000787 lysophospholipid transporter LplT; Provisional; Region: PRK11195 643561000788 alanine racemase; Reviewed; Region: dadX; PRK03646 643561000789 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 643561000790 active site 643561000791 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 643561000792 substrate binding site [chemical binding]; other site 643561000793 catalytic residues [active] 643561000794 dimer interface [polypeptide binding]; other site 643561000795 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 643561000796 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 643561000797 fumarylacetoacetase; Region: fum_ac_acetase; TIGR01266 643561000798 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 643561000799 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561000800 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561000801 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561000802 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000803 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561000804 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_N_Beta; cd03057 643561000805 C-terminal domain interface [polypeptide binding]; other site 643561000806 GSH binding site (G-site) [chemical binding]; other site 643561000807 dimer interface [polypeptide binding]; other site 643561000808 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 643561000809 N-terminal domain interface [polypeptide binding]; other site 643561000810 dimer interface [polypeptide binding]; other site 643561000811 substrate binding pocket (H-site) [chemical binding]; other site 643561000812 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 643561000813 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000814 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 643561000815 DNA repair protein RadA; Provisional; Region: PRK11823 643561000816 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 643561000817 Walker A motif/ATP binding site; other site 643561000818 ATP binding site [chemical binding]; other site 643561000819 Walker B motif; other site 643561000820 branched-chain amino acid aminotransferase; Provisional; Region: PRK12479 643561000821 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 643561000822 homodimer interface [polypeptide binding]; other site 643561000823 substrate-cofactor binding pocket; other site 643561000824 catalytic residue [active] 643561000825 Zinc-finger domain; Region: zf-CHCC; cl01821 643561000826 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 643561000827 O-Antigen ligase; Region: Wzy_C; cl04850 643561000828 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 643561000829 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 643561000830 active site 643561000831 Mannosyltransferase OCH1 and related enzymes [Cell envelope biogenesis, outer membrane]; Region: OCH1; COG3774 643561000832 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 643561000833 Nitronate monooxygenase; Region: NMO; pfam03060 643561000834 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin...; Region: NPD_like; cd04730 643561000835 FMN binding site [chemical binding]; other site 643561000836 substrate binding site [chemical binding]; other site 643561000837 putative catalytic residue [active] 643561000838 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561000839 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000840 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 643561000841 dimerization interface [polypeptide binding]; other site 643561000842 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 643561000843 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 643561000844 dimerization interface [polypeptide binding]; other site 643561000845 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 643561000846 dimer interface [polypeptide binding]; other site 643561000847 phosphorylation site [posttranslational modification] 643561000848 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 643561000849 ATP binding site [chemical binding]; other site 643561000850 G-X-G motif; other site 643561000851 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561000852 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561000853 active site 643561000854 phosphorylation site [posttranslational modification] 643561000855 intermolecular recognition site; other site 643561000856 dimerization interface [polypeptide binding]; other site 643561000857 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 643561000858 DNA binding site [nucleotide binding] 643561000859 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 643561000860 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561000861 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 643561000862 EamA-like transporter family; Region: EamA; cl01037 643561000863 Peptidase family M48; Region: Peptidase_M48; cl12018 643561000864 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 643561000865 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 643561000866 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561000867 hypothetical protein; Provisional; Region: PRK07338 643561000868 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 643561000869 metal binding site [ion binding]; metal-binding site 643561000870 dimer interface [polypeptide binding]; other site 643561000871 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561000872 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 643561000873 C-term; Region: GreA_GreB; pfam01272 643561000874 GAF domain; Region: GAF; cl00853 643561000875 transcriptional regulator; Provisional; Region: PRK10632 643561000876 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000877 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 643561000878 dimerization interface [polypeptide binding]; other site 643561000879 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 643561000880 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 643561000881 putative substrate translocation pore; other site 643561000882 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 643561000883 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 643561000884 active site 643561000885 catalytic tetrad [active] 643561000886 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 643561000887 putative active site [active] 643561000888 putative DNA binding site [nucleotide binding]; other site 643561000889 putative phosphate binding site [ion binding]; other site 643561000890 putative catalytic site [active] 643561000891 metal binding site A [ion binding]; metal-binding site 643561000892 putative AP binding site [nucleotide binding]; other site 643561000893 putative metal binding site B [ion binding]; other site 643561000894 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 643561000895 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 643561000896 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 643561000897 GatB domain; Region: GatB_Yqey; cl11497 643561000898 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 643561000899 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 643561000900 P-loop; other site 643561000901 Magnesium ion binding site [ion binding]; other site 643561000902 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 643561000903 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 643561000904 Divergent AAA domain; Region: AAA_4; pfam04326 643561000905 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 643561000906 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 643561000907 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 643561000908 rod shape-determining protein MreB; Provisional; Region: PRK13927 643561000909 Cell division protein FtsA; Region: FtsA; cl11496 643561000910 rod shape-determining protein MreC; Provisional; Region: PRK13922 643561000911 rod shape-determining protein MreC; Region: MreC; pfam04085 643561000912 rod shape-determining protein MreD; Region: MreD; cl01087 643561000913 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 643561000914 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 643561000915 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 643561000916 EamA-like transporter family; Region: EamA; cl01037 643561000917 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 643561000918 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 643561000919 Walker A/P-loop; other site 643561000920 ATP binding site [chemical binding]; other site 643561000921 Q-loop/lid; other site 643561000922 ABC transporter signature motif; other site 643561000923 Walker B; other site 643561000924 D-loop; other site 643561000925 H-loop/switch region; other site 643561000926 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 643561000927 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 643561000928 dimer interface [polypeptide binding]; other site 643561000929 conserved gate region; other site 643561000930 putative PBP binding loops; other site 643561000931 ABC-ATPase subunit interface; other site 643561000932 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 643561000933 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 643561000934 substrate binding pocket [chemical binding]; other site 643561000935 membrane-bound complex binding site; other site 643561000936 hinge residues; other site 643561000937 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 643561000938 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 643561000939 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 643561000940 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561000941 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561000942 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_6; cd08423 643561000943 putative dimerization interface [polypeptide binding]; other site 643561000944 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 643561000945 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 643561000946 choline dehydrogenase; Validated; Region: PRK02106 643561000947 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561000948 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 643561000949 Domain of unknown function DUF140; Region: DUF140; cl00510 643561000950 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 643561000951 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 643561000952 Walker A/P-loop; other site 643561000953 ATP binding site [chemical binding]; other site 643561000954 Q-loop/lid; other site 643561000955 ABC transporter signature motif; other site 643561000956 Walker B; other site 643561000957 D-loop; other site 643561000958 H-loop/switch region; other site 643561000959 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 643561000960 mce related protein; Region: MCE; pfam02470 643561000961 Protein of unknown function (DUF330); Region: DUF330; cl01135 643561000962 Quinolinate synthetase A protein; Region: NadA; cl00420 643561000963 Secretin and TonB N terminus short domain; Region: STN; cl06624 643561000964 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 643561000965 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 643561000966 N-terminal plug; other site 643561000967 ligand-binding site [chemical binding]; other site 643561000968 FecR protein; Region: FecR; pfam04773 643561000969 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 643561000970 RNA polymerase sigma factor; Reviewed; Region: PRK12527 643561000971 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 643561000972 DNA binding residues [nucleotide binding] 643561000973 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 643561000974 Active Sites [active] 643561000975 CsbD-like; Region: CsbD; cl01272 643561000976 cation-binding hemerythrin HHE family protein; Provisional; Region: PRK01917 643561000977 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 643561000978 octamerization interface [polypeptide binding]; other site 643561000979 diferric-oxygen binding site [ion binding]; other site 643561000980 Inner membrane protein CreD; Region: CreD; cl01844 643561000981 sensory histidine kinase CreC; Provisional; Region: PRK11100 643561000982 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 643561000983 dimer interface [polypeptide binding]; other site 643561000984 phosphorylation site [posttranslational modification] 643561000985 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 643561000986 ATP binding site [chemical binding]; other site 643561000987 Mg2+ binding site [ion binding]; other site 643561000988 G-X-G motif; other site 643561000989 DNA-binding response regulator CreB; Provisional; Region: PRK11083 643561000990 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561000991 active site 643561000992 phosphorylation site [posttranslational modification] 643561000993 intermolecular recognition site; other site 643561000994 dimerization interface [polypeptide binding]; other site 643561000995 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 643561000996 DNA binding site [nucleotide binding] 643561000997 MarC family integral membrane protein; Region: MarC; cl00919 643561000998 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561000999 classical (c) SDRs; Region: SDR_c; cd05233 643561001000 NAD(P) binding site [chemical binding]; other site 643561001001 active site 643561001002 Dienelactone hydrolase family; Region: DLH; pfam01738 643561001003 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 643561001004 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 643561001005 putative substrate translocation pore; other site 643561001006 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 643561001007 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 643561001008 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 643561001009 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 643561001010 Outer membrane efflux protein; Region: OEP; pfam02321 643561001011 Outer membrane efflux protein; Region: OEP; pfam02321 643561001012 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001013 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 643561001014 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 643561001015 catalytic triad [active] 643561001016 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 643561001017 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 643561001018 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 643561001019 dimer interface [polypeptide binding]; other site 643561001020 allosteric magnesium binding site [ion binding]; other site 643561001021 active site 643561001022 aspartate-rich active site metal binding site; other site 643561001023 Schiff base residues; other site 643561001024 Uncharacterised protein family (UPF0093); Region: UPF0093; cl00863 643561001025 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 643561001026 dimer interface [polypeptide binding]; other site 643561001027 [2Fe-2S] cluster binding site [ion binding]; other site 643561001028 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 643561001029 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 643561001030 Beta-lactamase; Region: Beta-lactamase; cl01009 643561001031 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 643561001032 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 643561001033 S17 interaction site [polypeptide binding]; other site 643561001034 S8 interaction site; other site 643561001035 16S rRNA interaction site [nucleotide binding]; other site 643561001036 streptomycin interaction site [chemical binding]; other site 643561001037 23S rRNA interaction site [nucleotide binding]; other site 643561001038 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 643561001039 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 643561001040 elongation factor G; Reviewed; Region: PRK00007 643561001041 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 643561001042 G1 box; other site 643561001043 putative GEF interaction site [polypeptide binding]; other site 643561001044 GTP/Mg2+ binding site [chemical binding]; other site 643561001045 Switch I region; other site 643561001046 G2 box; other site 643561001047 G3 box; other site 643561001048 Switch II region; other site 643561001049 G4 box; other site 643561001050 G5 box; other site 643561001051 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 643561001052 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 643561001053 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 643561001054 elongation factor Tu; Reviewed; Region: PRK00049 643561001055 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 643561001056 G1 box; other site 643561001057 GEF interaction site [polypeptide binding]; other site 643561001058 GTP/Mg2+ binding site [chemical binding]; other site 643561001059 Switch I region; other site 643561001060 G2 box; other site 643561001061 G3 box; other site 643561001062 Switch II region; other site 643561001063 G4 box; other site 643561001064 G5 box; other site 643561001065 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 643561001066 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 643561001067 Antibiotic Binding Site [chemical binding]; other site 643561001068 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 643561001069 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 643561001070 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 643561001071 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 643561001072 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 643561001073 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 643561001074 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 643561001075 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 643561001076 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 643561001077 putative translocon binding site; other site 643561001078 protein-rRNA interface [nucleotide binding]; other site 643561001079 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 643561001080 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 643561001081 G-X-X-G motif; other site 643561001082 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 643561001083 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 643561001084 23S rRNA interface [nucleotide binding]; other site 643561001085 5S rRNA interface [nucleotide binding]; other site 643561001086 putative antibiotic binding site [chemical binding]; other site 643561001087 L25 interface [polypeptide binding]; other site 643561001088 L27 interface [polypeptide binding]; other site 643561001089 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; cl09943 643561001090 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 643561001091 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 643561001092 catalytic triad [active] 643561001093 dimer interface [polypeptide binding]; other site 643561001094 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 643561001095 Coenzyme A binding pocket [chemical binding]; other site 643561001096 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing...; Region: TlpA_like_family; cd02966 643561001097 catalytic residues [active] 643561001098 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_man; cl00025 643561001099 active pocket/dimerization site; other site 643561001100 active site 643561001101 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 643561001102 dimerization domain swap beta strand [polypeptide binding]; other site 643561001103 regulatory protein interface [polypeptide binding]; other site 643561001104 active site 643561001105 regulatory phosphorylation site [posttranslational modification]; other site 643561001106 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 643561001107 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 643561001108 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 643561001109 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 643561001110 K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]; Region: KdpA; cl00903 643561001111 Potassium-transporting ATPase A subunit; Region: KdpA; pfam03814 643561001112 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 643561001113 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 643561001114 K+-transporting ATPase, c chain; Region: KdpC; cl00944 643561001115 sensor protein KdpD; Provisional; Region: PRK10490 643561001116 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 643561001117 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 643561001118 Ligand Binding Site [chemical binding]; other site 643561001119 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 643561001120 dimer interface [polypeptide binding]; other site 643561001121 phosphorylation site [posttranslational modification] 643561001122 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 643561001123 ATP binding site [chemical binding]; other site 643561001124 Mg2+ binding site [ion binding]; other site 643561001125 G-X-G motif; other site 643561001126 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 643561001127 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561001128 active site 643561001129 phosphorylation site [posttranslational modification] 643561001130 intermolecular recognition site; other site 643561001131 dimerization interface [polypeptide binding]; other site 643561001132 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 643561001133 DNA binding site [nucleotide binding] 643561001134 lipoyl synthase; Provisional; Region: PRK05481 643561001135 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 643561001136 FeS/SAM binding site; other site 643561001137 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 643561001138 Protein of unknown function (DUF493); Region: DUF493; cl01102 643561001139 ATP synthase A chain; Region: ATP-synt_A; cl00413 643561001140 ATP synthase subunit C; Region: ATP-synt_C; cl00466 643561001141 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 643561001142 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 643561001143 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 643561001144 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 643561001145 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 643561001146 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 643561001147 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 643561001148 beta subunit interaction interface [polypeptide binding]; other site 643561001149 Walker A motif; other site 643561001150 ATP binding site [chemical binding]; other site 643561001151 Walker B motif; other site 643561001152 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 643561001153 ATP synthase; Region: ATP-synt; cl00365 643561001154 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 643561001155 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 643561001156 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 643561001157 alpha subunit interaction interface [polypeptide binding]; other site 643561001158 Walker A motif; other site 643561001159 ATP binding site [chemical binding]; other site 643561001160 Walker B motif; other site 643561001161 inhibitor binding site; inhibition site 643561001162 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 643561001163 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 643561001164 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 643561001165 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 643561001166 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561001167 ATP-dependent DNA ligase; Validated; Region: PRK09247 643561001168 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 643561001169 active site 643561001170 DNA binding site [nucleotide binding] 643561001171 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 643561001172 DNA binding site [nucleotide binding] 643561001173 Lhr-like helicases [General function prediction only]; Region: Lhr; COG1201 643561001174 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561001175 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561001176 DEAD/H associated; Region: DEAD_assoc; pfam08494 643561001177 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 643561001178 putative active site [active] 643561001179 putative metal binding site [ion binding]; other site 643561001180 E3 ubiquitin-protein ligase SlrP; Provisional; Region: PRK15370 643561001181 Domain of unknown function (DUF477); Region: DUF477; cl01535 643561001182 Domain of unknown function (DUF477); Region: DUF477; cl01535 643561001183 LemA family; Region: LemA; cl00742 643561001184 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 643561001185 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 643561001186 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 643561001187 Cytochrome c; Region: Cytochrom_C; cl11414 643561001188 Cytochrome c; Region: Cytochrom_C; cl11414 643561001189 N-acetylneuraminic acid mutarotase; Provisional; Region: PRK14131 643561001190 Kelch motif; Region: Kelch_1; cl02701 643561001191 NodT family; Region: outer_NodT; TIGR01845 643561001192 Outer membrane efflux protein; Region: OEP; pfam02321 643561001193 Outer membrane efflux protein; Region: OEP; pfam02321 643561001194 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 643561001195 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 643561001196 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 643561001197 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561001198 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 643561001199 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 643561001200 putative active site [active] 643561001201 putative dimer interface [polypeptide binding]; other site 643561001202 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 643561001203 putative substrate translocation pore; other site 643561001204 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 643561001205 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 643561001206 active site 1 [active] 643561001207 dimer interface [polypeptide binding]; other site 643561001208 hexamer interface [polypeptide binding]; other site 643561001209 active site 2 [active] 643561001210 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561001211 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 643561001212 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 643561001213 dimerization interface [polypeptide binding]; other site 643561001214 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 643561001215 Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate...; Region: malate_synt_G; cd00728 643561001216 active site 643561001217 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001218 transcriptional activator TtdR; Provisional; Region: PRK09801 643561001219 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 643561001220 putative effector binding pocket; other site 643561001221 dimerization interface [polypeptide binding]; other site 643561001222 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 643561001223 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 643561001224 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 643561001225 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 643561001226 active site 643561001227 Trp docking motif; other site 643561001228 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 643561001229 Trp docking motif; other site 643561001230 active site 643561001231 'Velcro' closure; other site 643561001232 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 643561001233 psiF repeat; Region: PsiF_repeat; pfam07769 643561001234 psiF repeat; Region: PsiF_repeat; pfam07769 643561001235 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 643561001236 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 643561001237 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 643561001238 active site 643561001239 HIGH motif; other site 643561001240 nucleotide binding site [chemical binding]; other site 643561001241 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 643561001242 KMSK motif region; other site 643561001243 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 643561001244 tRNA binding surface [nucleotide binding]; other site 643561001245 anticodon binding site; other site 643561001246 Sporulation related domain; Region: SPOR; cl10051 643561001247 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 643561001248 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 643561001249 catalytic residues [active] 643561001250 hinge region; other site 643561001251 alpha helical domain; other site 643561001252 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 643561001253 OstA-like protein; Region: OstA; cl00844 643561001254 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 643561001255 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 643561001256 Walker A/P-loop; other site 643561001257 ATP binding site [chemical binding]; other site 643561001258 Q-loop/lid; other site 643561001259 ABC transporter signature motif; other site 643561001260 Walker B; other site 643561001261 D-loop; other site 643561001262 H-loop/switch region; other site 643561001263 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 643561001264 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 643561001265 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 643561001266 TspO/MBR family; Region: TspO_MBR; cl01379 643561001267 Cache domain; Region: Cache_1; pfam02743 643561001268 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 643561001269 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 643561001270 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 643561001271 Cache domain; Region: Cache_1; pfam02743 643561001272 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 643561001273 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 643561001274 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 643561001275 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 643561001276 THUMP domain; Region: THUMP; cl12076 643561001277 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 643561001278 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 643561001279 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561001280 heme ABC exporter, ATP-binding protein CcmA; Region: ccmA; TIGR01189 643561001281 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 643561001282 Uncharacterised protein family (UPF0149); Region: UPF0149; cl01173 643561001283 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 643561001284 Sulfate transporter family; Region: Sulfate_transp; cl00967 643561001285 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 643561001286 CHASE3 domain; Region: CHASE3; cl05000 643561001287 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561001288 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 643561001289 Competence-damaged protein; Region: CinA; cl00666 643561001290 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 643561001291 tetramer interfaces [polypeptide binding]; other site 643561001292 binuclear metal-binding site [ion binding]; other site 643561001293 conserved hypothetical protein; Region: TIGR02231 643561001294 thiamine monophosphate kinase; Provisional; Region: PRK05731 643561001295 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 643561001296 ATP binding site [chemical binding]; other site 643561001297 dimerization interface [polypeptide binding]; other site 643561001298 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561001299 ligand binding site [chemical binding]; other site 643561001300 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561001301 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561001302 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 643561001303 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 643561001304 phosphate binding site [ion binding]; other site 643561001305 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001306 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 643561001307 dimerization interface [polypeptide binding]; other site 643561001308 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 643561001309 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 643561001310 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 643561001311 Site-specific recombinase; Region: SpecificRecomb; pfam10136 643561001312 Site-specific recombinase [DNA replication, recombination, and repair]; Region: COG4389 643561001313 Protein of unknown function (DUF525); Region: DUF525; cl01119 643561001314 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 643561001315 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 643561001316 substrate binding site [chemical binding]; other site 643561001317 hexamer interface [polypeptide binding]; other site 643561001318 metal binding site [ion binding]; metal-binding site 643561001319 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 643561001320 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 643561001321 motif II; other site 643561001322 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 643561001323 anthranilate synthase component I; Provisional; Region: PRK13565 643561001324 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 643561001325 chorismate binding enzyme; Region: Chorismate_bind; cl10555 643561001326 Chorismate mutase type II; Region: CM_2; cl00693 643561001327 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561001328 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561001329 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 643561001330 DNA binding site [nucleotide binding] 643561001331 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 643561001332 FliP family; Region: FliP; cl00593 643561001333 type III secretion system apparatus protein YscQ/HrcQ; Region: SpaO_YscQ; TIGR02551 643561001334 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 643561001335 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 643561001336 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 643561001337 FHIPEP family; Region: FHIPEP; pfam00771 643561001338 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 643561001339 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 643561001340 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 643561001341 Pectate lyase; Region: Pectate_lyase; pfam03211 643561001342 RIB43A; Region: RIB43A; pfam05914 643561001343 type III secretion system ATPase; Provisional; Region: PRK09099 643561001344 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 643561001345 Walker A motif/ATP binding site; other site 643561001346 Walker B motif; other site 643561001347 type III secretion system protein; Reviewed; Region: PRK06937 643561001348 Bacterial type III secretion protein (HrpB4); Region: HrpB4; cl09735 643561001349 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 643561001350 Bacterial type III secretion protein (HrpB2); Region: HrpB2; cl09721 643561001351 Bacterial type III secretion protein (HrpB1_HrpK); Region: HrpB1_HrpK; cl09830 643561001352 outer membrane secretin SsaC; Provisional; Region: PRK15346 643561001353 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 643561001354 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 643561001355 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 643561001356 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 643561001357 S-adenosylmethionine binding site [chemical binding]; other site 643561001358 Predicted methyltransferase regulatory domain; Region: MethyTransf_Reg; pfam10119 643561001359 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 643561001360 N-acetyl-D-glucosamine binding site [chemical binding]; other site 643561001361 catalytic residue [active] 643561001362 Bacterial type III secretion protein (HrpB1_HrpK); Region: HrpB1_HrpK; cl09830 643561001363 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 643561001364 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 643561001365 glutamine binding [chemical binding]; other site 643561001366 catalytic triad [active] 643561001367 DinB superfamily; Region: DinB_2; cl00986 643561001368 LysE type translocator; Region: LysE; cl00565 643561001369 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 643561001370 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 643561001371 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 643561001372 active site 643561001373 phosphate binding site [ion binding]; other site 643561001374 ribulose/triose binding site [chemical binding]; other site 643561001375 substrate (anthranilate) binding pocket [chemical binding]; other site 643561001376 product (indole) binding pocket [chemical binding]; other site 643561001377 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 643561001378 ligand binding site [chemical binding]; other site 643561001379 active site 643561001380 UGI interface [polypeptide binding]; other site 643561001381 catalytic site [active] 643561001382 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 643561001383 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 643561001384 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 643561001385 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 643561001386 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 643561001387 amidase catalytic site [active] 643561001388 Zn binding residues [ion binding]; other site 643561001389 substrate binding site [chemical binding]; other site 643561001390 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561001391 Cupin domain; Region: Cupin_2; cl09118 643561001392 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561001393 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561001394 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 643561001395 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 643561001396 Zn2+ binding site [ion binding]; other site 643561001397 Mg2+ binding site [ion binding]; other site 643561001398 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 643561001399 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 643561001400 generic binding surface II; other site 643561001401 ssDNA binding site; other site 643561001402 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 643561001403 ATP binding site [chemical binding]; other site 643561001404 putative Mg++ binding site [ion binding]; other site 643561001405 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 643561001406 nucleotide binding region [chemical binding]; other site 643561001407 ATP-binding site [chemical binding]; other site 643561001408 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 643561001409 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001410 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 643561001411 dimerization interface [polypeptide binding]; other site 643561001412 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 643561001413 dimerization interface [polypeptide binding]; other site 643561001414 DPS ferroxidase diiron center [ion binding]; other site 643561001415 ion pore; other site 643561001416 UbiA prenyltransferase family; Region: UbiA; cl00337 643561001417 YdjC-like protein; Region: YdjC; cl01344 643561001418 GtrA-like protein; Region: GtrA; cl00971 643561001419 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 643561001420 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 643561001421 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561001422 glycerol kinase; Provisional; Region: glpK; PRK00047 643561001423 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 643561001424 N- and C-terminal domain interface [polypeptide binding]; other site 643561001425 active site 643561001426 MgATP binding site [chemical binding]; other site 643561001427 catalytic site [active] 643561001428 metal binding site [ion binding]; metal-binding site 643561001429 glycerol binding site [chemical binding]; other site 643561001430 homotetramer interface [polypeptide binding]; other site 643561001431 homodimer interface [polypeptide binding]; other site 643561001432 FBP binding site [chemical binding]; other site 643561001433 protein IIAGlc interface [polypeptide binding]; other site 643561001434 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001435 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 643561001436 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 643561001437 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 643561001438 Walker A/P-loop; other site 643561001439 ATP binding site [chemical binding]; other site 643561001440 Q-loop/lid; other site 643561001441 ABC transporter signature motif; other site 643561001442 Walker B; other site 643561001443 D-loop; other site 643561001444 H-loop/switch region; other site 643561001445 TOBE domain; Region: TOBE_2; cl01440 643561001446 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 643561001447 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 643561001448 Walker A/P-loop; other site 643561001449 ATP binding site [chemical binding]; other site 643561001450 Q-loop/lid; other site 643561001451 ABC transporter signature motif; other site 643561001452 Walker B; other site 643561001453 D-loop; other site 643561001454 H-loop/switch region; other site 643561001455 TOBE domain; Region: TOBE_2; cl01440 643561001456 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 643561001457 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 643561001458 putative PBP binding loops; other site 643561001459 ABC-ATPase subunit interface; other site 643561001460 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 643561001461 dimer interface [polypeptide binding]; other site 643561001462 conserved gate region; other site 643561001463 putative PBP binding loops; other site 643561001464 ABC-ATPase subunit interface; other site 643561001465 Predicted small integral membrane protein (DUF2160); Region: DUF2160; cl02294 643561001466 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 643561001467 glycerol-3-phosphate dehydrogenase; Region: PLN02464 643561001468 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561001469 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 643561001470 KOW motif; Region: KOW; cl00354 643561001471 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 643561001472 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 643561001473 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 643561001474 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 643561001475 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 643561001476 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 643561001477 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 643561001478 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 643561001479 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 643561001480 5S rRNA interface [nucleotide binding]; other site 643561001481 23S rRNA interface [nucleotide binding]; other site 643561001482 L5 interface [polypeptide binding]; other site 643561001483 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 643561001484 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 643561001485 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 643561001486 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 643561001487 23S rRNA binding site [nucleotide binding]; other site 643561001488 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 643561001489 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 643561001490 SecY translocase; Region: SecY; pfam00344 643561001491 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 643561001492 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 643561001493 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 643561001494 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 643561001495 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 643561001496 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 643561001497 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 643561001498 RNA binding surface [nucleotide binding]; other site 643561001499 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 643561001500 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 643561001501 alphaNTD homodimer interface [polypeptide binding]; other site 643561001502 alphaNTD - beta interaction site [polypeptide binding]; other site 643561001503 alphaNTD - beta' interaction site [polypeptide binding]; other site 643561001504 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 643561001505 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 643561001506 putative chaperone; Provisional; Region: PRK11678 643561001507 Predicted methyltransferases [General function prediction only]; Region: COG0313 643561001508 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 643561001509 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 643561001510 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 643561001511 dimer interface [polypeptide binding]; other site 643561001512 active site 643561001513 BON domain; Region: BON; cl02771 643561001514 BON domain; Region: BON; cl02771 643561001515 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 643561001516 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561001517 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 643561001518 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 643561001519 Walker A motif; other site 643561001520 ATP binding site [chemical binding]; other site 643561001521 Walker B motif; other site 643561001522 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 643561001523 ligand binding site [chemical binding]; other site 643561001524 flexible hinge region; other site 643561001525 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 643561001526 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 643561001527 Walker A motif; other site 643561001528 ATP binding site [chemical binding]; other site 643561001529 Walker B motif; other site 643561001530 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 643561001531 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 643561001532 catalytic residue [active] 643561001533 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 643561001534 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 643561001535 tetramer interface [polypeptide binding]; other site 643561001536 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561001537 catalytic residue [active] 643561001538 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 643561001539 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561001540 catalytic residue [active] 643561001541 Protein of unknown function (DUF445); Region: DUF445; pfam04286 643561001542 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 643561001543 FAD binding domain; Region: FAD_binding_4; pfam01565 643561001544 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 643561001545 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561001546 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561001547 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001548 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 643561001549 dimerization interface [polypeptide binding]; other site 643561001550 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 643561001551 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 643561001552 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 643561001553 putative active site [active] 643561001554 putative substrate binding site [chemical binding]; other site 643561001555 putative cosubstrate binding site; other site 643561001556 catalytic site [active] 643561001557 PAS domain S-box; Region: sensory_box; TIGR00229 643561001558 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 643561001559 putative active site [active] 643561001560 heme pocket [chemical binding]; other site 643561001561 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561001562 metal binding site [ion binding]; metal-binding site 643561001563 active site 643561001564 I-site; other site 643561001565 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 643561001566 MgtC family; Region: MgtC; cl12207 643561001567 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 643561001568 Protein of unknown function, DUF399; Region: DUF399; cl01139 643561001569 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 643561001570 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 643561001571 dimerization interface [polypeptide binding]; other site 643561001572 GAF domain; Region: GAF; cl00853 643561001573 Histidine kinase; Region: HisKA_3; pfam07730 643561001574 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 643561001575 ATP binding site [chemical binding]; other site 643561001576 Mg2+ binding site [ion binding]; other site 643561001577 G-X-G motif; other site 643561001578 transcriptional regulator NarL; Provisional; Region: PRK10651 643561001579 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561001580 active site 643561001581 phosphorylation site [posttranslational modification] 643561001582 intermolecular recognition site; other site 643561001583 dimerization interface [polypeptide binding]; other site 643561001584 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 643561001585 DNA binding residues [nucleotide binding] 643561001586 dimerization interface [polypeptide binding]; other site 643561001587 XamI restriction endonuclease; Region: RE_XamI; pfam09572 643561001588 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 643561001589 S-adenosylmethionine binding site [chemical binding]; other site 643561001590 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 643561001591 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 643561001592 putative substrate translocation pore; other site 643561001593 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 643561001594 respiratory nitrate reductase, alpha subunit; Region: narG; TIGR01580 643561001595 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_Nitrate-R-NarG-like; cd02750 643561001596 [4Fe-4S] binding site [ion binding]; other site 643561001597 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 643561001598 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 643561001599 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 643561001600 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 643561001601 molybdopterin cofactor binding site; other site 643561001602 nitrate reductase, beta subunit; Region: narH; TIGR01660 643561001603 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 643561001604 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 643561001605 PPIC-type PPIASE domain; Region: Rotamase; cl08278 643561001606 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_cladeB; cd00884 643561001607 active site clefts [active] 643561001608 zinc binding site [ion binding]; other site 643561001609 dimer interface [polypeptide binding]; other site 643561001610 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 643561001611 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 643561001612 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cd00081 643561001613 protein-splicing catalytic site; other site 643561001614 thioester formation/cholesterol transfer; other site 643561001615 Intein/homing endonuclease [DNA replication, recombination, and repair]; Region: COG1372 643561001616 Hint (Hedgehog/Intein) domain C-terminal region; Region: HintC; cl09966 643561001617 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 643561001618 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 643561001619 Cupin domain; Region: Cupin_2; cl09118 643561001620 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 643561001621 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 643561001622 Protein of unknown function (DUF3567); Region: DUF3567; pfam12091 643561001623 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 643561001624 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001625 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561001626 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561001627 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561001628 TraB family; Region: TraB; cl12050 643561001629 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561001630 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561001631 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561001632 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001633 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 643561001634 putative effector binding pocket; other site 643561001635 putative dimerization interface [polypeptide binding]; other site 643561001636 phenylcoumaran benzylic ether reductase (PCBER) like, atypical (a) SDRs; Region: PCBER_SDR_a; cd05259 643561001637 NmrA-like family; Region: NmrA; pfam05368 643561001638 NAD(P) binding site [chemical binding]; other site 643561001639 active site lysine 643561001640 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 643561001641 potential catalytic triad [active] 643561001642 conserved cys residue [active] 643561001643 Kelch motif; Region: Kelch_1; cl02701 643561001644 Kelch motif; Region: Kelch_1; cl02701 643561001645 kelch-like protein; Provisional; Region: PHA03098 643561001646 Kelch motif; Region: Kelch_1; cl02701 643561001647 Kelch motif; Region: Kelch_1; cl02701 643561001648 kelch-like protein; Provisional; Region: PHA03098 643561001649 Kelch motif; Region: Kelch_1; cl02701 643561001650 Kelch motif; Region: Kelch_1; cl02701 643561001651 Kelch motif; Region: Kelch_1; cl02701 643561001652 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 643561001653 Interdomain contacts; other site 643561001654 Cytokine receptor motif; other site 643561001655 EamA-like transporter family; Region: EamA; cl01037 643561001656 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 643561001657 non-specific DNA binding site [nucleotide binding]; other site 643561001658 salt bridge; other site 643561001659 sequence-specific DNA binding site [nucleotide binding]; other site 643561001660 Cupin domain; Region: Cupin_2; cl09118 643561001661 Haemolysin-III related; Region: HlyIII; cl03831 643561001662 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561001663 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561001664 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561001665 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561001666 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561001667 Transposase domain (DUF772); Region: DUF772; cl12084 643561001668 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 643561001669 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 643561001670 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 643561001671 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 643561001672 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 643561001673 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 643561001674 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 643561001675 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 643561001676 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 643561001677 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 643561001678 DctM-like transporters; Region: DctM; pfam06808 643561001679 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 643561001680 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 643561001681 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561001682 dihydroxy-acid dehydratase; Provisional; Region: PRK13017 643561001683 Dehydratase family; Region: ILVD_EDD; cl00340 643561001684 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561001685 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 643561001686 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001687 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 643561001688 dimerization interface [polypeptide binding]; other site 643561001689 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 643561001690 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001691 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 643561001692 dimerization interface [polypeptide binding]; other site 643561001693 Pirin-related protein [General function prediction only]; Region: COG1741 643561001694 Cupin domain; Region: Cupin_2; cl09118 643561001695 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them...; Region: YcaC_related; cd01012 643561001696 catalytic triad [active] 643561001697 dimer interface [polypeptide binding]; other site 643561001698 conserved cis-peptide bond; other site 643561001699 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 643561001700 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 643561001701 active site 643561001702 Bacterial protein of unknown function (DUF894); Region: DUF894; pfam05977 643561001703 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 643561001704 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These...; Region: MopB_3; cd02766 643561001705 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 643561001706 putative [4Fe-4S] binding site [ion binding]; other site 643561001707 putative molybdopterin cofactor binding site [chemical binding]; other site 643561001708 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_3; cd02786 643561001709 putative molybdopterin cofactor binding site; other site 643561001710 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561001711 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 643561001712 putative ligand binding site [chemical binding]; other site 643561001713 acetylornithine deacetylase (ArgE); Region: AcOrn-deacetyl; TIGR01892 643561001714 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 643561001715 metal binding site [ion binding]; metal-binding site 643561001716 putative dimer interface [polypeptide binding]; other site 643561001717 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 643561001718 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 643561001719 metal binding site [ion binding]; metal-binding site 643561001720 putative dimer interface [polypeptide binding]; other site 643561001721 Peptidase M14-like domain of 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...; Region: Peptidase_M14-like_6; cd06233 643561001722 putative active site [active] 643561001723 Zn-binding site [ion binding]; other site 643561001724 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561001725 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561001726 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 643561001727 Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a...; Region: ACBP; cl00221 643561001728 acyl-CoA binding pocket [chemical binding]; other site 643561001729 CoA binding site [chemical binding]; other site 643561001730 Predicted aminopeptidase (DUF2265); Region: DUF2265; pfam10023 643561001731 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 643561001732 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 643561001733 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 643561001734 S-adenosylmethionine binding site [chemical binding]; other site 643561001735 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 643561001736 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561001737 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561001738 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561001739 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561001740 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561001741 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 643561001742 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561001743 Walker A/P-loop; other site 643561001744 ATP binding site [chemical binding]; other site 643561001745 Q-loop/lid; other site 643561001746 ABC transporter signature motif; other site 643561001747 Walker B; other site 643561001748 D-loop; other site 643561001749 H-loop/switch region; other site 643561001750 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 643561001751 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561001752 putative ligand binding site [chemical binding]; other site 643561001753 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561001754 TM-ABC transporter signature motif; other site 643561001755 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561001756 TM-ABC transporter signature motif; other site 643561001757 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 643561001758 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561001759 Walker A/P-loop; other site 643561001760 ATP binding site [chemical binding]; other site 643561001761 Q-loop/lid; other site 643561001762 ABC transporter signature motif; other site 643561001763 Walker B; other site 643561001764 D-loop; other site 643561001765 H-loop/switch region; other site 643561001766 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 643561001767 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561001768 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561001769 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 643561001770 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561001771 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 643561001772 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 643561001773 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 643561001774 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 643561001775 magnesium chelatase subunit I; Provisional; Region: bchI; PRK13407 643561001776 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 643561001777 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 643561001778 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561001779 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561001780 Peptidase family M48; Region: Peptidase_M48; cl12018 643561001781 Bacterial protein of unknown function (DUF898); Region: DUF898; cl01738 643561001782 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 643561001783 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 643561001784 RNA binding surface [nucleotide binding]; other site 643561001785 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 643561001786 active site 643561001787 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 643561001788 nudix motif; other site 643561001789 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561001790 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561001791 hypothetical protein; Provisional; Region: PRK07538 643561001792 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001793 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561001794 Chromate transporter; Region: Chromate_transp; pfam02417 643561001795 Chromate transporter; Region: Chromate_transp; pfam02417 643561001796 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001797 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561001798 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 643561001799 NAD binding site [chemical binding]; other site 643561001800 substrate binding site [chemical binding]; other site 643561001801 putative active site [active] 643561001802 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 643561001803 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 643561001804 catalytic residues [active] 643561001805 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 643561001806 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 643561001807 C-terminal domain interface [polypeptide binding]; other site 643561001808 GSH binding site (G-site) [chemical binding]; other site 643561001809 dimer interface [polypeptide binding]; other site 643561001810 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 643561001811 dimer interface [polypeptide binding]; other site 643561001812 N-terminal domain interface [polypeptide binding]; other site 643561001813 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 643561001814 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 643561001815 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 643561001816 Protein of unknown function, DUF484; Region: DUF484; cl01228 643561001817 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 643561001818 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 643561001819 DNA binding site [nucleotide binding] 643561001820 Int/Topo IB signature motif; other site 643561001821 active site 643561001822 Uncharacterised BCR, COG1649; Region: DUF187; pfam02638 643561001823 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561001824 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 643561001825 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 643561001826 PUA domain; Region: PUA; cl00607 643561001827 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 643561001828 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 643561001829 S-adenosylmethionine binding site [chemical binding]; other site 643561001830 PAS fold; Region: PAS_7; pfam12860 643561001831 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 643561001832 PAS fold; Region: PAS_7; pfam12860 643561001833 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561001834 metal binding site [ion binding]; metal-binding site 643561001835 active site 643561001836 I-site; other site 643561001837 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 643561001838 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 643561001839 P-loop, Walker A motif; other site 643561001840 Base recognition motif; other site 643561001841 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 643561001842 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 643561001843 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 643561001844 active site 643561001845 HslU subunit interaction site [polypeptide binding]; other site 643561001846 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 643561001847 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 643561001848 Walker A motif; other site 643561001849 ATP binding site [chemical binding]; other site 643561001850 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561001851 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 643561001852 cell division protein MraZ; Reviewed; Region: PRK00326 643561001853 MraZ protein; Region: MraZ; pfam02381 643561001854 MraZ protein; Region: MraZ; pfam02381 643561001855 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 643561001856 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 643561001857 Septum formation initiator; Region: DivIC; cl11433 643561001858 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 643561001859 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 643561001860 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 643561001861 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 643561001862 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 643561001863 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 643561001864 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 643561001865 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 643561001866 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 643561001867 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 643561001868 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 643561001869 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 643561001870 Mg++ binding site [ion binding]; other site 643561001871 putative catalytic motif [active] 643561001872 putative substrate binding site [chemical binding]; other site 643561001873 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 643561001874 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 643561001875 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 643561001876 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 643561001877 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 643561001878 active site 643561001879 homodimer interface [polypeptide binding]; other site 643561001880 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 643561001881 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 643561001882 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 643561001883 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 643561001884 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 643561001885 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 643561001886 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561001887 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 643561001888 Cell division protein FtsQ; Region: FtsQ; pfam03799 643561001889 cell division protein FtsA; Region: ftsA; TIGR01174 643561001890 Cell division protein FtsA; Region: FtsA; cl11496 643561001891 Cell division protein FtsA; Region: FtsA; cl11496 643561001892 cell division protein FtsZ; Validated; Region: PRK09330 643561001893 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 643561001894 nucleotide binding site [chemical binding]; other site 643561001895 SulA interaction site; other site 643561001896 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 643561001897 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 643561001898 ThiC family; Region: ThiC; cl08031 643561001899 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 643561001900 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561001901 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 643561001902 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 643561001903 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561001904 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 643561001905 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 643561001906 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 643561001907 active site 643561001908 putative DNA-binding cleft [nucleotide binding]; other site 643561001909 dimer interface [polypeptide binding]; other site 643561001910 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 643561001911 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561001912 putative acyl-acceptor binding pocket; other site 643561001913 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 643561001914 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561001915 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561001916 Cupin domain; Region: Cupin_2; cl09118 643561001917 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 643561001918 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 643561001919 DNA-binding transcriptional activator MhpR; Provisional; Region: PRK09834 643561001920 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561001921 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561001922 Transglycosylase; Region: Transgly; cl07896 643561001923 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 643561001924 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 643561001925 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 643561001926 NAD(P) binding site [chemical binding]; other site 643561001927 shikimate binding site; other site 643561001928 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 643561001929 Gram-negative bacterial tonB protein; Region: TonB; cl10048 643561001930 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 643561001931 RNB domain; Region: RNB; pfam00773 643561001932 O-Antigen ligase; Region: Wzy_C; cl04850 643561001933 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 643561001934 Uncharacterised protein family (UPF0227); Region: UPF0227; cl14886 643561001935 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561001936 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 643561001937 amidase; Provisional; Region: PRK07056 643561001938 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 643561001939 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 643561001940 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 643561001941 NeuB family; Region: NeuB; cl00496 643561001942 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 643561001943 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 643561001944 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 643561001945 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 643561001946 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 643561001947 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing...; Region: TlpA_like_family; cd02966 643561001948 catalytic residues [active] 643561001949 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 643561001950 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 643561001951 carboxyltransferase (CT) interaction site; other site 643561001952 biotinylation site [posttranslational modification]; other site 643561001953 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 643561001954 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 643561001955 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561001956 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 643561001957 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 643561001958 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 643561001959 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 643561001960 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 643561001961 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 643561001962 substrate binding site [chemical binding]; other site 643561001963 ATP binding site [chemical binding]; other site 643561001964 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 643561001965 dimer interface [polypeptide binding]; other site 643561001966 putative radical transfer pathway; other site 643561001967 diiron center [ion binding]; other site 643561001968 tyrosyl radical; other site 643561001969 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 643561001970 ATP cone domain; Region: ATP-cone; pfam03477 643561001971 Class I ribonucleotide reductase; Region: RNR_I; cd01679 643561001972 active site 643561001973 dimer interface [polypeptide binding]; other site 643561001974 catalytic residues [active] 643561001975 effector binding site; other site 643561001976 R2 peptide binding site; other site 643561001977 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 643561001978 amidase catalytic site [active] 643561001979 Zn binding residues [ion binding]; other site 643561001980 substrate binding site [chemical binding]; other site 643561001981 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 643561001982 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561001983 active site 643561001984 phosphorylation site [posttranslational modification] 643561001985 intermolecular recognition site; other site 643561001986 dimerization interface [polypeptide binding]; other site 643561001987 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 643561001988 Walker A motif; other site 643561001989 ATP binding site [chemical binding]; other site 643561001990 Walker B motif; other site 643561001991 arginine finger; other site 643561001992 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561001993 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 643561001994 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 643561001995 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 643561001996 dimer interface [polypeptide binding]; other site 643561001997 phosphorylation site [posttranslational modification] 643561001998 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 643561001999 ATP binding site [chemical binding]; other site 643561002000 Mg2+ binding site [ion binding]; other site 643561002001 G-X-G motif; other site 643561002002 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 643561002003 signal recognition particle protein; Provisional; Region: PRK10867 643561002004 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 643561002005 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 643561002006 Signal peptide binding domain; Region: SRP_SPB; pfam02978 643561002007 Membrane glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: MdoH; COG2943 643561002008 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 643561002009 Ligand binding site [chemical binding]; other site 643561002010 DXD motif; other site 643561002011 response regulator GlrR; Provisional; Region: PRK15115 643561002012 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561002013 active site 643561002014 phosphorylation site [posttranslational modification] 643561002015 intermolecular recognition site; other site 643561002016 dimerization interface [polypeptide binding]; other site 643561002017 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 643561002018 Walker A motif; other site 643561002019 ATP binding site [chemical binding]; other site 643561002020 Walker B motif; other site 643561002021 arginine finger; other site 643561002022 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 643561002023 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 643561002024 ATP binding site [chemical binding]; other site 643561002025 Mg2+ binding site [ion binding]; other site 643561002026 G-X-G motif; other site 643561002027 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 643561002028 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 643561002029 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 643561002030 FeS/SAM binding site; other site 643561002031 TRAM domain; Region: TRAM; cl01282 643561002032 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561002033 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 643561002034 Secretin and TonB N terminus short domain; Region: STN; cl06624 643561002035 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561002036 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 643561002037 N-terminal plug; other site 643561002038 ligand-binding site [chemical binding]; other site 643561002039 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 643561002040 FecR protein; Region: FecR; pfam04773 643561002041 RNA polymerase sigma factor; Reviewed; Region: PRK12523 643561002042 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561002043 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 643561002044 DNA binding residues [nucleotide binding] 643561002045 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 643561002046 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561002047 active site 643561002048 phosphorylation site [posttranslational modification] 643561002049 intermolecular recognition site; other site 643561002050 dimerization interface [polypeptide binding]; other site 643561002051 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 643561002052 DNA binding site [nucleotide binding] 643561002053 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 643561002054 sensor protein BasS/PmrB; Provisional; Region: PRK10755 643561002055 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 643561002056 dimer interface [polypeptide binding]; other site 643561002057 phosphorylation site [posttranslational modification] 643561002058 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 643561002059 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 643561002060 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 643561002061 NodT family; Region: outer_NodT; TIGR01845 643561002062 Outer membrane efflux protein; Region: OEP; pfam02321 643561002063 Outer membrane efflux protein; Region: OEP; pfam02321 643561002064 Uncharacterized protein conserved in bacteria (DUF2252); Region: DUF2252; cl12088 643561002065 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 643561002066 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561002067 Walker A/P-loop; other site 643561002068 ATP binding site [chemical binding]; other site 643561002069 Q-loop/lid; other site 643561002070 ABC transporter signature motif; other site 643561002071 Walker B; other site 643561002072 D-loop; other site 643561002073 H-loop/switch region; other site 643561002074 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 643561002075 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 643561002076 Flavin binding site [chemical binding]; other site 643561002077 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 643561002078 putative ligand binding site [chemical binding]; other site 643561002079 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561002080 TM-ABC transporter signature motif; other site 643561002081 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561002082 TM-ABC transporter signature motif; other site 643561002083 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 643561002084 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561002085 Walker A/P-loop; other site 643561002086 ATP binding site [chemical binding]; other site 643561002087 Q-loop/lid; other site 643561002088 ABC transporter signature motif; other site 643561002089 Walker B; other site 643561002090 D-loop; other site 643561002091 H-loop/switch region; other site 643561002092 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 643561002093 active site 643561002094 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 643561002095 dimer interface [polypeptide binding]; other site 643561002096 non-prolyl cis peptide bond; other site 643561002097 insertion regions; other site 643561002098 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561002099 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 643561002100 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561002101 active site 643561002102 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 643561002103 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 643561002104 Flavin binding site [chemical binding]; other site 643561002105 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 643561002106 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 643561002107 Walker A motif; other site 643561002108 ATP binding site [chemical binding]; other site 643561002109 Walker B motif; other site 643561002110 arginine finger; other site 643561002111 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561002112 enoyl-CoA hydratase; Provisional; Region: PRK05862 643561002113 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 643561002114 substrate binding site [chemical binding]; other site 643561002115 oxyanion hole (OAH) forming residues; other site 643561002116 trimer interface [polypeptide binding]; other site 643561002117 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 643561002118 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 643561002119 Zn binding site [ion binding]; other site 643561002120 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated...; Region: PDZ; cl00117 643561002121 protein binding site [polypeptide binding]; other site 643561002122 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 643561002123 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 643561002124 dimerization domain [polypeptide binding]; other site 643561002125 dimer interface [polypeptide binding]; other site 643561002126 catalytic residues [active] 643561002127 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561002128 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 643561002129 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 643561002130 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 643561002131 MOSC domain; Region: MOSC; pfam03473 643561002132 GTP-binding protein YchF; Reviewed; Region: PRK09601 643561002133 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 643561002134 G1 box; other site 643561002135 GTP/Mg2+ binding site [chemical binding]; other site 643561002136 Switch I region; other site 643561002137 G2 box; other site 643561002138 Switch II region; other site 643561002139 G3 box; other site 643561002140 G4 box; other site 643561002141 G5 box; other site 643561002142 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 643561002143 Divergent AAA domain; Region: AAA_4; pfam04326 643561002144 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 643561002145 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 643561002146 HPP family; Region: HPP; pfam04982 643561002147 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 643561002148 Predicted permeases [General function prediction only]; Region: RarD; COG2962 643561002149 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 643561002150 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]; Region: COG5001 643561002151 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561002152 metal binding site [ion binding]; metal-binding site 643561002153 active site 643561002154 I-site; other site 643561002155 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 643561002156 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 643561002157 FMN binding site [chemical binding]; other site 643561002158 active site 643561002159 catalytic residues [active] 643561002160 substrate binding site [chemical binding]; other site 643561002161 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561002162 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 643561002163 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 643561002164 purine monophosphate binding site [chemical binding]; other site 643561002165 dimer interface [polypeptide binding]; other site 643561002166 putative catalytic residues [active] 643561002167 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 643561002168 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 643561002169 Pectate lyase; Region: Pectate_lyase; pfam03211 643561002170 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 643561002171 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 643561002172 inhibitor-cofactor binding pocket; inhibition site 643561002173 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561002174 catalytic residue [active] 643561002175 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed; Region: PRK06427 643561002176 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 643561002177 substrate binding site [chemical binding]; other site 643561002178 ATP binding site [chemical binding]; other site 643561002179 Rubredoxin [Energy production and conversion]; Region: COG1773 643561002180 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They...; Region: rubredoxin; cd00730 643561002181 iron binding site [ion binding]; other site 643561002182 Response regulator receiver domain; Region: Response_reg; pfam00072 643561002183 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561002184 active site 643561002185 phosphorylation site [posttranslational modification] 643561002186 intermolecular recognition site; other site 643561002187 dimerization interface [polypeptide binding]; other site 643561002188 Response regulator receiver domain; Region: Response_reg; pfam00072 643561002189 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561002190 active site 643561002191 phosphorylation site [posttranslational modification] 643561002192 intermolecular recognition site; other site 643561002193 dimerization interface [polypeptide binding]; other site 643561002194 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 643561002195 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561002196 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 643561002197 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 643561002198 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 643561002199 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 643561002200 putative binding surface; other site 643561002201 active site 643561002202 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 643561002203 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 643561002204 ATP binding site [chemical binding]; other site 643561002205 Mg2+ binding site [ion binding]; other site 643561002206 G-X-G motif; other site 643561002207 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 643561002208 Response regulator receiver domain; Region: Response_reg; pfam00072 643561002209 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561002210 active site 643561002211 phosphorylation site [posttranslational modification] 643561002212 intermolecular recognition site; other site 643561002213 dimerization interface [polypeptide binding]; other site 643561002214 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 643561002215 DNA photolyase; Region: DNA_photolyase; pfam00875 643561002216 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 643561002217 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 643561002218 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 643561002219 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 643561002220 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 643561002221 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 643561002222 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561002223 dihydroorotase; Provisional; Region: PRK07627 643561002224 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 643561002225 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C...; Region: DHOase_IIa; cd01317 643561002226 active site 643561002227 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 643561002228 putative acyl-acceptor binding pocket; other site 643561002229 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561002230 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561002231 Uncharacterized protein conserved in bacteria (DUF2257); Region: DUF2257; cl01794 643561002232 Membrane protein of unknown function (DUF340); Region: DUF340; cl01028 643561002233 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 643561002234 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 643561002235 Walker A/P-loop; other site 643561002236 ATP binding site [chemical binding]; other site 643561002237 Q-loop/lid; other site 643561002238 ABC transporter signature motif; other site 643561002239 Walker B; other site 643561002240 D-loop; other site 643561002241 H-loop/switch region; other site 643561002242 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 643561002243 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 643561002244 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 643561002245 catalytic residues [active] 643561002246 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 643561002247 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 643561002248 Walker A motif; other site 643561002249 ATP binding site [chemical binding]; other site 643561002250 Walker B motif; other site 643561002251 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 643561002252 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 643561002253 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 643561002254 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 643561002255 GspL cytoplasmic actin-ATPase-like region; Region: GspL; pfam05134 643561002256 General secretion pathway protein K; Region: GspK; pfam03934 643561002257 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 643561002258 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 643561002259 Bacterial type II secretion system protein I/J; Region: GSPII_IJ; pfam02501 643561002260 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 643561002261 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 643561002262 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 643561002263 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 643561002264 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 643561002265 threonine dehydratase; Reviewed; Region: PRK09224 643561002266 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 643561002267 tetramer interface [polypeptide binding]; other site 643561002268 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561002269 catalytic residue [active] 643561002270 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 643561002271 putative Ile/Val binding site [chemical binding]; other site 643561002272 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 643561002273 putative Ile/Val binding site [chemical binding]; other site 643561002274 OsmC-like protein; Region: OsmC; cl00767 643561002275 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 643561002276 diiron binding motif [ion binding]; other site 643561002277 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 643561002278 trimer interface [polypeptide binding]; other site 643561002279 eyelet of channel; other site 643561002280 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 643561002281 trimer interface [polypeptide binding]; other site 643561002282 eyelet of channel; other site 643561002283 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 643561002284 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 643561002285 dimer interface [polypeptide binding]; other site 643561002286 conserved gate region; other site 643561002287 putative PBP binding loops; other site 643561002288 ABC-ATPase subunit interface; other site 643561002289 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 643561002290 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 643561002291 metal binding site [ion binding]; metal-binding site 643561002292 putative dimer interface [polypeptide binding]; other site 643561002293 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 643561002294 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 643561002295 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 643561002296 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 643561002297 dimer interface [polypeptide binding]; other site 643561002298 conserved gate region; other site 643561002299 putative PBP binding loops; other site 643561002300 ABC-ATPase subunit interface; other site 643561002301 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 643561002302 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 643561002303 Walker A/P-loop; other site 643561002304 ATP binding site [chemical binding]; other site 643561002305 Q-loop/lid; other site 643561002306 ABC transporter signature motif; other site 643561002307 Walker B; other site 643561002308 D-loop; other site 643561002309 H-loop/switch region; other site 643561002310 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561002311 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 643561002312 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 643561002313 Walker A/P-loop; other site 643561002314 ATP binding site [chemical binding]; other site 643561002315 Q-loop/lid; other site 643561002316 ABC transporter signature motif; other site 643561002317 Walker B; other site 643561002318 D-loop; other site 643561002319 H-loop/switch region; other site 643561002320 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561002321 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561002322 nitrate/nitrite sensor protein NarX; Provisional; Region: PRK10600 643561002323 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 643561002324 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 643561002325 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561002326 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 643561002327 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 643561002328 dimer interface [polypeptide binding]; other site 643561002329 active site 643561002330 Predicted Zn-dependent protease (DUF2268); Region: DUF2268; cl02316 643561002331 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 643561002332 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 643561002333 putative active site [active] 643561002334 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 643561002335 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 643561002336 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 643561002337 transaldolase-like protein; Provisional; Region: PTZ00411 643561002338 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 643561002339 active site 643561002340 dimer interface [polypeptide binding]; other site 643561002341 catalytic residue [active] 643561002342 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 643561002343 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 643561002344 active site 643561002345 dimer interface [polypeptide binding]; other site 643561002346 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 643561002347 dimer interface [polypeptide binding]; other site 643561002348 active site 643561002349 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 643561002350 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561002351 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 643561002352 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 643561002353 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 643561002354 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 643561002355 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 643561002356 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 643561002357 putative PBP binding loops; other site 643561002358 dimer interface [polypeptide binding]; other site 643561002359 ABC-ATPase subunit interface; other site 643561002360 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 643561002361 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 643561002362 dimer interface [polypeptide binding]; other site 643561002363 conserved gate region; other site 643561002364 putative PBP binding loops; other site 643561002365 ABC-ATPase subunit interface; other site 643561002366 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 643561002367 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 643561002368 Walker A/P-loop; other site 643561002369 ATP binding site [chemical binding]; other site 643561002370 Q-loop/lid; other site 643561002371 ABC transporter signature motif; other site 643561002372 Walker B; other site 643561002373 D-loop; other site 643561002374 H-loop/switch region; other site 643561002375 TOBE domain; Region: TOBE_2; cl01440 643561002376 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 643561002377 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 643561002378 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 643561002379 sorbitol dehydrogenase; Provisional; Region: PRK07067 643561002380 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561002381 NAD(P) binding site [chemical binding]; other site 643561002382 active site 643561002383 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 643561002384 catalytic residue [active] 643561002385 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 643561002386 putative substrate binding site [chemical binding]; other site 643561002387 putative ATP binding site [chemical binding]; other site 643561002388 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561002389 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561002390 D-xylulose kinases, Escherichia coli xylulokinase-like subgroup; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_EcXK-like; cd07808 643561002391 N- and C-terminal domain interface [polypeptide binding]; other site 643561002392 L-fuculokinase; Region: fuculo_kin_coli; TIGR02628 643561002393 active site 643561002394 catalytic site [active] 643561002395 metal binding site [ion binding]; metal-binding site 643561002396 xylulose binding site [chemical binding]; other site 643561002397 putative ATP binding site [chemical binding]; other site 643561002398 homodimer interface [polypeptide binding]; other site 643561002399 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 643561002400 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 643561002401 ring oligomerisation interface [polypeptide binding]; other site 643561002402 ATP/Mg binding site [chemical binding]; other site 643561002403 stacking interactions; other site 643561002404 hinge regions; other site 643561002405 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 643561002406 oligomerisation interface [polypeptide binding]; other site 643561002407 mobile loop; other site 643561002408 roof hairpin; other site 643561002409 elongation factor G; Reviewed; Region: PRK00007 643561002410 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 643561002411 G1 box; other site 643561002412 putative GEF interaction site [polypeptide binding]; other site 643561002413 GTP/Mg2+ binding site [chemical binding]; other site 643561002414 Switch I region; other site 643561002415 G2 box; other site 643561002416 G3 box; other site 643561002417 Switch II region; other site 643561002418 G4 box; other site 643561002419 G5 box; other site 643561002420 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 643561002421 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 643561002422 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 643561002423 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 643561002424 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 643561002425 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 643561002426 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 643561002427 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 643561002428 Substrate binding site [chemical binding]; other site 643561002429 Cupin domain; Region: Cupin_2; cl09118 643561002430 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 643561002431 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 643561002432 Ligand binding site [chemical binding]; other site 643561002433 Putative Catalytic site [active] 643561002434 DXD motif; other site 643561002435 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 643561002436 active site 643561002437 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561002438 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 643561002439 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 643561002440 inhibitor-cofactor binding pocket; inhibition site 643561002441 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561002442 catalytic residue [active] 643561002443 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 643561002444 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 643561002445 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 643561002446 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 643561002447 NADP-binding site; other site 643561002448 homotetramer interface [polypeptide binding]; other site 643561002449 substrate binding site [chemical binding]; other site 643561002450 homodimer interface [polypeptide binding]; other site 643561002451 active site 643561002452 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561002453 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 643561002454 NAD(P) binding site [chemical binding]; other site 643561002455 active site 643561002456 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 643561002457 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 643561002458 inhibitor-cofactor binding pocket; inhibition site 643561002459 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561002460 catalytic residue [active] 643561002461 Predicted membrane protein (DUF2079); Region: DUF2079; cl01374 643561002462 MatE; Region: MatE; cl10513 643561002463 This family is most closely related to the GT1 family of glycosyltransferases. wbaZ in Salmonella enterica has been shown to possess the mannosyl transferase activity. The members of this family are found in certain bacteria and Archaea; Region: GT1_wbaZ_like; cd03804 643561002464 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 643561002465 putative ADP-binding pocket [chemical binding]; other site 643561002466 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 643561002467 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 643561002468 putative ADP-binding pocket [chemical binding]; other site 643561002469 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 643561002470 active site 643561002471 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 643561002472 binding surface 643561002473 TPR motif; other site 643561002474 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 643561002475 binding surface 643561002476 TPR motif; other site 643561002477 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 643561002478 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561002479 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 643561002480 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 643561002481 dihydropyrimidine dehydrogenase subunit B; Validated; Region: PRK08318 643561002482 Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and...; Region: DHPD_FMN; cd02940 643561002483 homodimer interface [polypeptide binding]; other site 643561002484 active site 643561002485 FMN binding site [chemical binding]; other site 643561002486 substrate binding site [chemical binding]; other site 643561002487 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 643561002488 Sodium:solute symporter family; Region: SSF; cl00456 643561002489 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 643561002490 phenylhydantoinase; Validated; Region: PRK08323 643561002491 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like...; Region: D-HYD; cd01314 643561002492 tetramer interface [polypeptide binding]; other site 643561002493 active site 643561002494 allantoate amidohydrolase; Reviewed; Region: PRK12893 643561002495 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 643561002496 active site 643561002497 metal binding site [ion binding]; metal-binding site 643561002498 dimer interface [polypeptide binding]; other site 643561002499 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 643561002500 bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional; Region: PRK05379 643561002501 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 643561002502 active site 643561002503 nucleotide binding site [chemical binding]; other site 643561002504 HIGH motif; other site 643561002505 KMSKS motif; other site 643561002506 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 643561002507 nudix motif; other site 643561002508 NAD synthetase; Provisional; Region: PRK13981 643561002509 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 643561002510 multimer interface [polypeptide binding]; other site 643561002511 active site 643561002512 catalytic triad [active] 643561002513 protein interface 1 [polypeptide binding]; other site 643561002514 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 643561002515 homodimer interface [polypeptide binding]; other site 643561002516 NAD binding pocket [chemical binding]; other site 643561002517 ATP binding pocket [chemical binding]; other site 643561002518 Mg binding site [ion binding]; other site 643561002519 active-site loop [active] 643561002520 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 643561002521 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 643561002522 active site 643561002523 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 643561002524 catalytic triad [active] 643561002525 conserved cis-peptide bond; other site 643561002526 S-adenosylmethionine synthetase; Validated; Region: PRK05250 643561002527 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 643561002528 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 643561002529 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 643561002530 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 643561002531 putative acyl-acceptor binding pocket; other site 643561002532 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 643561002533 putative acyl-acceptor binding pocket; other site 643561002534 short chain dehydrogenase; Validated; Region: PRK05855 643561002535 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 643561002536 G1 box; other site 643561002537 GTP/Mg2+ binding site [chemical binding]; other site 643561002538 Switch I region; other site 643561002539 G2 box; other site 643561002540 G3 box; other site 643561002541 Switch II region; other site 643561002542 G4 box; other site 643561002543 G5 box; other site 643561002544 Cytochrome c; Region: Cytochrom_C; cl11414 643561002545 Cytochrome c; Region: Cytochrom_C; cl11414 643561002546 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 643561002547 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 643561002548 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 643561002549 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 643561002550 Moco binding site; other site 643561002551 metal coordination site [ion binding]; other site 643561002552 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 643561002553 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561002554 diaminopimelate decarboxylase; Region: lysA; TIGR01048 643561002555 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 643561002556 active site 643561002557 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 643561002558 substrate binding site [chemical binding]; other site 643561002559 catalytic residues [active] 643561002560 dimer interface [polypeptide binding]; other site 643561002561 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 643561002562 putative iron binding site [ion binding]; other site 643561002563 Transglycosylase; Region: Transgly; cl07896 643561002564 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 643561002565 Competence protein A; Region: Competence_A; pfam11104 643561002566 GspL cytoplasmic actin-ATPase-like region; Region: GspL; pfam05134 643561002567 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 643561002568 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 643561002569 Pilus assembly protein, PilO; Region: PilO; cl01234 643561002570 Pilus assembly protein, PilP; Region: PilP; cl01235 643561002571 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 643561002572 Secretin and TonB N terminus short domain; Region: STN; cl06624 643561002573 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 643561002574 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 643561002575 Bacterial Ig-like domain (group 1); Region: Big_1; cl10510 643561002576 shikimate kinase; Reviewed; Region: aroK; PRK00131 643561002577 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 643561002578 ADP binding site [chemical binding]; other site 643561002579 magnesium binding site [ion binding]; other site 643561002580 putative shikimate binding site; other site 643561002581 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 643561002582 active site 643561002583 dimer interface [polypeptide binding]; other site 643561002584 metal binding site [ion binding]; metal-binding site 643561002585 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561002586 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 643561002587 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 643561002588 Transposase IS200 like; Region: Y1_Tnp; cl00848 643561002589 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 643561002590 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 643561002591 active site 643561002592 dimer interface [polypeptide binding]; other site 643561002593 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 643561002594 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 643561002595 active site 643561002596 FMN binding site [chemical binding]; other site 643561002597 substrate binding site [chemical binding]; other site 643561002598 3Fe-4S cluster binding site [ion binding]; other site 643561002599 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 643561002600 domain interface; other site 643561002601 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 643561002602 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 643561002603 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 643561002604 substrate binding pocket [chemical binding]; other site 643561002605 membrane-bound complex binding site; other site 643561002606 hinge residues; other site 643561002607 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 643561002608 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 643561002609 dimer interface [polypeptide binding]; other site 643561002610 conserved gate region; other site 643561002611 putative PBP binding loops; other site 643561002612 ABC-ATPase subunit interface; other site 643561002613 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 643561002614 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 643561002615 Walker A/P-loop; other site 643561002616 ATP binding site [chemical binding]; other site 643561002617 Q-loop/lid; other site 643561002618 ABC transporter signature motif; other site 643561002619 Walker B; other site 643561002620 D-loop; other site 643561002621 H-loop/switch region; other site 643561002622 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 643561002623 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 643561002624 Walker A/P-loop; other site 643561002625 ATP binding site [chemical binding]; other site 643561002626 Q-loop/lid; other site 643561002627 ABC transporter signature motif; other site 643561002628 Walker B; other site 643561002629 D-loop; other site 643561002630 H-loop/switch region; other site 643561002631 Domain of unknown function DUF140; Region: DUF140; cl00510 643561002632 mce related protein; Region: MCE; pfam02470 643561002633 VacJ like lipoprotein; Region: VacJ; cl01073 643561002634 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 643561002635 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 643561002636 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 643561002637 tetratricopeptide repeat protein; Provisional; Region: PRK11788 643561002638 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 643561002639 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency...; Region: ABC_subfamily_A; cd03263 643561002640 Walker A/P-loop; other site 643561002641 ATP binding site [chemical binding]; other site 643561002642 Q-loop/lid; other site 643561002643 ABC transporter signature motif; other site 643561002644 Walker B; other site 643561002645 D-loop; other site 643561002646 H-loop/switch region; other site 643561002647 ABC-2 type transporter; Region: ABC2_membrane; cl11417 643561002648 BolA-like protein; Region: BolA; cl00386 643561002649 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated; Region: PRK09369 643561002650 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 643561002651 hinge; other site 643561002652 active site 643561002653 ATP phosphoribosyltransferase; Region: HisG; cl15266 643561002654 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 643561002655 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 643561002656 NAD binding site [chemical binding]; other site 643561002657 dimerization interface [polypeptide binding]; other site 643561002658 product binding site; other site 643561002659 substrate binding site [chemical binding]; other site 643561002660 zinc binding site [ion binding]; other site 643561002661 catalytic residues [active] 643561002662 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 643561002663 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 643561002664 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561002665 DNA-binding site [nucleotide binding]; DNA binding site 643561002666 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 643561002667 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561002668 homodimer interface [polypeptide binding]; other site 643561002669 catalytic residue [active] 643561002670 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 643561002671 putative active site [active] 643561002672 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 643561002673 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 643561002674 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561002675 homodimer interface [polypeptide binding]; other site 643561002676 catalytic residue [active] 643561002677 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 643561002678 putative active site pocket [active] 643561002679 4-fold oligomerization interface [polypeptide binding]; other site 643561002680 metal binding residues [ion binding]; metal-binding site 643561002681 3-fold/trimer interface [polypeptide binding]; other site 643561002682 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 643561002683 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 643561002684 putative active site [active] 643561002685 oxyanion strand; other site 643561002686 catalytic triad [active] 643561002687 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 643561002688 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 643561002689 catalytic residues [active] 643561002690 Spherulation-specific family 4; Region: Spherulin4; pfam12138 643561002691 Spherulation-specific family 4; Region: Spherulin4; pfam12138 643561002692 Predicted membrane protein [Function unknown]; Region: COG4267 643561002693 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_3; cd03813 643561002694 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 643561002695 poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA; Region: PGA_TPR_OMP; TIGR03939 643561002696 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 643561002697 TM1410 hypothetical-related protein; Region: DUF297; cl00997 643561002698 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 643561002699 UDP-glucose 4-epimerase; Region: PLN02240 643561002700 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 643561002701 NAD binding site [chemical binding]; other site 643561002702 homodimer interface [polypeptide binding]; other site 643561002703 active site 643561002704 substrate binding site [chemical binding]; other site 643561002705 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 643561002706 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 643561002707 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 643561002708 active site 643561002709 phosphate binding residues; other site 643561002710 catalytic residues [active] 643561002711 Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]; Region: HisF; COG0107 643561002712 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 643561002713 substrate binding site [chemical binding]; other site 643561002714 glutamase interaction surface [polypeptide binding]; other site 643561002715 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 643561002716 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 643561002717 Predicted membrane protein [Function unknown]; Region: COG3671 643561002718 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 643561002719 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 643561002720 active site 643561002721 nucleophile elbow; other site 643561002722 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 643561002723 nucleotide binding site/active site [active] 643561002724 HIT family signature motif; other site 643561002725 catalytic residue [active] 643561002726 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 643561002727 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 643561002728 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 643561002729 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561002730 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561002731 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561002732 Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide...; Region: CASc; cl00042 643561002733 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 643561002734 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 643561002735 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 643561002736 protein binding site [polypeptide binding]; other site 643561002737 metabolite-proton symporter; Region: 2A0106; TIGR00883 643561002738 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 643561002739 putative substrate translocation pore; other site 643561002740 Uncharacterized conserved protein [Function unknown]; Region: COG0327 643561002741 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 643561002742 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 643561002743 metal ion-dependent adhesion site (MIDAS); other site 643561002744 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 643561002745 Protein of unknown function DUF58; Region: DUF58; pfam01882 643561002746 MoxR-like ATPases [General function prediction only]; Region: COG0714 643561002747 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 643561002748 Walker A motif; other site 643561002749 ATP binding site [chemical binding]; other site 643561002750 Walker B motif; other site 643561002751 arginine finger; other site 643561002752 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 643561002753 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 643561002754 active site 643561002755 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 643561002756 putative active site [active] 643561002757 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 643561002758 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 643561002759 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 643561002760 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 643561002761 Walker A motif; other site 643561002762 ATP binding site [chemical binding]; other site 643561002763 Walker B motif; other site 643561002764 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 643561002765 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 643561002766 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 643561002767 EamA-like transporter family; Region: EamA; cl01037 643561002768 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 643561002769 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 643561002770 putative NAD(P) binding site [chemical binding]; other site 643561002771 putative active site [active] 643561002772 Pseudomonas putida Aldehyde dehydrogenase AlkH-like; Region: ALDH_AlkH-like; cd07134 643561002773 NAD(P) binding site [chemical binding]; other site 643561002774 catalytic residues [active] 643561002775 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 643561002776 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 643561002777 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 643561002778 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561002779 catalytic residue [active] 643561002780 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 643561002781 intersubunit interface [polypeptide binding]; other site 643561002782 active site 643561002783 Zn2+ binding site [ion binding]; other site 643561002784 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 643561002785 uncharacterized xylulose kinase-like proteins, subgroup 2; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_XK_like_2; cd07805 643561002786 N- and C-terminal domain interface [polypeptide binding]; other site 643561002787 active site 643561002788 catalytic site [active] 643561002789 metal binding site [ion binding]; metal-binding site 643561002790 xylulose binding site [chemical binding]; other site 643561002791 ATP binding site [chemical binding]; other site 643561002792 putative homodimer interface [polypeptide binding]; other site 643561002793 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 643561002794 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 643561002795 hopanoid-associated sugar epimerase; Region: HpnA; TIGR03466 643561002796 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561002797 NAD(P) binding site [chemical binding]; other site 643561002798 active site 643561002799 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561002800 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561002801 UreD urease accessory protein; Region: UreD; cl00530 643561002802 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 643561002803 nucleoside/Zn binding site; other site 643561002804 dimer interface [polypeptide binding]; other site 643561002805 catalytic motif [active] 643561002806 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561002807 NMT1/THI5 like; Region: NMT1; pfam09084 643561002808 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 643561002809 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 643561002810 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 643561002811 rRNA binding site [nucleotide binding]; other site 643561002812 predicted 30S ribosome binding site; other site 643561002813 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 643561002814 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561002815 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 643561002816 NAD(P) binding site [chemical binding]; other site 643561002817 active site 643561002818 Predicted ATPase [General function prediction only]; Region: COG3910 643561002819 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561002820 Walker A/P-loop; other site 643561002821 ATP binding site [chemical binding]; other site 643561002822 Q-loop/lid; other site 643561002823 ABC transporter signature motif; other site 643561002824 Walker B; other site 643561002825 D-loop; other site 643561002826 H-loop/switch region; other site 643561002827 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 643561002828 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 643561002829 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 643561002830 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 643561002831 Walker A/P-loop; other site 643561002832 ATP binding site [chemical binding]; other site 643561002833 Q-loop/lid; other site 643561002834 ABC transporter signature motif; other site 643561002835 Walker B; other site 643561002836 D-loop; other site 643561002837 H-loop/switch region; other site 643561002838 NMT1/THI5 like; Region: NMT1; pfam09084 643561002839 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 643561002840 nucleoside/Zn binding site; other site 643561002841 dimer interface [polypeptide binding]; other site 643561002842 catalytic motif [active] 643561002843 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 643561002844 Malic enzyme, N-terminal domain; Region: malic; pfam00390 643561002845 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 643561002846 putative NAD(P) binding site [chemical binding]; other site 643561002847 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 643561002848 Sulfate transporter family; Region: Sulfate_transp; cl00967 643561002849 Permease family; Region: Xan_ur_permease; pfam00860 643561002850 Transcriptional regulators [Transcription]; Region: GntR; COG1802 643561002851 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561002852 DNA-binding site [nucleotide binding]; DNA binding site 643561002853 FCD domain; Region: FCD; cl11656 643561002854 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 643561002855 Sodium:solute symporter family; Region: SSF; cl00456 643561002856 Purine-cytosine permease and related proteins [Nucleotide transport and metabolism]; Region: CodB; COG1457 643561002857 Transcriptional regulators [Transcription]; Region: FadR; COG2186 643561002858 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561002859 DNA-binding site [nucleotide binding]; DNA binding site 643561002860 FCD domain; Region: FCD; cl11656 643561002861 Cache domain; Region: Cache_1; pfam02743 643561002862 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 643561002863 dimerization interface [polypeptide binding]; other site 643561002864 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561002865 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 643561002866 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 643561002867 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 643561002868 dimer interface [polypeptide binding]; other site 643561002869 active site 643561002870 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 643561002871 Ligand Binding Site [chemical binding]; other site 643561002872 sulfotransferase; Region: PLN02164 643561002873 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 643561002874 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 643561002875 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561002876 Walker A/P-loop; other site 643561002877 ATP binding site [chemical binding]; other site 643561002878 Q-loop/lid; other site 643561002879 ABC transporter signature motif; other site 643561002880 Walker B; other site 643561002881 D-loop; other site 643561002882 H-loop/switch region; other site 643561002883 V-type ATPase 116kDa subunit family; Region: V_ATPase_I; pfam01496 643561002884 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561002885 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 643561002886 NAD(P) binding site [chemical binding]; other site 643561002887 active site 643561002888 Macrocin-O-methyltransferase (TylF); Region: TylF; pfam05711 643561002889 Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]; Region: AsnB; COG0367 643561002890 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 643561002891 active site 643561002892 dimer interface [polypeptide binding]; other site 643561002893 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 643561002894 Ligand Binding Site [chemical binding]; other site 643561002895 Molecular Tunnel; other site 643561002896 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 643561002897 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 643561002898 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 643561002899 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 643561002900 O-Antigen ligase; Region: Wzy_C; cl04850 643561002901 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 643561002902 Bacterial sugar transferase; Region: Bac_transf; cl00939 643561002903 M20 Zn-peptidases include exopeptidases; Region: M20_like; cd02697 643561002904 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK08651 643561002905 putative metal binding site [ion binding]; other site 643561002906 putative bifunctional OHCU decarboxylase/allantoate amidohydrolase; Provisional; Region: PRK13590 643561002907 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 643561002908 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 643561002909 active site 643561002910 metal binding site [ion binding]; metal-binding site 643561002911 dimer interface [polypeptide binding]; other site 643561002912 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 643561002913 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 643561002914 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 643561002915 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561002916 DNA-binding site [nucleotide binding]; DNA binding site 643561002917 FCD domain; Region: FCD; cl11656 643561002918 MOFRL family; Region: MOFRL; cl01013 643561002919 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 643561002920 esterase, PHB depolymerase family; Region: esterase_phb; TIGR01840 643561002921 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 643561002922 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 643561002923 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU)...; Region: TLP_HIUase; cd05822 643561002924 active site 643561002925 homotetramer interface [polypeptide binding]; other site 643561002926 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 643561002927 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 643561002928 Predicted membrane protein [Function unknown]; Region: COG3748 643561002929 Protein of unknown function (DUF989); Region: DUF989; pfam06181 643561002930 Cytochrome c; Region: Cytochrom_C; cl11414 643561002931 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 643561002932 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain...; Region: CBS_pair_GGDEF_assoc; cd04598 643561002933 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561002934 metal binding site [ion binding]; metal-binding site 643561002935 active site 643561002936 I-site; other site 643561002937 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 643561002938 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561002939 active site 643561002940 phosphorylation site [posttranslational modification] 643561002941 intermolecular recognition site; other site 643561002942 dimerization interface [polypeptide binding]; other site 643561002943 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 643561002944 DNA binding residues [nucleotide binding] 643561002945 dimerization interface [polypeptide binding]; other site 643561002946 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 643561002947 Cache domain; Region: Cache_2; cl07034 643561002948 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 643561002949 ATP binding site [chemical binding]; other site 643561002950 Mg2+ binding site [ion binding]; other site 643561002951 G-X-G motif; other site 643561002952 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 643561002953 homotrimer interaction site [polypeptide binding]; other site 643561002954 putative active site [active] 643561002955 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 643561002956 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 643561002957 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561002958 catalytic residue [active] 643561002959 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 643561002960 trimer interface [polypeptide binding]; other site 643561002961 eyelet of channel; other site 643561002962 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 643561002963 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561002964 flavanone-3-hydroxylase; Provisional; Region: PLN03176 643561002965 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 643561002966 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 643561002967 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 643561002968 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561002969 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 643561002970 PAS fold; Region: PAS; pfam00989 643561002971 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561002972 metal binding site [ion binding]; metal-binding site 643561002973 active site 643561002974 I-site; other site 643561002975 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 643561002976 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 643561002977 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 643561002978 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 643561002979 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 643561002980 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 643561002981 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 643561002982 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 643561002983 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 643561002984 Walker A/P-loop; other site 643561002985 ATP binding site [chemical binding]; other site 643561002986 Q-loop/lid; other site 643561002987 ABC transporter signature motif; other site 643561002988 Walker B; other site 643561002989 D-loop; other site 643561002990 H-loop/switch region; other site 643561002991 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 643561002992 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 643561002993 TM-ABC transporter signature motif; other site 643561002994 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 643561002995 TM-ABC transporter signature motif; other site 643561002996 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 643561002997 putative ligand binding site [chemical binding]; other site 643561002998 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 643561002999 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 643561003000 active site 643561003001 putative substrate binding pocket [chemical binding]; other site 643561003002 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561003003 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561003004 Predicted amidohydrolase [General function prediction only]; Region: COG0388 643561003005 N-carbamyl-D-amino acid amidohydrolase (DCase, class 6 nitrilases); Region: DCase; cd07569 643561003006 tetramer interface [polypeptide binding]; other site 643561003007 active site 643561003008 catalytic triad [active] 643561003009 dimer interface [polypeptide binding]; other site 643561003010 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561003011 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003012 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 643561003013 dimerization interface [polypeptide binding]; other site 643561003014 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561003015 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 643561003016 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 643561003017 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 643561003018 Walker A/P-loop; other site 643561003019 ATP binding site [chemical binding]; other site 643561003020 Q-loop/lid; other site 643561003021 ABC transporter signature motif; other site 643561003022 Walker B; other site 643561003023 D-loop; other site 643561003024 H-loop/switch region; other site 643561003025 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 643561003026 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 643561003027 dimer interface [polypeptide binding]; other site 643561003028 conserved gate region; other site 643561003029 putative PBP binding loops; other site 643561003030 ABC-ATPase subunit interface; other site 643561003031 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 643561003032 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561003033 substrate binding pocket [chemical binding]; other site 643561003034 membrane-bound complex binding site; other site 643561003035 hinge residues; other site 643561003036 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 643561003037 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003038 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561003039 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 643561003040 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1)...; Region: Rieske; cl00938 643561003041 iron-sulfur cluster [ion binding]; other site 643561003042 [2Fe-2S] cluster binding site [ion binding]; other site 643561003043 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 643561003044 hydrophobic ligand binding site; other site 643561003045 Glycogen debranching enzyme [Carbohydrate transport and metabolism]; Region: GDB1; COG3408 643561003046 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 643561003047 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 643561003048 active site 643561003049 purine riboside binding site [chemical binding]; other site 643561003050 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561003051 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 643561003052 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-...; Region: Ntn_hydrolase; cl00467 643561003053 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-...; Region: Ntn_hydrolase; cl00467 643561003054 active site 643561003055 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-...; Region: Ntn_hydrolase; cl00467 643561003056 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 643561003057 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003058 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 643561003059 putative ligand binding site [chemical binding]; other site 643561003060 guanine deaminase; Provisional; Region: PRK09228 643561003061 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 643561003062 active site 643561003063 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 643561003064 trimer interface [polypeptide binding]; other site 643561003065 active site 643561003066 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 643561003067 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 643561003068 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 643561003069 ATP binding site [chemical binding]; other site 643561003070 Mg++ binding site [ion binding]; other site 643561003071 motif III; other site 643561003072 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 643561003073 nucleotide binding region [chemical binding]; other site 643561003074 ATP-binding site [chemical binding]; other site 643561003075 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 643561003076 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 643561003077 active site 643561003078 metal binding site [ion binding]; metal-binding site 643561003079 H-NS histone family; Region: Histone_HNS; pfam00816 643561003080 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 643561003081 aconitate hydratase; Validated; Region: PRK09277 643561003082 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 643561003083 substrate binding site [chemical binding]; other site 643561003084 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 643561003085 ligand binding site [chemical binding]; other site 643561003086 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 643561003087 substrate binding site [chemical binding]; other site 643561003088 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 643561003089 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561003090 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 643561003091 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 643561003092 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 643561003093 putative active site [active] 643561003094 heme pocket [chemical binding]; other site 643561003095 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561003096 metal binding site [ion binding]; metal-binding site 643561003097 active site 643561003098 I-site; other site 643561003099 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 643561003100 PAS fold; Region: PAS_7; pfam12860 643561003101 PAS domain S-box; Region: sensory_box; TIGR00229 643561003102 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561003103 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561003104 metal binding site [ion binding]; metal-binding site 643561003105 active site 643561003106 I-site; other site 643561003107 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 643561003108 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003109 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 643561003110 Tryptophan 2,3-dioxygenase; Region: Trp_dioxygenase; cl03994 643561003111 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 643561003112 kynureninase; Region: kynureninase; TIGR01814 643561003113 Putative cyclase; Region: Cyclase; cl00814 643561003114 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561003115 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003116 Flagellin N-methylase; Region: FliB; cl00497 643561003117 FeoA domain; Region: FeoA; cl00838 643561003118 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 643561003119 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 643561003120 G1 box; other site 643561003121 GTP/Mg2+ binding site [chemical binding]; other site 643561003122 Switch I region; other site 643561003123 G2 box; other site 643561003124 G3 box; other site 643561003125 Switch II region; other site 643561003126 G4 box; other site 643561003127 G5 box; other site 643561003128 Nucleoside recognition; Region: Gate; cl00486 643561003129 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 643561003130 Nucleoside recognition; Region: Gate; cl00486 643561003131 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561003132 ornithine carbamoyltransferase; Provisional; Region: PRK00779 643561003133 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 643561003134 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003135 acetylornithine aminotransferase; Provisional; Region: PRK02627 643561003136 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 643561003137 inhibitor-cofactor binding pocket; inhibition site 643561003138 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561003139 catalytic residue [active] 643561003140 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 643561003141 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561003142 Predicted dehydrogenase [General function prediction only]; Region: COG0579 643561003143 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 643561003144 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 643561003145 hypothetical protein; Provisional; Region: PRK10941 643561003146 Uncharacterized conserved protein [Function unknown]; Region: COG2912 643561003147 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 643561003148 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 643561003149 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 643561003150 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 643561003151 Protein of unknown function (DUF328); Region: DUF328; cl01143 643561003152 ribonuclease E; Reviewed; Region: rne; PRK10811 643561003153 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 643561003154 homodimer interface [polypeptide binding]; other site 643561003155 oligonucleotide binding site [chemical binding]; other site 643561003156 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 643561003157 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 643561003158 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 643561003159 active site 643561003160 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 643561003161 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 643561003162 motif II; other site 643561003163 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1)...; Region: Rieske; cd03467 643561003164 iron-sulfur cluster [ion binding]; other site 643561003165 [2Fe-2S] cluster binding site [ion binding]; other site 643561003166 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 643561003167 tandem repeat interface [polypeptide binding]; other site 643561003168 oligomer interface [polypeptide binding]; other site 643561003169 active site residues [active] 643561003170 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 643561003171 Maf-like protein; Region: Maf; pfam02545 643561003172 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 643561003173 active site 643561003174 dimer interface [polypeptide binding]; other site 643561003175 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 643561003176 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 643561003177 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 643561003178 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 643561003179 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 643561003180 dimer interface [polypeptide binding]; other site 643561003181 active site 643561003182 CoA binding pocket [chemical binding]; other site 643561003183 Acyl transferase domain; Region: Acyl_transf_1; cl08282 643561003184 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 643561003185 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003186 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 643561003187 NAD(P) binding site [chemical binding]; other site 643561003188 active site 643561003189 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561003190 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 643561003191 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 643561003192 dimer interface [polypeptide binding]; other site 643561003193 active site 643561003194 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 643561003195 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561003196 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 643561003197 DNA binding residues [nucleotide binding] 643561003198 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 643561003199 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 643561003200 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 643561003201 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 643561003202 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 643561003203 protein binding site [polypeptide binding]; other site 643561003204 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 643561003205 GTP-binding protein LepA; Provisional; Region: PRK05433 643561003206 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 643561003207 G1 box; other site 643561003208 putative GEF interaction site [polypeptide binding]; other site 643561003209 GTP/Mg2+ binding site [chemical binding]; other site 643561003210 Switch I region; other site 643561003211 G2 box; other site 643561003212 G3 box; other site 643561003213 Switch II region; other site 643561003214 G4 box; other site 643561003215 G5 box; other site 643561003216 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding...; Region: Translation_Factor_II_like; cl02787 643561003217 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 643561003218 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 643561003219 signal peptidase I; Provisional; Region: PRK10861 643561003220 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 643561003221 Catalytic site [active] 643561003222 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 643561003223 ribonuclease III; Reviewed; Region: rnc; PRK00102 643561003224 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 643561003225 dimerization interface [polypeptide binding]; other site 643561003226 active site 643561003227 metal binding site [ion binding]; metal-binding site 643561003228 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 643561003229 dsRNA binding site [nucleotide binding]; other site 643561003230 GTPase Era; Reviewed; Region: era; PRK00089 643561003231 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 643561003232 G1 box; other site 643561003233 GTP/Mg2+ binding site [chemical binding]; other site 643561003234 Switch I region; other site 643561003235 G2 box; other site 643561003236 Switch II region; other site 643561003237 G3 box; other site 643561003238 G4 box; other site 643561003239 G5 box; other site 643561003240 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 643561003241 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 643561003242 Recombination protein O N terminal; Region: RecO_N; pfam11967 643561003243 Recombination protein O C terminal; Region: RecO_C; pfam02565 643561003244 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 643561003245 active site 643561003246 hydrophilic channel; other site 643561003247 dimerization interface [polypeptide binding]; other site 643561003248 catalytic residues [active] 643561003249 active site lid [active] 643561003250 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 643561003251 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 643561003252 Protein of unknown function (DUF3300); Region: DUF3300; pfam11737 643561003253 Mechanosensitive ion channel; Region: MS_channel; pfam00924 643561003254 Response regulator receiver domain; Region: Response_reg; pfam00072 643561003255 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561003256 active site 643561003257 phosphorylation site [posttranslational modification] 643561003258 intermolecular recognition site; other site 643561003259 dimerization interface [polypeptide binding]; other site 643561003260 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561003261 metal binding site [ion binding]; metal-binding site 643561003262 active site 643561003263 I-site; other site 643561003264 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 643561003265 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 643561003266 dimer interface [polypeptide binding]; other site 643561003267 putative anticodon binding site; other site 643561003268 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 643561003269 motif 1; other site 643561003270 active site 643561003271 motif 2; other site 643561003272 motif 3; other site 643561003273 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 643561003274 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 643561003275 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 643561003276 ubiquinone biosynthesis O-methyltransferase; Region: UbiG; TIGR01983 643561003277 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 643561003278 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 643561003279 Bacterial sugar transferase; Region: Bac_transf; cl00939 643561003280 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 643561003281 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 643561003282 putative ADP-binding pocket [chemical binding]; other site 643561003283 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 643561003284 YGGT family; Region: YGGT; cl00508 643561003285 YGGT family; Region: YGGT; cl00508 643561003286 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 643561003287 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561003288 tryptophan synthase; Region: PLN02591 643561003289 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 643561003290 substrate binding site [chemical binding]; other site 643561003291 active site 643561003292 catalytic residues [active] 643561003293 heterodimer interface [polypeptide binding]; other site 643561003294 tryptophan synthase, beta chain; Region: PLN02618 643561003295 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 643561003296 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561003297 catalytic residue [active] 643561003298 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 643561003299 active site 643561003300 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 643561003301 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 643561003302 dimerization interface 3.5A [polypeptide binding]; other site 643561003303 active site 643561003304 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 643561003305 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 643561003306 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 643561003307 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 643561003308 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 643561003309 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003310 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 643561003311 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003312 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561003313 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 643561003314 isocitrate dehydrogenase; Validated; Region: PRK06451 643561003315 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 643561003316 substrate binding site [chemical binding]; other site 643561003317 Entericidin EcnA/B family; Region: Entericidin; cl02322 643561003318 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 643561003319 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 643561003320 substrate binding site [chemical binding]; other site 643561003321 ligand binding site [chemical binding]; other site 643561003322 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561003323 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003324 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 643561003325 putative dimerization interface [polypeptide binding]; other site 643561003326 chaperone protein DnaJ; Provisional; Region: PRK10767 643561003327 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 643561003328 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 643561003329 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 643561003330 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 643561003331 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 643561003332 dimer interface [polypeptide binding]; other site 643561003333 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 643561003334 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 643561003335 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 643561003336 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 643561003337 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 643561003338 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 643561003339 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 643561003340 replicative DNA helicase; Region: DnaB; TIGR00665 643561003341 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 643561003342 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 643561003343 Walker A motif; other site 643561003344 ATP binding site [chemical binding]; other site 643561003345 Walker B motif; other site 643561003346 DNA binding loops [nucleotide binding] 643561003347 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 643561003348 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 643561003349 putative active site [active] 643561003350 PhoH-like protein; Region: PhoH; cl12134 643561003351 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 643561003352 catalytic triad [active] 643561003353 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome...; Region: Xcc1710_like; cd05560 643561003354 alanine aminotransferase; Provisional; Region: PTZ00377 643561003355 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 643561003356 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561003357 homodimer interface [polypeptide binding]; other site 643561003358 catalytic residue [active] 643561003359 homoserine dehydrogenase; Provisional; Region: PRK06349 643561003360 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003361 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 643561003362 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 643561003363 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 643561003364 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants...; Region: Thr-synth_2; cd01560 643561003365 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561003366 catalytic residue [active] 643561003367 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 643561003368 Walker A motif; other site 643561003369 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 643561003370 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 643561003371 dimer interface [polypeptide binding]; other site 643561003372 putative functional site; other site 643561003373 putative MPT binding site; other site 643561003374 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 643561003375 MoaE interaction surface [polypeptide binding]; other site 643561003376 MoeB interaction surface [polypeptide binding]; other site 643561003377 thiocarboxylated glycine; other site 643561003378 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 643561003379 dihydrodipicolinate synthase; Region: dapA; TIGR00674 643561003380 dimer interface [polypeptide binding]; other site 643561003381 active site 643561003382 catalytic residue [active] 643561003383 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 643561003384 MoaE homodimer interface [polypeptide binding]; other site 643561003385 MoaD interaction [polypeptide binding]; other site 643561003386 active site residues [active] 643561003387 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 643561003388 Clp amino terminal domain; Region: Clp_N; pfam02861 643561003389 Clp amino terminal domain; Region: Clp_N; pfam02861 643561003390 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 643561003391 Walker A motif; other site 643561003392 ATP binding site [chemical binding]; other site 643561003393 Walker B motif; other site 643561003394 arginine finger; other site 643561003395 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 643561003396 Walker A motif; other site 643561003397 ATP binding site [chemical binding]; other site 643561003398 Walker B motif; other site 643561003399 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 643561003400 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 643561003401 NAD(P) binding site [chemical binding]; other site 643561003402 catalytic residues [active] 643561003403 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 643561003404 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 643561003405 Coenzyme A binding pocket [chemical binding]; other site 643561003406 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 643561003407 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 643561003408 FMN binding site [chemical binding]; other site 643561003409 active site 643561003410 catalytic residues [active] 643561003411 substrate binding site [chemical binding]; other site 643561003412 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 643561003413 putative active site [active] 643561003414 catalytic site [active] 643561003415 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 643561003416 putative active site [active] 643561003417 catalytic site [active] 643561003418 aspartate aminotransferase; Provisional; Region: PRK08361 643561003419 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 643561003420 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561003421 homodimer interface [polypeptide binding]; other site 643561003422 catalytic residue [active] 643561003423 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 643561003424 16S/18S rRNA binding site [nucleotide binding]; other site 643561003425 S13e-L30e interaction site [polypeptide binding]; other site 643561003426 25S rRNA binding site [nucleotide binding]; other site 643561003427 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 643561003428 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 643561003429 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 643561003430 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 643561003431 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 643561003432 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 643561003433 putative nucleic acid binding region [nucleotide binding]; other site 643561003434 G-X-X-G motif; other site 643561003435 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 643561003436 RNA binding site [nucleotide binding]; other site 643561003437 domain interface; other site 643561003438 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 643561003439 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 643561003440 NAD(P) binding site [chemical binding]; other site 643561003441 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 643561003442 substrate binding site [chemical binding]; other site 643561003443 dimer interface [polypeptide binding]; other site 643561003444 catalytic triad [active] 643561003445 Preprotein translocase SecG subunit; Region: SecG; cl09123 643561003446 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 643561003447 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 643561003448 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 643561003449 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 643561003450 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 643561003451 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of...; Region: TRX_Fd_NuoE; cd03064 643561003452 putative dimer interface [polypeptide binding]; other site 643561003453 [2Fe-2S] cluster binding site [ion binding]; other site 643561003454 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 643561003455 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 643561003456 SLBB domain; Region: SLBB; pfam10531 643561003457 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 643561003458 NADH dehydrogenase subunit G; Validated; Region: PRK09129 643561003459 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 643561003460 catalytic loop [active] 643561003461 iron binding site [ion binding]; other site 643561003462 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 643561003463 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions...; Region: MopB_NDH-1_NuoG2; cd02772 643561003464 NADH dehydrogenase; Region: NADHdh; cl00469 643561003465 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 643561003466 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 643561003467 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 643561003468 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 643561003469 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 643561003470 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 643561003471 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 643561003472 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 643561003473 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 643561003474 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 643561003475 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 643561003476 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 643561003477 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 643561003478 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 643561003479 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561003480 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561003481 Walker A/P-loop; other site 643561003482 ATP binding site [chemical binding]; other site 643561003483 Q-loop/lid; other site 643561003484 ABC transporter signature motif; other site 643561003485 Walker B; other site 643561003486 D-loop; other site 643561003487 H-loop/switch region; other site 643561003488 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 643561003489 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561003490 Walker A/P-loop; other site 643561003491 ATP binding site [chemical binding]; other site 643561003492 Q-loop/lid; other site 643561003493 ABC transporter signature motif; other site 643561003494 Walker B; other site 643561003495 D-loop; other site 643561003496 H-loop/switch region; other site 643561003497 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 643561003498 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561003499 Walker A/P-loop; other site 643561003500 ATP binding site [chemical binding]; other site 643561003501 Q-loop/lid; other site 643561003502 ABC transporter signature motif; other site 643561003503 Walker B; other site 643561003504 D-loop; other site 643561003505 H-loop/switch region; other site 643561003506 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561003507 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 643561003508 putative ligand binding site [chemical binding]; other site 643561003509 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561003510 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 643561003511 putative ligand binding site [chemical binding]; other site 643561003512 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561003513 TM-ABC transporter signature motif; other site 643561003514 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561003515 TM-ABC transporter signature motif; other site 643561003516 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 643561003517 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 643561003518 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 643561003519 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561003520 catalytic residue [active] 643561003521 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 643561003522 active site 643561003523 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 643561003524 putative dimer interface [polypeptide binding]; other site 643561003525 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 643561003526 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 643561003527 Walker A/P-loop; other site 643561003528 ATP binding site [chemical binding]; other site 643561003529 Q-loop/lid; other site 643561003530 ABC transporter signature motif; other site 643561003531 Walker B; other site 643561003532 D-loop; other site 643561003533 H-loop/switch region; other site 643561003534 IPP transferase; Region: IPPT; cl00403 643561003535 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003536 NmrA-like family; Region: NmrA; pfam05368 643561003537 NAD(P) binding site [chemical binding]; other site 643561003538 active site 643561003539 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003540 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 643561003541 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 643561003542 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 643561003543 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 643561003544 putative active site [active] 643561003545 catalytic site [active] 643561003546 putative metal binding site [ion binding]; other site 643561003547 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 643561003548 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 643561003549 ATP binding site [chemical binding]; other site 643561003550 Mg2+ binding site [ion binding]; other site 643561003551 G-X-G motif; other site 643561003552 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 643561003553 ATP binding site [chemical binding]; other site 643561003554 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 643561003555 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 643561003556 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 643561003557 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561003558 Localisation of periplasmic protein complexes; Region: AMIN; pfam11741 643561003559 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 643561003560 active site 643561003561 metal binding site [ion binding]; metal-binding site 643561003562 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 643561003563 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 643561003564 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 643561003565 Membrane transport protein; Region: Mem_trans; cl09117 643561003566 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561003567 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003568 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 643561003569 dimerization interface [polypeptide binding]; other site 643561003570 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 643561003571 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 643561003572 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003573 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 643561003574 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561003575 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561003576 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 643561003577 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 643561003578 Int/Topo IB signature motif; other site 643561003579 active site 643561003580 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561003581 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561003582 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 643561003583 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 643561003584 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561003585 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 643561003586 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561003587 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 643561003588 dinuclear metal binding motif [ion binding]; other site 643561003589 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 643561003590 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 643561003591 trimer interface [polypeptide binding]; other site 643561003592 putative metal binding site [ion binding]; other site 643561003593 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 643561003594 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 643561003595 dimerization interface [polypeptide binding]; other site 643561003596 domain crossover interface; other site 643561003597 redox-dependent activation switch; other site 643561003598 Septum formation initiator; Region: DivIC; cl11433 643561003599 enolase; Provisional; Region: eno; PRK00077 643561003600 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 643561003601 dimer interface [polypeptide binding]; other site 643561003602 metal binding site [ion binding]; metal-binding site 643561003603 substrate binding pocket [chemical binding]; other site 643561003604 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 643561003605 NeuB family; Region: NeuB; cl00496 643561003606 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 643561003607 CTP synthetase; Validated; Region: pyrG; PRK05380 643561003608 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 643561003609 Catalytic site [active] 643561003610 Active site [active] 643561003611 UTP binding site [chemical binding]; other site 643561003612 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 643561003613 active site 643561003614 putative oxyanion hole; other site 643561003615 catalytic triad [active] 643561003616 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 643561003617 Flavoprotein; Region: Flavoprotein; cl08021 643561003618 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 643561003619 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 643561003620 trimer interface [polypeptide binding]; other site 643561003621 active site 643561003622 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 643561003623 Cupin superfamily protein; Region: Cupin_4; pfam08007 643561003624 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561003625 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 643561003626 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 643561003627 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 643561003628 dihydrodipicolinate synthase; Region: dapA; TIGR00674 643561003629 dimer interface [polypeptide binding]; other site 643561003630 active site 643561003631 catalytic residue [active] 643561003632 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 643561003633 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 643561003634 S-adenosylmethionine binding site [chemical binding]; other site 643561003635 Major Facilitator Superfamily; Region: MFS_1; pfam07690 643561003636 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 643561003637 putative substrate translocation pore; other site 643561003638 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 643561003639 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 643561003640 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 643561003641 anchoring element; other site 643561003642 dimer interface [polypeptide binding]; other site 643561003643 ATP binding site [chemical binding]; other site 643561003644 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 643561003645 active site 643561003646 metal binding site [ion binding]; metal-binding site 643561003647 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 643561003648 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 643561003649 N-acetyl-D-glucosamine binding site [chemical binding]; other site 643561003650 catalytic residue [active] 643561003651 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 643561003652 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 643561003653 CAP-like domain; other site 643561003654 Active site [active] 643561003655 primary dimer interface [polypeptide binding]; other site 643561003656 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561003657 methyl-accepting chemotaxis protein II; Provisional; Region: PRK15048 643561003658 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 643561003659 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 643561003660 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561003661 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 643561003662 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 643561003663 pyridoxal binding site [chemical binding]; other site 643561003664 dimer interface [polypeptide binding]; other site 643561003665 ATP binding site [chemical binding]; other site 643561003666 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_1; cd02199 643561003667 homotrimer interaction site [polypeptide binding]; other site 643561003668 putative active site [active] 643561003669 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 643561003670 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561003671 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 643561003672 Competence protein; Region: Competence; cl00471 643561003673 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561003674 Uncharacterized conserved protein [Function unknown]; Region: COG2308 643561003675 Domain of unknown function (DUF404); Region: DUF404; pfam04169 643561003676 Domain of unknown function (DUF407); Region: DUF407; pfam04174 643561003677 Bacterial domain of unknown function (DUF403); Region: DUF403; cl00980 643561003678 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. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 643561003679 nudix motif; other site 643561003680 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003681 active site 643561003682 NAD+ binding site [chemical binding]; other site 643561003683 oligomerization interface [polypeptide binding]; other site 643561003684 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 643561003685 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 643561003686 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 643561003687 S-adenosylmethionine binding site [chemical binding]; other site 643561003688 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 643561003689 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 643561003690 dimer interface [polypeptide binding]; other site 643561003691 active site 643561003692 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 643561003693 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 643561003694 dimer interface [polypeptide binding]; other site 643561003695 active site 643561003696 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 643561003697 3-oxoacyl-(acyl-carrier-protein) reductase, putative; Region: fabG_rel; TIGR01831 643561003698 NAD(P) binding site [chemical binding]; other site 643561003699 homotetramer interface [polypeptide binding]; other site 643561003700 homodimer interface [polypeptide binding]; other site 643561003701 active site 643561003702 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 643561003703 putative active site 1 [active] 643561003704 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 643561003705 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 643561003706 dimer interface [polypeptide binding]; other site 643561003707 active site 643561003708 Protein of unknown function (DUF3261); Region: DUF3261; pfam11659 643561003709 Predicted exporter [General function prediction only]; Region: COG4258 643561003710 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 643561003711 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 643561003712 active site 643561003713 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 643561003714 Ligand binding site [chemical binding]; other site 643561003715 Putative Catalytic site [active] 643561003716 DXD motif; other site 643561003717 Predicted acyltransferase [General function prediction only]; Region: COG4261 643561003718 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 643561003719 putative acyl-acceptor binding pocket; other site 643561003720 FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid...; Region: FabA_FabZ; cd00493 643561003721 active site 2 [active] 643561003722 dimer interface [polypeptide binding]; other site 643561003723 active site 1 [active] 643561003724 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 643561003725 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561003726 Predicted membrane protein [Function unknown]; Region: COG4648 643561003727 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561003728 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561003729 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 643561003730 putative acyl-acceptor binding pocket; other site 643561003731 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 643561003732 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 643561003733 transcriptional regulator; Provisional; Region: PRK10632 643561003734 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003735 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 643561003736 putative effector binding pocket; other site 643561003737 putative dimerization interface [polypeptide binding]; other site 643561003738 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 643561003739 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 643561003740 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 643561003741 NodT family; Region: outer_NodT; TIGR01845 643561003742 Outer membrane efflux protein; Region: OEP; pfam02321 643561003743 Outer membrane efflux protein; Region: OEP; pfam02321 643561003744 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561003745 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 643561003746 tetramerization interface [polypeptide binding]; other site 643561003747 NAD(P) binding site [chemical binding]; other site 643561003748 catalytic residues [active] 643561003749 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 643561003750 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 643561003751 N-terminal plug; other site 643561003752 ligand-binding site [chemical binding]; other site 643561003753 Nickel uptake substrate-specific transmembrane region; Region: NikM; pfam10670 643561003754 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 643561003755 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 643561003756 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561003757 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 643561003758 N-terminal plug; other site 643561003759 ligand-binding site [chemical binding]; other site 643561003760 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 643561003761 Ferritin-like domain; Region: Ferritin; pfam00210 643561003762 heme binding site [chemical binding]; other site 643561003763 ferroxidase pore; other site 643561003764 ferroxidase diiron center [ion binding]; other site 643561003765 peroxiredoxin; Region: AhpC; TIGR03137 643561003766 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 643561003767 dimer interface [polypeptide binding]; other site 643561003768 decamer (pentamer of dimers) interface [polypeptide binding]; other site 643561003769 catalytic triad [active] 643561003770 peroxidatic and resolving cysteines [active] 643561003771 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 643561003772 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the...; Region: AhpF_NTD_N; cd02974 643561003773 catalytic residue [active] 643561003774 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 643561003775 catalytic residues [active] 643561003776 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003777 Transposase domain (DUF772); Region: DUF772; cl12084 643561003778 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 643561003779 Restriction endonuclease; Region: Mrr_cat; cl00747 643561003780 DNA topoisomerase I; Validated; Region: PRK05582 643561003781 Domain of unknown function (DUF299); Region: DUF299; cl00780 643561003782 phosphoenolpyruvate synthase; Validated; Region: PRK06464 643561003783 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 643561003784 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 643561003785 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 643561003786 Predicted membrane protein [Function unknown]; Region: COG4327; cl01781 643561003787 Sodium:solute symporter family; Region: SSF; cl00456 643561003788 Sodium:solute symporter family; Region: SSF; cl00456 643561003789 TIGR03118 family protein; Region: PEPCTERM_chp_1 643561003790 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 643561003791 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003792 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561003793 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003794 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 643561003795 dimerization interface [polypeptide binding]; other site 643561003796 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 643561003797 active site 643561003798 catalytic residues [active] 643561003799 metal binding site [ion binding]; metal-binding site 643561003800 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561003801 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561003802 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561003803 aromatic amino acid exporter; Provisional; Region: PRK11689 643561003804 VirK protein; Region: VirK; pfam06903 643561003805 cell density-dependent motility repressor; Provisional; Region: PRK10082 643561003806 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561003807 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 643561003808 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 643561003809 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 643561003810 inhibitor site; inhibition site 643561003811 active site 643561003812 dimer interface [polypeptide binding]; other site 643561003813 catalytic residue [active] 643561003814 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561003815 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561003816 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 643561003817 classical (c) SDRs; Region: SDR_c; cd05233 643561003818 NAD(P) binding site [chemical binding]; other site 643561003819 active site 643561003820 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 643561003821 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved...; Region: MR_like_1; cd03326 643561003822 putative active site pocket [active] 643561003823 metal binding site [ion binding]; metal-binding site 643561003824 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 643561003825 Domain of unknown function (DUF955); Region: DUF955; cl01076 643561003826 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 643561003827 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561003828 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 643561003829 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561003830 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 643561003831 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561003832 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 643561003833 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 643561003834 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 643561003835 Trp docking motif; other site 643561003836 active site 643561003837 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 643561003838 'Velcro' closure; other site 643561003839 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 643561003840 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 643561003841 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 643561003842 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 643561003843 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561003844 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 643561003845 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 643561003846 DNA binding residues [nucleotide binding] 643561003847 DNA primase, catalytic core; Region: dnaG; TIGR01391 643561003848 CHC2 zinc finger; Region: zf-CHC2; cl02597 643561003849 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 643561003850 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 643561003851 active site 643561003852 metal binding site [ion binding]; metal-binding site 643561003853 interdomain interaction site; other site 643561003854 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 643561003855 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 643561003856 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561003857 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 643561003858 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 643561003859 PhoD-like phosphatase; Region: PhoD; pfam09423 643561003860 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 643561003861 putative active site [active] 643561003862 putative metal binding site [ion binding]; other site 643561003863 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 643561003864 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 643561003865 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561003866 metal binding site [ion binding]; metal-binding site 643561003867 active site 643561003868 I-site; other site 643561003869 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 643561003870 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 643561003871 NAD(P) binding site [chemical binding]; other site 643561003872 Survival protein SurE; Region: SurE; cl00448 643561003873 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 643561003874 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 643561003875 putative peptidoglycan binding site; other site 643561003876 Peptidase family M23; Region: Peptidase_M23; pfam01551 643561003877 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 643561003878 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 643561003879 RNA binding surface [nucleotide binding]; other site 643561003880 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 643561003881 active site 643561003882 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 643561003883 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 643561003884 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 643561003885 RNA binding surface [nucleotide binding]; other site 643561003886 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 643561003887 probable active site [active] 643561003888 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 643561003889 active site 643561003890 multimer interface [polypeptide binding]; other site 643561003891 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 643561003892 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 643561003893 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 643561003894 binding surface 643561003895 TPR motif; other site 643561003896 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 643561003897 binding surface 643561003898 TPR motif; other site 643561003899 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 643561003900 cytoskeletal protein RodZ; Provisional; Region: PRK10856 643561003901 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 643561003902 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 643561003903 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 643561003904 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 643561003905 dimer interface [polypeptide binding]; other site 643561003906 motif 1; other site 643561003907 active site 643561003908 motif 2; other site 643561003909 motif 3; other site 643561003910 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 643561003911 anticodon binding site; other site 643561003912 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 643561003913 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 643561003914 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 643561003915 GTP-binding protein Der; Reviewed; Region: PRK00093 643561003916 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 643561003917 G1 box; other site 643561003918 GTP/Mg2+ binding site [chemical binding]; other site 643561003919 Switch I region; other site 643561003920 G2 box; other site 643561003921 Switch II region; other site 643561003922 G3 box; other site 643561003923 G4 box; other site 643561003924 G5 box; other site 643561003925 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 643561003926 G1 box; other site 643561003927 GTP/Mg2+ binding site [chemical binding]; other site 643561003928 Switch I region; other site 643561003929 G2 box; other site 643561003930 G3 box; other site 643561003931 Switch II region; other site 643561003932 G4 box; other site 643561003933 G5 box; other site 643561003934 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 643561003935 Sm1 motif; other site 643561003936 intra - hexamer interaction site; other site 643561003937 inter - hexamer interaction site [polypeptide binding]; other site 643561003938 nucleotide binding pocket [chemical binding]; other site 643561003939 Sm2 motif; other site 643561003940 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 643561003941 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 643561003942 G1 box; other site 643561003943 GTP/Mg2+ binding site [chemical binding]; other site 643561003944 Switch I region; other site 643561003945 G2 box; other site 643561003946 G3 box; other site 643561003947 Switch II region; other site 643561003948 G4 box; other site 643561003949 G5 box; other site 643561003950 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 643561003951 HflK protein; Region: hflK; TIGR01933 643561003952 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 643561003953 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 643561003954 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 643561003955 dimer interface [polypeptide binding]; other site 643561003956 motif 1; other site 643561003957 active site 643561003958 motif 2; other site 643561003959 motif 3; other site 643561003960 adenylosuccinate synthetase; Provisional; Region: PRK01117 643561003961 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 643561003962 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 643561003963 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 643561003964 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 643561003965 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 643561003966 active site 643561003967 uracil binding [chemical binding]; other site 643561003968 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 643561003969 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 643561003970 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 643561003971 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 643561003972 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 643561003973 putative MPT binding site; other site 643561003974 glutamine synthetase; Provisional; Region: glnA; PRK09469 643561003975 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 643561003976 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 643561003977 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 643561003978 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 643561003979 dimer interface [polypeptide binding]; other site 643561003980 phosphorylation site [posttranslational modification] 643561003981 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 643561003982 ATP binding site [chemical binding]; other site 643561003983 Mg2+ binding site [ion binding]; other site 643561003984 G-X-G motif; other site 643561003985 nitrogen regulation protein NR(I); Provisional; Region: glnG; PRK10923 643561003986 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561003987 active site 643561003988 phosphorylation site [posttranslational modification] 643561003989 intermolecular recognition site; other site 643561003990 dimerization interface [polypeptide binding]; other site 643561003991 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 643561003992 Walker A motif; other site 643561003993 ATP binding site [chemical binding]; other site 643561003994 Walker B motif; other site 643561003995 arginine finger; other site 643561003996 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561003997 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 643561003998 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 643561003999 putative phosphate binding site [ion binding]; other site 643561004000 putative catalytic site [active] 643561004001 active site 643561004002 metal binding site A [ion binding]; metal-binding site 643561004003 DNA binding site [nucleotide binding] 643561004004 putative AP binding site [nucleotide binding]; other site 643561004005 putative metal binding site B [ion binding]; other site 643561004006 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 643561004007 folate binding site [chemical binding]; other site 643561004008 NADP+ binding site [chemical binding]; other site 643561004009 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 643561004010 dimerization interface [polypeptide binding]; other site 643561004011 active site 643561004012 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 643561004013 FAD binding domain; Region: FAD_binding_4; pfam01565 643561004014 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 643561004015 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 643561004016 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561004017 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 643561004018 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 643561004019 catalytic residues [active] 643561004020 substrate binding pocket [chemical binding]; other site 643561004021 substrate-Mg2+ binding site; other site 643561004022 aspartate-rich region 1; other site 643561004023 aspartate-rich region 2; other site 643561004024 Found in ATP-dependent protease La (LON); Region: LON; smart00464 643561004025 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 643561004026 Found in ATP-dependent protease La (LON); Region: LON; smart00464 643561004027 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 643561004028 Walker A motif; other site 643561004029 ATP binding site [chemical binding]; other site 643561004030 Walker B motif; other site 643561004031 arginine finger; other site 643561004032 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 643561004033 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 643561004034 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 643561004035 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 643561004036 Walker A motif; other site 643561004037 ATP binding site [chemical binding]; other site 643561004038 Walker B motif; other site 643561004039 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 643561004040 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 643561004041 oligomer interface [polypeptide binding]; other site 643561004042 active site residues [active] 643561004043 trigger factor; Provisional; Region: tig; PRK01490 643561004044 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 643561004045 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 643561004046 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 643561004047 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 643561004048 putative membrane fusion protein; Region: TIGR02828 643561004049 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 643561004050 active site lid residues [active] 643561004051 substrate binding pocket [chemical binding]; other site 643561004052 catalytic residues [active] 643561004053 substrate-Mg2+ binding site; other site 643561004054 aspartate-rich region 1; other site 643561004055 aspartate-rich region 2; other site 643561004056 Protein of unknown function (DUF796); Region: DUF796; cl01226 643561004057 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 643561004058 Catalytic domain of Protein Kinases; Region: PKc; cd00180 643561004059 active site 643561004060 ATP binding site [chemical binding]; other site 643561004061 substrate binding site [chemical binding]; other site 643561004062 activation loop (A-loop); other site 643561004063 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 643561004064 phosphopeptide binding site; other site 643561004065 type VI secretion system FHA domain protein; Region: VI_FHA; TIGR03354 643561004066 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 643561004067 Active site [active] 643561004068 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 643561004069 Bacterial protein of unknown function (DUF876); Region: DUF876; cl01406 643561004070 hypothetical protein; Provisional; Region: PRK07033 643561004071 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 643561004072 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561004073 ligand binding site [chemical binding]; other site 643561004074 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 643561004075 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 643561004076 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 643561004077 Uncharacterized protein conserved in bacteria (DUF2094); Region: DUF2094; cl01611 643561004078 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 643561004079 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 643561004080 Protein of unknown function (DUF770); Region: DUF770; cl01402 643561004081 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 643561004082 Protein of unknown function (DUF877); Region: DUF877; pfam05943 643561004083 Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]; Region: ImpE; COG4455 643561004084 ImpE protein; Region: ImpE; pfam07024 643561004085 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 643561004086 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 643561004087 type VI secretion protein, VC_A0110 family; Region: VI_chp_6; TIGR03359 643561004088 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 643561004089 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 643561004090 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 643561004091 Walker A motif; other site 643561004092 ATP binding site [chemical binding]; other site 643561004093 Walker B motif; other site 643561004094 arginine finger; other site 643561004095 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 643561004096 Walker A motif; other site 643561004097 ATP binding site [chemical binding]; other site 643561004098 Walker B motif; other site 643561004099 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 643561004100 Protein of unknown function DUF45; Region: DUF45; cl00636 643561004101 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 643561004102 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 643561004103 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 643561004104 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 643561004105 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 643561004106 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 643561004107 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 643561004108 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 643561004109 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 643561004110 Fumarase C-terminus; Region: Fumerase_C; cl00795 643561004111 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 643561004112 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 643561004113 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561004114 metal binding site [ion binding]; metal-binding site 643561004115 active site 643561004116 I-site; other site 643561004117 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 643561004118 fumarate hydratase; Reviewed; Region: fumC; PRK00485 643561004119 Class II fumarases; Region: Fumarase_classII; cd01362 643561004120 active site 643561004121 tetramer interface [polypeptide binding]; other site 643561004122 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 643561004123 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes...; Region: Topo_IB_C; cd00659 643561004124 DNA binding site [nucleotide binding] 643561004125 active site 643561004126 Int/Topo IB signature motif; other site 643561004127 catalytic residues [active] 643561004128 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 643561004129 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561004130 active site 643561004131 phosphorylation site [posttranslational modification] 643561004132 intermolecular recognition site; other site 643561004133 dimerization interface [polypeptide binding]; other site 643561004134 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 643561004135 DNA binding site [nucleotide binding] 643561004136 signal transduction histidine-protein kinase BaeS; Provisional; Region: PRK10549 643561004137 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 643561004138 dimerization interface [polypeptide binding]; other site 643561004139 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 643561004140 dimer interface [polypeptide binding]; other site 643561004141 phosphorylation site [posttranslational modification] 643561004142 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 643561004143 ATP binding site [chemical binding]; other site 643561004144 Mg2+ binding site [ion binding]; other site 643561004145 G-X-G motif; other site 643561004146 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561004147 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 643561004148 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 643561004149 dimer interface [polypeptide binding]; other site 643561004150 conserved gate region; other site 643561004151 putative PBP binding loops; other site 643561004152 ABC-ATPase subunit interface; other site 643561004153 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 643561004154 This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these...; Region: ABC_Pro_Gly_Bertaine; cd03294 643561004155 Walker A/P-loop; other site 643561004156 ATP binding site [chemical binding]; other site 643561004157 Q-loop/lid; other site 643561004158 ABC transporter signature motif; other site 643561004159 Walker B; other site 643561004160 D-loop; other site 643561004161 H-loop/switch region; other site 643561004162 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc2; cd04583 643561004163 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 643561004164 acetyl-CoA synthetase; Provisional; Region: PRK00174 643561004165 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 643561004166 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561004167 Cytochrome c; Region: Cytochrom_C; cl11414 643561004168 Dehydratase family; Region: ILVD_EDD; cl00340 643561004169 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 643561004170 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 643561004171 Ferritin-like domain; Region: Ferritin; pfam00210 643561004172 heme binding site [chemical binding]; other site 643561004173 ferroxidase pore; other site 643561004174 ferroxidase diiron center [ion binding]; other site 643561004175 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 643561004176 Transcriptional regulators [Transcription]; Region: GntR; COG1802 643561004177 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561004178 DNA-binding site [nucleotide binding]; DNA binding site 643561004179 FCD domain; Region: FCD; cl11656 643561004180 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 643561004181 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561004182 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561004183 enoyl-CoA hydratase; Provisional; Region: PRK06144 643561004184 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 643561004185 substrate binding site [chemical binding]; other site 643561004186 oxyanion hole (OAH) forming residues; other site 643561004187 trimer interface [polypeptide binding]; other site 643561004188 malonyl-CoA synthase; Validated; Region: PRK07514 643561004189 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561004190 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561004191 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561004192 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 643561004193 dimerization interface [polypeptide binding]; other site 643561004194 substrate binding pocket [chemical binding]; other site 643561004195 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 643561004196 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 643561004197 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, 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...; Region: Met_dep_hydrolase_A; cd01299 643561004198 active site 643561004199 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561004200 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 643561004201 ligand binding site [chemical binding]; other site 643561004202 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561004203 TM-ABC transporter signature motif; other site 643561004204 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561004205 TM-ABC transporter signature motif; other site 643561004206 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 643561004207 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561004208 Walker A/P-loop; other site 643561004209 ATP binding site [chemical binding]; other site 643561004210 Q-loop/lid; other site 643561004211 ABC transporter signature motif; other site 643561004212 Walker B; other site 643561004213 D-loop; other site 643561004214 H-loop/switch region; other site 643561004215 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 643561004216 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561004217 Walker A/P-loop; other site 643561004218 ATP binding site [chemical binding]; other site 643561004219 Q-loop/lid; other site 643561004220 ABC transporter signature motif; other site 643561004221 Walker B; other site 643561004222 D-loop; other site 643561004223 H-loop/switch region; other site 643561004224 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 643561004225 Ligand Binding Site [chemical binding]; other site 643561004226 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 643561004227 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 643561004228 metal-binding site [ion binding] 643561004229 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 643561004230 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 643561004231 Low-spin heme binding site [chemical binding]; other site 643561004232 Putative water exit pathway; other site 643561004233 Binuclear center (active site) [active] 643561004234 Putative proton exit pathway; other site 643561004235 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 643561004236 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; cl00282 643561004237 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 643561004238 Cytochrome c; Region: Cytochrom_C; cl11414 643561004239 Cytochrome c; Region: Cytochrom_C; cl11414 643561004240 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 643561004241 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 643561004242 FixH; Region: FixH; cl01254 643561004243 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 643561004244 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 643561004245 ligand binding site [chemical binding]; other site 643561004246 flexible hinge region; other site 643561004247 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 643561004248 putative switch regulator; other site 643561004249 non-specific DNA interactions [nucleotide binding]; other site 643561004250 DNA binding site [nucleotide binding] 643561004251 sequence specific DNA binding site [nucleotide binding]; other site 643561004252 putative cAMP binding site [chemical binding]; other site 643561004253 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 643561004254 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 643561004255 FeS/SAM binding site; other site 643561004256 HemN C-terminal region; Region: HemN_C; pfam06969 643561004257 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 643561004258 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 643561004259 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 643561004260 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 643561004261 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561004262 metal binding site [ion binding]; metal-binding site 643561004263 active site 643561004264 I-site; other site 643561004265 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 643561004266 Cell division protein ZapA; Region: ZapA; cl01146 643561004267 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 643561004268 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 643561004269 N-terminal plug; other site 643561004270 ligand-binding site [chemical binding]; other site 643561004271 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 643561004272 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 643561004273 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 643561004274 catalytic triad [active] 643561004275 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 643561004276 homotrimer interface [polypeptide binding]; other site 643561004277 Walker A motif; other site 643561004278 GTP binding site [chemical binding]; other site 643561004279 Walker B motif; other site 643561004280 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 643561004281 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface...; Region: TroA-like; cl00262 643561004282 intersubunit interface [polypeptide binding]; other site 643561004283 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 643561004284 dimer interface [polypeptide binding]; other site 643561004285 putative PBP binding regions; other site 643561004286 ABC-ATPase subunit interface; other site 643561004287 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 643561004288 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561004289 Walker A/P-loop; other site 643561004290 ATP binding site [chemical binding]; other site 643561004291 Q-loop/lid; other site 643561004292 ABC transporter signature motif; other site 643561004293 Walker B; other site 643561004294 D-loop; other site 643561004295 H-loop/switch region; other site 643561004296 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 643561004297 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 643561004298 homodimer interface [polypeptide binding]; other site 643561004299 Walker A motif; other site 643561004300 ATP binding site [chemical binding]; other site 643561004301 hydroxycobalamin binding site [chemical binding]; other site 643561004302 Walker B motif; other site 643561004303 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(; Region: BluB; cd02145 643561004304 putative FMN binding site [chemical binding]; other site 643561004305 CobD/Cbib protein; Region: CobD_Cbib; cl00561 643561004306 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 643561004307 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 643561004308 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561004309 catalytic residue [active] 643561004310 Protein of unknown function (DUF3037); Region: DUF3037; pfam11236 643561004311 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561004312 classical (c) SDRs; Region: SDR_c; cd05233 643561004313 NAD(P) binding site [chemical binding]; other site 643561004314 active site 643561004315 cobyric acid synthase; Provisional; Region: PRK00784 643561004316 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 643561004317 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 643561004318 catalytic triad [active] 643561004319 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 643561004320 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 643561004321 putative dimer interface [polypeptide binding]; other site 643561004322 active site pocket [active] 643561004323 putative cataytic base [active] 643561004324 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 643561004325 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561004326 Walker A/P-loop; other site 643561004327 ATP binding site [chemical binding]; other site 643561004328 Q-loop/lid; other site 643561004329 ABC transporter signature motif; other site 643561004330 Walker B; other site 643561004331 D-loop; other site 643561004332 H-loop/switch region; other site 643561004333 TOBE domain; Region: TOBE_2; cl01440 643561004334 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 643561004335 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 643561004336 dimer interface [polypeptide binding]; other site 643561004337 conserved gate region; other site 643561004338 putative PBP binding loops; other site 643561004339 ABC-ATPase subunit interface; other site 643561004340 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 643561004341 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 643561004342 dimer interface [polypeptide binding]; other site 643561004343 conserved gate region; other site 643561004344 putative PBP binding loops; other site 643561004345 ABC-ATPase subunit interface; other site 643561004346 Transcriptional regulators [Transcription]; Region: GntR; COG1802 643561004347 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561004348 DNA-binding site [nucleotide binding]; DNA binding site 643561004349 FCD domain; Region: FCD; cl11656 643561004350 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 643561004351 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 643561004352 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 643561004353 putative substrate translocation pore; other site 643561004354 tellurite resistance protein terB; Region: terB; cd07176 643561004355 putative metal binding site [ion binding]; other site 643561004356 Domain of unknown function (DUF697); Region: DUF697; cl12064 643561004357 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561004358 endonuclease III; Provisional; Region: PRK10702 643561004359 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 643561004360 minor groove reading motif; other site 643561004361 helix-hairpin-helix signature motif; other site 643561004362 substrate binding pocket [chemical binding]; other site 643561004363 active site 643561004364 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 643561004365 aspartate aminotransferase; Provisional; Region: PRK08361 643561004366 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 643561004367 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561004368 homodimer interface [polypeptide binding]; other site 643561004369 catalytic residue [active] 643561004370 SlyX; Region: SlyX; cl01090 643561004371 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 643561004372 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 643561004373 active site 643561004374 catalytic tetrad [active] 643561004375 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 643561004376 DEAD-like helicases superfamily; Region: DEXDc; smart00487 643561004377 ATP binding site [chemical binding]; other site 643561004378 Mg++ binding site [ion binding]; other site 643561004379 motif III; other site 643561004380 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 643561004381 nucleotide binding region [chemical binding]; other site 643561004382 ATP-binding site [chemical binding]; other site 643561004383 translation initiation factor Sui1; Validated; Region: PRK06824 643561004384 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 643561004385 Predicted RNA interaction site [nucleotide binding]; other site 643561004386 putative binding site; other site 643561004387 Mutations affecting start-site selection; other site 643561004388 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 643561004389 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 643561004390 heme-binding site [chemical binding]; other site 643561004391 iron-sulfur cluster repair di-iron protein; Provisional; Region: PRK10992 643561004392 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 643561004393 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 643561004394 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 643561004395 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561004396 Rrf2 family protein; Region: rrf2_super; TIGR00738 643561004397 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 643561004398 Strictosidine synthase; Region: Str_synth; pfam03088 643561004399 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 643561004400 active site 643561004401 metal binding site [ion binding]; metal-binding site 643561004402 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 643561004403 active site 643561004404 Cupin domain; Region: Cupin_2; cl09118 643561004405 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561004406 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 643561004407 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 643561004408 chromosome replication initiation inhibitor protein; Provisional; Region: PRK13348 643561004409 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561004410 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 643561004411 dimerization interface [polypeptide binding]; other site 643561004412 LysE type translocator; Region: LysE; cl00565 643561004413 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561004414 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 643561004415 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 643561004416 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 643561004417 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 643561004418 DNA binding residues [nucleotide binding] 643561004419 dimerization interface [polypeptide binding]; other site 643561004420 Tannase and feruloyl esterase; Region: Tannase; pfam07519 643561004421 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 643561004422 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 643561004423 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 643561004424 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 643561004425 ATP binding site [chemical binding]; other site 643561004426 putative Mg++ binding site [ion binding]; other site 643561004427 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 643561004428 nucleotide binding region [chemical binding]; other site 643561004429 ATP-binding site [chemical binding]; other site 643561004430 TRCF domain; Region: TRCF; cl04088 643561004431 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 643561004432 substrate binding site [chemical binding]; other site 643561004433 dimer interface [polypeptide binding]; other site 643561004434 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 643561004435 homotrimer interaction site [polypeptide binding]; other site 643561004436 zinc binding site [ion binding]; other site 643561004437 CDP-binding sites; other site 643561004438 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 643561004439 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 643561004440 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 643561004441 ATP binding site [chemical binding]; other site 643561004442 Mg2+ binding site [ion binding]; other site 643561004443 G-X-G motif; other site 643561004444 osmolarity response regulator; Provisional; Region: ompR; PRK09468 643561004445 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561004446 active site 643561004447 phosphorylation site [posttranslational modification] 643561004448 intermolecular recognition site; other site 643561004449 dimerization interface [polypeptide binding]; other site 643561004450 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 643561004451 DNA binding site [nucleotide binding] 643561004452 Protein of unknown function (DUF541); Region: SIMPL; cl01077 643561004453 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 643561004454 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 643561004455 NAD binding site [chemical binding]; other site 643561004456 homotetramer interface [polypeptide binding]; other site 643561004457 homodimer interface [polypeptide binding]; other site 643561004458 substrate binding site [chemical binding]; other site 643561004459 active site 643561004460 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561004461 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 643561004462 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 643561004463 synthetase active site [active] 643561004464 NTP binding site [chemical binding]; other site 643561004465 metal binding site [ion binding]; metal-binding site 643561004466 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 643561004467 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 643561004468 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561004469 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 643561004470 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 643561004471 OsmC-like protein; Region: OsmC; cl00767 643561004472 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 643561004473 proposed catalytic triad [active] 643561004474 conserved cys residue [active] 643561004475 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 643561004476 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 643561004477 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 643561004478 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 643561004479 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 643561004480 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 643561004481 substrate binding site [chemical binding]; other site 643561004482 ATP binding site [chemical binding]; other site 643561004483 galactarate dehydratase; Region: galactar-dH20; TIGR03248 643561004484 SAF domain; Region: SAF; cl00555 643561004485 SAF domain; Region: SAF; cl00555 643561004486 Domain of unknown function (DUF718); Region: DUF718; cl01281 643561004487 altronate oxidoreductase; Provisional; Region: PRK03643 643561004488 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 643561004489 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 643561004490 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH7; cd08261 643561004491 putative NAD(P) binding site [chemical binding]; other site 643561004492 catalytic Zn binding site [ion binding]; other site 643561004493 structural Zn binding site [ion binding]; other site 643561004494 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 643561004495 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 643561004496 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 643561004497 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 643561004498 active site 643561004499 catalytic tetrad [active] 643561004500 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 643561004501 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_2; cd06310 643561004502 putative ligand binding site [chemical binding]; other site 643561004503 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 643561004504 TM-ABC transporter signature motif; other site 643561004505 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 643561004506 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 643561004507 Walker A/P-loop; other site 643561004508 ATP binding site [chemical binding]; other site 643561004509 Q-loop/lid; other site 643561004510 ABC transporter signature motif; other site 643561004511 Walker B; other site 643561004512 D-loop; other site 643561004513 H-loop/switch region; other site 643561004514 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 643561004515 Transcriptional regulators [Transcription]; Region: FadR; COG2186 643561004516 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561004517 DNA-binding site [nucleotide binding]; DNA binding site 643561004518 FCD domain; Region: FCD; cl11656 643561004519 2-keto-3-deoxygluconate permease; Region: KdgT; cl14653 643561004520 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561004521 human DHRS6-like, classical (c) SDRs; Region: DHRS6_like_SDR_c; cd05368 643561004522 NAD binding site [chemical binding]; other site 643561004523 homotetramer interface [polypeptide binding]; other site 643561004524 homodimer interface [polypeptide binding]; other site 643561004525 active site 643561004526 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 643561004527 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561004528 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561004529 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561004530 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561004531 Uncharacterized conserved protein (DUF2267); Region: DUF2267; cl02314 643561004532 Domain of unknown function (DUF1905); Region: DUF1905; pfam08922 643561004533 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 643561004534 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 643561004535 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 643561004536 FeS/SAM binding site; other site 643561004537 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 643561004538 active site 643561004539 NTP binding site [chemical binding]; other site 643561004540 metal binding triad [ion binding]; metal-binding site 643561004541 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 643561004542 citrate-proton symporter; Provisional; Region: PRK15075 643561004543 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 643561004544 putative substrate translocation pore; other site 643561004545 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 643561004546 non-specific DNA binding site [nucleotide binding]; other site 643561004547 salt bridge; other site 643561004548 sequence-specific DNA binding site [nucleotide binding]; other site 643561004549 elongation factor P; Validated; Region: PRK00529 643561004550 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 643561004551 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 643561004552 RNA binding site [nucleotide binding]; other site 643561004553 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 643561004554 RNA binding site [nucleotide binding]; other site 643561004555 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 643561004556 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561004557 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 643561004558 putative dimerization interface [polypeptide binding]; other site 643561004559 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561004560 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 643561004561 active site 643561004562 catalytic residues [active] 643561004563 metal binding site [ion binding]; metal-binding site 643561004564 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561004565 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561004566 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561004567 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561004568 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 643561004569 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 643561004570 putative active site [active] 643561004571 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 643561004572 catalytic nucleophile [active] 643561004573 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 643561004574 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 643561004575 Walker A/P-loop; other site 643561004576 ATP binding site [chemical binding]; other site 643561004577 Q-loop/lid; other site 643561004578 ABC transporter signature motif; other site 643561004579 Walker B; other site 643561004580 D-loop; other site 643561004581 H-loop/switch region; other site 643561004582 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561004583 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 643561004584 Walker A/P-loop; other site 643561004585 ATP binding site [chemical binding]; other site 643561004586 Q-loop/lid; other site 643561004587 ABC transporter signature motif; other site 643561004588 Walker B; other site 643561004589 D-loop; other site 643561004590 H-loop/switch region; other site 643561004591 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561004592 The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold; Region: PBP2_Ylib_like; cd08499 643561004593 glutathione ABC transporter substrate-binding protein GsiB; Provisional; Region: PRK15413 643561004594 glutathione ABC transporter permease GsiC; Provisional; Region: PRK15081 643561004595 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 643561004596 dimer interface [polypeptide binding]; other site 643561004597 conserved gate region; other site 643561004598 putative PBP binding loops; other site 643561004599 ABC-ATPase subunit interface; other site 643561004600 glutathione ABC transporter permease GsiD; Provisional; Region: PRK15082 643561004601 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 643561004602 dimer interface [polypeptide binding]; other site 643561004603 conserved gate region; other site 643561004604 putative PBP binding loops; other site 643561004605 ABC-ATPase subunit interface; other site 643561004606 L-Aminopeptidase D-amidase/D-esterase (DmpA) family; DmpA catalyzes the release of N-terminal D and L amino acids from peptide susbtrates. DmpA is synthesized as a single polypeptide precursor, which is autocatalytically cleaved to the active...; Region: DmpA; cd02253 643561004607 homodimer interface [polypeptide binding]; other site 643561004608 homotetramer interface [polypeptide binding]; other site 643561004609 active site pocket [active] 643561004610 cleavage site 643561004611 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA_1; cd08663 643561004612 SxDxEG motif; other site 643561004613 active site 643561004614 metal binding site [ion binding]; metal-binding site 643561004615 homopentamer interface [polypeptide binding]; other site 643561004616 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 643561004617 aspartate racemase; Region: asp_race; TIGR00035 643561004618 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 643561004619 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 643561004620 GIY-YIG motif/motif A; other site 643561004621 active site 643561004622 catalytic site [active] 643561004623 putative DNA binding site [nucleotide binding]; other site 643561004624 metal binding site [ion binding]; metal-binding site 643561004625 UvrB/uvrC motif; Region: UVR; pfam02151 643561004626 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 643561004627 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 643561004628 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 643561004629 IHF dimer interface [polypeptide binding]; other site 643561004630 IHF - DNA interface [nucleotide binding]; other site 643561004631 periplasmic folding chaperone; Provisional; Region: PRK10788 643561004632 SurA N-terminal domain; Region: SurA_N; pfam09312 643561004633 PPIC-type PPIASE domain; Region: Rotamase; cl08278 643561004634 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561004635 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561004636 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 643561004637 argininosuccinate lyase; Provisional; Region: PRK00855 643561004638 active sites [active] 643561004639 tetramer interface [polypeptide binding]; other site 643561004640 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561004641 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 643561004642 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 643561004643 dimerization interface [polypeptide binding]; other site 643561004644 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 643561004645 methionine aminopeptidase; Reviewed; Region: PRK07281 643561004646 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 643561004647 active site 643561004648 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 643561004649 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561004650 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561004651 hypothetical protein; Validated; Region: PRK07586 643561004652 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 643561004653 PYR/PP interface [polypeptide binding]; other site 643561004654 dimer interface [polypeptide binding]; other site 643561004655 TPP binding site [chemical binding]; other site 643561004656 TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of benzoylformate to benzaldehyde and carbon dioxide. This...; Region: TPP_BFDC; cd02002 643561004657 TPP-binding site [chemical binding]; other site 643561004658 dimer interface [polypeptide binding]; other site 643561004659 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 643561004660 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561004661 NAD(P) binding site [chemical binding]; other site 643561004662 active site 643561004663 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 643561004664 Ycf48-like protein; Provisional; Region: PRK13684 643561004665 The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC 1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6 and BphC3-RGP6, and similar proteins; Region: BphC2-C3-RGP6_C_like; cd08348 643561004666 putative active site [active] 643561004667 putative metal binding site [ion binding]; other site 643561004668 Protein of unknown function (DUF1185); Region: DUF1185; pfam06684 643561004669 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 643561004670 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561004671 NIPSNAP; Region: NIPSNAP; pfam07978 643561004672 3-(3-hydroxyphenyl)propionate hydroxylase; Validated; Region: mhpA; PRK06183 643561004673 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561004674 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561004675 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561004676 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 643561004677 tetramerization interface [polypeptide binding]; other site 643561004678 NAD(P) binding site [chemical binding]; other site 643561004679 catalytic residues [active] 643561004680 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561004681 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 643561004682 tetramerization interface [polypeptide binding]; other site 643561004683 NAD(P) binding site [chemical binding]; other site 643561004684 catalytic residues [active] 643561004685 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_2; cd02138 643561004686 putative FMN binding site [chemical binding]; other site 643561004687 Ycf48-like protein; Provisional; Region: PRK13684 643561004688 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 643561004689 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 643561004690 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 643561004691 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 643561004692 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 643561004693 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561004694 NAD(P) binding site [chemical binding]; other site 643561004695 catalytic residues [active] 643561004696 transcriptional regulator EutR; Provisional; Region: PRK10130 643561004697 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561004698 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 643561004699 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 643561004700 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561004701 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 643561004702 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]; Region: GabT; COG0160 643561004703 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 643561004704 inhibitor-cofactor binding pocket; inhibition site 643561004705 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561004706 catalytic residue [active] 643561004707 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561004708 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561004709 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561004710 putative cation:proton antiport protein; Provisional; Region: PRK10669 643561004711 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 643561004712 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561004713 The M14 family of metallocarboxypeptidases (MCPs) are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key...; Region: Peptidase_M14_like; cl11393 643561004714 active site 643561004715 Zn-binding site [ion binding]; other site 643561004716 helicase 45; Provisional; Region: PTZ00424 643561004717 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 643561004718 ATP binding site [chemical binding]; other site 643561004719 Mg++ binding site [ion binding]; other site 643561004720 motif III; other site 643561004721 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 643561004722 nucleotide binding region [chemical binding]; other site 643561004723 ATP-binding site [chemical binding]; other site 643561004724 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 643561004725 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 643561004726 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 643561004727 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561004728 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 643561004729 ABC transporter; Region: ABC_tran_2; pfam12848 643561004730 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 643561004731 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 643561004732 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561004733 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 643561004734 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of highly-; Region: nylC_like; cd02252 643561004735 putative active site pocket [active] 643561004736 cleavage site 643561004737 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 643561004738 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561004739 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561004740 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 643561004741 NAD(P) binding site [chemical binding]; other site 643561004742 catalytic residues [active] 643561004743 choline dehydrogenase; Validated; Region: PRK02106 643561004744 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 643561004745 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 643561004746 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 643561004747 Enterobacterial TraT complement resistance protein; Region: TraT; cl05410 643561004748 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 643561004749 Cupin domain; Region: Cupin_2; cl09118 643561004750 Protein of unknown function, DUF; Region: DUF411; cl01142 643561004751 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 643561004752 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 643561004753 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 643561004754 Outer membrane efflux protein; Region: OEP; pfam02321 643561004755 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 643561004756 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 643561004757 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 643561004758 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 643561004759 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 643561004760 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 643561004761 DNA binding residues [nucleotide binding] 643561004762 Domain of unknown function DUF140; Region: DUF140; cl00510 643561004763 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 643561004764 mce related protein; Region: MCE; pfam02470 643561004765 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 643561004766 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 643561004767 putative substrate binding site [chemical binding]; other site 643561004768 putative ATP binding site [chemical binding]; other site 643561004769 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 643561004770 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561004771 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 643561004772 rRNA interaction site [nucleotide binding]; other site 643561004773 S8 interaction site; other site 643561004774 putative laminin-1 binding site; other site 643561004775 elongation factor Ts; Provisional; Region: tsf; PRK09377 643561004776 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 643561004777 Elongation factor TS; Region: EF_TS; pfam00889 643561004778 Elongation factor TS; Region: EF_TS; pfam00889 643561004779 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 643561004780 putative nucleotide binding site [chemical binding]; other site 643561004781 uridine monophosphate binding site [chemical binding]; other site 643561004782 homohexameric interface [polypeptide binding]; other site 643561004783 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 643561004784 hinge region; other site 643561004785 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 643561004786 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 643561004787 catalytic residue [active] 643561004788 putative FPP diphosphate binding site; other site 643561004789 putative FPP binding hydrophobic cleft; other site 643561004790 dimer interface [polypeptide binding]; other site 643561004791 putative IPP diphosphate binding site; other site 643561004792 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 643561004793 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 643561004794 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 643561004795 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 643561004796 zinc metallopeptidase RseP; Provisional; Region: PRK10779 643561004797 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 643561004798 active site 643561004799 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 643561004800 protein binding site [polypeptide binding]; other site 643561004801 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 643561004802 putative substrate binding region [chemical binding]; other site 643561004803 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 643561004804 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 643561004805 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 643561004806 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 643561004807 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 643561004808 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 643561004809 Surface antigen; Region: Bac_surface_Ag; cl03097 643561004810 periplasmic chaperone; Provisional; Region: PRK10780 643561004811 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 643561004812 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 643561004813 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 643561004814 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 643561004815 trimer interface [polypeptide binding]; other site 643561004816 active site 643561004817 UDP-GlcNAc binding site [chemical binding]; other site 643561004818 lipid binding site [chemical binding]; lipid-binding site 643561004819 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 643561004820 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 643561004821 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 643561004822 active site 643561004823 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 643561004824 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 643561004825 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 643561004826 RNA/DNA hybrid binding site [nucleotide binding]; other site 643561004827 active site 643561004828 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 643561004829 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 643561004830 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 643561004831 Secretin and TonB N terminus short domain; Region: STN; cl06624 643561004832 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561004833 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 643561004834 N-terminal plug; other site 643561004835 ligand-binding site [chemical binding]; other site 643561004836 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 643561004837 FecR protein; Region: FecR; pfam04773 643561004838 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561004839 RNA polymerase sigma factor; Reviewed; Region: PRK12527 643561004840 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 643561004841 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 643561004842 AMP binding site [chemical binding]; other site 643561004843 metal binding site [ion binding]; metal-binding site 643561004844 active site 643561004845 aminopeptidase N; Provisional; Region: pepN; PRK14015 643561004846 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 643561004847 active site 643561004848 Zn binding site [ion binding]; other site 643561004849 Predicted ATPase [General function prediction only]; Region: COG4637 643561004850 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561004851 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561004852 ABC transporter signature motif; other site 643561004853 Walker B; other site 643561004854 D-loop; other site 643561004855 H-loop/switch region; other site 643561004856 peptide chain release factor 2; Validated; Region: prfB; PRK00578 643561004857 RF-1 domain; Region: RF-1; cl02875 643561004858 RF-1 domain; Region: RF-1; cl02875 643561004859 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561004860 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 643561004861 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 643561004862 Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]; Region: Nei; COG0266 643561004863 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; Region: BaFpgNei_N_2; cd08974 643561004864 putative DNA binding site [nucleotide binding]; other site 643561004865 catalytic residue [active] 643561004866 putative H2TH interface [polypeptide binding]; other site 643561004867 putative catalytic residues [active] 643561004868 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 643561004869 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 643561004870 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 643561004871 active site 643561004872 catalytic tetrad [active] 643561004873 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 643561004874 putative deacylase active site [active] 643561004875 Domain of unknown function (DUF205); Region: DUF205; cl00410 643561004876 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 643561004877 Predicted aspartyl protease [General function prediction only]; Region: COG3577 643561004878 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 643561004879 catalytic motif [active] 643561004880 Catalytic residue [active] 643561004881 Protein of unknown function (DUF520); Region: DUF520; cl00723 643561004882 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 643561004883 FAD binding domain; Region: FAD_binding_4; pfam01565 643561004884 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 643561004885 argininosuccinate synthase; Region: argG; TIGR00032 643561004886 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 643561004887 Ligand Binding Site [chemical binding]; other site 643561004888 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 643561004889 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 643561004890 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 643561004891 putative catalytic residues [active] 643561004892 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 643561004893 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 643561004894 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 643561004895 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DedD; COG3147 643561004896 Sporulation related domain; Region: SPOR; cl10051 643561004897 Colicin V production protein; Region: Colicin_V; cl00567 643561004898 amidophosphoribosyltransferase; Provisional; Region: PRK09246 643561004899 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 643561004900 active site 643561004901 tetramer interface [polypeptide binding]; other site 643561004902 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 643561004903 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 643561004904 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 643561004905 homodimer interface [polypeptide binding]; other site 643561004906 substrate-cofactor binding pocket; other site 643561004907 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561004908 catalytic residue [active] 643561004909 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 643561004910 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 643561004911 active site 643561004912 HIGH motif; other site 643561004913 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 643561004914 active site 643561004915 KMSKS motif; other site 643561004916 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 643561004917 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 643561004918 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 643561004919 putative substrate translocation pore; other site 643561004920 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 643561004921 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 643561004922 putative substrate translocation pore; other site 643561004923 Protein of unknown function DUF72; Region: DUF72; cl00777 643561004924 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 643561004925 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 643561004926 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 643561004927 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 643561004928 RNA binding site [nucleotide binding]; other site 643561004929 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 643561004930 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561004931 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 643561004932 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 643561004933 putative active site [active] 643561004934 metal binding site [ion binding]; metal-binding site 643561004935 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561004936 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 643561004937 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 643561004938 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 643561004939 active site 643561004940 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561004941 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 643561004942 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 643561004943 YceG-like family; Region: YceG; pfam02618 643561004944 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 643561004945 dimerization interface [polypeptide binding]; other site 643561004946 thymidylate kinase; Validated; Region: tmk; PRK00698 643561004947 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 643561004948 TMP-binding site; other site 643561004949 ATP-binding site [chemical binding]; other site 643561004950 DNA polymerase III subunit delta'; Validated; Region: PRK06964 643561004951 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561004952 PilZ domain; Region: PilZ; cl01260 643561004953 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 643561004954 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 643561004955 active site 643561004956 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 643561004957 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 643561004958 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 643561004959 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 643561004960 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561004961 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 643561004962 Walker A/P-loop; other site 643561004963 ATP binding site [chemical binding]; other site 643561004964 Q-loop/lid; other site 643561004965 ABC transporter signature motif; other site 643561004966 Walker B; other site 643561004967 D-loop; other site 643561004968 H-loop/switch region; other site 643561004969 translocation protein TolB; Provisional; Region: tolB; PRK02889 643561004970 TolB amino-terminal domain; Region: TolB_N; pfam04052 643561004971 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 643561004972 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 643561004973 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 643561004974 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561004975 ligand binding site [chemical binding]; other site 643561004976 Rice tungro bacilliform virus P46 protein; Region: RTBV_P46; pfam06216 643561004977 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 643561004978 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 643561004979 binding surface 643561004980 TPR motif; other site 643561004981 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 643561004982 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 643561004983 putative ATP binding site [chemical binding]; other site 643561004984 putative substrate interface [chemical binding]; other site 643561004985 Protein of unknown function (DUF1810); Region: DUF1810; cl02370 643561004986 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561004987 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 643561004988 dimerization interface [polypeptide binding]; other site 643561004989 ligand binding site [chemical binding]; other site 643561004990 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561004991 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cd00091 643561004992 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 643561004993 active site 643561004994 substrate binding site [chemical binding]; other site 643561004995 Mg2+ binding site [ion binding]; other site 643561004996 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 643561004997 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl02184 643561004998 Endoglucanase C-terminal domain/subunit and related proteins [Carbohydrate transport and metabolism]; Region: COG4305 643561004999 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 643561005000 Cellulose binding domain; Region: CBM_2; cl02709 643561005001 Cache domain; Region: Cache_1; pfam02743 643561005002 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561005003 metal binding site [ion binding]; metal-binding site 643561005004 active site 643561005005 I-site; other site 643561005006 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 643561005007 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005008 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 643561005009 putative dimerization interface [polypeptide binding]; other site 643561005010 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 643561005011 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005012 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005013 Cytochrome c; Region: Cytochrom_C; cl11414 643561005014 Cytochrome c; Region: Cytochrom_C; cl11414 643561005015 Cytochrome c; Region: Cytochrom_C; cl11414 643561005016 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 643561005017 Cytochrome c; Region: Cytochrom_C; cl11414 643561005018 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 643561005019 catalytic residues [active] 643561005020 ribosome maturation protein RimP; Reviewed; Region: PRK00092 643561005021 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 643561005022 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 643561005023 Sm1 motif; other site 643561005024 D3 - B interaction site; other site 643561005025 D1 - D2 interaction site; other site 643561005026 Hfq - Hfq interaction site; other site 643561005027 RNA binding pocket [nucleotide binding]; other site 643561005028 Sm2 motif; other site 643561005029 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 643561005030 NusA N-terminal domain; Region: NusA_N; pfam08529 643561005031 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 643561005032 RNA binding site [nucleotide binding]; other site 643561005033 homodimer interface [polypeptide binding]; other site 643561005034 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 643561005035 G-X-X-G motif; other site 643561005036 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 643561005037 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 643561005038 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 643561005039 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 643561005040 translation initiation factor IF-2; Region: IF-2; TIGR00487 643561005041 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 643561005042 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 643561005043 G1 box; other site 643561005044 putative GEF interaction site [polypeptide binding]; other site 643561005045 GTP/Mg2+ binding site [chemical binding]; other site 643561005046 Switch I region; other site 643561005047 G2 box; other site 643561005048 G3 box; other site 643561005049 Switch II region; other site 643561005050 G4 box; other site 643561005051 G5 box; other site 643561005052 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 643561005053 Translation-initiation factor 2; Region: IF-2; pfam11987 643561005054 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 643561005055 Ribosome-binding factor A; Region: RBFA; cl00542 643561005056 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01851 643561005057 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 643561005058 RNA binding site [nucleotide binding]; other site 643561005059 active site 643561005060 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 643561005061 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 643561005062 G1 box; other site 643561005063 putative GEF interaction site [polypeptide binding]; other site 643561005064 GTP/Mg2+ binding site [chemical binding]; other site 643561005065 Switch I region; other site 643561005066 G2 box; other site 643561005067 G3 box; other site 643561005068 Switch II region; other site 643561005069 G4 box; other site 643561005070 G5 box; other site 643561005071 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 643561005072 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 643561005073 Integral membrane protein TerC family; Region: TerC; cl10468 643561005074 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 643561005075 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 643561005076 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 643561005077 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 643561005078 substrate binding site [chemical binding]; other site 643561005079 oxyanion hole (OAH) forming residues; other site 643561005080 trimer interface [polypeptide binding]; other site 643561005081 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 643561005082 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 643561005083 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561005084 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 643561005085 DNA binding residues [nucleotide binding] 643561005086 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 643561005087 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 643561005088 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 643561005089 SmpB-tmRNA interface; other site 643561005090 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 643561005091 putative coenzyme Q binding site [chemical binding]; other site 643561005092 GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but...; Region: TGS; cl03735 643561005093 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 643561005094 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 643561005095 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 643561005096 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 643561005097 active site 643561005098 Phd_YefM; Region: PhdYeFM; cl09153 643561005099 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 643561005100 putative active site [active] 643561005101 homotetrameric interface [polypeptide binding]; other site 643561005102 metal binding site [ion binding]; metal-binding site 643561005103 GMP synthase; Reviewed; Region: guaA; PRK00074 643561005104 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 643561005105 AMP/PPi binding site [chemical binding]; other site 643561005106 candidate oxyanion hole; other site 643561005107 catalytic triad [active] 643561005108 potential glutamine specificity residues [chemical binding]; other site 643561005109 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 643561005110 ATP Binding subdomain [chemical binding]; other site 643561005111 Ligand Binding sites [chemical binding]; other site 643561005112 Dimerization subdomain; other site 643561005113 integrase; Provisional; Region: PRK09692 643561005114 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 643561005115 active site 643561005116 Int/Topo IB signature motif; other site 643561005117 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 643561005118 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561005119 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561005120 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 643561005121 putative active site [active] 643561005122 putative metal-binding site [ion binding]; other site 643561005123 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 643561005124 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561005125 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 643561005126 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 643561005127 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005128 LysR family transcriptional regulator; Provisional; Region: PRK14997 643561005129 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005130 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 643561005131 dimerization interface [polypeptide binding]; other site 643561005132 putative effector binding pocket; other site 643561005133 NodT family; Region: outer_NodT; TIGR01845 643561005134 Outer membrane efflux protein; Region: OEP; pfam02321 643561005135 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 643561005136 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 643561005137 Fusaric acid resistance protein family; Region: FUSC; pfam04632 643561005138 Bacterial protein of unknown function (DUF939); Region: DUF939; cl12136 643561005139 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005140 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561005141 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005142 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 643561005143 dimerization interface [polypeptide binding]; other site 643561005144 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561005145 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 643561005146 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 643561005147 NADP binding site [chemical binding]; other site 643561005148 active site 643561005149 steroid binding site; other site 643561005150 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 643561005151 classical (c) SDRs; Region: SDR_c; cd05233 643561005152 NAD(P) binding site [chemical binding]; other site 643561005153 active site 643561005154 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005155 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 643561005156 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 643561005157 N-terminal plug; other site 643561005158 ligand-binding site [chemical binding]; other site 643561005159 Cupin domain; Region: Cupin_2; cl09118 643561005160 Helix-turn-helix domain; Region: HTH_18; pfam12833 643561005161 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561005162 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561005163 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_8; cd07246 643561005164 putative dimer interface [polypeptide binding]; other site 643561005165 FAD binding domain; Region: FAD_binding_3; pfam01494 643561005166 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005167 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561005168 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 643561005169 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 643561005170 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 643561005171 Domain of unknown function (DUF1795); Region: DUF1795; cl02256 643561005172 Uncharacterized conserved protein [Function unknown]; Region: COG4104 643561005173 PAAR motif; Region: PAAR_motif; pfam05488 643561005174 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561005175 RHS Repeat; Region: RHS_repeat; cl11982 643561005176 RHS Repeat; Region: RHS_repeat; cl11982 643561005177 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561005178 RHS Repeat; Region: RHS_repeat; cl11982 643561005179 RHS Repeat; Region: RHS_repeat; cl11982 643561005180 RHS protein; Region: RHS; pfam03527 643561005181 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561005182 Transposase domain (DUF772); Region: DUF772; cl12084 643561005183 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 643561005184 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 643561005185 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 643561005186 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl10040 643561005187 Rrf2 family protein; Region: rrf2_super; TIGR00738 643561005188 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005189 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 643561005190 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 643561005191 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 643561005192 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 643561005193 ATP binding site [chemical binding]; other site 643561005194 Mg2+ binding site [ion binding]; other site 643561005195 G-X-G motif; other site 643561005196 Response regulator receiver domain; Region: Response_reg; pfam00072 643561005197 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561005198 active site 643561005199 phosphorylation site [posttranslational modification] 643561005200 intermolecular recognition site; other site 643561005201 dimerization interface [polypeptide binding]; other site 643561005202 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 643561005203 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 643561005204 dimer interface [polypeptide binding]; other site 643561005205 ADP-ribose binding site [chemical binding]; other site 643561005206 active site 643561005207 nudix motif; other site 643561005208 metal binding site [ion binding]; metal-binding site 643561005209 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 643561005210 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 643561005211 active site 643561005212 PAS fold; Region: PAS_4; pfam08448 643561005213 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 643561005214 putative active site [active] 643561005215 heme pocket [chemical binding]; other site 643561005216 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561005217 metal binding site [ion binding]; metal-binding site 643561005218 active site 643561005219 I-site; other site 643561005220 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561005221 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005222 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561005223 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005224 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005225 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005226 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005227 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005228 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005229 glutathionine S-transferase; Provisional; Region: PRK10542 643561005230 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens...; Region: GST_N_Beta; cd03057 643561005231 C-terminal domain interface [polypeptide binding]; other site 643561005232 GSH binding site (G-site) [chemical binding]; other site 643561005233 dimer interface [polypeptide binding]; other site 643561005234 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 643561005235 dimer interface [polypeptide binding]; other site 643561005236 N-terminal domain interface [polypeptide binding]; other site 643561005237 substrate binding pocket (H-site) [chemical binding]; other site 643561005238 Activator of aromatic catabolism; Region: XylR_N; pfam06505 643561005239 Heme NO binding; Region: HNOB; cl15268 643561005240 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 643561005241 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 643561005242 Walker A motif; other site 643561005243 ATP binding site [chemical binding]; other site 643561005244 Walker B motif; other site 643561005245 arginine finger; other site 643561005246 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561005247 NAD-dependent benzaldehyde dehydrogenase II-like; Region: ALDH_BenzADH; cd07152 643561005248 NAD(P) binding site [chemical binding]; other site 643561005249 catalytic residues [active] 643561005250 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005251 NAD(P) binding site [chemical binding]; other site 643561005252 3-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK12428 643561005253 active site 643561005254 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561005255 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 643561005256 N-terminal plug; other site 643561005257 ligand-binding site [chemical binding]; other site 643561005258 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 643561005259 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 643561005260 Walker A/P-loop; other site 643561005261 ATP binding site [chemical binding]; other site 643561005262 Q-loop/lid; other site 643561005263 ABC transporter signature motif; other site 643561005264 Walker B; other site 643561005265 D-loop; other site 643561005266 H-loop/switch region; other site 643561005267 Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and...; Region: TroA_a; cd01148 643561005268 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 643561005269 putative ligand binding residues [chemical binding]; other site 643561005270 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 643561005271 dimer interface [polypeptide binding]; other site 643561005272 putative PBP binding regions; other site 643561005273 ABC-ATPase subunit interface; other site 643561005274 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 643561005275 trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: putA; PRK11809 643561005276 Proline dehydrogenase; Region: Pro_dh; cl03282 643561005277 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 643561005278 NAD(P) binding site [chemical binding]; other site 643561005279 catalytic residues [active] 643561005280 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 643561005281 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005282 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005283 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 643561005284 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 643561005285 YccA-like proteins; Region: YccA_like; cd10433 643561005286 Domain of unknown function (DUF336); Region: DUF336; cl01249 643561005287 Hemin uptake protein hemP; Region: hemP; cl10043 643561005288 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 643561005289 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 643561005290 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 643561005291 Gram-negative bacterial tonB protein; Region: TonB; cl10048 643561005292 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 643561005293 Phasin protein; Region: Phasin_2; cl11491 643561005294 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 643561005295 active site 643561005296 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 643561005297 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 643561005298 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 643561005299 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 643561005300 active site 643561005301 glyoxylate reductase; Reviewed; Region: PRK13243 643561005302 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005303 RmuC family; Region: RmuC; pfam02646 643561005304 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 643561005305 Major Facilitator Superfamily; Region: MFS_1; pfam07690 643561005306 putative substrate translocation pore; other site 643561005307 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 643561005308 CrcB-like protein; Region: CRCB; cl09114 643561005309 DctM-like transporters; Region: DctM; pfam06808 643561005310 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 643561005311 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561005312 The M14 family of metallocarboxypeptidases (MCPs) are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key...; Region: Peptidase_M14_like; cl11393 643561005313 active site 643561005314 Zn-binding site [ion binding]; other site 643561005315 5-oxoprolinase; Region: PLN02666 643561005316 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 643561005317 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 643561005318 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 643561005319 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 643561005320 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 643561005321 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 643561005322 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 643561005323 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 643561005324 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 643561005325 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 643561005326 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 643561005327 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 643561005328 Domain related to MnhB subunit of Na+/H+ antiporter; Region: MnhB; cl00676 643561005329 tetratricopeptide repeat protein; Provisional; Region: PRK11788 643561005330 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 643561005331 binding surface 643561005332 TPR motif; other site 643561005333 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561005334 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 643561005335 IHF dimer interface [polypeptide binding]; other site 643561005336 IHF - DNA interface [nucleotide binding]; other site 643561005337 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 643561005338 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 643561005339 RNA binding site [nucleotide binding]; other site 643561005340 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 643561005341 RNA binding site [nucleotide binding]; other site 643561005342 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 643561005343 RNA binding site [nucleotide binding]; other site 643561005344 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 643561005345 RNA binding site [nucleotide binding]; other site 643561005346 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 643561005347 RNA binding site [nucleotide binding]; other site 643561005348 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 643561005349 RNA binding site [nucleotide binding]; other site 643561005350 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 643561005351 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 643561005352 hinge; other site 643561005353 active site 643561005354 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 643561005355 CMP-binding site; other site 643561005356 The sites determining sugar specificity; other site 643561005357 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005358 Prephenate dehydrogenase; Region: PDH; pfam02153 643561005359 Chorismate mutase type II; Region: CM_2; cl00693 643561005360 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 643561005361 Prephenate dehydratase; Region: PDT; pfam00800 643561005362 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 643561005363 putative L-Phe binding site [chemical binding]; other site 643561005364 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 643561005365 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561005366 catalytic residue [active] 643561005367 DNA gyrase subunit A; Validated; Region: PRK05560 643561005368 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 643561005369 CAP-like domain; other site 643561005370 Active site [active] 643561005371 primary dimer interface [polypeptide binding]; other site 643561005372 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 643561005373 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 643561005374 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 643561005375 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 643561005376 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 643561005377 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 643561005378 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561005379 ligand binding site [chemical binding]; other site 643561005380 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 643561005381 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 643561005382 S-adenosylmethionine binding site [chemical binding]; other site 643561005383 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 643561005384 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 643561005385 motif II; other site 643561005386 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase_like_1; cd01832 643561005387 active site 643561005388 catalytic triad [active] 643561005389 oxyanion hole [active] 643561005390 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 643561005391 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 643561005392 dimer interface [polypeptide binding]; other site 643561005393 phosphorylation site [posttranslational modification] 643561005394 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 643561005395 ATP binding site [chemical binding]; other site 643561005396 Mg2+ binding site [ion binding]; other site 643561005397 G-X-G motif; other site 643561005398 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561005399 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561005400 active site 643561005401 phosphorylation site [posttranslational modification] 643561005402 intermolecular recognition site; other site 643561005403 dimerization interface [polypeptide binding]; other site 643561005404 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 643561005405 DNA binding site [nucleotide binding] 643561005406 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 643561005407 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 643561005408 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005409 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005410 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 643561005411 trimer interface [polypeptide binding]; other site 643561005412 eyelet of channel; other site 643561005413 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 643561005414 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005415 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005416 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561005417 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005418 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 643561005419 putative dimerization interface [polypeptide binding]; other site 643561005420 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 643561005421 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 643561005422 arginine decarboxylase; Provisional; Region: PRK15029 643561005423 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 643561005424 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 643561005425 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561005426 catalytic residue [active] 643561005427 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 643561005428 Fasciclin domain; Region: Fasciclin; cl02663 643561005429 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 643561005430 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 643561005431 NAD binding site [chemical binding]; other site 643561005432 homotetramer interface [polypeptide binding]; other site 643561005433 homodimer interface [polypeptide binding]; other site 643561005434 substrate binding site [chemical binding]; other site 643561005435 active site 643561005436 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 643561005437 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 643561005438 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 643561005439 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 643561005440 dimer interface [polypeptide binding]; other site 643561005441 conserved gate region; other site 643561005442 putative PBP binding loops; other site 643561005443 ABC-ATPase subunit interface; other site 643561005444 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 643561005445 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 643561005446 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 643561005447 dimer interface [polypeptide binding]; other site 643561005448 conserved gate region; other site 643561005449 putative PBP binding loops; other site 643561005450 ABC-ATPase subunit interface; other site 643561005451 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 643561005452 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 643561005453 Walker A/P-loop; other site 643561005454 ATP binding site [chemical binding]; other site 643561005455 Q-loop/lid; other site 643561005456 ABC transporter signature motif; other site 643561005457 Walker B; other site 643561005458 D-loop; other site 643561005459 H-loop/switch region; other site 643561005460 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561005461 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 643561005462 Walker A/P-loop; other site 643561005463 ATP binding site [chemical binding]; other site 643561005464 Q-loop/lid; other site 643561005465 ABC transporter signature motif; other site 643561005466 Walker B; other site 643561005467 D-loop; other site 643561005468 H-loop/switch region; other site 643561005469 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561005470 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 643561005471 PAS fold; Region: PAS_4; pfam08448 643561005472 PAS domain S-box; Region: sensory_box; TIGR00229 643561005473 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 643561005474 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561005475 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561005476 metal binding site [ion binding]; metal-binding site 643561005477 active site 643561005478 I-site; other site 643561005479 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 643561005480 Domain of unknown function DUF20; Region: UPF0118; cl00465 643561005481 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 643561005482 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 643561005483 TPP-binding site [chemical binding]; other site 643561005484 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 643561005485 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 643561005486 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 643561005487 E3 interaction surface; other site 643561005488 lipoyl attachment site [posttranslational modification]; other site 643561005489 e3 binding domain; Region: E3_binding; pfam02817 643561005490 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 643561005491 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 643561005492 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005493 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 643561005494 Predicted ATPase [General function prediction only]; Region: COG1485 643561005495 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 643561005496 Active site [active] 643561005497 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 643561005498 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561005499 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561005500 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 643561005501 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 643561005502 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 643561005503 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 643561005504 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 643561005505 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 643561005506 generic binding surface II; other site 643561005507 generic binding surface I; other site 643561005508 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 643561005509 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 643561005510 Clp amino terminal domain; Region: Clp_N; pfam02861 643561005511 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 643561005512 Walker A motif; other site 643561005513 ATP binding site [chemical binding]; other site 643561005514 Walker B motif; other site 643561005515 arginine finger; other site 643561005516 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 643561005517 Walker A motif; other site 643561005518 ATP binding site [chemical binding]; other site 643561005519 Walker B motif; other site 643561005520 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 643561005521 Predicted dienelactone hydrolase [General function prediction only]; Region: COG4188 643561005522 isoform II; Region: PAF-AH_p_II; pfam03403 643561005523 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561005524 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561005525 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 643561005526 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 643561005527 lytic murein transglycosylase; Region: MltB_2; TIGR02283 643561005528 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 643561005529 exonuclease I; Provisional; Region: sbcB; PRK11779 643561005530 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 643561005531 active site 643561005532 substrate binding site [chemical binding]; other site 643561005533 catalytic site [active] 643561005534 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 643561005535 NAD-dependent deacetylase; Provisional; Region: PRK05333 643561005536 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 643561005537 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 643561005538 GAF domain; Region: GAF; cl00853 643561005539 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 643561005540 Walker A motif; other site 643561005541 ATP binding site [chemical binding]; other site 643561005542 Walker B motif; other site 643561005543 arginine finger; other site 643561005544 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561005545 Protein of unknown function (DUF779); Region: DUF779; cl01432 643561005546 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 643561005547 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 643561005548 NAD binding site [chemical binding]; other site 643561005549 substrate binding site [chemical binding]; other site 643561005550 catalytic Zn binding site [ion binding]; other site 643561005551 tetramer interface [polypeptide binding]; other site 643561005552 structural Zn binding site [ion binding]; other site 643561005553 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 643561005554 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561005555 NAD(P) binding site [chemical binding]; other site 643561005556 catalytic residues [active] 643561005557 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 643561005558 HSP70 interaction site [polypeptide binding]; other site 643561005559 Cupin domain; Region: Cupin_2; cl09118 643561005560 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561005561 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561005562 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561005563 LysE type translocator; Region: LysE; cl00565 643561005564 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 643561005565 DNA binding site [nucleotide binding] 643561005566 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 643561005567 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 643561005568 cytosine deaminase; Provisional; Region: PRK05985 643561005569 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and...; Region: Bact_CD; cd01293 643561005570 active site 643561005571 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_15; cd07264 643561005572 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 643561005573 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561005574 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 643561005575 TM-ABC transporter signature motif; other site 643561005576 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 643561005577 TM-ABC transporter signature motif; other site 643561005578 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 643561005579 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 643561005580 Walker A/P-loop; other site 643561005581 ATP binding site [chemical binding]; other site 643561005582 Q-loop/lid; other site 643561005583 ABC transporter signature motif; other site 643561005584 Walker B; other site 643561005585 D-loop; other site 643561005586 H-loop/switch region; other site 643561005587 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 643561005588 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 643561005589 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 643561005590 putative ligand binding site [chemical binding]; other site 643561005591 A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine'...; Region: Peptidase_C39_likeA; cd02417 643561005592 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 643561005593 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561005594 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561005595 Walker A/P-loop; other site 643561005596 ATP binding site [chemical binding]; other site 643561005597 Q-loop/lid; other site 643561005598 ABC transporter signature motif; other site 643561005599 Walker B; other site 643561005600 D-loop; other site 643561005601 H-loop/switch region; other site 643561005602 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 643561005603 Transposase domain (DUF772); Region: DUF772; cl12084 643561005604 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 643561005605 sulfite reductase (NADPH) hemoprotein, beta-component; Region: CysI; TIGR02041 643561005606 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 643561005607 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 643561005608 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 643561005609 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 643561005610 sulfite reductase (NADPH) hemoprotein, beta-component; Region: CysI; TIGR02041 643561005611 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 643561005612 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 643561005613 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 643561005614 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 643561005615 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 643561005616 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 643561005617 serine/threonine dehydratase; Validated; Region: PRK07048 643561005618 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 643561005619 tetramer interface [polypeptide binding]; other site 643561005620 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561005621 catalytic residue [active] 643561005622 enoyl-CoA hydratase; Provisional; Region: PRK06142 643561005623 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 643561005624 substrate binding site [chemical binding]; other site 643561005625 oxyanion hole (OAH) forming residues; other site 643561005626 trimer interface [polypeptide binding]; other site 643561005627 Membrane transport protein; Region: Mem_trans; cl09117 643561005628 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 643561005629 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005630 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 643561005631 dimerization interface [polypeptide binding]; other site 643561005632 substrate binding pocket [chemical binding]; other site 643561005633 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 643561005634 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 643561005635 C-terminal domain interface [polypeptide binding]; other site 643561005636 GSH binding site (G-site) [chemical binding]; other site 643561005637 dimer interface [polypeptide binding]; other site 643561005638 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 643561005639 N-terminal domain interface [polypeptide binding]; other site 643561005640 putative dimer interface [polypeptide binding]; other site 643561005641 active site 643561005642 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 643561005643 Domain of unknown function DUF28; Region: DUF28; cl00361 643561005644 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 643561005645 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 643561005646 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561005647 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 643561005648 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 643561005649 Domain of unknown function DUF143; Region: DUF143; cl00519 643561005650 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 643561005651 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 643561005652 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561005653 Maf-like protein; Region: Maf; pfam02545 643561005654 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 643561005655 active site 643561005656 dimer interface [polypeptide binding]; other site 643561005657 ribonuclease G; Provisional; Region: PRK11712 643561005658 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 643561005659 homodimer interface [polypeptide binding]; other site 643561005660 oligonucleotide binding site [chemical binding]; other site 643561005661 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 643561005662 PAS fold; Region: PAS; pfam00989 643561005663 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 643561005664 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 643561005665 dimer interface [polypeptide binding]; other site 643561005666 phosphorylation site [posttranslational modification] 643561005667 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 643561005668 ATP binding site [chemical binding]; other site 643561005669 Mg2+ binding site [ion binding]; other site 643561005670 G-X-G motif; other site 643561005671 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561005672 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 643561005673 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005674 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005675 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 643561005676 active site 643561005677 FMN binding site [chemical binding]; other site 643561005678 substrate binding site [chemical binding]; other site 643561005679 homotetramer interface [polypeptide binding]; other site 643561005680 catalytic residue [active] 643561005681 classical (c) SDRs; Region: SDR_c; cd05233 643561005682 NAD(P) binding site [chemical binding]; other site 643561005683 active site 643561005684 Transcriptional regulators [Transcription]; Region: MarR; COG1846 643561005685 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005686 enoyl-CoA hydratase; Provisional; Region: PRK08258 643561005687 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 643561005688 substrate binding site [chemical binding]; other site 643561005689 oxyanion hole (OAH) forming residues; other site 643561005690 trimer interface [polypeptide binding]; other site 643561005691 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561005692 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561005693 active site 643561005694 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 643561005695 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561005696 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561005697 Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; Region: PBP1_Nba_like; cd06359 643561005698 putative ligand binding site [chemical binding]; other site 643561005699 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561005700 TM-ABC transporter signature motif; other site 643561005701 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561005702 TM-ABC transporter signature motif; other site 643561005703 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 643561005704 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561005705 Walker A/P-loop; other site 643561005706 ATP binding site [chemical binding]; other site 643561005707 Q-loop/lid; other site 643561005708 ABC transporter signature motif; other site 643561005709 Walker B; other site 643561005710 D-loop; other site 643561005711 H-loop/switch region; other site 643561005712 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 643561005713 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561005714 Walker A/P-loop; other site 643561005715 ATP binding site [chemical binding]; other site 643561005716 Q-loop/lid; other site 643561005717 ABC transporter signature motif; other site 643561005718 Walker B; other site 643561005719 D-loop; other site 643561005720 H-loop/switch region; other site 643561005721 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 643561005722 homotrimer interaction site [polypeptide binding]; other site 643561005723 putative active site [active] 643561005724 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 643561005725 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 643561005726 substrate binding pocket [chemical binding]; other site 643561005727 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 643561005728 methionine aminotransferase; Validated; Region: PRK09082 643561005729 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 643561005730 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561005731 homodimer interface [polypeptide binding]; other site 643561005732 catalytic residue [active] 643561005733 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 643561005734 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005735 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 643561005736 substrate binding site [chemical binding]; other site 643561005737 dimerization interface [polypeptide binding]; other site 643561005738 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a...; Region: CbiX_SirB_N; cd03416 643561005739 putative active site [active] 643561005740 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 643561005741 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 643561005742 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 643561005743 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 643561005744 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 643561005745 interface (dimer of trimers) [polypeptide binding]; other site 643561005746 Substrate-binding/catalytic site; other site 643561005747 Zn-binding sites [ion binding]; other site 643561005748 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 643561005749 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561005750 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 643561005751 dimerization interface [polypeptide binding]; other site 643561005752 ligand binding site [chemical binding]; other site 643561005753 LysE type translocator; Region: LysE; cl00565 643561005754 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 643561005755 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (...; Region: CS_ACL-C_CCL; cl00416 643561005756 Citrate synthase; Region: Citrate_synt; pfam00285 643561005757 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the...; Region: citrate_synt_like_2; cd06102 643561005758 dimer interface [polypeptide binding]; other site 643561005759 active site 643561005760 oxalacetate/citrate binding site [chemical binding]; other site 643561005761 citrylCoA binding site [chemical binding]; other site 643561005762 coenzyme A binding site [chemical binding]; other site 643561005763 catalytic triad [active] 643561005764 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561005765 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 643561005766 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005767 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08314 643561005768 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561005769 PilZ domain; Region: PilZ; cl01260 643561005770 Uncharacterized protein conserved in bacteria (DUF2257); Region: DUF2257; cl01794 643561005771 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 643561005772 Ligand Binding Site [chemical binding]; other site 643561005773 Transposase domain (DUF772); Region: DUF772; cl12084 643561005774 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 643561005775 potassium uptake protein; Region: kup; TIGR00794 643561005776 K+ potassium transporter; Region: K_trans; cl01227 643561005777 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005778 short chain dehydrogenase; Provisional; Region: PRK06924 643561005779 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005780 NAD(P) binding site [chemical binding]; other site 643561005781 active site 643561005782 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 643561005783 active site 643561005784 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 643561005785 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 643561005786 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 643561005787 dimer interface [polypeptide binding]; other site 643561005788 phosphorylation site [posttranslational modification] 643561005789 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 643561005790 ATP binding site [chemical binding]; other site 643561005791 Mg2+ binding site [ion binding]; other site 643561005792 G-X-G motif; other site 643561005793 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 643561005794 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561005795 active site 643561005796 phosphorylation site [posttranslational modification] 643561005797 intermolecular recognition site; other site 643561005798 dimerization interface [polypeptide binding]; other site 643561005799 H+ Antiporter protein; Region: 2A0121; TIGR00900 643561005800 Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Region: HTH_NolA-AlbR; cd04788 643561005801 DNA binding residues [nucleotide binding] 643561005802 putative dimer interface [polypeptide binding]; other site 643561005803 TipAS antibiotic-recognition domain; Region: TipAS; pfam07739 643561005804 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 643561005805 glycine dehydrogenase; Provisional; Region: PRK05367 643561005806 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 643561005807 tetramer interface [polypeptide binding]; other site 643561005808 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561005809 catalytic residue [active] 643561005810 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 643561005811 tetramer interface [polypeptide binding]; other site 643561005812 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561005813 catalytic residue [active] 643561005814 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 643561005815 lipoyl attachment site [posttranslational modification]; other site 643561005816 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 643561005817 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 643561005818 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561005819 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005820 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 643561005821 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561005822 Walker A/P-loop; other site 643561005823 ATP binding site [chemical binding]; other site 643561005824 Q-loop/lid; other site 643561005825 ABC transporter signature motif; other site 643561005826 Walker B; other site 643561005827 D-loop; other site 643561005828 H-loop/switch region; other site 643561005829 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 643561005830 TM-ABC transporter signature motif; other site 643561005831 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 643561005832 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 643561005833 zinc binding site [ion binding]; other site 643561005834 putative ligand binding site [chemical binding]; other site 643561005835 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 643561005836 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 643561005837 tetramer interface [polypeptide binding]; other site 643561005838 active site 643561005839 Mg2+/Mn2+ binding site [ion binding]; other site 643561005840 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 643561005841 phosphonopyruvate decarboxylase; Region: Ppyr-DeCO2ase; TIGR03297 643561005842 PYR/PP interface [polypeptide binding]; other site 643561005843 dimer interface [polypeptide binding]; other site 643561005844 TPP binding site [chemical binding]; other site 643561005845 TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus...; Region: TPP_PpyrDC; cd03371 643561005846 TPP-binding site; other site 643561005847 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 643561005848 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 643561005849 active site 643561005850 metal binding site [ion binding]; metal-binding site 643561005851 exosortase 1 system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 643561005852 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 643561005853 active site 643561005854 dimer interface [polypeptide binding]; other site 643561005855 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 643561005856 Ligand Binding Site [chemical binding]; other site 643561005857 Molecular Tunnel; other site 643561005858 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561005859 Streptomyces putative phosphonoformaldehyde dehydrogenase PhpJ-like; Region: ALDH_PhpJ; cd07146 643561005860 NAD(P) binding site [chemical binding]; other site 643561005861 catalytic residues [active] 643561005862 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 643561005863 S-adenosylmethionine binding site [chemical binding]; other site 643561005864 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 643561005865 active site 643561005866 metal binding site [ion binding]; metal-binding site 643561005867 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 643561005868 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 643561005869 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005870 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 643561005871 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 643561005872 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 643561005873 classical (c) SDRs; Region: SDR_c; cd05233 643561005874 NAD(P) binding site [chemical binding]; other site 643561005875 active site 643561005876 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 643561005877 Clade 1 of the heme-binding enzyme catalase; Region: catalase_clade_1; cd08154 643561005878 tetramer interface [polypeptide binding]; other site 643561005879 heme binding pocket [chemical binding]; other site 643561005880 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 643561005881 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 643561005882 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 643561005883 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 643561005884 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561005885 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561005886 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 643561005887 conserved cys residue [active] 643561005888 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 643561005889 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 643561005890 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 643561005891 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 643561005892 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 643561005893 Transposase; Region: DEDD_Tnp_IS110; pfam01548 643561005894 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 643561005895 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561005896 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005897 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561005898 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005899 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005900 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 643561005901 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 643561005902 active site 643561005903 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005904 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005905 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 643561005906 hypothetical protein; Validated; Region: PRK06201 643561005907 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 643561005908 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005909 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005910 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005911 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561005912 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561005913 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 643561005914 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 643561005915 active site 643561005916 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 643561005917 Strictosidine synthase; Region: Str_synth; pfam03088 643561005918 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 643561005919 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 643561005920 dimer interface [polypeptide binding]; other site 643561005921 active site 643561005922 heme binding site [chemical binding]; other site 643561005923 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 643561005924 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 643561005925 hypothetical protein; Provisional; Region: PRK11367 643561005926 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 643561005927 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005928 PAS fold; Region: PAS; pfam00989 643561005929 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 643561005930 putative active site [active] 643561005931 heme pocket [chemical binding]; other site 643561005932 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 643561005933 DNA binding residues [nucleotide binding] 643561005934 dimerization interface [polypeptide binding]; other site 643561005935 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 643561005936 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 643561005937 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 643561005938 FemAB family; Region: FemAB; cl11444 643561005939 Protein of unknown function, DUF482; Region: DUF482; pfam04339 643561005940 NAD synthetase; Provisional; Region: PRK13981 643561005941 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 643561005942 multimer interface [polypeptide binding]; other site 643561005943 active site 643561005944 catalytic triad [active] 643561005945 protein interface 1 [polypeptide binding]; other site 643561005946 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 643561005947 homodimer interface [polypeptide binding]; other site 643561005948 NAD binding pocket [chemical binding]; other site 643561005949 ATP binding pocket [chemical binding]; other site 643561005950 Mg binding site [ion binding]; other site 643561005951 active-site loop [active] 643561005952 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 643561005953 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 643561005954 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 643561005955 RDD family; Region: RDD; cl00746 643561005956 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 643561005957 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 643561005958 RNA polymerase factor sigma-70; Validated; Region: PRK09047 643561005959 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 643561005960 DNA binding residues [nucleotide binding] 643561005961 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 643561005962 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 643561005963 PYR/PP interface [polypeptide binding]; other site 643561005964 dimer interface [polypeptide binding]; other site 643561005965 TPP binding site [chemical binding]; other site 643561005966 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 643561005967 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 643561005968 TPP-binding site [chemical binding]; other site 643561005969 dimer interface [polypeptide binding]; other site 643561005970 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 643561005971 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 643561005972 putative valine binding site [chemical binding]; other site 643561005973 dimer interface [polypeptide binding]; other site 643561005974 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 643561005975 ketol-acid reductoisomerase; Provisional; Region: PRK05479 643561005976 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561005977 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 643561005978 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 643561005979 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 643561005980 2-isopropylmalate synthase; Validated; Region: PRK00915 643561005981 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 643561005982 active site 643561005983 catalytic residues [active] 643561005984 metal binding site [ion binding]; metal-binding site 643561005985 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 643561005986 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 643561005987 Beta-lactamase; Region: Beta-lactamase; cl01009 643561005988 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561005989 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561005990 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561005991 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 643561005992 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 643561005993 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 643561005994 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 643561005995 Protein of unknown function (DUF454); Region: DUF454; cl01063 643561005996 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 643561005997 active site 643561005998 catalytic residues [active] 643561005999 metal binding site [ion binding]; metal-binding site 643561006000 PII uridylyl-transferase; Provisional; Region: PRK03059 643561006001 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 643561006002 metal binding triad; other site 643561006003 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 643561006004 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561006005 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 643561006006 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 643561006007 methionine aminopeptidase; Reviewed; Region: PRK07281 643561006008 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 643561006009 active site 643561006010 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 643561006011 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 643561006012 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 643561006013 dimerization interface [polypeptide binding]; other site 643561006014 ATP binding site [chemical binding]; other site 643561006015 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP...; Region: PurL_repeat2; cd02204 643561006016 dimerization interface [polypeptide binding]; other site 643561006017 ATP binding site [chemical binding]; other site 643561006018 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 643561006019 putative active site [active] 643561006020 catalytic triad [active] 643561006021 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cl02712 643561006022 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 643561006023 GAF domain; Region: GAF; cl00853 643561006024 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 643561006025 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 643561006026 Protein of unknown function (DUF808); Region: DUF808; cl01002 643561006027 Surface antigen; Region: Surface_Ag_2; cl01155 643561006028 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 643561006029 dimer interface [polypeptide binding]; other site 643561006030 phosphorylation site [posttranslational modification] 643561006031 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 643561006032 ATP binding site [chemical binding]; other site 643561006033 Mg2+ binding site [ion binding]; other site 643561006034 G-X-G motif; other site 643561006035 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 643561006036 probable methyltransferase; Region: TIGR03438 643561006037 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 643561006038 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 643561006039 TIGR03440 family protein; Region: unchr_TIGR03440 643561006040 DinB superfamily; Region: DinB_2; cl00986 643561006041 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl00556 643561006042 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 643561006043 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 643561006044 homodimer interface [polypeptide binding]; other site 643561006045 substrate-cofactor binding pocket; other site 643561006046 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561006047 catalytic residue [active] 643561006048 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 643561006049 Peptidase family U32; Region: Peptidase_U32; cl03113 643561006050 Collagenase; Region: DUF3656; pfam12392 643561006051 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561006052 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 643561006053 dimerization interface [polypeptide binding]; other site 643561006054 ligand binding site [chemical binding]; other site 643561006055 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 643561006056 nucleoside/Zn binding site; other site 643561006057 dimer interface [polypeptide binding]; other site 643561006058 catalytic motif [active] 643561006059 haloalkane dehalogenase; Provisional; Region: PRK00870 643561006060 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 643561006061 dimer interface [polypeptide binding]; other site 643561006062 catalytic triad [active] 643561006063 cyclase homology domain; Region: CHD; cd07302 643561006064 nucleotidyl binding site; other site 643561006065 metal binding site [ion binding]; metal-binding site 643561006066 dimer interface [polypeptide binding]; other site 643561006067 type VI secretion system FHA domain protein; Region: VI_FHA; TIGR03354 643561006068 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cl00062 643561006069 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 643561006070 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-...; Region: Ntn_hydrolase; cl00467 643561006071 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-...; Region: Ntn_PGA_like; cd03747 643561006072 active site 643561006073 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561006074 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561006075 active site 643561006076 Predicted aminoglycoside phosphotransferase [General function prediction only]; Region: COG3173 643561006077 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: ACAD10_11_like; cd05154 643561006078 putative active site [active] 643561006079 putative substrate binding site [chemical binding]; other site 643561006080 ATP binding site [chemical binding]; other site 643561006081 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 643561006082 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 643561006083 ligand binding site [chemical binding]; other site 643561006084 flexible hinge region; other site 643561006085 enoyl-CoA hydratase; Provisional; Region: PRK07511 643561006086 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 643561006087 substrate binding site [chemical binding]; other site 643561006088 oxyanion hole (OAH) forming residues; other site 643561006089 trimer interface [polypeptide binding]; other site 643561006090 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 643561006091 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 643561006092 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561006093 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561006094 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 643561006095 thiamine phosphate binding site [chemical binding]; other site 643561006096 active site 643561006097 pyrophosphate binding site [ion binding]; other site 643561006098 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 643561006099 ThiS interaction site; other site 643561006100 putative active site [active] 643561006101 tetramer interface [polypeptide binding]; other site 643561006102 Ubiquitin-like proteins; Region: UBQ; cl00155 643561006103 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 643561006104 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561006105 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 643561006106 dimer interface [polypeptide binding]; other site 643561006107 substrate binding site [chemical binding]; other site 643561006108 ATP binding site [chemical binding]; other site 643561006109 Catalytic domain of Protein Kinases; Region: PKc; cd00180 643561006110 active site 643561006111 ATP binding site [chemical binding]; other site 643561006112 substrate binding site [chemical binding]; other site 643561006113 TOMM system kinase/cyclase multidomain protein; Region: TOMM_kin_cyc; TIGR03903 643561006114 activation loop (A-loop); other site 643561006115 cyclase homology domain; Region: CHD; cd07302 643561006116 conserved hypothetical protein, BMA_0021 family; Region: chp_BMA0021; TIGR03795 643561006117 conserved hypothetical protein, BMA_0021 family; Region: chp_BMA0021; TIGR03795 643561006118 Leucine carboxyl methyltransferase; Region: LCM; cl01306 643561006119 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561006120 MoeZ/MoeB domain; Region: MoeZ_MoeB; cl14816 643561006121 YcaO-like family; Region: YcaO; cl09146 643561006122 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 643561006123 type VI secretion system FHA domain protein; Region: VI_FHA; TIGR03354 643561006124 phosphopeptide binding site; other site 643561006125 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 643561006126 Ferredoxin [Energy production and conversion]; Region: COG1146 643561006127 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 643561006128 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 643561006129 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 643561006130 G1 box; other site 643561006131 GTP/Mg2+ binding site [chemical binding]; other site 643561006132 G2 box; other site 643561006133 Switch I region; other site 643561006134 G3 box; other site 643561006135 Switch II region; other site 643561006136 G4 box; other site 643561006137 G5 box; other site 643561006138 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 643561006139 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 643561006140 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 643561006141 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 643561006142 Active Sites [active] 643561006143 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 643561006144 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 643561006145 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 643561006146 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 643561006147 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 643561006148 Major Facilitator Superfamily; Region: MFS_1; pfam07690 643561006149 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 643561006150 putative substrate translocation pore; other site 643561006151 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 643561006152 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561006153 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 643561006154 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 643561006155 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561006156 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 643561006157 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 643561006158 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561006159 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 643561006160 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 643561006161 substrate binding pocket [chemical binding]; other site 643561006162 membrane-bound complex binding site; other site 643561006163 hinge residues; other site 643561006164 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 643561006165 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 643561006166 active site 643561006167 dimer interface [polypeptide binding]; other site 643561006168 non-prolyl cis peptide bond; other site 643561006169 insertion regions; other site 643561006170 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_9; cd07245 643561006171 dimer interface [polypeptide binding]; other site 643561006172 putative metal binding site [ion binding]; other site 643561006173 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 643561006174 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 643561006175 putative PBP binding loops; other site 643561006176 dimer interface [polypeptide binding]; other site 643561006177 ABC-ATPase subunit interface; other site 643561006178 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 643561006179 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 643561006180 Walker A/P-loop; other site 643561006181 ATP binding site [chemical binding]; other site 643561006182 Q-loop/lid; other site 643561006183 ABC transporter signature motif; other site 643561006184 Walker B; other site 643561006185 D-loop; other site 643561006186 H-loop/switch region; other site 643561006187 TOBE domain; Region: TOBE_2; cl01440 643561006188 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12683 643561006189 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561006190 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 643561006191 substrate binding site [chemical binding]; other site 643561006192 dimerization interface [polypeptide binding]; other site 643561006193 Cytochrome c; Region: Cytochrom_C; cl11414 643561006194 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 643561006195 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 643561006196 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 643561006197 motif 1; other site 643561006198 active site 643561006199 motif 2; other site 643561006200 motif 3; other site 643561006201 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 643561006202 DHHA1 domain; Region: DHHA1; pfam02272 643561006203 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561006204 metal binding site [ion binding]; metal-binding site 643561006205 active site 643561006206 I-site; other site 643561006207 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 643561006208 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 643561006209 active site 643561006210 HIGH motif; other site 643561006211 nucleotide binding site [chemical binding]; other site 643561006212 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 643561006213 active site 643561006214 KMSKS motif; other site 643561006215 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 643561006216 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561006217 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 643561006218 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 643561006219 dimerization interface [polypeptide binding]; other site 643561006220 Pirin-related protein [General function prediction only]; Region: COG1741 643561006221 Cupin domain; Region: Cupin_2; cl09118 643561006222 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561006223 Pirin-related protein [General function prediction only]; Region: COG1741 643561006224 Cupin domain; Region: Cupin_2; cl09118 643561006225 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 643561006226 rhodanese superfamily protein; Provisional; Region: PRK05320 643561006227 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 643561006228 active site residue [active] 643561006229 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 643561006230 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 643561006231 P-loop; other site 643561006232 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561006233 metal binding site [ion binding]; metal-binding site 643561006234 active site 643561006235 I-site; other site 643561006236 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 643561006237 Sulfate transporter family; Region: Sulfate_transp; cl00967 643561006238 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 643561006239 BON domain; Region: BON; cl02771 643561006240 cystathionine beta-lyase; Provisional; Region: PRK07050 643561006241 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 643561006242 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561006243 catalytic residue [active] 643561006244 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 643561006245 active site 643561006246 catalytic triad [active] 643561006247 oxyanion hole [active] 643561006248 switch loop; other site 643561006249 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 643561006250 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 643561006251 Walker A/P-loop; other site 643561006252 ATP binding site [chemical binding]; other site 643561006253 Q-loop/lid; other site 643561006254 ABC transporter signature motif; other site 643561006255 Walker B; other site 643561006256 D-loop; other site 643561006257 H-loop/switch region; other site 643561006258 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 643561006259 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 643561006260 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 643561006261 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 643561006262 NAD+ binding site [chemical binding]; other site 643561006263 substrate binding site [chemical binding]; other site 643561006264 Zn binding site [ion binding]; other site 643561006265 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 643561006266 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 643561006267 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 643561006268 active site 643561006269 catalytic tetrad [active] 643561006270 Chromate transporter; Region: Chromate_transp; pfam02417 643561006271 Chromate transporter; Region: Chromate_transp; pfam02417 643561006272 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 643561006273 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 643561006274 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 643561006275 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 643561006276 active site 643561006277 multifunctional aminopeptidase A; Provisional; Region: PRK00913 643561006278 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 643561006279 interface (dimer of trimers) [polypeptide binding]; other site 643561006280 Substrate-binding/catalytic site; other site 643561006281 Zn-binding sites [ion binding]; other site 643561006282 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 643561006283 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 643561006284 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 643561006285 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 643561006286 Gram-negative bacterial tonB protein; Region: TonB; cl10048 643561006287 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 643561006288 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 643561006289 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561006290 catalytic residue [active] 643561006291 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 643561006292 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 643561006293 substrate binding pocket [chemical binding]; other site 643561006294 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 643561006295 catalytic residues [active] 643561006296 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 643561006297 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561006298 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 643561006299 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561006300 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 643561006301 N-terminal plug; other site 643561006302 ligand-binding site [chemical binding]; other site 643561006303 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 643561006304 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561006305 DNA-binding site [nucleotide binding]; DNA binding site 643561006306 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 643561006307 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561006308 homodimer interface [polypeptide binding]; other site 643561006309 catalytic residue [active] 643561006310 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 643561006311 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 643561006312 dimer interface [polypeptide binding]; other site 643561006313 phosphorylation site [posttranslational modification] 643561006314 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 643561006315 ATP binding site [chemical binding]; other site 643561006316 Mg2+ binding site [ion binding]; other site 643561006317 G-X-G motif; other site 643561006318 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 643561006319 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561006320 active site 643561006321 phosphorylation site [posttranslational modification] 643561006322 intermolecular recognition site; other site 643561006323 dimerization interface [polypeptide binding]; other site 643561006324 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 643561006325 DNA binding site [nucleotide binding] 643561006326 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561006327 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 643561006328 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 643561006329 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 643561006330 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 643561006331 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561006332 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 643561006333 N-terminal plug; other site 643561006334 ligand-binding site [chemical binding]; other site 643561006335 3HB-oligomer hydrolase (3HBOH); Region: 3HBOH; pfam10605 643561006336 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 643561006337 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 643561006338 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561006339 active site 643561006340 phosphorylation site [posttranslational modification] 643561006341 intermolecular recognition site; other site 643561006342 dimerization interface [polypeptide binding]; other site 643561006343 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 643561006344 DNA binding site [nucleotide binding] 643561006345 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 643561006346 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 643561006347 dimer interface [polypeptide binding]; other site 643561006348 phosphorylation site [posttranslational modification] 643561006349 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 643561006350 ATP binding site [chemical binding]; other site 643561006351 Mg2+ binding site [ion binding]; other site 643561006352 G-X-G motif; other site 643561006353 ferrochelatase; Reviewed; Region: hemH; PRK00035 643561006354 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 643561006355 C-terminal domain interface [polypeptide binding]; other site 643561006356 active site 643561006357 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 643561006358 active site 643561006359 N-terminal domain interface [polypeptide binding]; other site 643561006360 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 643561006361 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 643561006362 active site 643561006363 motif I; other site 643561006364 motif II; other site 643561006365 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 643561006366 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561006367 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK08134 643561006368 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 643561006369 homodimer interface [polypeptide binding]; other site 643561006370 substrate-cofactor binding pocket; other site 643561006371 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561006372 catalytic residue [active] 643561006373 FOG: CBS domain [General function prediction only]; Region: COG0517 643561006374 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 643561006375 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 643561006376 Tetramer interface [polypeptide binding]; other site 643561006377 Active site [active] 643561006378 FMN-binding site [chemical binding]; other site 643561006379 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 643561006380 ATP cone domain; Region: ATP-cone; pfam03477 643561006381 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 643561006382 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 643561006383 dimer interface [polypeptide binding]; other site 643561006384 glycine-pyridoxal phosphate binding site [chemical binding]; other site 643561006385 active site 643561006386 folate binding site [chemical binding]; other site 643561006387 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 643561006388 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 643561006389 N-acetyl-D-glucosamine binding site [chemical binding]; other site 643561006390 catalytic residue [active] 643561006391 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 643561006392 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 643561006393 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 643561006394 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 643561006395 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 643561006396 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 643561006397 ribonuclease R; Region: RNase_R; TIGR02063 643561006398 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 643561006399 RNB domain; Region: RNB; pfam00773 643561006400 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 643561006401 RNA binding site [nucleotide binding]; other site 643561006402 classical (c) SDRs; Region: SDR_c; cd05233 643561006403 NAD(P) binding site [chemical binding]; other site 643561006404 active site 643561006405 glycogen synthase; Provisional; Region: glgA; PRK00654 643561006406 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 643561006407 ADP-binding pocket [chemical binding]; other site 643561006408 homodimer interface [polypeptide binding]; other site 643561006409 putative bifunctional 4-alpha-glucanotransferase/malto-oligosyltrehalose synthase; Provisional; Region: PRK14507 643561006410 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 643561006411 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 643561006412 Maltooligosyl trehalose synthase (MTSase) N-terminus domain. MTSase and maltooligosyl trehalose trehalohydrolase (MTHase) work together to produce trehalose. MTSase is responsible for converting the alpha-1,4-glucosidic linkage to an alpha,alpha-1,1-...; Region: MTHase_N_term; cd02853 643561006413 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 643561006414 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 643561006415 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 643561006416 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 643561006417 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 643561006418 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 643561006419 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00844 643561006420 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 643561006421 ligand binding site [chemical binding]; other site 643561006422 oligomer interface [polypeptide binding]; other site 643561006423 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 643561006424 dimer interface [polypeptide binding]; other site 643561006425 N-terminal domain interface [polypeptide binding]; other site 643561006426 sulfate 1 binding site; other site 643561006427 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 643561006428 active site 643561006429 phosphorylation site [posttranslational modification] 643561006430 intermolecular recognition site; other site 643561006431 dimerization interface [polypeptide binding]; other site 643561006432 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 643561006433 GAF domain; Region: GAF; cl00853 643561006434 Phytochrome region; Region: PHY; pfam00360 643561006435 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 643561006436 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 643561006437 ATP binding site [chemical binding]; other site 643561006438 Mg2+ binding site [ion binding]; other site 643561006439 G-X-G motif; other site 643561006440 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 643561006441 heme binding pocket [chemical binding]; other site 643561006442 PAS fold; Region: PAS_4; pfam08448 643561006443 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 643561006444 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 643561006445 dimer interface [polypeptide binding]; other site 643561006446 phosphorylation site [posttranslational modification] 643561006447 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 643561006448 ATP binding site [chemical binding]; other site 643561006449 Mg2+ binding site [ion binding]; other site 643561006450 G-X-G motif; other site 643561006451 Response regulator receiver domain; Region: Response_reg; pfam00072 643561006452 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561006453 active site 643561006454 phosphorylation site [posttranslational modification] 643561006455 intermolecular recognition site; other site 643561006456 dimerization interface [polypeptide binding]; other site 643561006457 Response regulator receiver domain; Region: Response_reg; pfam00072 643561006458 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561006459 active site 643561006460 phosphorylation site [posttranslational modification] 643561006461 intermolecular recognition site; other site 643561006462 dimerization interface [polypeptide binding]; other site 643561006463 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 643561006464 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 643561006465 putative active site [active] 643561006466 heme pocket [chemical binding]; other site 643561006467 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 643561006468 dimer interface [polypeptide binding]; other site 643561006469 phosphorylation site [posttranslational modification] 643561006470 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 643561006471 ATP binding site [chemical binding]; other site 643561006472 Mg2+ binding site [ion binding]; other site 643561006473 G-X-G motif; other site 643561006474 Response regulator receiver domain; Region: Response_reg; pfam00072 643561006475 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561006476 active site 643561006477 phosphorylation site [posttranslational modification] 643561006478 intermolecular recognition site; other site 643561006479 dimerization interface [polypeptide binding]; other site 643561006480 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 643561006481 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 643561006482 dimer interface [polypeptide binding]; other site 643561006483 phosphorylation site [posttranslational modification] 643561006484 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 643561006485 ATP binding site [chemical binding]; other site 643561006486 Mg2+ binding site [ion binding]; other site 643561006487 G-X-G motif; other site 643561006488 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 643561006489 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 643561006490 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 643561006491 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 643561006492 Sulphate Transporter and Anti-Sigma factor antagonist domain of the 'stressosome' complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation; Region: STAS_RsbR_RsbS_like; cd07041 643561006493 Sulphate Transporter and Anti-Sigma factor antagonist domain of the 'stressosome' complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation; Region: STAS_RsbR_RsbS_like; cd07041 643561006494 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561006495 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 643561006496 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 643561006497 dimer interface [polypeptide binding]; other site 643561006498 conserved gate region; other site 643561006499 putative PBP binding loops; other site 643561006500 ABC-ATPase subunit interface; other site 643561006501 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 643561006502 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 643561006503 Walker A/P-loop; other site 643561006504 ATP binding site [chemical binding]; other site 643561006505 Q-loop/lid; other site 643561006506 ABC transporter signature motif; other site 643561006507 Walker B; other site 643561006508 D-loop; other site 643561006509 H-loop/switch region; other site 643561006510 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 643561006511 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561006512 DNA-binding site [nucleotide binding]; DNA binding site 643561006513 UTRA domain; Region: UTRA; cl01230 643561006514 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 643561006515 tyrosine 2,3-aminomutase; Region: Tyr_2_3_mutase; TIGR03832 643561006516 active sites [active] 643561006517 tetramer interface [polypeptide binding]; other site 643561006518 urocanate hydratase; Provisional; Region: PRK05414 643561006519 urocanate hydratase; Region: hutU; TIGR01228 643561006520 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl02184 643561006521 HutD; Region: HutD; cl01532 643561006522 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 643561006523 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 643561006524 active site 643561006525 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 643561006526 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 643561006527 active site 643561006528 N-formylglutamate amidohydrolase; Region: FGase; cl01522 643561006529 threonine and homoserine efflux system; Provisional; Region: PRK10532 643561006530 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 643561006531 active site 643561006532 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 643561006533 Pertactin-like passenger domains (virulence factors) of autotransporter proteins of the type V secretion system. Autotransporters are proteins used by Gram-negative bacteria to transport proteins across their outer membranes. The C-terminal (beta)...; Region: PL_Passenger_AT; cl00185 643561006534 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 643561006535 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 643561006536 rRNA binding site [nucleotide binding]; other site 643561006537 predicted 30S ribosome binding site; other site 643561006538 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 643561006539 active site 643561006540 catalytic triad [active] 643561006541 oxyanion hole [active] 643561006542 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 643561006543 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 643561006544 PPIC-type PPIASE domain; Region: Rotamase; cl08278 643561006545 BolA-like protein; Region: BolA; cl00386 643561006546 Intracellular septation protein A; Region: IspA; cl01098 643561006547 SelR domain; Region: SelR; cl00369 643561006548 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 643561006549 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 643561006550 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561006551 putative acyl-CoA synthetase; Provisional; Region: PRK06018 643561006552 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561006553 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 643561006554 putative ligand binding site [chemical binding]; other site 643561006555 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561006556 TM-ABC transporter signature motif; other site 643561006557 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561006558 TM-ABC transporter signature motif; other site 643561006559 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 643561006560 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561006561 Walker A/P-loop; other site 643561006562 ATP binding site [chemical binding]; other site 643561006563 Q-loop/lid; other site 643561006564 ABC transporter signature motif; other site 643561006565 Walker B; other site 643561006566 D-loop; other site 643561006567 H-loop/switch region; other site 643561006568 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 643561006569 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561006570 Walker A/P-loop; other site 643561006571 ATP binding site [chemical binding]; other site 643561006572 Q-loop/lid; other site 643561006573 ABC transporter signature motif; other site 643561006574 Walker B; other site 643561006575 D-loop; other site 643561006576 H-loop/switch region; other site 643561006577 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain...; Region: CBS_pair_GGDEF_assoc; cd04598 643561006578 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 643561006579 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 643561006580 Domain of unknown function (DUF1987); Region: DUF1987; pfam09345 643561006581 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561006582 metal binding site [ion binding]; metal-binding site 643561006583 active site 643561006584 I-site; other site 643561006585 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 643561006586 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561006587 metal binding site [ion binding]; metal-binding site 643561006588 active site 643561006589 I-site; other site 643561006590 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 643561006591 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; cl14895 643561006592 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 643561006593 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 643561006594 substrate binding site [chemical binding]; other site 643561006595 oxyanion hole (OAH) forming residues; other site 643561006596 trimer interface [polypeptide binding]; other site 643561006597 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 643561006598 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561006599 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561006600 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 643561006601 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 643561006602 dimer interface [polypeptide binding]; other site 643561006603 active site 643561006604 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 643561006605 CoenzymeA binding site [chemical binding]; other site 643561006606 subunit interaction site [polypeptide binding]; other site 643561006607 PHB binding site; other site 643561006608 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561006609 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561006610 active site 643561006611 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 643561006612 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 643561006613 classical (c) SDRs; Region: SDR_c; cd05233 643561006614 NAD(P) binding site [chemical binding]; other site 643561006615 active site 643561006616 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 643561006617 CoenzymeA binding site [chemical binding]; other site 643561006618 subunit interaction site [polypeptide binding]; other site 643561006619 PHB binding site; other site 643561006620 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 643561006621 Prostaglandin dehydrogenases; Region: PGDH; cd05288 643561006622 NAD(P) binding site [chemical binding]; other site 643561006623 substrate binding site [chemical binding]; other site 643561006624 dimer interface [polypeptide binding]; other site 643561006625 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561006626 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 643561006627 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 643561006628 C-terminal domain interface [polypeptide binding]; other site 643561006629 GSH binding site (G-site) [chemical binding]; other site 643561006630 dimer interface [polypeptide binding]; other site 643561006631 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 643561006632 N-terminal domain interface [polypeptide binding]; other site 643561006633 hypothetical protein; Provisional; Region: PRK06194 643561006634 classical (c) SDRs; Region: SDR_c; cd05233 643561006635 NAD(P) binding site [chemical binding]; other site 643561006636 active site 643561006637 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561006638 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 643561006639 NAD binding site [chemical binding]; other site 643561006640 homotetramer interface [polypeptide binding]; other site 643561006641 homodimer interface [polypeptide binding]; other site 643561006642 active site 643561006643 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 643561006644 SWIB/MDM2 domain; Region: SWIB; cl02489 643561006645 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 643561006646 EamA-like transporter family; Region: EamA; cl01037 643561006647 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561006648 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561006649 EamA-like transporter family; Region: EamA; cl01037 643561006650 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 643561006651 EamA-like transporter family; Region: EamA; cl01037 643561006652 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 643561006653 putative active site pocket [active] 643561006654 dimerization interface [polypeptide binding]; other site 643561006655 putative catalytic residue [active] 643561006656 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 643561006657 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 643561006658 tetramer interface [polypeptide binding]; other site 643561006659 active site 643561006660 Mg2+/Mn2+ binding site [ion binding]; other site 643561006661 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 643561006662 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 643561006663 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 643561006664 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 643561006665 active site 643561006666 dimer interface [polypeptide binding]; other site 643561006667 motif 1; other site 643561006668 motif 2; other site 643561006669 motif 3; other site 643561006670 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 643561006671 anticodon binding site; other site 643561006672 translation initiation factor IF-3; Region: infC; TIGR00168 643561006673 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 643561006674 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 643561006675 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 643561006676 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 643561006677 23S rRNA binding site [nucleotide binding]; other site 643561006678 L21 binding site [polypeptide binding]; other site 643561006679 L13 binding site [polypeptide binding]; other site 643561006680 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 643561006681 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 643561006682 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 643561006683 dimer interface [polypeptide binding]; other site 643561006684 motif 1; other site 643561006685 active site 643561006686 motif 2; other site 643561006687 motif 3; other site 643561006688 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 643561006689 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 643561006690 putative tRNA-binding site [nucleotide binding]; other site 643561006691 B3/4 domain; Region: B3_4; cl11458 643561006692 tRNA synthetase B5 domain; Region: B5; cl08394 643561006693 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 643561006694 dimer interface [polypeptide binding]; other site 643561006695 motif 1; other site 643561006696 motif 3; other site 643561006697 motif 2; other site 643561006698 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 643561006699 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 643561006700 IHF - DNA interface [nucleotide binding]; other site 643561006701 IHF dimer interface [polypeptide binding]; other site 643561006702 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 643561006703 DNA binding residues [nucleotide binding] 643561006704 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 643561006705 maltose O-acetyltransferase; Provisional; Region: PRK10092 643561006706 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 643561006707 active site 643561006708 substrate binding site [chemical binding]; other site 643561006709 trimer interface [polypeptide binding]; other site 643561006710 CoA binding site [chemical binding]; other site 643561006711 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 643561006712 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561006713 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561006714 Walker A/P-loop; other site 643561006715 ATP binding site [chemical binding]; other site 643561006716 Q-loop/lid; other site 643561006717 ABC transporter signature motif; other site 643561006718 Walker B; other site 643561006719 D-loop; other site 643561006720 H-loop/switch region; other site 643561006721 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 643561006722 transmembrane helices; other site 643561006723 CHASE domain; Region: CHASE; cl01369 643561006724 PAS domain S-box; Region: sensory_box; TIGR00229 643561006725 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 643561006726 putative active site [active] 643561006727 heme pocket [chemical binding]; other site 643561006728 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561006729 metal binding site [ion binding]; metal-binding site 643561006730 active site 643561006731 I-site; other site 643561006732 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 643561006733 Uncharacterised BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 643561006734 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 643561006735 active site flap/lid [active] 643561006736 nucleophilic elbow; other site 643561006737 catalytic triad [active] 643561006738 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 643561006739 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 643561006740 Walker A/P-loop; other site 643561006741 ATP binding site [chemical binding]; other site 643561006742 Q-loop/lid; other site 643561006743 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 643561006744 ABC transporter signature motif; other site 643561006745 Walker B; other site 643561006746 D-loop; other site 643561006747 H-loop/switch region; other site 643561006748 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cl12038 643561006749 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 643561006750 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 643561006751 nucleotide binding pocket [chemical binding]; other site 643561006752 K-X-D-G motif; other site 643561006753 catalytic site [active] 643561006754 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 643561006755 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 643561006756 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 643561006757 Dimer interface [polypeptide binding]; other site 643561006758 BRCT sequence motif; other site 643561006759 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 643561006760 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 643561006761 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 643561006762 Domain of unknown function (DUF1795); Region: DUF1795; cl02256 643561006763 Uncharacterized conserved protein [Function unknown]; Region: COG4104 643561006764 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561006765 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561006766 RHS Repeat; Region: RHS_repeat; cl11982 643561006767 RHS Repeat; Region: RHS_repeat; cl11982 643561006768 RHS Repeat; Region: RHS_repeat; cl11982 643561006769 RHS Repeat; Region: RHS_repeat; cl11982 643561006770 RHS protein; Region: RHS; pfam03527 643561006771 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561006772 Transposase domain (DUF772); Region: DUF772; cl12084 643561006773 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 643561006774 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 643561006775 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561006776 substrate binding pocket [chemical binding]; other site 643561006777 membrane-bound complex binding site; other site 643561006778 hinge residues; other site 643561006779 EVE domain; Region: EVE; cl00728 643561006780 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 643561006781 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 643561006782 ATP binding site [chemical binding]; other site 643561006783 putative Mg++ binding site [ion binding]; other site 643561006784 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 643561006785 nucleotide binding region [chemical binding]; other site 643561006786 ATP-binding site [chemical binding]; other site 643561006787 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 643561006788 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 643561006789 NlpC/P60 family; Region: NLPC_P60; cl11438 643561006790 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 643561006791 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 643561006792 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them...; Region: YcaC_related; cd01012 643561006793 Isochorismatase family; Region: Isochorismatase; pfam00857 643561006794 catalytic triad [active] 643561006795 dimer interface [polypeptide binding]; other site 643561006796 conserved cis-peptide bond; other site 643561006797 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 643561006798 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 643561006799 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561006800 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 643561006801 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561006802 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 643561006803 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 643561006804 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 643561006805 active site 643561006806 FMN binding site [chemical binding]; other site 643561006807 2,4-decadienoyl-CoA binding site; other site 643561006808 catalytic residue [active] 643561006809 4Fe-4S cluster binding site [ion binding]; other site 643561006810 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 643561006811 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561006812 PAS fold; Region: PAS_3; pfam08447 643561006813 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561006814 PAS domain S-box; Region: sensory_box; TIGR00229 643561006815 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 643561006816 hypothetical protein; Provisional; Region: PRK13560 643561006817 PAS domain S-box; Region: sensory_box; TIGR00229 643561006818 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 643561006819 putative diguanylate cyclase; Provisional; Region: PRK09776 643561006820 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561006821 metal binding site [ion binding]; metal-binding site 643561006822 active site 643561006823 I-site; other site 643561006824 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 643561006825 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 643561006826 EamA-like transporter family; Region: EamA; cl01037 643561006827 EamA-like transporter family; Region: EamA; cl01037 643561006828 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 643561006829 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 643561006830 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 643561006831 DNA binding site [nucleotide binding] 643561006832 active site 643561006833 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 643561006834 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561006835 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561006836 AlkA N-terminal domain; Region: AlkA_N; cl05528 643561006837 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 643561006838 minor groove reading motif; other site 643561006839 helix-hairpin-helix signature motif; other site 643561006840 active site 643561006841 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 643561006842 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 643561006843 active site 643561006844 substrate binding site [chemical binding]; other site 643561006845 metal binding site [ion binding]; metal-binding site 643561006846 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 643561006847 active site 643561006848 catalytic triad [active] 643561006849 dimer interface [polypeptide binding]; other site 643561006850 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 643561006851 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 643561006852 Protein involved in meta-pathway of phenol degradation [Energy production and conversion]; Region: COG4313 643561006853 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 643561006854 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561006855 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 643561006856 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 643561006857 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 643561006858 Nitrile hydratase beta subunit; Region: NHase_beta; pfam02211 643561006859 nitrile hydratase, beta subunit; Region: nitrile_beta; cl03486 643561006860 Nitrile hydratase, alpha chain; Region: NHase_alpha; pfam02979 643561006861 TOMM propeptide domain; Region: TOMM_pelo; TIGR03793 643561006862 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 643561006863 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 643561006864 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561006865 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561006866 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 643561006867 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561006868 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561006869 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 643561006870 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561006871 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 643561006872 active site 643561006873 ATP binding site [chemical binding]; other site 643561006874 substrate binding site [chemical binding]; other site 643561006875 activation loop (A-loop); other site 643561006876 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 643561006877 Outer membrane efflux protein; Region: OEP; pfam02321 643561006878 Outer membrane efflux protein; Region: OEP; pfam02321 643561006879 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561006880 active site residue [active] 643561006881 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 643561006882 S-adenosylmethionine binding site [chemical binding]; other site 643561006883 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561006884 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561006885 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 643561006886 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561006887 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 643561006888 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561006889 Walker A/P-loop; other site 643561006890 ATP binding site [chemical binding]; other site 643561006891 Q-loop/lid; other site 643561006892 ABC transporter signature motif; other site 643561006893 Walker B; other site 643561006894 D-loop; other site 643561006895 H-loop/switch region; other site 643561006896 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 643561006897 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 643561006898 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 643561006899 N-terminal plug; other site 643561006900 ligand-binding site [chemical binding]; other site 643561006901 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561006902 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 643561006903 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 643561006904 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561006905 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561006906 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 643561006907 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561006908 NAD binding site [chemical binding]; other site 643561006909 catalytic residues [active] 643561006910 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 643561006911 C-terminal peptidase (prc); Region: prc; TIGR00225 643561006912 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 643561006913 protein binding site [polypeptide binding]; other site 643561006914 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 643561006915 Catalytic dyad [active] 643561006916 Membrane transport protein; Region: Mem_trans; cl09117 643561006917 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_1; cd05678 643561006918 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 643561006919 putative metal binding site [ion binding]; other site 643561006920 putative dimer interface [polypeptide binding]; other site 643561006921 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 643561006922 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 643561006923 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 643561006924 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 643561006925 putative active site pocket [active] 643561006926 dimerization interface [polypeptide binding]; other site 643561006927 putative catalytic residue [active] 643561006928 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561006929 ligand binding site [chemical binding]; other site 643561006930 Predicted small integral membrane protein (DUF2165); Region: DUF2165; cl02290 643561006931 Uncharacterised protein family (UPF0156); Region: RHH_2; cl01448 643561006932 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 643561006933 Transcriptional regulators [Transcription]; Region: PurR; COG1609 643561006934 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 643561006935 DNA binding site [nucleotide binding] 643561006936 domain linker motif; other site 643561006937 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 643561006938 putative ligand binding site [chemical binding]; other site 643561006939 putative dimerization interface [polypeptide binding]; other site 643561006940 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 643561006941 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 643561006942 ATP-binding site [chemical binding]; other site 643561006943 Gluconate-6-phosphate binding site [chemical binding]; other site 643561006944 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 643561006945 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 643561006946 DctM-like transporters; Region: DctM; pfam06808 643561006947 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561006948 Dehydratase family; Region: ILVD_EDD; cl00340 643561006949 6-phosphogluconate dehydratase; Region: edd; TIGR01196 643561006950 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 643561006951 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 643561006952 active site 643561006953 intersubunit interface [polypeptide binding]; other site 643561006954 catalytic residue [active] 643561006955 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 643561006956 dimer interface [polypeptide binding]; other site 643561006957 active site 643561006958 metal binding site [ion binding]; metal-binding site 643561006959 glutathione binding site [chemical binding]; other site 643561006960 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561006961 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561006962 NAD(P) binding site [chemical binding]; other site 643561006963 active site 643561006964 anaerobic benzoate catabolism transcriptional regulator; Reviewed; Region: PRK08154 643561006965 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 643561006966 non-specific DNA binding site [nucleotide binding]; other site 643561006967 salt bridge; other site 643561006968 sequence-specific DNA binding site [nucleotide binding]; other site 643561006969 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 643561006970 Domain of unknown function (DUF955); Region: DUF955; cl01076 643561006971 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 643561006972 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 643561006973 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (...; Region: CS_ACL-C_CCL; cl00416 643561006974 oxalacetate binding site [chemical binding]; other site 643561006975 citrylCoA binding site [chemical binding]; other site 643561006976 coenzyme A binding site [chemical binding]; other site 643561006977 catalytic triad [active] 643561006978 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 643561006979 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 643561006980 substrate binding site [chemical binding]; other site 643561006981 ligand binding site [chemical binding]; other site 643561006982 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 643561006983 substrate binding site [chemical binding]; other site 643561006984 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 643561006985 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 643561006986 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 643561006987 tetramer interface [polypeptide binding]; other site 643561006988 active site 643561006989 Mg2+/Mn2+ binding site [ion binding]; other site 643561006990 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 643561006991 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561006992 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 643561006993 putative dimerization interface [polypeptide binding]; other site 643561006994 Domain of unknown function (DUF1852); Region: DUF1852; pfam08908 643561006995 methionine synthase; Provisional; Region: PRK01207 643561006996 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 643561006997 substrate binding site [chemical binding]; other site 643561006998 THF binding site; other site 643561006999 zinc-binding site [ion binding]; other site 643561007000 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561007001 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 643561007002 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 643561007003 DNA binding site [nucleotide binding] 643561007004 Int/Topo IB signature motif; other site 643561007005 active site 643561007006 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 643561007007 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 643561007008 Peptidase S8 family domain, uncharacterized subfamily 12; Region: Peptidases_S8_12; cd07480 643561007009 active site 643561007010 catalytic triad [active] 643561007011 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cl00179 643561007012 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 643561007013 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 643561007014 eyelet of channel; other site 643561007015 trimer interface [polypeptide binding]; other site 643561007016 proline-specific peptidases, Bacillus coagulans-type subfamily; Region: pro_imino_pep_2; TIGR01250 643561007017 Predicted amidohydrolase [General function prediction only]; Region: COG0388 643561007018 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 643561007019 putative active site [active] 643561007020 catalytic triad [active] 643561007021 dimer interface [polypeptide binding]; other site 643561007022 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 643561007023 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 643561007024 dimer interface [polypeptide binding]; other site 643561007025 conserved gate region; other site 643561007026 ABC-ATPase subunit interface; other site 643561007027 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 643561007028 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 643561007029 putative PBP binding loops; other site 643561007030 dimer interface [polypeptide binding]; other site 643561007031 ABC-ATPase subunit interface; other site 643561007032 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 643561007033 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 643561007034 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 643561007035 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 643561007036 Walker A/P-loop; other site 643561007037 ATP binding site [chemical binding]; other site 643561007038 Q-loop/lid; other site 643561007039 ABC transporter signature motif; other site 643561007040 Walker B; other site 643561007041 D-loop; other site 643561007042 H-loop/switch region; other site 643561007043 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561007044 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 643561007045 Walker A/P-loop; other site 643561007046 ATP binding site [chemical binding]; other site 643561007047 Q-loop/lid; other site 643561007048 ABC transporter signature motif; other site 643561007049 Walker B; other site 643561007050 D-loop; other site 643561007051 H-loop/switch region; other site 643561007052 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561007053 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 643561007054 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 643561007055 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 643561007056 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561007057 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561007058 Autoinducer binding domain; Region: Autoind_bind; pfam03472 643561007059 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 643561007060 DNA binding residues [nucleotide binding] 643561007061 dimerization interface [polypeptide binding]; other site 643561007062 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 643561007063 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561007064 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007065 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 643561007066 putative dimerization interface [polypeptide binding]; other site 643561007067 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 643561007068 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561007069 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561007070 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561007071 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 643561007072 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 643561007073 active site 643561007074 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561007075 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561007076 hypothetical protein; Provisional; Region: PRK09936 643561007077 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561007078 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561007079 active site 643561007080 D-alanine--poly(phosphoribitol) ligase subunit 2; Validated; Region: PRK05087; cl07963 643561007081 D-alanine--poly(phosphoribitol) ligase subunit 1; Provisional; Region: PRK04813 643561007082 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561007083 Alginate O-acetyl transferase AlgF; Region: AlgF; pfam11182 643561007084 MBOAT family; Region: MBOAT; cl00738 643561007085 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 643561007086 TPR motif; other site 643561007087 binding surface 643561007088 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 643561007089 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 643561007090 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 643561007091 active site 643561007092 homodimer interface [polypeptide binding]; other site 643561007093 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 643561007094 intersubunit interface [polypeptide binding]; other site 643561007095 active site 643561007096 Zn2+ binding site [ion binding]; other site 643561007097 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 643561007098 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 643561007099 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PSRA_1; cd02558 643561007100 probable active site [active] 643561007101 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 643561007102 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 643561007103 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 643561007104 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 643561007105 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 643561007106 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 643561007107 generic binding surface II; other site 643561007108 generic binding surface I; other site 643561007109 Y-family of DNA polymerases; Region: PolY; cl12025 643561007110 Cell division inhibitor SulA; Region: SulA; cl01880 643561007111 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 643561007112 Zn2+ binding site [ion binding]; other site 643561007113 Mg2+ binding site [ion binding]; other site 643561007114 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 643561007115 dimer interface [polypeptide binding]; other site 643561007116 substrate binding site [chemical binding]; other site 643561007117 metal binding sites [ion binding]; metal-binding site 643561007118 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561007119 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561007120 D-aminoacyl-tRNA deacylase; Region: tRNA_deacylase; cl00716 643561007121 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 643561007122 Formyl transferase catalytic core domain found in a group of proteins with unknown functions; Region: FMT_core_like_3; cd08653 643561007123 putative active site [active] 643561007124 putative cosubstrate binding site; other site 643561007125 putative substrate binding site [chemical binding]; other site 643561007126 catalytic site [active] 643561007127 argininosuccinate lyase; Provisional; Region: PRK02186 643561007128 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561007129 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 643561007130 tetramer interface [polypeptide binding]; other site 643561007131 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 643561007132 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 643561007133 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561007134 catalytic residue [active] 643561007135 Protein involved in propanediol utilization, and related proteins (includes coumermycin biosynthetic protein), possible kinase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PduX; COG4542 643561007136 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 643561007137 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 643561007138 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 643561007139 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 643561007140 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 643561007141 putative metal binding site [ion binding]; other site 643561007142 Protein of unknown function (DUF962); Region: DUF962; cl01879 643561007143 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 643561007144 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007145 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561007146 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like; Region: ALDH_AAS00426; cd07109 643561007147 NAD(P) binding site [chemical binding]; other site 643561007148 catalytic residues [active] 643561007149 catalytic residues [active] 643561007150 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 643561007151 superoxide dismutase; Provisional; Region: PRK10925 643561007152 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 643561007153 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 643561007154 GntP family permease; Region: GntP_permease; cl15264 643561007155 gluconate transporter; Region: gntP; TIGR00791 643561007156 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 643561007157 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561007158 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561007159 NAD(P) binding site [chemical binding]; other site 643561007160 active site 643561007161 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 643561007162 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 643561007163 FeS/SAM binding site; other site 643561007164 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 643561007165 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 643561007166 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 643561007167 GTP binding site [chemical binding]; other site 643561007168 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561007169 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 643561007170 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 643561007171 dimer interface [polypeptide binding]; other site 643561007172 putative functional site; other site 643561007173 putative MPT binding site; other site 643561007174 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 643561007175 catalytic residues [active] 643561007176 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 643561007177 RNA/DNA hybrid binding site [nucleotide binding]; other site 643561007178 active site 643561007179 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 643561007180 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561007181 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 643561007182 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 643561007183 N-acetyl-D-glucosamine binding site [chemical binding]; other site 643561007184 catalytic residue [active] 643561007185 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 643561007186 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 643561007187 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561007188 MAPEG family; Region: MAPEG; cl09190 643561007189 recombination protein RecR; Reviewed; Region: recR; PRK00076 643561007190 RecR protein; Region: RecR; pfam02132 643561007191 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 643561007192 putative active site [active] 643561007193 putative metal-binding site [ion binding]; other site 643561007194 tetramer interface [polypeptide binding]; other site 643561007195 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 643561007196 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14951 643561007197 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 643561007198 Walker A motif; other site 643561007199 ATP binding site [chemical binding]; other site 643561007200 Walker B motif; other site 643561007201 arginine finger; other site 643561007202 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 643561007203 Cache domain; Region: Cache_2; cl07034 643561007204 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561007205 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 643561007206 Predicted flavoproteins [General function prediction only]; Region: COG2081 643561007207 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561007208 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561007209 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 643561007210 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561007211 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 643561007212 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561007213 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 643561007214 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 643561007215 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 643561007216 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 643561007217 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 643561007218 catalytic residues [active] 643561007219 transcription termination factor Rho; Provisional; Region: rho; PRK09376 643561007220 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 643561007221 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 643561007222 RNA binding site [nucleotide binding]; other site 643561007223 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 643561007224 multimer interface [polypeptide binding]; other site 643561007225 Walker A motif; other site 643561007226 ATP binding site [chemical binding]; other site 643561007227 Walker B motif; other site 643561007228 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561007229 Walker A/P-loop; other site 643561007230 ATP binding site [chemical binding]; other site 643561007231 Q-loop/lid; other site 643561007232 exonuclease subunit SbcC; Provisional; Region: PRK10246 643561007233 exonuclease subunit SbcC; Provisional; Region: PRK10246 643561007234 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561007235 ABC transporter signature motif; other site 643561007236 Walker B; other site 643561007237 D-loop; other site 643561007238 H-loop/switch region; other site 643561007239 exonuclease subunit SbcD; Provisional; Region: PRK10966 643561007240 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 643561007241 active site 643561007242 metal binding site [ion binding]; metal-binding site 643561007243 DNA binding site [nucleotide binding] 643561007244 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 643561007245 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 643561007246 multidrug efflux protein; Reviewed; Region: PRK01766 643561007247 MatE; Region: MatE; cl10513 643561007248 MatE; Region: MatE; cl10513 643561007249 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 643561007250 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 643561007251 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 643561007252 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 643561007253 dimer interface [polypeptide binding]; other site 643561007254 phosphorylation site [posttranslational modification] 643561007255 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 643561007256 ATP binding site [chemical binding]; other site 643561007257 Mg2+ binding site [ion binding]; other site 643561007258 G-X-G motif; other site 643561007259 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 643561007260 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561007261 active site 643561007262 phosphorylation site [posttranslational modification] 643561007263 intermolecular recognition site; other site 643561007264 dimerization interface [polypeptide binding]; other site 643561007265 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 643561007266 DNA binding site [nucleotide binding] 643561007267 transcriptional regulator PhoU; Provisional; Region: PRK11115 643561007268 PhoU domain; Region: PhoU; pfam01895 643561007269 PhoU domain; Region: PhoU; pfam01895 643561007270 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 643561007271 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 643561007272 Walker A/P-loop; other site 643561007273 ATP binding site [chemical binding]; other site 643561007274 Q-loop/lid; other site 643561007275 ABC transporter signature motif; other site 643561007276 Walker B; other site 643561007277 D-loop; other site 643561007278 H-loop/switch region; other site 643561007279 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 643561007280 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 643561007281 dimer interface [polypeptide binding]; other site 643561007282 conserved gate region; other site 643561007283 putative PBP binding loops; other site 643561007284 ABC-ATPase subunit interface; other site 643561007285 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 643561007286 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 643561007287 dimer interface [polypeptide binding]; other site 643561007288 conserved gate region; other site 643561007289 putative PBP binding loops; other site 643561007290 ABC-ATPase subunit interface; other site 643561007291 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 643561007292 guanosine pentaphosphate phosphohydrolase; Provisional; Region: PRK11031 643561007293 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 643561007294 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 643561007295 catalytic core [active] 643561007296 polyphosphate kinase; Provisional; Region: PRK05443 643561007297 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 643561007298 putative active site [active] 643561007299 catalytic site [active] 643561007300 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 643561007301 putative domain interface [polypeptide binding]; other site 643561007302 putative active site [active] 643561007303 catalytic site [active] 643561007304 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561007305 PAS domain S-box; Region: sensory_box; TIGR00229 643561007306 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561007307 PAS domain S-box; Region: sensory_box; TIGR00229 643561007308 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 643561007309 putative active site [active] 643561007310 heme pocket [chemical binding]; other site 643561007311 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 643561007312 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561007313 metal binding site [ion binding]; metal-binding site 643561007314 active site 643561007315 I-site; other site 643561007316 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 643561007317 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 643561007318 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 643561007319 active site 643561007320 substrate binding site [chemical binding]; other site 643561007321 metal binding site [ion binding]; metal-binding site 643561007322 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 643561007323 dihydropteroate synthase; Region: DHPS; TIGR01496 643561007324 substrate binding pocket [chemical binding]; other site 643561007325 dimer interface [polypeptide binding]; other site 643561007326 inhibitor binding site; inhibition site 643561007327 FtsH Extracellular; Region: FtsH_ext; pfam06480 643561007328 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 643561007329 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 643561007330 Walker A motif; other site 643561007331 ATP binding site [chemical binding]; other site 643561007332 Walker B motif; other site 643561007333 arginine finger; other site 643561007334 Peptidase family M41; Region: Peptidase_M41; pfam01434 643561007335 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 643561007336 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 643561007337 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 643561007338 domain; Region: GreA_GreB_N; pfam03449 643561007339 C-term; Region: GreA_GreB; pfam01272 643561007340 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 643561007341 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 643561007342 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561007343 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 643561007344 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 643561007345 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561007346 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 643561007347 IMP binding site; other site 643561007348 dimer interface [polypeptide binding]; other site 643561007349 interdomain contacts; other site 643561007350 partial ornithine binding site; other site 643561007351 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 643561007352 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 643561007353 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 643561007354 catalytic site [active] 643561007355 subunit interface [polypeptide binding]; other site 643561007356 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading...; Region: EFh; cd00051 643561007357 Ca2+ binding site [ion binding]; other site 643561007358 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading...; Region: EFh; cd00051 643561007359 Ca2+ binding site [ion binding]; other site 643561007360 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 643561007361 Amino acid permease; Region: AA_permease; pfam00324 643561007362 hypothetical protein; Provisional; Region: PRK07206 643561007363 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561007364 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007365 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 643561007366 dimerization interface [polypeptide binding]; other site 643561007367 Transposase; Region: DEDD_Tnp_IS110; pfam01548 643561007368 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 643561007369 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 643561007370 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561007371 tetrameric interface [polypeptide binding]; other site 643561007372 NAD binding site [chemical binding]; other site 643561007373 catalytic residues [active] 643561007374 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 643561007375 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561007376 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561007377 active site 643561007378 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561007379 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 643561007380 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 643561007381 E-class dimer interface [polypeptide binding]; other site 643561007382 P-class dimer interface [polypeptide binding]; other site 643561007383 active site 643561007384 Cu2+ binding site [ion binding]; other site 643561007385 Zn2+ binding site [ion binding]; other site 643561007386 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 643561007387 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561007388 N-terminal plug; other site 643561007389 ligand-binding site [chemical binding]; other site 643561007390 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561007391 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561007392 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 643561007393 galactarate dehydratase; Region: galactar-dH20; TIGR03248 643561007394 SAF domain; Region: SAF; cl00555 643561007395 SAF domain; Region: SAF; cl00555 643561007396 DctM-like transporters; Region: DctM; pfam06808 643561007397 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 643561007398 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 643561007399 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561007400 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 643561007401 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561007402 NAD(P) binding site [chemical binding]; other site 643561007403 active site 643561007404 Transcriptional regulators [Transcription]; Region: FadR; COG2186 643561007405 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561007406 DNA-binding site [nucleotide binding]; DNA binding site 643561007407 FCD domain; Region: FCD; cl11656 643561007408 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561007409 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561007410 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 643561007411 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH); Region: KDGDH; cd00951 643561007412 putative active site [active] 643561007413 catalytic residue [active] 643561007414 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 643561007415 RNA polymerase sigma factor; Provisional; Region: PRK12515 643561007416 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 643561007417 DNA binding residues [nucleotide binding] 643561007418 Peptidase S8 family domain, uncharacterized subfamily 8; Region: Peptidases_S8_8; cd07492 643561007419 active site 643561007420 catalytic triad [active] 643561007421 major facilitator superfamily transporter; Provisional; Region: PRK05122 643561007422 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561007423 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561007424 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561007425 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 643561007426 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 643561007427 H-NS histone family; Region: Histone_HNS; pfam00816 643561007428 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 643561007429 putative metal dependent hydrolase; Provisional; Region: PRK11598 643561007430 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 643561007431 Sulfatase; Region: Sulfatase; cl10460 643561007432 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 643561007433 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 643561007434 dimer interface [polypeptide binding]; other site 643561007435 phosphorylation site [posttranslational modification] 643561007436 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 643561007437 ATP binding site [chemical binding]; other site 643561007438 Mg2+ binding site [ion binding]; other site 643561007439 G-X-G motif; other site 643561007440 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561007441 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561007442 active site 643561007443 phosphorylation site [posttranslational modification] 643561007444 intermolecular recognition site; other site 643561007445 dimerization interface [polypeptide binding]; other site 643561007446 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 643561007447 DNA binding site [nucleotide binding] 643561007448 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 643561007449 Protein of unknown function (DUF1260); Region: DUF1260; cl01170 643561007450 D-galactonate transporter; Region: 2A0114; TIGR00893 643561007451 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 643561007452 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007453 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 643561007454 CoenzymeA binding site [chemical binding]; other site 643561007455 subunit interaction site [polypeptide binding]; other site 643561007456 PHB binding site; other site 643561007457 isocitrate dehydrogenase; Validated; Region: PRK07362 643561007458 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 643561007459 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 643561007460 superoxide dismutase; Provisional; Region: PRK10543 643561007461 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 643561007462 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 643561007463 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 643561007464 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 643561007465 generic binding surface II; other site 643561007466 generic binding surface I; other site 643561007467 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 643561007468 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 643561007469 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 643561007470 tetraacyldisaccharide 4'-kinase; Provisional; Region: PRK01906 643561007471 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 643561007472 Trm112p-like protein; Region: Trm112p; cl01066 643561007473 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 643561007474 Ligand binding site [chemical binding]; other site 643561007475 oligomer interface [polypeptide binding]; other site 643561007476 adenylate kinase; Reviewed; Region: adk; PRK00279 643561007477 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 643561007478 AMP-binding site [chemical binding]; other site 643561007479 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 643561007480 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 643561007481 active site/substrate binding site [active] 643561007482 tetramer interface [polypeptide binding]; other site 643561007483 LexA repressor; Validated; Region: PRK00215 643561007484 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007485 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 643561007486 Catalytic site [active] 643561007487 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 643561007488 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 643561007489 ATP binding site [chemical binding]; other site 643561007490 putative Mg++ binding site [ion binding]; other site 643561007491 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 643561007492 nucleotide binding region [chemical binding]; other site 643561007493 ATP-binding site [chemical binding]; other site 643561007494 Helicase associated domain (HA2); Region: HA2; cl04503 643561007495 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 643561007496 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 643561007497 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 643561007498 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561007499 N-acetylglutamate synthase; Validated; Region: PRK05279 643561007500 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 643561007501 putative feedback inhibition sensing region; other site 643561007502 putative nucleotide binding site [chemical binding]; other site 643561007503 putative substrate binding site [chemical binding]; other site 643561007504 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561007505 Beta-lactamase; Region: Beta-lactamase; cl01009 643561007506 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561007507 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007508 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 643561007509 dimerization interface [polypeptide binding]; other site 643561007510 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 643561007511 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 643561007512 active site residue [active] 643561007513 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 643561007514 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 643561007515 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 643561007516 putative N-terminal domain interface [polypeptide binding]; other site 643561007517 putative dimer interface [polypeptide binding]; other site 643561007518 putative substrate binding pocket (H-site) [chemical binding]; other site 643561007519 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 643561007520 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 643561007521 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 643561007522 Walker A/P-loop; other site 643561007523 ATP binding site [chemical binding]; other site 643561007524 Q-loop/lid; other site 643561007525 ABC transporter signature motif; other site 643561007526 Walker B; other site 643561007527 D-loop; other site 643561007528 H-loop/switch region; other site 643561007529 TOBE-like domain; Region: TOBE_3; pfam12857 643561007530 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 643561007531 dimer interface [polypeptide binding]; other site 643561007532 conserved gate region; other site 643561007533 putative PBP binding loops; other site 643561007534 ABC-ATPase subunit interface; other site 643561007535 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 643561007536 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 643561007537 dimer interface [polypeptide binding]; other site 643561007538 conserved gate region; other site 643561007539 putative PBP binding loops; other site 643561007540 ABC-ATPase subunit interface; other site 643561007541 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 643561007542 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 643561007543 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 643561007544 LysR family transcriptional regulator; Provisional; Region: PRK14997 643561007545 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007546 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 643561007547 putative effector binding pocket; other site 643561007548 putative dimerization interface [polypeptide binding]; other site 643561007549 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561007550 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561007551 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561007552 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561007553 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 643561007554 SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and...; Region: XynE_like; cd01830 643561007555 active site 643561007556 catalytic triad [active] 643561007557 oxyanion hole [active] 643561007558 Transposase; Region: DEDD_Tnp_IS110; pfam01548 643561007559 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 643561007560 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561007561 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561007562 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561007563 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 643561007564 dimer interface [polypeptide binding]; other site 643561007565 conserved gate region; other site 643561007566 ABC-ATPase subunit interface; other site 643561007567 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 643561007568 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 643561007569 Walker A/P-loop; other site 643561007570 ATP binding site [chemical binding]; other site 643561007571 Q-loop/lid; other site 643561007572 ABC transporter signature motif; other site 643561007573 Walker B; other site 643561007574 D-loop; other site 643561007575 H-loop/switch region; other site 643561007576 NIL domain; Region: NIL; cl09633 643561007577 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 643561007578 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 643561007579 histidine kinase; Provisional; Region: PRK13557 643561007580 putative active site [active] 643561007581 heme pocket [chemical binding]; other site 643561007582 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 643561007583 ATP binding site [chemical binding]; other site 643561007584 Mg2+ binding site [ion binding]; other site 643561007585 G-X-G motif; other site 643561007586 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561007587 active site 643561007588 phosphorylation site [posttranslational modification] 643561007589 intermolecular recognition site; other site 643561007590 dimerization interface [polypeptide binding]; other site 643561007591 transcriptional regulator; Provisional; Region: PRK10632 643561007592 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007593 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 643561007594 putative effector binding pocket; other site 643561007595 dimerization interface [polypeptide binding]; other site 643561007596 NodT family; Region: outer_NodT; TIGR01845 643561007597 Outer membrane efflux protein; Region: OEP; pfam02321 643561007598 Outer membrane efflux protein; Region: OEP; pfam02321 643561007599 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 643561007600 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 643561007601 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561007602 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561007603 active site 643561007604 phosphorylation site [posttranslational modification] 643561007605 intermolecular recognition site; other site 643561007606 dimerization interface [polypeptide binding]; other site 643561007607 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 643561007608 DNA binding site [nucleotide binding] 643561007609 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 643561007610 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 643561007611 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 643561007612 ATP binding site [chemical binding]; other site 643561007613 Mg2+ binding site [ion binding]; other site 643561007614 G-X-G motif; other site 643561007615 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007616 LysR family transcriptional regulator; Provisional; Region: PRK14997 643561007617 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_7; cd08476 643561007618 putative effector binding pocket; other site 643561007619 putative dimerization interface [polypeptide binding]; other site 643561007620 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561007621 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561007622 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561007623 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 643561007624 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 643561007625 putative DNA binding site [nucleotide binding]; other site 643561007626 putative homodimer interface [polypeptide binding]; other site 643561007627 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 643561007628 DNA polymerase LigD, ligase domain; Region: NHEJ_ligase_lig; TIGR02779 643561007629 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 643561007630 active site 643561007631 DNA binding site [nucleotide binding] 643561007632 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 643561007633 DNA binding site [nucleotide binding] 643561007634 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-...; Region: PaeLigD_Pol_like; cd04862 643561007635 nucleotide binding site [chemical binding]; other site 643561007636 biotin synthase; Provisional; Region: PRK15108 643561007637 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 643561007638 FeS/SAM binding site; other site 643561007639 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 643561007640 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 643561007641 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561007642 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 643561007643 substrate binding pocket [chemical binding]; other site 643561007644 membrane-bound complex binding site; other site 643561007645 hinge residues; other site 643561007646 hypothetical protein; Provisional; Region: PRK07483 643561007647 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 643561007648 inhibitor-cofactor binding pocket; inhibition site 643561007649 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561007650 catalytic residue [active] 643561007651 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 643561007652 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 643561007653 putative active site [active] 643561007654 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 643561007655 dimer interface [polypeptide binding]; other site 643561007656 substrate binding site [chemical binding]; other site 643561007657 metal binding site [ion binding]; metal-binding site 643561007658 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 643561007659 putative active site [active] 643561007660 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 643561007661 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 643561007662 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561007663 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 643561007664 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 643561007665 carboxyltransferase (CT) interaction site; other site 643561007666 biotinylation site [posttranslational modification]; other site 643561007667 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 643561007668 putative metal binding site [ion binding]; other site 643561007669 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 643561007670 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 643561007671 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561007672 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561007673 membrane ATPase/protein kinase; Provisional; Region: PRK09435 643561007674 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 643561007675 Walker A; other site 643561007676 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561007677 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 643561007678 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily...; Region: MM_CoA_mutase_alpha_like; cd03679 643561007679 active site 643561007680 substrate binding site [chemical binding]; other site 643561007681 coenzyme B12 binding site [chemical binding]; other site 643561007682 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen...; Region: MM_CoA_mut_B12_BD; cd02071 643561007683 B12 binding site [chemical binding]; other site 643561007684 cobalt ligand [ion binding]; other site 643561007685 Transcriptional regulators [Transcription]; Region: GntR; COG1802 643561007686 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561007687 DNA-binding site [nucleotide binding]; DNA binding site 643561007688 FCD domain; Region: FCD; cl11656 643561007689 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 643561007690 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 643561007691 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 643561007692 PAS domain S-box; Region: sensory_box; TIGR00229 643561007693 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 643561007694 putative active site [active] 643561007695 heme pocket [chemical binding]; other site 643561007696 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 643561007697 PAS domain S-box; Region: sensory_box; TIGR00229 643561007698 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561007699 metal binding site [ion binding]; metal-binding site 643561007700 active site 643561007701 I-site; other site 643561007702 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 643561007703 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 643561007704 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 643561007705 Outer membrane efflux protein; Region: OEP; pfam02321 643561007706 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 643561007707 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561007708 active site 643561007709 phosphorylation site [posttranslational modification] 643561007710 intermolecular recognition site; other site 643561007711 dimerization interface [polypeptide binding]; other site 643561007712 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 643561007713 DNA binding residues [nucleotide binding] 643561007714 dimerization interface [polypeptide binding]; other site 643561007715 CHASE3 domain; Region: CHASE3; cl05000 643561007716 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 643561007717 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561007718 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 643561007719 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 643561007720 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 643561007721 FMN binding site [chemical binding]; other site 643561007722 active site 643561007723 catalytic residues [active] 643561007724 substrate binding site [chemical binding]; other site 643561007725 CHASE domain; Region: CHASE; cl01369 643561007726 PAS fold; Region: PAS_4; pfam08448 643561007727 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561007728 metal binding site [ion binding]; metal-binding site 643561007729 active site 643561007730 I-site; other site 643561007731 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 643561007732 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 643561007733 synthetase active site [active] 643561007734 NTP binding site [chemical binding]; other site 643561007735 metal binding site [ion binding]; metal-binding site 643561007736 polyhydroxyalkanoate depolymerase, intracellular; Region: PHB_depoly_PhaZ; TIGR01849 643561007737 PHB de-polymerase C-terminus; Region: PHB_depo_C; cl14907 643561007738 ferredoxin; Provisional; Region: PRK06991 643561007739 Putative Fe-S cluster; Region: FeS; pfam04060 643561007740 4Fe-4S binding domain; Region: Fer4; cl02805 643561007741 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 643561007742 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561007743 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 643561007744 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 643561007745 hypothetical protein; Validated; Region: PRK07682 643561007746 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 643561007747 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561007748 homodimer interface [polypeptide binding]; other site 643561007749 catalytic residue [active] 643561007750 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 643561007751 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA...; Region: LbH_THP_succinylT; cd03350 643561007752 active site 643561007753 substrate binding site [chemical binding]; other site 643561007754 trimer interface [polypeptide binding]; other site 643561007755 CoA binding site [chemical binding]; other site 643561007756 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 643561007757 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561007758 Walker A motif; other site 643561007759 ATP binding site [chemical binding]; other site 643561007760 Walker B motif; other site 643561007761 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 643561007762 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 643561007763 metal binding site [ion binding]; metal-binding site 643561007764 dimer interface [polypeptide binding]; other site 643561007765 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 643561007766 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 643561007767 S-adenosylmethionine binding site [chemical binding]; other site 643561007768 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 643561007769 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 643561007770 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 643561007771 ABC transporter; Region: ABC_tran_2; pfam12848 643561007772 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 643561007773 acetyacetyl-CoA reductase; Provisional; Region: PRK12938 643561007774 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 643561007775 NAD(P) binding site [chemical binding]; other site 643561007776 homotetramer interface [polypeptide binding]; other site 643561007777 homodimer interface [polypeptide binding]; other site 643561007778 active site 643561007779 putative acyltransferase; Provisional; Region: PRK05790 643561007780 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 643561007781 dimer interface [polypeptide binding]; other site 643561007782 active site 643561007783 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 643561007784 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 643561007785 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 643561007786 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 643561007787 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 643561007788 maleylacetoacetate isomerase; Region: maiA; TIGR01262 643561007789 C-terminal domain interface [polypeptide binding]; other site 643561007790 GSH binding site (G-site) [chemical binding]; other site 643561007791 putative dimer interface [polypeptide binding]; other site 643561007792 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 643561007793 dimer interface [polypeptide binding]; other site 643561007794 N-terminal domain interface [polypeptide binding]; other site 643561007795 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 643561007796 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561007797 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 643561007798 nudix motif; other site 643561007799 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 643561007800 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 643561007801 active site 643561007802 ATP binding site [chemical binding]; other site 643561007803 substrate binding site [chemical binding]; other site 643561007804 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 643561007805 Cupin domain; Region: Cupin_2; cl09118 643561007806 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561007807 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561007808 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561007809 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 643561007810 substrate binding pocket [chemical binding]; other site 643561007811 membrane-bound complex binding site; other site 643561007812 hinge residues; other site 643561007813 Transglycosylase; Region: Transgly; cl07896 643561007814 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 643561007815 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 643561007816 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 643561007817 Protein of unknown function (DUF2167); Region: DUF2167; cl01938 643561007818 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561007819 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561007820 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 643561007821 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 643561007822 E3 interaction surface; other site 643561007823 lipoyl attachment site [posttranslational modification]; other site 643561007824 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561007825 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 643561007826 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 643561007827 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 643561007828 E3 interaction surface; other site 643561007829 lipoyl attachment site [posttranslational modification]; other site 643561007830 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 643561007831 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 643561007832 E3 interaction surface; other site 643561007833 lipoyl attachment site [posttranslational modification]; other site 643561007834 e3 binding domain; Region: E3_binding; pfam02817 643561007835 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 643561007836 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 643561007837 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 643561007838 dimer interface [polypeptide binding]; other site 643561007839 TPP-binding site [chemical binding]; other site 643561007840 PAS domain S-box; Region: sensory_box; TIGR00229 643561007841 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 643561007842 putative active site [active] 643561007843 heme pocket [chemical binding]; other site 643561007844 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 643561007845 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 643561007846 ATP binding site [chemical binding]; other site 643561007847 Mg2+ binding site [ion binding]; other site 643561007848 G-X-G motif; other site 643561007849 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 643561007850 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561007851 active site 643561007852 phosphorylation site [posttranslational modification] 643561007853 intermolecular recognition site; other site 643561007854 dimerization interface [polypeptide binding]; other site 643561007855 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 643561007856 DNA binding residues [nucleotide binding] 643561007857 dimerization interface [polypeptide binding]; other site 643561007858 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 643561007859 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 643561007860 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 643561007861 homodimer interface [polypeptide binding]; other site 643561007862 NADP binding site [chemical binding]; other site 643561007863 substrate binding site [chemical binding]; other site 643561007864 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 643561007865 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 643561007866 active site 643561007867 Zn binding site [ion binding]; other site 643561007868 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 643561007869 catalytic residues [active] 643561007870 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 643561007871 tetramer (dimer of dimers) interface [polypeptide binding]; other site 643561007872 active site 643561007873 dimer interface [polypeptide binding]; other site 643561007874 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 643561007875 quinone interaction residues [chemical binding]; other site 643561007876 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 643561007877 active site 643561007878 catalytic residues [active] 643561007879 FMN binding site [chemical binding]; other site 643561007880 substrate binding site [chemical binding]; other site 643561007881 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 643561007882 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561007883 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 643561007884 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 643561007885 Proteobacterial; Region: dnaQ_proteo; TIGR01406 643561007886 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 643561007887 active site 643561007888 substrate binding site [chemical binding]; other site 643561007889 catalytic site [active] 643561007890 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 643561007891 catalytic loop [active] 643561007892 iron binding site [ion binding]; other site 643561007893 chaperone protein HscA; Provisional; Region: hscA; PRK05183 643561007894 co-chaperone HscB; Provisional; Region: hscB; PRK03578 643561007895 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 643561007896 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 643561007897 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 643561007898 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 643561007899 trimerization site [polypeptide binding]; other site 643561007900 active site 643561007901 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 643561007902 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 643561007903 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561007904 catalytic residue [active] 643561007905 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007906 Rrf2 family protein; Region: rrf2_super; TIGR00738 643561007907 excinuclease ABC subunit B; Provisional; Region: PRK05298 643561007908 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 643561007909 ATP binding site [chemical binding]; other site 643561007910 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 643561007911 nucleotide binding region [chemical binding]; other site 643561007912 ATP-binding site [chemical binding]; other site 643561007913 Ultra-violet resistance protein B; Region: UvrB; pfam12344 643561007914 UvrB/uvrC motif; Region: UVR; pfam02151 643561007915 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 643561007916 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561007917 homodimer interface [polypeptide binding]; other site 643561007918 catalytic residue [active] 643561007919 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561007920 hypothetical protein; Provisional; Region: PRK01254 643561007921 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 643561007922 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561007923 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 643561007924 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 643561007925 Uncharacterized conserved protein [Function unknown]; Region: COG1739 643561007926 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 643561007927 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 643561007928 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 643561007929 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561007930 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 643561007931 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561007932 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 643561007933 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561007934 amidase; Provisional; Region: PRK07486 643561007935 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 643561007936 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561007937 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561007938 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 643561007939 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561007940 catalytic residue [active] 643561007941 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007942 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561007943 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 643561007944 dimerization interface [polypeptide binding]; other site 643561007945 Membrane bound L-sorbosone dehydrogenase; Region: SNDH; pfam12303 643561007946 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 643561007947 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 643561007948 RNA binding surface [nucleotide binding]; other site 643561007949 Uncharacterized protein involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: MukB; COG3096 643561007950 CheB methylesterase; Region: CheB_methylest; pfam01339 643561007951 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 643561007952 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 643561007953 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 643561007954 Tat binding protein 1(TBP-1)-interacting protein (TBPIP); Region: TBPIP; pfam07106 643561007955 PAS domain S-box; Region: sensory_box; TIGR00229 643561007956 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 643561007957 putative active site [active] 643561007958 heme pocket [chemical binding]; other site 643561007959 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 643561007960 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 643561007961 putative active site [active] 643561007962 heme pocket [chemical binding]; other site 643561007963 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 643561007964 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 643561007965 ATP binding site [chemical binding]; other site 643561007966 Mg2+ binding site [ion binding]; other site 643561007967 G-X-G motif; other site 643561007968 Response regulator receiver domain; Region: Response_reg; pfam00072 643561007969 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561007970 active site 643561007971 phosphorylation site [posttranslational modification] 643561007972 intermolecular recognition site; other site 643561007973 dimerization interface [polypeptide binding]; other site 643561007974 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 643561007975 dinuclear metal binding motif [ion binding]; other site 643561007976 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561007977 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 643561007978 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561007979 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_3; cd08461 643561007980 putative substrate binding pocket [chemical binding]; other site 643561007981 putative dimerization interface [polypeptide binding]; other site 643561007982 CsbD-like; Region: CsbD; cl01272 643561007983 aspartate kinase; Reviewed; Region: PRK06635 643561007984 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 643561007985 putative nucleotide binding site [chemical binding]; other site 643561007986 putative catalytic residues [active] 643561007987 putative Mg ion binding site [ion binding]; other site 643561007988 putative aspartate binding site [chemical binding]; other site 643561007989 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 643561007990 putative allosteric regulatory site; other site 643561007991 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 643561007992 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 643561007993 Ligand Binding Site [chemical binding]; other site 643561007994 TilS substrate binding domain; Region: TilS; pfam09179 643561007995 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561007996 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 643561007997 endonuclease III; Region: ENDO3c; smart00478 643561007998 minor groove reading motif; other site 643561007999 helix-hairpin-helix signature motif; other site 643561008000 substrate binding pocket [chemical binding]; other site 643561008001 active site 643561008002 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 643561008003 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 643561008004 active site 643561008005 HIGH motif; other site 643561008006 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 643561008007 KMSKS motif; other site 643561008008 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 643561008009 tRNA binding surface [nucleotide binding]; other site 643561008010 anticodon binding site; other site 643561008011 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 643561008012 binding surface 643561008013 TPR motif; other site 643561008014 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 643561008015 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 643561008016 substrate binding site [chemical binding]; other site 643561008017 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 643561008018 substrate binding site [chemical binding]; other site 643561008019 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 643561008020 putative active site [active] 643561008021 putative metal binding site [ion binding]; other site 643561008022 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 643561008023 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561008024 ligand binding site [chemical binding]; other site 643561008025 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 643561008026 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561008027 metal binding site [ion binding]; metal-binding site 643561008028 active site 643561008029 I-site; other site 643561008030 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 643561008031 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 643561008032 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561008033 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561008034 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 643561008035 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008036 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 643561008037 dimerization interface [polypeptide binding]; other site 643561008038 2-oxoacid dehydrogenase subunit E1; Provisional; Region: PRK13012 643561008039 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 643561008040 dimer interface [polypeptide binding]; other site 643561008041 TPP-binding site [chemical binding]; other site 643561008042 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 643561008043 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008044 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 643561008045 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 643561008046 Predicted esterase [General function prediction only]; Region: COG0400 643561008047 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 643561008048 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 643561008049 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 643561008050 putative active site [active] 643561008051 metal binding site [ion binding]; metal-binding site 643561008052 RF-1 domain; Region: RF-1; cl02875 643561008053 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561008054 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 643561008055 trimer interface [polypeptide binding]; other site 643561008056 active site 643561008057 dimer interface [polypeptide binding]; other site 643561008058 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 643561008059 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 643561008060 active site 643561008061 HIGH motif; other site 643561008062 nucleotide binding site [chemical binding]; other site 643561008063 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 643561008064 KMSKS motif; other site 643561008065 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 643561008066 Membrane protein of unknown function; Region: DUF360; cl00850 643561008067 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561008068 active site residue [active] 643561008069 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561008070 active site residue [active] 643561008071 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561008072 active site residue [active] 643561008073 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561008074 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561008075 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 643561008076 substrate binding pocket [chemical binding]; other site 643561008077 membrane-bound complex binding site; other site 643561008078 hinge residues; other site 643561008079 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 643561008080 dimer interface [polypeptide binding]; other site 643561008081 conserved gate region; other site 643561008082 putative PBP binding loops; other site 643561008083 ABC-ATPase subunit interface; other site 643561008084 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 643561008085 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 643561008086 dimer interface [polypeptide binding]; other site 643561008087 conserved gate region; other site 643561008088 putative PBP binding loops; other site 643561008089 ABC-ATPase subunit interface; other site 643561008090 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 643561008091 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 643561008092 Walker A/P-loop; other site 643561008093 ATP binding site [chemical binding]; other site 643561008094 Q-loop/lid; other site 643561008095 ABC transporter signature motif; other site 643561008096 Walker B; other site 643561008097 D-loop; other site 643561008098 H-loop/switch region; other site 643561008099 Cysteine dioxygenase type I; Region: CDO_I; cl02350 643561008100 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 643561008101 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 643561008102 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561008103 catalytic residue [active] 643561008104 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561008105 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561008106 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561008107 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008108 NAD(P) binding site [chemical binding]; other site 643561008109 active site 643561008110 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561008111 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008112 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 643561008113 dimerization interface [polypeptide binding]; other site 643561008114 substrate binding pocket [chemical binding]; other site 643561008115 Cysteine dioxygenase type I; Region: CDO_I; cl02350 643561008116 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561008117 active site residue [active] 643561008118 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561008119 active site residue [active] 643561008120 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative...; Region: 4RHOD_Repeat_3; cd01534 643561008121 active site residue [active] 643561008122 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561008123 active site residue [active] 643561008124 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561008125 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561008126 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; cl01820 643561008127 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 643561008128 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 643561008129 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 643561008130 putative hydrophobic ligand binding site [chemical binding]; other site 643561008131 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 643561008132 putative active site [active] 643561008133 catalytic site [active] 643561008134 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 643561008135 putative active site [active] 643561008136 catalytic site [active] 643561008137 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 643561008138 Peptidase family M23; Region: Peptidase_M23; pfam01551 643561008139 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 643561008140 active site 643561008141 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 643561008142 Sel1 repeat; Region: Sel1; cl02723 643561008143 enterobactin exporter EntS; Provisional; Region: PRK10489 643561008144 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 643561008145 putative substrate translocation pore; other site 643561008146 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561008147 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561008148 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 643561008149 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 643561008150 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 643561008151 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 643561008152 Protein of unknown function (DUF1501); Region: DUF1501; cl01699 643561008153 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 643561008154 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 643561008155 active site 643561008156 MgtC family; Region: MgtC; cl12207 643561008157 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 643561008158 Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Region: HTH_SoxR; cd01110 643561008159 DNA binding residues [nucleotide binding] 643561008160 dimer interface [polypeptide binding]; other site 643561008161 [2Fe-2S] cluster binding site [ion binding]; other site 643561008162 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 643561008163 homotrimer interaction site [polypeptide binding]; other site 643561008164 putative active site [active] 643561008165 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008166 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561008167 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 643561008168 trimer interface [polypeptide binding]; other site 643561008169 eyelet of channel; other site 643561008170 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 643561008171 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 643561008172 GTP/Mg2+ binding site [chemical binding]; other site 643561008173 G4 box; other site 643561008174 G5 box; other site 643561008175 G1 box; other site 643561008176 Switch I region; other site 643561008177 G2 box; other site 643561008178 G3 box; other site 643561008179 Switch II region; other site 643561008180 GAF domain; Region: GAF; cl00853 643561008181 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 643561008182 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 643561008183 ATP binding site [chemical binding]; other site 643561008184 Mg2+ binding site [ion binding]; other site 643561008185 G-X-G motif; other site 643561008186 LysE type translocator; Region: LysE; cl00565 643561008187 thiamine pyrophosphate protein; Validated; Region: PRK08199 643561008188 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 643561008189 PYR/PP interface [polypeptide binding]; other site 643561008190 dimer interface [polypeptide binding]; other site 643561008191 TPP binding site [chemical binding]; other site 643561008192 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 643561008193 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; cd00568 643561008194 TPP-binding site [chemical binding]; other site 643561008195 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl01099 643561008196 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 643561008197 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 643561008198 classical (c) SDRs; Region: SDR_c; cd05233 643561008199 NAD(P) binding site [chemical binding]; other site 643561008200 active site 643561008201 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 643561008202 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008203 The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Region: PBP2_GbpR; cd08435 643561008204 putative dimerization interface [polypeptide binding]; other site 643561008205 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 643561008206 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561008207 NAD(P) binding site [chemical binding]; other site 643561008208 catalytic residues [active] 643561008209 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 643561008210 putative ligand binding site [chemical binding]; other site 643561008211 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 643561008212 putative ligand binding site [chemical binding]; other site 643561008213 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 643561008214 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 643561008215 Walker A/P-loop; other site 643561008216 ATP binding site [chemical binding]; other site 643561008217 Q-loop/lid; other site 643561008218 ABC transporter signature motif; other site 643561008219 Walker B; other site 643561008220 D-loop; other site 643561008221 H-loop/switch region; other site 643561008222 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 643561008223 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 643561008224 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 643561008225 TM-ABC transporter signature motif; other site 643561008226 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 643561008227 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 643561008228 Walker A/P-loop; other site 643561008229 ATP binding site [chemical binding]; other site 643561008230 Q-loop/lid; other site 643561008231 ABC transporter signature motif; other site 643561008232 Walker B; other site 643561008233 D-loop; other site 643561008234 H-loop/switch region; other site 643561008235 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 643561008236 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 643561008237 TM-ABC transporter signature motif; other site 643561008238 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 643561008239 TM-ABC transporter signature motif; other site 643561008240 dihydroxy-acid dehydratase; Provisional; Region: PRK13017 643561008241 Dehydratase family; Region: ILVD_EDD; cl00340 643561008242 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 643561008243 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 643561008244 inhibitor site; inhibition site 643561008245 active site 643561008246 dimer interface [polypeptide binding]; other site 643561008247 catalytic residue [active] 643561008248 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism]; Region: DgoK; COG3734 643561008249 2-keto-3-deoxy-galactonokinase; Region: DGOK; pfam05035 643561008250 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 643561008251 active site 643561008252 intersubunit interface [polypeptide binding]; other site 643561008253 catalytic residue [active] 643561008254 galactonate dehydratase; Provisional; Region: PRK14017 643561008255 D-galactonate dehydratase catalyses the dehydration of galactonate to 2-keto-3-deoxygalactnate (KDGal), as part of the D-galactonate nonphosphorolytic catabolic Entner-Doudoroff pathway. D-galactonate dehydratase belongs to the enolase superfamily of...; Region: D-galactonate_dehydratase; cd03325 643561008256 putative active site pocket [active] 643561008257 putative metal binding site [ion binding]; other site 643561008258 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 643561008259 hypothetical membrane protein, TIGR01666; Region: YCCS 643561008260 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561008261 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 643561008262 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561008263 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 643561008264 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561008265 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 643561008266 Response regulator receiver domain; Region: Response_reg; pfam00072 643561008267 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008268 active site 643561008269 phosphorylation site [posttranslational modification] 643561008270 intermolecular recognition site; other site 643561008271 dimerization interface [polypeptide binding]; other site 643561008272 Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Region: HTH_MerR-trunc; cd04762 643561008273 DNA binding residues [nucleotide binding] 643561008274 Response regulator receiver domain; Region: Response_reg; pfam00072 643561008275 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008276 active site 643561008277 phosphorylation site [posttranslational modification] 643561008278 intermolecular recognition site; other site 643561008279 dimerization interface [polypeptide binding]; other site 643561008280 Response regulator receiver domain; Region: Response_reg; pfam00072 643561008281 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008282 active site 643561008283 phosphorylation site [posttranslational modification] 643561008284 intermolecular recognition site; other site 643561008285 dimerization interface [polypeptide binding]; other site 643561008286 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 643561008287 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 643561008288 substrate binding pocket [chemical binding]; other site 643561008289 membrane-bound complex binding site; other site 643561008290 hinge residues; other site 643561008291 PAS fold; Region: PAS_4; pfam08448 643561008292 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 643561008293 putative active site [active] 643561008294 heme pocket [chemical binding]; other site 643561008295 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 643561008296 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 643561008297 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 643561008298 dimer interface [polypeptide binding]; other site 643561008299 phosphorylation site [posttranslational modification] 643561008300 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 643561008301 ATP binding site [chemical binding]; other site 643561008302 Mg2+ binding site [ion binding]; other site 643561008303 G-X-G motif; other site 643561008304 Domain of unknown function (DUF427); Region: DUF427; cl00998 643561008305 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 643561008306 catalytic loop [active] 643561008307 iron binding site [ion binding]; other site 643561008308 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 643561008309 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 643561008310 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 643561008311 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 643561008312 dimerization interface [polypeptide binding]; other site 643561008313 active site 643561008314 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 643561008315 homopentamer interface [polypeptide binding]; other site 643561008316 active site 643561008317 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 643561008318 hypothetical protein; Validated; Region: PRK07682 643561008319 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 643561008320 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561008321 homodimer interface [polypeptide binding]; other site 643561008322 catalytic residue [active] 643561008323 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 643561008324 active site 643561008325 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 643561008326 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 643561008327 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 643561008328 Gram-negative bacterial tonB protein; Region: TonB; cl10048 643561008329 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 643561008330 Phospholipase C [Cell envelope biogenesis, outer membrane]; Region: PlcC; COG3511 643561008331 Sulfatase; Region: Sulfatase; cl10460 643561008332 metabolite-proton symporter; Region: 2A0106; TIGR00883 643561008333 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 643561008334 putative substrate translocation pore; other site 643561008335 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 643561008336 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 643561008337 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 643561008338 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 643561008339 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 643561008340 D-pathway; other site 643561008341 Putative ubiquinol binding site [chemical binding]; other site 643561008342 Low-spin heme (heme b) binding site [chemical binding]; other site 643561008343 Putative water exit pathway; other site 643561008344 Binuclear center (heme o3/CuB) [ion binding]; other site 643561008345 K-pathway; other site 643561008346 Putative proton exit pathway; other site 643561008347 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 643561008348 Subunit I/III interface [polypeptide binding]; other site 643561008349 Subunit III/IV interface [polypeptide binding]; other site 643561008350 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 643561008351 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 643561008352 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 643561008353 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 643561008354 ATP binding site [chemical binding]; other site 643561008355 Mg2+ binding site [ion binding]; other site 643561008356 G-X-G motif; other site 643561008357 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 643561008358 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008359 active site 643561008360 phosphorylation site [posttranslational modification] 643561008361 intermolecular recognition site; other site 643561008362 dimerization interface [polypeptide binding]; other site 643561008363 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561008364 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561008365 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008366 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 643561008367 dimerization interface [polypeptide binding]; other site 643561008368 putative protease; Provisional; Region: PRK15452 643561008369 Peptidase family U32; Region: Peptidase_U32; cl03113 643561008370 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 643561008371 non-specific DNA binding site [nucleotide binding]; other site 643561008372 salt bridge; other site 643561008373 sequence-specific DNA binding site [nucleotide binding]; other site 643561008374 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561008375 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 643561008376 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 643561008377 substrate binding site [chemical binding]; other site 643561008378 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 643561008379 substrate binding site [chemical binding]; other site 643561008380 ligand binding site [chemical binding]; other site 643561008381 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 643561008382 trans-aconitate 2-methyltransferase; Provisional; Region: PRK01683 643561008383 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 643561008384 S-adenosylmethionine binding site [chemical binding]; other site 643561008385 malate dehydrogenase; Provisional; Region: PRK05442 643561008386 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 643561008387 NAD(P) binding site [chemical binding]; other site 643561008388 dimer interface [polypeptide binding]; other site 643561008389 malate binding site [chemical binding]; other site 643561008390 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 643561008391 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561008392 DNA-binding site [nucleotide binding]; DNA binding site 643561008393 UTRA domain; Region: UTRA; cl01230 643561008394 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 643561008395 Iron-sulfur protein interface; other site 643561008396 proximal quinone binding site [chemical binding]; other site 643561008397 SdhD (CybS) interface [polypeptide binding]; other site 643561008398 proximal heme binding site [chemical binding]; other site 643561008399 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 643561008400 SdhC subunit interface [polypeptide binding]; other site 643561008401 proximal heme binding site [chemical binding]; other site 643561008402 cardiolipin binding site; other site 643561008403 Iron-sulfur protein interface; other site 643561008404 proximal quinone binding site [chemical binding]; other site 643561008405 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 643561008406 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008407 domain; Region: Succ_DH_flav_C; pfam02910 643561008408 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 643561008409 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 643561008410 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 643561008411 dimer interface [polypeptide binding]; other site 643561008412 Citrate synthase; Region: Citrate_synt; pfam00285 643561008413 active site 643561008414 citrylCoA binding site [chemical binding]; other site 643561008415 NADH binding [chemical binding]; other site 643561008416 cationic pore residues; other site 643561008417 oxalacetate/citrate binding site [chemical binding]; other site 643561008418 coenzyme A binding site [chemical binding]; other site 643561008419 catalytic triad [active] 643561008420 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 643561008421 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561008422 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 643561008423 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 643561008424 conserved cys residue [active] 643561008425 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561008426 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561008427 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 643561008428 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 643561008429 substrate binding site [chemical binding]; other site 643561008430 catalytic Zn binding site [ion binding]; other site 643561008431 NAD binding site [chemical binding]; other site 643561008432 structural Zn binding site [ion binding]; other site 643561008433 dimer interface [polypeptide binding]; other site 643561008434 Predicted esterase [General function prediction only]; Region: COG0627 643561008435 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 643561008436 putative metal dependent hydrolase; Provisional; Region: PRK11598 643561008437 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 643561008438 Sulfatase; Region: Sulfatase; cl10460 643561008439 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561008440 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008441 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 643561008442 dimerization interface [polypeptide binding]; other site 643561008443 Cache domain; Region: Cache_2; cl07034 643561008444 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561008445 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 643561008446 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561008447 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 643561008448 tetramerization interface [polypeptide binding]; other site 643561008449 NAD(P) binding site [chemical binding]; other site 643561008450 catalytic residues [active] 643561008451 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 643561008452 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 643561008453 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 643561008454 Walker A/P-loop; other site 643561008455 ATP binding site [chemical binding]; other site 643561008456 Q-loop/lid; other site 643561008457 ABC transporter signature motif; other site 643561008458 Walker B; other site 643561008459 D-loop; other site 643561008460 H-loop/switch region; other site 643561008461 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 643561008462 Walker A/P-loop; other site 643561008463 ATP binding site [chemical binding]; other site 643561008464 Q-loop/lid; other site 643561008465 ABC transporter signature motif; other site 643561008466 Walker B; other site 643561008467 D-loop; other site 643561008468 H-loop/switch region; other site 643561008469 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561008470 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 643561008471 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 643561008472 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 643561008473 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 643561008474 dimer interface [polypeptide binding]; other site 643561008475 conserved gate region; other site 643561008476 putative PBP binding loops; other site 643561008477 ABC-ATPase subunit interface; other site 643561008478 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 643561008479 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_17; cd08503 643561008480 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561008481 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 643561008482 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 643561008483 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 643561008484 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 643561008485 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561008486 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 643561008487 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008488 hypothetical protein; Provisional; Region: PRK05965 643561008489 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 643561008490 inhibitor-cofactor binding pocket; inhibition site 643561008491 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561008492 catalytic residue [active] 643561008493 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561008494 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008495 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 643561008496 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 643561008497 metal binding site [ion binding]; metal-binding site 643561008498 putative dimer interface [polypeptide binding]; other site 643561008499 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 643561008500 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 643561008501 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK12323 643561008502 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 643561008503 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 643561008504 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 643561008505 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 643561008506 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin...; Region: NPD_like; cd04730 643561008507 FMN binding site [chemical binding]; other site 643561008508 substrate binding site [chemical binding]; other site 643561008509 putative catalytic residue [active] 643561008510 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 643561008511 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 643561008512 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561008513 active site 643561008514 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 643561008515 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 643561008516 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 643561008517 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 643561008518 Electron transfer flavoprotein, beta subunit [Energy production and conversion]; Region: FixA; COG2086 643561008519 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 643561008520 Ligand binding site [chemical binding]; other site 643561008521 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 643561008522 Mechanosensitive ion channel; Region: MS_channel; pfam00924 643561008523 YopJ Serine/Threonine acetyltransferase; Region: YopJ; cl07849 643561008524 enoyl-CoA hydratase; Validated; Region: PRK08139 643561008525 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 643561008526 substrate binding site [chemical binding]; other site 643561008527 oxyanion hole (OAH) forming residues; other site 643561008528 trimer interface [polypeptide binding]; other site 643561008529 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 643561008530 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 643561008531 MoxR-like ATPases [General function prediction only]; Region: COG0714 643561008532 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 643561008533 Walker A motif; other site 643561008534 ATP binding site [chemical binding]; other site 643561008535 Walker B motif; other site 643561008536 arginine finger; other site 643561008537 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561008538 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 643561008539 Protein of unknown function DUF58; Region: DUF58; pfam01882 643561008540 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 643561008541 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 643561008542 lytic murein transglycosylase; Region: MltB_2; TIGR02283 643561008543 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 643561008544 N-acetyl-D-glucosamine binding site [chemical binding]; other site 643561008545 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 643561008546 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561008547 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561008548 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008549 NAD(P) binding site [chemical binding]; other site 643561008550 active site 643561008551 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008552 NAD(P) binding site [chemical binding]; other site 643561008553 active site 643561008554 acyl-CoA synthetase; Validated; Region: PRK06188 643561008555 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561008556 lipid-transfer protein; Provisional; Region: PRK08256 643561008557 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal 3-ketacyl-; Region: SCP-x_thiolase; cd00829 643561008558 active site 643561008559 NnrS protein; Region: NnrS; cl01258 643561008560 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 643561008561 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561008562 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561008563 adhesin; Provisional; Region: PRK09752 643561008564 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561008565 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 643561008566 putative ligand binding site [chemical binding]; other site 643561008567 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 643561008568 This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa...; Region: ACD_sHsps_p23-like; cd00298 643561008569 UGMP family protein; Validated; Region: PRK09604 643561008570 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561008571 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 643561008572 dimerization interface [polypeptide binding]; other site 643561008573 ligand binding site [chemical binding]; other site 643561008574 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 643561008575 ANTAR domain; Region: ANTAR; cl04297 643561008576 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 643561008577 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 643561008578 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 643561008579 dimer interface [polypeptide binding]; other site 643561008580 conserved gate region; other site 643561008581 putative PBP binding loops; other site 643561008582 ABC-ATPase subunit interface; other site 643561008583 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 643561008584 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 643561008585 Walker A/P-loop; other site 643561008586 ATP binding site [chemical binding]; other site 643561008587 Q-loop/lid; other site 643561008588 ABC transporter signature motif; other site 643561008589 Walker B; other site 643561008590 D-loop; other site 643561008591 H-loop/switch region; other site 643561008592 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 643561008593 NADP+ binding site [chemical binding]; other site 643561008594 folate binding site [chemical binding]; other site 643561008595 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561008596 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561008597 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 643561008598 Major Facilitator Superfamily; Region: MFS_1; pfam07690 643561008599 putative substrate translocation pore; other site 643561008600 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561008601 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008602 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 643561008603 dimerization interface [polypeptide binding]; other site 643561008604 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561008605 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 643561008606 FAD binding domain; Region: FAD_binding_4; pfam01565 643561008607 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561008608 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 643561008609 NAD(P) binding site [chemical binding]; other site 643561008610 catalytic residues [active] 643561008611 Subunit B of Class III Extradiol ring-cleavage dioxygenases; Region: Extradiol_Dioxygenase_3B_like; cl00599 643561008612 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 643561008613 active site 643561008614 metal binding site [ion binding]; metal-binding site 643561008615 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 643561008616 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 643561008617 putative substrate translocation pore; other site 643561008618 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561008619 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 643561008620 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008621 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 643561008622 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561008623 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561008624 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008625 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 643561008626 putative effector binding pocket; other site 643561008627 dimerization interface [polypeptide binding]; other site 643561008628 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561008629 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 643561008630 DoxX; Region: DoxX; cl00976 643561008631 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 643561008632 Carboxylesterase type B [Lipid metabolism]; Region: PnbA; COG2272 643561008633 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 643561008634 substrate binding pocket [chemical binding]; other site 643561008635 catalytic triad [active] 643561008636 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 643561008637 putative phosphate binding site [ion binding]; other site 643561008638 putative catalytic site [active] 643561008639 active site 643561008640 metal binding site A [ion binding]; metal-binding site 643561008641 DNA binding site [nucleotide binding] 643561008642 putative AP binding site [nucleotide binding]; other site 643561008643 putative metal binding site B [ion binding]; other site 643561008644 Response regulator receiver domain; Region: Response_reg; pfam00072 643561008645 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008646 active site 643561008647 phosphorylation site [posttranslational modification] 643561008648 intermolecular recognition site; other site 643561008649 dimerization interface [polypeptide binding]; other site 643561008650 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 643561008651 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 643561008652 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 643561008653 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 643561008654 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 643561008655 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 643561008656 ATP binding site [chemical binding]; other site 643561008657 Mg2+ binding site [ion binding]; other site 643561008658 G-X-G motif; other site 643561008659 classical (c) SDRs; Region: SDR_c; cd05233 643561008660 NAD(P) binding site [chemical binding]; other site 643561008661 active site 643561008662 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561008663 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008664 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 643561008665 putative effector binding pocket; other site 643561008666 putative dimerization interface [polypeptide binding]; other site 643561008667 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 643561008668 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 643561008669 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561008670 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 643561008671 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 643561008672 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 643561008673 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_10; cd04623 643561008674 FOG: CBS domain [General function prediction only]; Region: COG0517 643561008675 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 643561008676 PAS fold; Region: PAS_3; pfam08447 643561008677 putative active site [active] 643561008678 heme pocket [chemical binding]; other site 643561008679 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561008680 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 643561008681 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 643561008682 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 643561008683 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 643561008684 Outer membrane efflux protein; Region: OEP; pfam02321 643561008685 Outer membrane efflux protein; Region: OEP; pfam02321 643561008686 CheD chemotactic sensory transduction; Region: CheD; cl00810 643561008687 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 643561008688 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 643561008689 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 643561008690 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 643561008691 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 643561008692 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 643561008693 PAS fold; Region: PAS_3; pfam08447 643561008694 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561008695 PAS fold; Region: PAS_3; pfam08447 643561008696 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561008697 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561008698 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 643561008699 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 643561008700 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008701 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 643561008702 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 643561008703 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 643561008704 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 643561008705 [2Fe-2S] cluster binding site [ion binding]; other site 643561008706 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 643561008707 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 643561008708 [4Fe-4S] binding site [ion binding]; other site 643561008709 molybdopterin cofactor binding site; other site 643561008710 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 643561008711 molybdopterin cofactor binding site; other site 643561008712 nitrite reductase [NAD(P)H], large subunit; Region: nitri_red_nirB; TIGR02374 643561008713 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 643561008714 glycosyl transferase family protein; Provisional; Region: PRK08136 643561008715 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 643561008716 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 643561008717 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; cl14895 643561008718 Cellulose binding domain; Region: CBM_2; cl02709 643561008719 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 643561008720 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 643561008721 active site clefts [active] 643561008722 zinc binding site [ion binding]; other site 643561008723 dimer interface [polypeptide binding]; other site 643561008724 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 643561008725 Sulfate transporter family; Region: Sulfate_transp; cl00967 643561008726 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 643561008727 Predicted flavoproteins [General function prediction only]; Region: COG2081 643561008728 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008729 NIPSNAP; Region: NIPSNAP; pfam07978 643561008730 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 643561008731 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 643561008732 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 643561008733 PAS domain S-box; Region: sensory_box; TIGR00229 643561008734 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 643561008735 putative active site [active] 643561008736 heme pocket [chemical binding]; other site 643561008737 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561008738 metal binding site [ion binding]; metal-binding site 643561008739 active site 643561008740 I-site; other site 643561008741 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 643561008742 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 643561008743 GatB domain; Region: GatB_Yqey; cl11497 643561008744 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 643561008745 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins...; Region: GST_N_GTT1_like; cd03046 643561008746 putative C-terminal domain interface [polypeptide binding]; other site 643561008747 putative GSH binding site (G-site) [chemical binding]; other site 643561008748 putative dimer interface [polypeptide binding]; other site 643561008749 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 643561008750 dimer interface [polypeptide binding]; other site 643561008751 N-terminal domain interface [polypeptide binding]; other site 643561008752 putative substrate binding pocket (H-site) [chemical binding]; other site 643561008753 Predicted transcriptional regulator [Transcription]; Region: COG2378 643561008754 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008755 transcriptional activator TtdR; Provisional; Region: PRK09801 643561008756 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008757 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_9; cd08479 643561008758 putative effector binding pocket; other site 643561008759 putative dimerization interface [polypeptide binding]; other site 643561008760 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 643561008761 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 643561008762 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 643561008763 active site 643561008764 nucleophile elbow; other site 643561008765 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 643561008766 Sugar (and other) transporter; Region: Sugar_tr; pfam00083 643561008767 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 643561008768 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1; Region: PLPDE_III_DSD_D-TA_like_1; cd06812 643561008769 dimer interface [polypeptide binding]; other site 643561008770 active site 643561008771 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 643561008772 substrate binding site [chemical binding]; other site 643561008773 catalytic residue [active] 643561008774 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561008775 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008776 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 643561008777 dimerization interface [polypeptide binding]; other site 643561008778 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561008779 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008780 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 643561008781 dimerization interface [polypeptide binding]; other site 643561008782 Transposase; Region: DEDD_Tnp_IS110; pfam01548 643561008783 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 643561008784 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561008785 galactarate dehydratase; Region: galactar-dH20; TIGR03248 643561008786 SAF domain; Region: SAF; cl00555 643561008787 SAF domain; Region: SAF; cl00555 643561008788 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561008789 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 643561008790 tetramerization interface [polypeptide binding]; other site 643561008791 NAD(P) binding site [chemical binding]; other site 643561008792 catalytic residues [active] 643561008793 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 643561008794 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 643561008795 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 643561008796 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 643561008797 Protein of unknown function (DUF615); Region: DUF615; cl01147 643561008798 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 643561008799 MPT binding site; other site 643561008800 trimer interface [polypeptide binding]; other site 643561008801 serine O-acetyltransferase; Region: cysE; TIGR01172 643561008802 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 643561008803 trimer interface [polypeptide binding]; other site 643561008804 active site 643561008805 substrate binding site [chemical binding]; other site 643561008806 CoA binding site [chemical binding]; other site 643561008807 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 643561008808 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 643561008809 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 643561008810 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is...; Region: GT1_TPS; cd03788 643561008811 active site 643561008812 homotetramer interface [polypeptide binding]; other site 643561008813 Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake. NatB possess six...; Region: ABC_NatA_like; cd03267 643561008814 PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 643561008815 Walker A/P-loop; other site 643561008816 ATP binding site [chemical binding]; other site 643561008817 Q-loop/lid; other site 643561008818 ABC transporter signature motif; other site 643561008819 Walker B; other site 643561008820 D-loop; other site 643561008821 H-loop/switch region; other site 643561008822 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4587 643561008823 Protein of unknown function (DUF990); Region: DUF990; cl01496 643561008824 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 643561008825 active site 643561008826 dimerization interface [polypeptide binding]; other site 643561008827 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 643561008828 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008829 active site 643561008830 phosphorylation site [posttranslational modification] 643561008831 intermolecular recognition site; other site 643561008832 dimerization interface [polypeptide binding]; other site 643561008833 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 643561008834 Zn2+ binding site [ion binding]; other site 643561008835 Mg2+ binding site [ion binding]; other site 643561008836 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 643561008837 PAS domain S-box; Region: sensory_box; TIGR00229 643561008838 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 643561008839 putative active site [active] 643561008840 heme pocket [chemical binding]; other site 643561008841 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 643561008842 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 643561008843 putative active site [active] 643561008844 heme pocket [chemical binding]; other site 643561008845 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 643561008846 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561008847 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 643561008848 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 643561008849 dimer interface [polypeptide binding]; other site 643561008850 phosphorylation site [posttranslational modification] 643561008851 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 643561008852 ATP binding site [chemical binding]; other site 643561008853 Mg2+ binding site [ion binding]; other site 643561008854 G-X-G motif; other site 643561008855 Response regulator receiver domain; Region: Response_reg; pfam00072 643561008856 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008857 active site 643561008858 phosphorylation site [posttranslational modification] 643561008859 intermolecular recognition site; other site 643561008860 dimerization interface [polypeptide binding]; other site 643561008861 Response regulator receiver domain; Region: Response_reg; pfam00072 643561008862 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008863 active site 643561008864 phosphorylation site [posttranslational modification] 643561008865 intermolecular recognition site; other site 643561008866 dimerization interface [polypeptide binding]; other site 643561008867 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 643561008868 Mechanosensitive ion channel; Region: MS_channel; pfam00924 643561008869 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 643561008870 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 643561008871 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561008872 enoyl-CoA hydratase; Provisional; Region: PRK06688 643561008873 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 643561008874 substrate binding site [chemical binding]; other site 643561008875 oxyanion hole (OAH) forming residues; other site 643561008876 trimer interface [polypeptide binding]; other site 643561008877 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561008878 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561008879 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008880 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561008881 GAF domain; Region: GAF; cl00853 643561008882 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 643561008883 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 643561008884 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 643561008885 MutS domain I; Region: MutS_I; pfam01624 643561008886 MutS domain II; Region: MutS_II; pfam05188 643561008887 MutS family domain IV; Region: MutS_IV; pfam05190 643561008888 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 643561008889 Walker A/P-loop; other site 643561008890 ATP binding site [chemical binding]; other site 643561008891 Q-loop/lid; other site 643561008892 ABC transporter signature motif; other site 643561008893 Walker B; other site 643561008894 D-loop; other site 643561008895 H-loop/switch region; other site 643561008896 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 643561008897 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 643561008898 NAD binding site [chemical binding]; other site 643561008899 homotetramer interface [polypeptide binding]; other site 643561008900 homodimer interface [polypeptide binding]; other site 643561008901 substrate binding site [chemical binding]; other site 643561008902 active site 643561008903 Transposase domain (DUF772); Region: DUF772; cl12084 643561008904 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 643561008905 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561008906 RHS Repeat; Region: RHS_repeat; cl11982 643561008907 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561008908 RHS protein; Region: RHS; pfam03527 643561008909 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561008910 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 643561008911 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 643561008912 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 643561008913 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 643561008914 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings...; Region: proteasome_beta_bacterial; cd03765 643561008915 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561008916 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 643561008917 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 643561008918 FAD binding domain; Region: FAD_binding_4; pfam01565 643561008919 Berberine and berberine like; Region: BBE; pfam08031 643561008920 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 643561008921 PAS fold; Region: PAS_4; pfam08448 643561008922 PAS fold; Region: PAS_4; pfam08448 643561008923 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561008924 metal binding site [ion binding]; metal-binding site 643561008925 active site 643561008926 I-site; other site 643561008927 Bacitracin resistance protein BacA; Region: BacA; cl00858 643561008928 NodT family; Region: outer_NodT; TIGR01845 643561008929 Outer membrane efflux protein; Region: OEP; pfam02321 643561008930 Outer membrane efflux protein; Region: OEP; pfam02321 643561008931 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 643561008932 Protein export membrane protein; Region: SecD_SecF; cl14618 643561008933 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 643561008934 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 643561008935 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 643561008936 Histidine kinase; Region: His_kinase; pfam06580 643561008937 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 643561008938 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 643561008939 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561008940 active site 643561008941 phosphorylation site [posttranslational modification] 643561008942 intermolecular recognition site; other site 643561008943 dimerization interface [polypeptide binding]; other site 643561008944 LytTr DNA-binding domain; Region: LytTR; cl04498 643561008945 LysE type translocator; Region: LysE; cl00565 643561008946 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561008947 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561008948 heme ABC exporter, ATP-binding protein CcmA; Region: ccmA; TIGR01189 643561008949 Walker A/P-loop; other site 643561008950 ATP binding site [chemical binding]; other site 643561008951 Q-loop/lid; other site 643561008952 ABC transporter signature motif; other site 643561008953 Walker B; other site 643561008954 D-loop; other site 643561008955 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561008956 TOBE domain; Region: TOBE_2; cl01440 643561008957 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561008958 RHS Repeat; Region: RHS_repeat; cl11982 643561008959 RHS Repeat; Region: RHS_repeat; cl11982 643561008960 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561008961 RHS protein; Region: RHS; pfam03527 643561008962 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561008963 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 643561008964 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 643561008965 dimer interface [polypeptide binding]; other site 643561008966 ABC-ATPase subunit interface; other site 643561008967 putative PBP binding loops; other site 643561008968 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 643561008969 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561008970 Walker A/P-loop; other site 643561008971 ATP binding site [chemical binding]; other site 643561008972 Q-loop/lid; other site 643561008973 ABC transporter signature motif; other site 643561008974 Walker B; other site 643561008975 D-loop; other site 643561008976 H-loop/switch region; other site 643561008977 TOBE domain; Region: TOBE_2; cl01440 643561008978 Adenylosuccinate lyase [Nucleotide transport and metabolism]; Region: PurB; COG0015 643561008979 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 643561008980 tetramer interface [polypeptide binding]; other site 643561008981 active site 643561008982 BCCT family transporter; Region: BCCT; cl00569 643561008983 glycogen branching enzyme; Provisional; Region: PRK05402 643561008984 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 643561008985 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 643561008986 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 643561008987 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 643561008988 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 643561008989 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 643561008990 trehalose synthase; Region: treS_nterm; TIGR02456 643561008991 trehalose synthase; Region: treS_nterm; TIGR02456 643561008992 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 643561008993 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; cl01286 643561008994 Conserved TM helix; Region: TM_helix; pfam05552 643561008995 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 643561008996 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 643561008997 DctM-like transporters; Region: DctM; pfam06808 643561008998 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561008999 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 643561009000 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 643561009001 TPP-binding site; other site 643561009002 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 643561009003 PYR/PP interface [polypeptide binding]; other site 643561009004 dimer interface [polypeptide binding]; other site 643561009005 TPP binding site [chemical binding]; other site 643561009006 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 643561009007 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 643561009008 substrate binding pocket [chemical binding]; other site 643561009009 substrate-Mg2+ binding site; other site 643561009010 aspartate-rich region 1; other site 643561009011 aspartate-rich region 2; other site 643561009012 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 643561009013 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 643561009014 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 643561009015 [2Fe-2S] cluster binding site [ion binding]; other site 643561009016 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 643561009017 alpha subunit interface [polypeptide binding]; other site 643561009018 active site 643561009019 substrate binding site [chemical binding]; other site 643561009020 Fe binding site [ion binding]; other site 643561009021 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 643561009022 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 643561009023 active site residue [active] 643561009024 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 643561009025 active site residue [active] 643561009026 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561009027 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 643561009028 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 643561009029 Walker A/P-loop; other site 643561009030 ATP binding site [chemical binding]; other site 643561009031 Q-loop/lid; other site 643561009032 ABC transporter signature motif; other site 643561009033 Walker B; other site 643561009034 D-loop; other site 643561009035 H-loop/switch region; other site 643561009036 NIL domain; Region: NIL; cl09633 643561009037 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 643561009038 dimer interface [polypeptide binding]; other site 643561009039 conserved gate region; other site 643561009040 ABC-ATPase subunit interface; other site 643561009041 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 643561009042 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561009043 active site 643561009044 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 643561009045 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561009046 active site 643561009047 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 643561009048 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 643561009049 active site 643561009050 non-prolyl cis peptide bond; other site 643561009051 Flagellar transcriptional activator (FlhD); Region: FlhD; cl05012 643561009052 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 643561009053 Domain of unknown function DUF20; Region: UPF0118; cl00465 643561009054 integral membrane protein, YccS/YhfK family; Region: YCCS_YHJK; TIGR01667 643561009055 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 643561009056 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 643561009057 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 643561009058 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 643561009059 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 643561009060 domain interfaces; other site 643561009061 active site 643561009062 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 643561009063 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 643561009064 active site 643561009065 HemX; Region: HemX; cl14667 643561009066 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 643561009067 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 643561009068 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 643561009069 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 643561009070 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 643561009071 Zn binding site [ion binding]; other site 643561009072 Peptidase family M48; Region: Peptidase_M48; cl12018 643561009073 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 643561009074 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 643561009075 HIGH motif; other site 643561009076 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 643561009077 active site 643561009078 KMSKS motif; other site 643561009079 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 643561009080 tRNA binding surface [nucleotide binding]; other site 643561009081 anticodon binding site; other site 643561009082 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 643561009083 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 643561009084 active site 643561009085 tetramer interface [polypeptide binding]; other site 643561009086 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 643561009087 CPxP motif; other site 643561009088 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 643561009089 nudix motif; other site 643561009090 cysteine synthases; Region: cysKM; TIGR01136 643561009091 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 643561009092 dimer interface [polypeptide binding]; other site 643561009093 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561009094 catalytic residue [active] 643561009095 DNA topoisomerase; Region: Topoisom_bac; pfam01131 643561009096 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561009097 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009098 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 643561009099 dimerization interface [polypeptide binding]; other site 643561009100 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 643561009101 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561009102 FAD binding site [chemical binding]; other site 643561009103 substrate binding pocket [chemical binding]; other site 643561009104 catalytic base [active] 643561009105 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561009106 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 643561009107 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561009108 NAD(P) binding site [chemical binding]; other site 643561009109 active site 643561009110 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 643561009111 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 643561009112 catalytic loop [active] 643561009113 iron binding site [ion binding]; other site 643561009114 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 643561009115 FAD binding pocket [chemical binding]; other site 643561009116 FAD binding motif [chemical binding]; other site 643561009117 phosphate binding motif [ion binding]; other site 643561009118 beta-alpha-beta structure motif; other site 643561009119 NAD binding pocket [chemical binding]; other site 643561009120 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561009121 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 643561009122 catalytic center binding site [active] 643561009123 ATP binding site [chemical binding]; other site 643561009124 poly(A) polymerase; Region: pcnB; TIGR01942 643561009125 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 643561009126 active site 643561009127 NTP binding site [chemical binding]; other site 643561009128 metal binding triad [ion binding]; metal-binding site 643561009129 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 643561009130 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 643561009131 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 643561009132 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 643561009133 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561009134 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 643561009135 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 643561009136 dimerization interface [polypeptide binding]; other site 643561009137 putative ATP binding site [chemical binding]; other site 643561009138 Domain of unknown function DUF20; Region: UPF0118; cl00465 643561009139 Isochorismatase family; Region: Isochorismatase; pfam00857 643561009140 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 643561009141 catalytic triad [active] 643561009142 conserved cis-peptide bond; other site 643561009143 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 643561009144 conserved cys residue [active] 643561009145 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 643561009146 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 643561009147 conserved cys residue [active] 643561009148 DNA polymerase IV; Validated; Region: PRK03352 643561009149 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 643561009150 active site 643561009151 DNA binding site [nucleotide binding] 643561009152 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is...; Region: Trunc_globin; cd00454 643561009153 apolar tunnel; other site 643561009154 heme binding site [chemical binding]; other site 643561009155 dimerization interface [polypeptide binding]; other site 643561009156 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 643561009157 Protein of unknown function (DUF3455); Region: DUF3455; pfam11937 643561009158 Nitrate and nitrite sensing; Region: NIT; pfam08376 643561009159 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 643561009160 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 643561009161 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 643561009162 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 643561009163 phosphate binding site [ion binding]; other site 643561009164 EamA-like transporter family; Region: EamA; cl01037 643561009165 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 643561009166 Transglycosylase; Region: Transgly; cl07896 643561009167 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 643561009168 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 643561009169 CHASE3 domain; Region: CHASE3; cl05000 643561009170 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 643561009171 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561009172 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 643561009173 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 643561009174 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 643561009175 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 643561009176 MG2 domain; Region: A2M_N; pfam01835 643561009177 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 643561009178 Alpha-2-macroglobulin family; Region: A2M; pfam00207 643561009179 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 643561009180 OpgC protein; Region: OpgC_C; cl10497 643561009181 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase_like_7; cd04502 643561009182 active site 643561009183 catalytic triad [active] 643561009184 oxyanion hole [active] 643561009185 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 643561009186 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 643561009187 putative substrate translocation pore; other site 643561009188 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 643561009189 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009190 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 643561009191 putative dimerization interface [polypeptide binding]; other site 643561009192 putative substrate binding pocket [chemical binding]; other site 643561009193 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561009194 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561009195 argininosuccinate lyase; Provisional; Region: PRK00855 643561009196 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 643561009197 active sites [active] 643561009198 tetramer interface [polypeptide binding]; other site 643561009199 Histidine kinase; Region: His_kinase; pfam06580 643561009200 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 643561009201 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 643561009202 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009203 active site 643561009204 phosphorylation site [posttranslational modification] 643561009205 intermolecular recognition site; other site 643561009206 dimerization interface [polypeptide binding]; other site 643561009207 LytTr DNA-binding domain; Region: LytTR; cl04498 643561009208 Transposase; Region: DEDD_Tnp_IS110; pfam01548 643561009209 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 643561009210 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 643561009211 Argininosuccinate lyase [Amino acid transport and metabolism]; Region: ArgH; COG0165 643561009212 active sites [active] 643561009213 tetramer interface [polypeptide binding]; other site 643561009214 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 643561009215 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 643561009216 Dienelactone hydrolase family; Region: DLH; pfam01738 643561009217 Predicted transcriptional regulators [Transcription]; Region: COG1510 643561009218 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009219 Protein of unknown function, DUF393; Region: DUF393; cl01136 643561009220 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 643561009221 putative NAD(P) binding site [chemical binding]; other site 643561009222 active site 643561009223 Predicted integral membrane protein (DUF2269); Region: DUF2269; cl02335 643561009224 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 643561009225 aspartate racemase; Region: asp_race; TIGR00035 643561009226 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561009227 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 643561009228 substrate binding pocket [chemical binding]; other site 643561009229 membrane-bound complex binding site; other site 643561009230 hinge residues; other site 643561009231 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561009232 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 643561009233 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 643561009234 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009235 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 643561009236 dimerization interface [polypeptide binding]; other site 643561009237 DNA polymerase I; Provisional; Region: PRK05755 643561009238 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 643561009239 active site 643561009240 metal binding site 1 [ion binding]; metal-binding site 643561009241 putative 5' ssDNA interaction site; other site 643561009242 metal binding site 3; metal-binding site 643561009243 metal binding site 2 [ion binding]; metal-binding site 643561009244 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 643561009245 putative DNA binding site [nucleotide binding]; other site 643561009246 putative metal binding site [ion binding]; other site 643561009247 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 643561009248 active site 643561009249 catalytic site [active] 643561009250 substrate binding site [chemical binding]; other site 643561009251 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 643561009252 active site 643561009253 DNA binding site [nucleotide binding] 643561009254 catalytic site [active] 643561009255 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 643561009256 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 643561009257 Phosphotransferase enzyme family; Region: APH; pfam01636 643561009258 putative active site [active] 643561009259 putative substrate binding site [chemical binding]; other site 643561009260 ATP binding site [chemical binding]; other site 643561009261 Bacterial protein of unknown function (DUF839); Region: DUF839; pfam05787 643561009262 Imelysin; Region: Peptidase_M75; cl09159 643561009263 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 643561009264 Imelysin; Region: Peptidase_M75; cl09159 643561009265 Protein of unknown function (DUF1513); Region: DUF1513; pfam07433 643561009266 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl01426 643561009267 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 643561009268 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 643561009269 Phage Tail Collar Domain; Region: Collar; pfam07484 643561009270 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 643561009271 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561009272 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561009273 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 643561009274 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 643561009275 putative active site [active] 643561009276 hypothetical protein; Provisional; Region: PRK07338 643561009277 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 643561009278 metal binding site [ion binding]; metal-binding site 643561009279 dimer interface [polypeptide binding]; other site 643561009280 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561009281 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561009282 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 643561009283 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 643561009284 active site 643561009285 Protein of unknown function (DUF1348); Region: DUF1348; pfam07080 643561009286 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 643561009287 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561009288 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561009289 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 643561009290 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009291 active site 643561009292 phosphorylation site [posttranslational modification] 643561009293 intermolecular recognition site; other site 643561009294 dimerization interface [polypeptide binding]; other site 643561009295 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 643561009296 Walker A motif; other site 643561009297 ATP binding site [chemical binding]; other site 643561009298 Walker B motif; other site 643561009299 arginine finger; other site 643561009300 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561009301 hypothetical protein; Provisional; Region: PRK13560 643561009302 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 643561009303 dimer interface [polypeptide binding]; other site 643561009304 phosphorylation site [posttranslational modification] 643561009305 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 643561009306 ATP binding site [chemical binding]; other site 643561009307 Mg2+ binding site [ion binding]; other site 643561009308 G-X-G motif; other site 643561009309 Response regulator receiver domain; Region: Response_reg; pfam00072 643561009310 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009311 active site 643561009312 phosphorylation site [posttranslational modification] 643561009313 intermolecular recognition site; other site 643561009314 dimerization interface [polypeptide binding]; other site 643561009315 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 643561009316 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 643561009317 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 643561009318 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 643561009319 Protein of unknown function (DUF461); Region: DUF461; cl01071 643561009320 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 643561009321 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 643561009322 putative substrate translocation pore; other site 643561009323 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 643561009324 putative active site [active] 643561009325 heme pocket [chemical binding]; other site 643561009326 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561009327 metal binding site [ion binding]; metal-binding site 643561009328 active site 643561009329 I-site; other site 643561009330 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 643561009331 ATP binding site [chemical binding]; other site 643561009332 Mg++ binding site [ion binding]; other site 643561009333 motif III; other site 643561009334 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 643561009335 nucleotide binding region [chemical binding]; other site 643561009336 ATP-binding site [chemical binding]; other site 643561009337 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 643561009338 putative active site [active] 643561009339 putative substrate binding site [chemical binding]; other site 643561009340 catalytic site [active] 643561009341 dimer interface [polypeptide binding]; other site 643561009342 Peptidase family M48; Region: Peptidase_M48; cl12018 643561009343 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 643561009344 aromatic arch; other site 643561009345 DCoH dimer interaction site [polypeptide binding]; other site 643561009346 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 643561009347 DCoH tetramer interaction site [polypeptide binding]; other site 643561009348 substrate binding site [chemical binding]; other site 643561009349 GTPase RsgA; Reviewed; Region: PRK00098 643561009350 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 643561009351 GTPase/OB domain interface [polypeptide binding]; other site 643561009352 GTPase/Zn-binding domain interface [polypeptide binding]; other site 643561009353 GTP/Mg2+ binding site [chemical binding]; other site 643561009354 G4 box; other site 643561009355 G5 box; other site 643561009356 G1 box; other site 643561009357 Switch I region; other site 643561009358 G2 box; other site 643561009359 G3 box; other site 643561009360 Switch II region; other site 643561009361 CobD/Cbib protein; Region: CobD_Cbib; cl00561 643561009362 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 643561009363 putative active site [active] 643561009364 putative CoA binding site [chemical binding]; other site 643561009365 nudix motif; other site 643561009366 metal binding site [ion binding]; metal-binding site 643561009367 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 643561009368 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 643561009369 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 643561009370 RimM N-terminal domain; Region: RimM; pfam01782 643561009371 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 643561009372 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 643561009373 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 643561009374 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 643561009375 Coenzyme A binding pocket [chemical binding]; other site 643561009376 Phosphate transporter family; Region: PHO4; cl00396 643561009377 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 643561009378 Surface antigen; Region: Surface_Ag_2; cl01155 643561009379 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 643561009380 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561009381 Walker A/P-loop; other site 643561009382 ATP binding site [chemical binding]; other site 643561009383 Q-loop/lid; other site 643561009384 ABC transporter signature motif; other site 643561009385 Walker B; other site 643561009386 D-loop; other site 643561009387 H-loop/switch region; other site 643561009388 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 643561009389 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561009390 Walker A/P-loop; other site 643561009391 ATP binding site [chemical binding]; other site 643561009392 Q-loop/lid; other site 643561009393 ABC transporter signature motif; other site 643561009394 Walker B; other site 643561009395 D-loop; other site 643561009396 H-loop/switch region; other site 643561009397 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561009398 TM-ABC transporter signature motif; other site 643561009399 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561009400 TM-ABC transporter signature motif; other site 643561009401 recombination factor protein RarA; Reviewed; Region: PRK13342 643561009402 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 643561009403 Walker A motif; other site 643561009404 ATP binding site [chemical binding]; other site 643561009405 Walker B motif; other site 643561009406 arginine finger; other site 643561009407 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 643561009408 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 643561009409 Walker A motif; other site 643561009410 ATP binding site [chemical binding]; other site 643561009411 Walker B motif; other site 643561009412 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 643561009413 putative uracil binding site [chemical binding]; other site 643561009414 putative active site [active] 643561009415 Protein of unknown function (DUF1304); Region: DUF1304; cl01533 643561009416 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 643561009417 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 643561009418 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561009419 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 643561009420 thioredoxin reductase; Provisional; Region: PRK10262 643561009421 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561009422 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 643561009423 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 643561009424 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 643561009425 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561009426 DNA-binding site [nucleotide binding]; DNA binding site 643561009427 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 643561009428 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561009429 homodimer interface [polypeptide binding]; other site 643561009430 catalytic residue [active] 643561009431 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 643561009432 Di-iron ligands [ion binding]; other site 643561009433 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 643561009434 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 643561009435 Pectate lyase; Region: Pec_lyase_C; cl01593 643561009436 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 643561009437 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 643561009438 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 643561009439 Mg2+ binding site [ion binding]; other site 643561009440 G-X-G motif; other site 643561009441 osmolarity response regulator; Provisional; Region: ompR; PRK09468 643561009442 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009443 active site 643561009444 phosphorylation site [posttranslational modification] 643561009445 intermolecular recognition site; other site 643561009446 dimerization interface [polypeptide binding]; other site 643561009447 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 643561009448 DNA binding site [nucleotide binding] 643561009449 Secreted protein acidic and rich in cysteine Ca binding region; Region: SPARC_Ca_bdg; pfam10591 643561009450 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 643561009451 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 643561009452 active site 643561009453 substrate binding site [chemical binding]; other site 643561009454 cosubstrate binding site; other site 643561009455 catalytic site [active] 643561009456 Protein of unknown function, DUF480; Region: DUF480; cl01209 643561009457 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 643561009458 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561009459 active site 643561009460 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 643561009461 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 643561009462 active site 643561009463 Glyco_18 domain; Region: Glyco_18; smart00636 643561009464 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 643561009465 active site 643561009466 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 643561009467 TPR motif; other site 643561009468 binding surface 643561009469 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 643561009470 binding surface 643561009471 TPR motif; other site 643561009472 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 643561009473 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 643561009474 TPR motif; other site 643561009475 binding surface 643561009476 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 643561009477 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 643561009478 DctM-like transporters; Region: DctM; pfam06808 643561009479 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 643561009480 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 643561009481 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561009482 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561009483 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 643561009484 N-terminal plug; other site 643561009485 ligand-binding site [chemical binding]; other site 643561009486 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 643561009487 active site 643561009488 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 643561009489 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 643561009490 active site 643561009491 Riboflavin kinase; Region: Flavokinase; cl03312 643561009492 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 643561009493 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 643561009494 active site 643561009495 HIGH motif; other site 643561009496 nucleotide binding site [chemical binding]; other site 643561009497 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 643561009498 active site 643561009499 KMSKS motif; other site 643561009500 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 643561009501 tRNA binding surface [nucleotide binding]; other site 643561009502 anticodon binding site; other site 643561009503 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 643561009504 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 643561009505 Transcriptional regulators [Transcription]; Region: PurR; COG1609 643561009506 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 643561009507 DNA binding site [nucleotide binding] 643561009508 domain linker motif; other site 643561009509 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR_like_2; cd06282 643561009510 putative dimerization interface [polypeptide binding]; other site 643561009511 putative ligand binding site [chemical binding]; other site 643561009512 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 643561009513 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 643561009514 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 643561009515 dimer interface [polypeptide binding]; other site 643561009516 conserved gate region; other site 643561009517 putative PBP binding loops; other site 643561009518 ABC-ATPase subunit interface; other site 643561009519 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 643561009520 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561009521 Walker A/P-loop; other site 643561009522 ATP binding site [chemical binding]; other site 643561009523 Q-loop/lid; other site 643561009524 ABC transporter signature motif; other site 643561009525 Walker B; other site 643561009526 D-loop; other site 643561009527 H-loop/switch region; other site 643561009528 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 643561009529 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 643561009530 active site 643561009531 metal binding site [ion binding]; metal-binding site 643561009532 hexamer interface [polypeptide binding]; other site 643561009533 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 643561009534 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 643561009535 PhoU domain; Region: PhoU; pfam01895 643561009536 PhoU domain; Region: PhoU; pfam01895 643561009537 YopJ Serine/Threonine acetyltransferase; Region: YopJ; cl07849 643561009538 YopJ Serine/Threonine acetyltransferase; Region: YopJ; cl07849 643561009539 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561009540 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009541 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 643561009542 dimerization interface [polypeptide binding]; other site 643561009543 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 643561009544 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 643561009545 putative NAD(P) binding site [chemical binding]; other site 643561009546 putative substrate binding site [chemical binding]; other site 643561009547 catalytic Zn binding site [ion binding]; other site 643561009548 structural Zn binding site [ion binding]; other site 643561009549 dimer interface [polypeptide binding]; other site 643561009550 Membrane transport protein; Region: Mem_trans; cl09117 643561009551 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009552 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 643561009553 Predicted amidohydrolase [General function prediction only]; Region: COG0388 643561009554 Nitrilases, cyanide hydratase (CH)s, and similar proteins (class 1 nitrilases); Region: nitrilases_CHs; cd07564 643561009555 putative active site [active] 643561009556 catalytic triad [active] 643561009557 putative dimer interface [polypeptide binding]; other site 643561009558 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 643561009559 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561009560 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3435 643561009561 Cupin domain; Region: Cupin_2; cl09118 643561009562 Cupin domain; Region: Cupin_2; cl09118 643561009563 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 643561009564 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561009565 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 643561009566 active site 643561009567 FMN binding site [chemical binding]; other site 643561009568 substrate binding site [chemical binding]; other site 643561009569 homotetramer interface [polypeptide binding]; other site 643561009570 catalytic residue [active] 643561009571 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 643561009572 active site 643561009573 putative indolepyruvate oxidoreductase subunit B; Reviewed; Region: PRK08312 643561009574 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 643561009575 benzoate transport; Region: 2A0115; TIGR00895 643561009576 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 643561009577 putative substrate translocation pore; other site 643561009578 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 643561009579 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]; Region: COG4231 643561009580 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 643561009581 dimer interface [polypeptide binding]; other site 643561009582 PYR/PP interface [polypeptide binding]; other site 643561009583 TPP binding site [chemical binding]; other site 643561009584 substrate binding site [chemical binding]; other site 643561009585 TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the...; Region: TPP_IOR_alpha; cd02008 643561009586 TPP-binding site; other site 643561009587 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561009588 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561009589 Protein involved in meta-pathway of phenol degradation [Energy production and conversion]; Region: COG4313 643561009590 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 643561009591 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561009592 Putative cyclase; Region: Cyclase; cl00814 643561009593 Flavin Reductases; Region: FlaRed; cl00801 643561009594 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 643561009595 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561009596 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561009597 classical (c) SDRs; Region: SDR_c; cd05233 643561009598 NAD(P) binding site [chemical binding]; other site 643561009599 active site 643561009600 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 643561009601 nudix motif; other site 643561009602 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 643561009603 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 643561009604 NADP binding site [chemical binding]; other site 643561009605 dimer interface [polypeptide binding]; other site 643561009606 EamA-like transporter family; Region: EamA; cl01037 643561009607 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 643561009608 EamA-like transporter family; Region: EamA; cl01037 643561009609 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 643561009610 binding surface 643561009611 TPR motif; other site 643561009612 SMI1 / KNR4 family; Region: SMI1_KNR4; cl01747 643561009613 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561009614 RHS Repeat; Region: RHS_repeat; cl11982 643561009615 RHS Repeat; Region: RHS_repeat; cl11982 643561009616 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561009617 RHS Repeat; Region: RHS_repeat; cl11982 643561009618 RHS protein; Region: RHS; pfam03527 643561009619 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561009620 3-oxoacyl-(acyl carrier protein) synthase; Validated; Region: PRK06147 643561009621 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 643561009622 Protein of unknown function (DUF3540); Region: DUF3540; pfam12059 643561009623 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 643561009624 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 643561009625 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 643561009626 PAS fold; Region: PAS_7; pfam12860 643561009627 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561009628 metal binding site [ion binding]; metal-binding site 643561009629 active site 643561009630 I-site; other site 643561009631 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 643561009632 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561009633 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 643561009634 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 643561009635 active site 643561009636 metal binding site [ion binding]; metal-binding site 643561009637 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 643561009638 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 643561009639 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 643561009640 active site 643561009641 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 643561009642 putative substrate translocation pore; other site 643561009643 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 643561009644 DNA-binding site [nucleotide binding]; DNA binding site 643561009645 RNA-binding motif; other site 643561009646 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 643561009647 cyclase homology domain; Region: CHD; cd07302 643561009648 nucleotidyl binding site; other site 643561009649 metal binding site [ion binding]; metal-binding site 643561009650 dimer interface [polypeptide binding]; other site 643561009651 PilZ domain; Region: PilZ; cl01260 643561009652 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 643561009653 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561009654 Walker A/P-loop; other site 643561009655 ATP binding site [chemical binding]; other site 643561009656 Q-loop/lid; other site 643561009657 ABC transporter signature motif; other site 643561009658 Walker B; other site 643561009659 D-loop; other site 643561009660 H-loop/switch region; other site 643561009661 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 643561009662 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561009663 Walker A/P-loop; other site 643561009664 ATP binding site [chemical binding]; other site 643561009665 Q-loop/lid; other site 643561009666 ABC transporter signature motif; other site 643561009667 Walker B; other site 643561009668 D-loop; other site 643561009669 H-loop/switch region; other site 643561009670 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561009671 TM-ABC transporter signature motif; other site 643561009672 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561009673 TM-ABC transporter signature motif; other site 643561009674 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561009675 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 643561009676 putative ligand binding site [chemical binding]; other site 643561009677 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 643561009678 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 643561009679 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 643561009680 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 643561009681 C-terminal domain interface [polypeptide binding]; other site 643561009682 GSH binding site (G-site) [chemical binding]; other site 643561009683 dimer interface [polypeptide binding]; other site 643561009684 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 643561009685 dimer interface [polypeptide binding]; other site 643561009686 N-terminal domain interface [polypeptide binding]; other site 643561009687 putative substrate binding pocket (H-site) [chemical binding]; other site 643561009688 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009689 YceI-like domain; Region: YceI; cl01001 643561009690 YceI-like domain; Region: YceI; cl01001 643561009691 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 643561009692 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009693 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561009694 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561009695 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561009696 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561009697 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA)...; Region: CCL_ACL-C; cd06100 643561009698 active site 643561009699 oxalacetate binding site [chemical binding]; other site 643561009700 citrylCoA binding site [chemical binding]; other site 643561009701 coenzyme A binding site [chemical binding]; other site 643561009702 catalytic triad [active] 643561009703 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 643561009704 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 643561009705 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 643561009706 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561009707 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 643561009708 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 643561009709 carboxyltransferase (CT) interaction site; other site 643561009710 biotinylation site [posttranslational modification]; other site 643561009711 Allophanate hydrolase subunit 1; Region: AHS1; smart00796 643561009712 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 643561009713 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 643561009714 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 643561009715 Protein of unknown function (DUF1445); Region: DUF1445; cl01790 643561009716 LamB/YcsF family; Region: LamB_YcsF; cl00664 643561009717 benzoate transport; Region: 2A0115; TIGR00895 643561009718 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 643561009719 putative substrate translocation pore; other site 643561009720 Transcriptional regulators [Transcription]; Region: GntR; COG1802 643561009721 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561009722 DNA-binding site [nucleotide binding]; DNA binding site 643561009723 FCD domain; Region: FCD; cl11656 643561009724 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 643561009725 nickel responsive regulator; Provisional; Region: PRK02967 643561009726 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 643561009727 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 643561009728 N-terminal plug; other site 643561009729 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561009730 ligand-binding site [chemical binding]; other site 643561009731 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 643561009732 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 643561009733 phosphate binding site [ion binding]; other site 643561009734 DNA-binding transcriptional repressor LldR; Provisional; Region: PRK10421 643561009735 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561009736 DNA-binding site [nucleotide binding]; DNA binding site 643561009737 FCD domain; Region: FCD; cl11656 643561009738 L-lactate permease; Region: Lactate_perm; cl00701 643561009739 glycolate transporter; Provisional; Region: PRK09695 643561009740 Predicted integral membrane protein (DUF2269); Region: DUF2269; cl02335 643561009741 CHASE4 domain; Region: CHASE4; cl01308 643561009742 PAS domain S-box; Region: sensory_box; TIGR00229 643561009743 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 643561009744 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561009745 metal binding site [ion binding]; metal-binding site 643561009746 active site 643561009747 I-site; other site 643561009748 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 643561009749 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009750 active site 643561009751 phosphorylation site [posttranslational modification] 643561009752 intermolecular recognition site; other site 643561009753 dimerization interface [polypeptide binding]; other site 643561009754 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 643561009755 DNA binding residues [nucleotide binding] 643561009756 dimerization interface [polypeptide binding]; other site 643561009757 Sodium:solute symporter family; Region: SSF; cl00456 643561009758 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 643561009759 dimer interface [polypeptide binding]; other site 643561009760 phosphorylation site [posttranslational modification] 643561009761 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 643561009762 ATP binding site [chemical binding]; other site 643561009763 Mg2+ binding site [ion binding]; other site 643561009764 G-X-G motif; other site 643561009765 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 643561009766 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009767 active site 643561009768 phosphorylation site [posttranslational modification] 643561009769 intermolecular recognition site; other site 643561009770 dimerization interface [polypeptide binding]; other site 643561009771 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 643561009772 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 643561009773 active site 643561009774 metal binding site [ion binding]; metal-binding site 643561009775 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 643561009776 alpha-gamma subunit interface [polypeptide binding]; other site 643561009777 beta-gamma subunit interface [polypeptide binding]; other site 643561009778 HupE / UreJ protein; Region: HupE_UreJ; cl01011 643561009779 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_beta; cd00407 643561009780 gamma-beta subunit interface [polypeptide binding]; other site 643561009781 alpha-beta subunit interface [polypeptide binding]; other site 643561009782 urease subunit alpha; Reviewed; Region: ureC; PRK13207 643561009783 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 643561009784 subunit interactions [polypeptide binding]; other site 643561009785 active site 643561009786 flap region; other site 643561009787 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The C-...; Region: UreE; cd00571 643561009788 dimer interface [polypeptide binding]; other site 643561009789 catalytic residues [active] 643561009790 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 643561009791 UreF; Region: UreF; pfam01730 643561009792 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 643561009793 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 643561009794 FRG domain; Region: FRG; cl07460 643561009795 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 643561009796 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 643561009797 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 643561009798 Walker A/P-loop; other site 643561009799 ATP binding site [chemical binding]; other site 643561009800 Q-loop/lid; other site 643561009801 ABC transporter signature motif; other site 643561009802 Walker B; other site 643561009803 D-loop; other site 643561009804 H-loop/switch region; other site 643561009805 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 643561009806 Walker A/P-loop; other site 643561009807 ATP binding site [chemical binding]; other site 643561009808 Q-loop/lid; other site 643561009809 ABC transporter signature motif; other site 643561009810 Walker B; other site 643561009811 D-loop; other site 643561009812 H-loop/switch region; other site 643561009813 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561009814 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 643561009815 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 643561009816 dimer interface [polypeptide binding]; other site 643561009817 conserved gate region; other site 643561009818 putative PBP binding loops; other site 643561009819 ABC-ATPase subunit interface; other site 643561009820 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 643561009821 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 643561009822 putative PBP binding loops; other site 643561009823 dimer interface [polypeptide binding]; other site 643561009824 ABC-ATPase subunit interface; other site 643561009825 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 643561009826 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 643561009827 Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase; Region: AAT; pfam03417 643561009828 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561009829 DNA-binding site [nucleotide binding]; DNA binding site 643561009830 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561009831 DNA-binding site [nucleotide binding]; DNA binding site 643561009832 FCD domain; Region: FCD; cl11656 643561009833 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 643561009834 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 643561009835 inhibitor-cofactor binding pocket; inhibition site 643561009836 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561009837 catalytic residue [active] 643561009838 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561009839 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561009840 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561009841 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 643561009842 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 643561009843 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 643561009844 putative NAD(P) binding site [chemical binding]; other site 643561009845 catalytic Zn binding site [ion binding]; other site 643561009846 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 643561009847 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 643561009848 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 643561009849 Walker A motif; other site 643561009850 ATP binding site [chemical binding]; other site 643561009851 Walker B motif; other site 643561009852 arginine finger; other site 643561009853 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 643561009854 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 643561009855 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561009856 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561009857 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 643561009858 Response regulator receiver domain; Region: Response_reg; pfam00072 643561009859 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009860 active site 643561009861 phosphorylation site [posttranslational modification] 643561009862 intermolecular recognition site; other site 643561009863 dimerization interface [polypeptide binding]; other site 643561009864 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 643561009865 anti sigma factor interaction site; other site 643561009866 regulatory phosphorylation site [posttranslational modification]; other site 643561009867 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 643561009868 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 643561009869 putative binding surface; other site 643561009870 active site 643561009871 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 643561009872 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 643561009873 ATP binding site [chemical binding]; other site 643561009874 Mg2+ binding site [ion binding]; other site 643561009875 G-X-G motif; other site 643561009876 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 643561009877 CHASE3 domain; Region: CHASE3; cl05000 643561009878 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 643561009879 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 643561009880 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561009881 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 643561009882 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 643561009883 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 643561009884 putative CheA interaction surface; other site 643561009885 Response regulator receiver domain; Region: Response_reg; pfam00072 643561009886 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009887 active site 643561009888 phosphorylation site [posttranslational modification] 643561009889 intermolecular recognition site; other site 643561009890 dimerization interface [polypeptide binding]; other site 643561009891 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 643561009892 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 643561009893 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 643561009894 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 643561009895 CheD chemotactic sensory transduction; Region: CheD; cl00810 643561009896 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 643561009897 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009898 active site 643561009899 phosphorylation site [posttranslational modification] 643561009900 intermolecular recognition site; other site 643561009901 dimerization interface [polypeptide binding]; other site 643561009902 CheB methylesterase; Region: CheB_methylest; pfam01339 643561009903 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 643561009904 Type II transport protein GspH; Region: GspH; pfam12019 643561009905 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 643561009906 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 643561009907 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 643561009908 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 643561009909 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 643561009910 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 643561009911 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 643561009912 catalytic motif [active] 643561009913 Zn binding site [ion binding]; other site 643561009914 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 643561009915 Predicted outer membrane protein [Function unknown]; Region: COG3652 643561009916 Predicted membrane protein (DUF2243); Region: DUF2243; cl01783 643561009917 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 643561009918 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 643561009919 catalytic triad [active] 643561009920 conserved cis-peptide bond; other site 643561009921 Protein of unknown function (DUF421); Region: DUF421; cl00990 643561009922 histidine kinase; Provisional; Region: PRK13557 643561009923 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 643561009924 putative active site [active] 643561009925 heme pocket [chemical binding]; other site 643561009926 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 643561009927 dimer interface [polypeptide binding]; other site 643561009928 phosphorylation site [posttranslational modification] 643561009929 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 643561009930 ATP binding site [chemical binding]; other site 643561009931 Mg2+ binding site [ion binding]; other site 643561009932 G-X-G motif; other site 643561009933 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561009934 active site 643561009935 phosphorylation site [posttranslational modification] 643561009936 intermolecular recognition site; other site 643561009937 dimerization interface [polypeptide binding]; other site 643561009938 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 643561009939 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 643561009940 S-adenosylmethionine binding site [chemical binding]; other site 643561009941 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 643561009942 Predicted membrane protein (DUF2177); Region: DUF2177; cl02014 643561009943 Transcriptional activator [Transcription]; Region: ChrR; COG3806 643561009944 Cupin domain; Region: Cupin_2; cl09118 643561009945 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 643561009946 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561009947 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 643561009948 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 643561009949 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561009950 Protein of unknown function (DUF1365); Region: DUF1365; cl01388 643561009951 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 643561009952 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 643561009953 S-adenosylmethionine binding site [chemical binding]; other site 643561009954 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 643561009955 classical (c) SDRs; Region: SDR_c; cd05233 643561009956 NAD(P) binding site [chemical binding]; other site 643561009957 active site 643561009958 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 643561009959 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 643561009960 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 643561009961 FeS/SAM binding site; other site 643561009962 HemN C-terminal region; Region: HemN_C; pfam06969 643561009963 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 643561009964 active site 643561009965 dimerization interface [polypeptide binding]; other site 643561009966 ribonuclease PH; Reviewed; Region: rph; PRK00173 643561009967 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 643561009968 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 643561009969 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 643561009970 Protein phosphatase 2C; Region: PP2C; pfam00481 643561009971 Active site [active] 643561009972 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 643561009973 Catalytic domain of Protein Kinases; Region: PKc; cd00180 643561009974 active site 643561009975 ATP binding site [chemical binding]; other site 643561009976 substrate binding site [chemical binding]; other site 643561009977 activation loop (A-loop); other site 643561009978 hypothetical protein; Provisional; Region: PRK11820 643561009979 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 643561009980 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 643561009981 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 643561009982 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 643561009983 catalytic site [active] 643561009984 G-X2-G-X-G-K; other site 643561009985 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 643561009986 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 643561009987 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561009988 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 643561009989 synthetase active site [active] 643561009990 NTP binding site [chemical binding]; other site 643561009991 metal binding site [ion binding]; metal-binding site 643561009992 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 643561009993 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 643561009994 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 643561009995 domain; Region: GreA_GreB_N; pfam03449 643561009996 C-term; Region: GreA_GreB; pfam01272 643561009997 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 643561009998 catalytic residues [active] 643561009999 Phage related hypothetical protein (DUF1799); Region: DUF1799; pfam08809 643561010000 Domain of unknown function (DUF1789); Region: DUF1789; pfam08748 643561010001 Phage tail protein; Region: Phage_tail_3; pfam08813 643561010002 Predicted transcriptional regulator [Transcription]; Region: COG2932 643561010003 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 643561010004 Catalytic site [active] 643561010005 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 643561010006 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561010007 active site 643561010008 phosphorylation site [posttranslational modification] 643561010009 intermolecular recognition site; other site 643561010010 dimerization interface [polypeptide binding]; other site 643561010011 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 643561010012 DNA binding residues [nucleotide binding] 643561010013 dimerization interface [polypeptide binding]; other site 643561010014 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 643561010015 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561010016 HrcA protein C terminal domain; Region: HrcA; pfam01628 643561010017 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 643561010018 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 643561010019 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 643561010020 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 643561010021 Walker A/P-loop; other site 643561010022 ATP binding site [chemical binding]; other site 643561010023 Q-loop/lid; other site 643561010024 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 643561010025 ABC transporter signature motif; other site 643561010026 Walker B; other site 643561010027 D-loop; other site 643561010028 H-loop/switch region; other site 643561010029 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561010030 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 643561010031 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 643561010032 minor groove reading motif; other site 643561010033 helix-hairpin-helix signature motif; other site 643561010034 substrate binding pocket [chemical binding]; other site 643561010035 active site 643561010036 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 643561010037 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 643561010038 DNA binding and oxoG recognition site [nucleotide binding] 643561010039 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 643561010040 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 643561010041 Switch II region; other site 643561010042 G3 box; other site 643561010043 G4 box; other site 643561010044 G5 box; other site 643561010045 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 643561010046 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 643561010047 DNA binding site [nucleotide binding] 643561010048 catalytic residue [active] 643561010049 H2TH interface [polypeptide binding]; other site 643561010050 putative catalytic residues [active] 643561010051 turnover-facilitating residue; other site 643561010052 intercalation triad [nucleotide binding]; other site 643561010053 8OG recognition residue [nucleotide binding]; other site 643561010054 putative reading head residues; other site 643561010055 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 643561010056 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 643561010057 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 643561010058 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 643561010059 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 643561010060 binding surface 643561010061 TPR motif; other site 643561010062 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 643561010063 binding surface 643561010064 TPR motif; other site 643561010065 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 643561010066 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 643561010067 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 643561010068 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK04923 643561010069 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 643561010070 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 643561010071 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 643561010072 5S rRNA interface [nucleotide binding]; other site 643561010073 CTC domain interface [polypeptide binding]; other site 643561010074 L16 interface [polypeptide binding]; other site 643561010075 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 643561010076 putative active site [active] 643561010077 catalytic residue [active] 643561010078 hypothetical protein; Provisional; Region: PRK13795 643561010079 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 643561010080 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 643561010081 dimer interface [polypeptide binding]; other site 643561010082 conserved gate region; other site 643561010083 putative PBP binding loops; other site 643561010084 ABC-ATPase subunit interface; other site 643561010085 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 643561010086 dimer interface [polypeptide binding]; other site 643561010087 conserved gate region; other site 643561010088 putative PBP binding loops; other site 643561010089 ABC-ATPase subunit interface; other site 643561010090 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 643561010091 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 643561010092 Walker A/P-loop; other site 643561010093 ATP binding site [chemical binding]; other site 643561010094 Q-loop/lid; other site 643561010095 ABC transporter signature motif; other site 643561010096 Walker B; other site 643561010097 D-loop; other site 643561010098 H-loop/switch region; other site 643561010099 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561010100 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 643561010101 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 643561010102 Walker A/P-loop; other site 643561010103 ATP binding site [chemical binding]; other site 643561010104 Q-loop/lid; other site 643561010105 ABC transporter signature motif; other site 643561010106 Walker B; other site 643561010107 D-loop; other site 643561010108 H-loop/switch region; other site 643561010109 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561010110 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 643561010111 HipA-like N-terminal domain; Region: HipA_N; pfam07805 643561010112 HipA-like C-terminal domain; Region: HipA_C; pfam07804 643561010113 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 643561010114 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_6; cd08494 643561010115 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09775 643561010116 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561010117 HipA-like N-terminal domain; Region: HipA_N; pfam07805 643561010118 HipA-like C-terminal domain; Region: HipA_C; pfam07804 643561010119 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561010120 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 643561010121 tetramerization interface [polypeptide binding]; other site 643561010122 NAD(P) binding site [chemical binding]; other site 643561010123 catalytic residues [active] 643561010124 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 643561010125 D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of...; Region: D-glucarate_dehydratase; cd03323 643561010126 active site 643561010127 tetramer interface [polypeptide binding]; other site 643561010128 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561010129 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561010130 Transposase; Region: DEDD_Tnp_IS110; pfam01548 643561010131 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 643561010132 Transcriptional regulators [Transcription]; Region: PurR; COG1609 643561010133 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 643561010134 DNA binding site [nucleotide binding] 643561010135 domain linker motif; other site 643561010136 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 643561010137 putative dimerization interface [polypeptide binding]; other site 643561010138 putative ligand binding site [chemical binding]; other site 643561010139 nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal...; Region: nuc_hydro; cl00226 643561010140 active site 643561010141 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 643561010142 Sensors of blue-light using FAD; Region: BLUF; cl04855 643561010143 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 643561010144 active site 643561010145 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 643561010146 putative active site [active] 643561010147 catalytic site [active] 643561010148 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 643561010149 putative active site [active] 643561010150 catalytic site [active] 643561010151 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 643561010152 putative catalytic site [active] 643561010153 putative metal binding site [ion binding]; other site 643561010154 putative phosphate binding site [ion binding]; other site 643561010155 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), 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 643561010156 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 643561010157 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 643561010158 binding surface 643561010159 TPR motif; other site 643561010160 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 643561010161 nudix motif; other site 643561010162 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 643561010163 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 643561010164 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 643561010165 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 643561010166 dimer interface [polypeptide binding]; other site 643561010167 anticodon binding site; other site 643561010168 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 643561010169 homodimer interface [polypeptide binding]; other site 643561010170 motif 1; other site 643561010171 active site 643561010172 motif 2; other site 643561010173 GAD domain; Region: GAD; pfam02938 643561010174 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 643561010175 motif 3; other site 643561010176 Protein of unknown function (DUF502); Region: DUF502; cl01107 643561010177 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 643561010178 Sodium:solute symporter family; Region: SSF; cl00456 643561010179 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 643561010180 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 643561010181 SCP-2 sterol transfer family; Region: SCP2; cl01225 643561010182 Tim44-like domain; Region: Tim44; cl09208 643561010183 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 643561010184 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 643561010185 S-adenosylmethionine binding site [chemical binding]; other site 643561010186 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 643561010187 Protein of unknown function (DUF971); Region: DUF971; cl01414 643561010188 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561010189 metal binding site [ion binding]; metal-binding site 643561010190 active site 643561010191 I-site; other site 643561010192 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 643561010193 nucleotide binding site/active site [active] 643561010194 HIT family signature motif; other site 643561010195 catalytic residue [active] 643561010196 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 643561010197 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 643561010198 FAD binding domain; Region: FAD_binding_4; pfam01565 643561010199 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 643561010200 Heterodisulfide reductase, subunit C [Energy production and conversion]; Region: HdrC; COG1150 643561010201 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 643561010202 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 643561010203 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561010204 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 643561010205 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561010206 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 643561010207 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 643561010208 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561010209 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 643561010210 L-serine binding site [chemical binding]; other site 643561010211 ACT domain interface; other site 643561010212 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 643561010213 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 643561010214 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 643561010215 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 643561010216 dimer interface [polypeptide binding]; other site 643561010217 conserved gate region; other site 643561010218 putative PBP binding loops; other site 643561010219 ABC-ATPase subunit interface; other site 643561010220 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 643561010221 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 643561010222 dimer interface [polypeptide binding]; other site 643561010223 conserved gate region; other site 643561010224 putative PBP binding loops; other site 643561010225 ABC-ATPase subunit interface; other site 643561010226 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 643561010227 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 643561010228 Walker A/P-loop; other site 643561010229 ATP binding site [chemical binding]; other site 643561010230 Q-loop/lid; other site 643561010231 ABC transporter signature motif; other site 643561010232 Walker B; other site 643561010233 D-loop; other site 643561010234 H-loop/switch region; other site 643561010235 TOBE domain; Region: TOBE_2; cl01440 643561010236 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 643561010237 active site 643561010238 metal binding site [ion binding]; metal-binding site 643561010239 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 643561010240 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 643561010241 active site 643561010242 catalytic site [active] 643561010243 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561010244 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 643561010245 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561010246 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 643561010247 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 643561010248 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 643561010249 Mechanosensitive ion channel; Region: MS_channel; pfam00924 643561010250 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561010251 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561010252 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561010253 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561010254 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 643561010255 dimerization interface [polypeptide binding]; other site 643561010256 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 643561010257 putative substrate translocation pore; other site 643561010258 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 643561010259 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 643561010260 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 643561010261 tRNA; other site 643561010262 putative tRNA binding site [nucleotide binding]; other site 643561010263 putative NADP binding site [chemical binding]; other site 643561010264 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 643561010265 peptide chain release factor 1; Validated; Region: prfA; PRK00591 643561010266 RF-1 domain; Region: RF-1; cl02875 643561010267 RF-1 domain; Region: RF-1; cl02875 643561010268 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 643561010269 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 643561010270 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 643561010271 putative GSH binding site [chemical binding]; other site 643561010272 catalytic residues [active] 643561010273 Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]; Region: RecJ; COG0608 643561010274 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 643561010275 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 643561010276 Walker A motif; other site 643561010277 ATP binding site [chemical binding]; other site 643561010278 Walker B motif; other site 643561010279 arginine finger; other site 643561010280 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 643561010281 Domain of unknown function DUF21; Region: DUF21; pfam01595 643561010282 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 643561010283 Transporter associated domain; Region: CorC_HlyC; cl08393 643561010284 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 643561010285 N-acetyl-D-glucosamine binding site [chemical binding]; other site 643561010286 catalytic residue [active] 643561010287 prolyl-tRNA synthetase; Provisional; Region: PRK09194 643561010288 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 643561010289 dimer interface [polypeptide binding]; other site 643561010290 motif 1; other site 643561010291 active site 643561010292 motif 2; other site 643561010293 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 643561010294 putative deacylase active site [active] 643561010295 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 643561010296 active site 643561010297 motif 3; other site 643561010298 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 643561010299 anticodon binding site; other site 643561010300 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 643561010301 putative active site [active] 643561010302 Ap4A binding site [chemical binding]; other site 643561010303 nudix motif; other site 643561010304 putative metal binding site [ion binding]; other site 643561010305 gamma-glutamyl kinase; Provisional; Region: PRK05429 643561010306 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 643561010307 nucleotide binding site [chemical binding]; other site 643561010308 homotetrameric interface [polypeptide binding]; other site 643561010309 putative phosphate binding site [ion binding]; other site 643561010310 putative allosteric binding site; other site 643561010311 PUA domain; Region: PUA; cl00607 643561010312 GTPase CgtA; Reviewed; Region: obgE; PRK12299 643561010313 GTP1/OBG; Region: GTP1_OBG; pfam01018 643561010314 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 643561010315 G1 box; other site 643561010316 GTP/Mg2+ binding site [chemical binding]; other site 643561010317 Switch I region; other site 643561010318 G2 box; other site 643561010319 G3 box; other site 643561010320 Switch II region; other site 643561010321 G4 box; other site 643561010322 G5 box; other site 643561010323 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 643561010324 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 643561010325 octaprenyl diphosphate synthase; Provisional; Region: PRK10888 643561010326 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 643561010327 substrate binding pocket [chemical binding]; other site 643561010328 chain length determination region; other site 643561010329 substrate-Mg2+ binding site; other site 643561010330 catalytic residues [active] 643561010331 aspartate-rich region 1; other site 643561010332 active site lid residues [active] 643561010333 aspartate-rich region 2; other site 643561010334 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 643561010335 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 643561010336 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 643561010337 Walker A motif; other site 643561010338 ATP binding site [chemical binding]; other site 643561010339 Walker B motif; other site 643561010340 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 643561010341 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 643561010342 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 643561010343 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 643561010344 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 643561010345 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 643561010346 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 643561010347 CoA-binding site [chemical binding]; other site 643561010348 ATP-binding [chemical binding]; other site 643561010349 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 643561010350 Domain of unknown function (DUF329); Region: DUF329; cl01144 643561010351 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 643561010352 active site 643561010353 8-oxo-dGMP binding site [chemical binding]; other site 643561010354 nudix motif; other site 643561010355 metal binding site [ion binding]; metal-binding site 643561010356 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 643561010357 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561010358 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group...; Region: OAT; cd02152 643561010359 heterotetramer interface [polypeptide binding]; other site 643561010360 active site pocket [active] 643561010361 cleavage site 643561010362 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 643561010363 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 643561010364 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 643561010365 nucleotide binding region [chemical binding]; other site 643561010366 hypothetical protein; Provisional; Region: PRK02250 643561010367 SEC-C motif; Region: SEC-C; cl12132 643561010368 Peptidase family M23; Region: Peptidase_M23; pfam01551 643561010369 Stringent starvation protein B; Region: SspB; cl01120 643561010370 stringent starvation protein A; Provisional; Region: sspA; PRK09481 643561010371 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 643561010372 C-terminal domain interface [polypeptide binding]; other site 643561010373 putative GSH binding site (G-site) [chemical binding]; other site 643561010374 dimer interface [polypeptide binding]; other site 643561010375 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 643561010376 dimer interface [polypeptide binding]; other site 643561010377 N-terminal domain interface [polypeptide binding]; other site 643561010378 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 643561010379 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 643561010380 Qi binding site; other site 643561010381 intrachain domain interface; other site 643561010382 interchain domain interface [polypeptide binding]; other site 643561010383 cytochrome b; Provisional; Region: CYTB; MTH00145 643561010384 heme bH binding site [chemical binding]; other site 643561010385 heme bL binding site [chemical binding]; other site 643561010386 Qo binding site; other site 643561010387 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: cytochrome_b_C; cl00193 643561010388 interchain domain interface [polypeptide binding]; other site 643561010389 intrachain domain interface; other site 643561010390 Qi binding site; other site 643561010391 Qo binding site; other site 643561010392 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 643561010393 [2Fe-2S] cluster binding site [ion binding]; other site 643561010394 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 643561010395 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 643561010396 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 643561010397 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 643561010398 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 643561010399 Walker A/P-loop; other site 643561010400 ATP binding site [chemical binding]; other site 643561010401 Q-loop/lid; other site 643561010402 ABC transporter signature motif; other site 643561010403 Walker B; other site 643561010404 D-loop; other site 643561010405 H-loop/switch region; other site 643561010406 LolC/E family; Region: lolCE; TIGR02212 643561010407 FtsX-like permease family; Region: FtsX; pfam02687 643561010408 Sulfatase; Region: Sulfatase; cl10460 643561010409 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 643561010410 DHH family; Region: DHH; pfam01368 643561010411 DHHA1 domain; Region: DHHA1; pfam02272 643561010412 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 643561010413 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561010414 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 643561010415 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 643561010416 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 643561010417 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 643561010418 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561010419 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 643561010420 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 643561010421 active site 643561010422 putative substrate binding region [chemical binding]; other site 643561010423 tryptophanyl-tRNA synthetase; Region: trpS; TIGR00233 643561010424 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 643561010425 active site 643561010426 HIGH motif; other site 643561010427 dimer interface [polypeptide binding]; other site 643561010428 KMSKS motif; other site 643561010429 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 643561010430 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561010431 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 643561010432 catalytic residues [active] 643561010433 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 643561010434 dimerization interface [polypeptide binding]; other site 643561010435 putative DNA binding site [nucleotide binding]; other site 643561010436 putative Zn2+ binding site [ion binding]; other site 643561010437 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561010438 RHS Repeat; Region: RHS_repeat; cl11982 643561010439 RHS Repeat; Region: RHS_repeat; cl11982 643561010440 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561010441 RHS protein; Region: RHS; pfam03527 643561010442 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561010443 Piwi_piwi-like_ProArk: PIWI domain, Piwi-like subfamily found in Archaea and Bacteria. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide...; Region: Piwi_piwi-like_ProArk; cd04659 643561010444 5' RNA guide strand anchoring site; other site 643561010445 active site 643561010446 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 643561010447 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 643561010448 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 643561010449 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism]; Region: BioA; COG0161 643561010450 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 643561010451 inhibitor-cofactor binding pocket; inhibition site 643561010452 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561010453 catalytic residue [active] 643561010454 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 643561010455 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 643561010456 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 643561010457 cyclic peptide transporter; Region: cyc_pep_trnsptr; TIGR01194 643561010458 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561010459 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with...; Region: ABCC_MRP_Like; cd03228 643561010460 Walker A/P-loop; other site 643561010461 ATP binding site [chemical binding]; other site 643561010462 Q-loop/lid; other site 643561010463 ABC transporter signature motif; other site 643561010464 Walker B; other site 643561010465 D-loop; other site 643561010466 H-loop/switch region; other site 643561010467 siderophore-iron reductase FhuF; Region: Fe_III_red_FhuF; TIGR03951 643561010468 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 643561010469 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 643561010470 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 643561010471 catalytic site [active] 643561010472 Siderophore biosynthesis protein domain; Region: AlcB; cl11000 643561010473 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 643561010474 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 643561010475 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 643561010476 N-terminal plug; other site 643561010477 ligand-binding site [chemical binding]; other site 643561010478 Condensation domain; Region: Condensation; cl09290 643561010479 peptide synthase; Provisional; Region: PRK12467 643561010480 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010481 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561010482 peptide synthase; Provisional; Region: PRK12467 643561010483 Condensation domain; Region: Condensation; cl09290 643561010484 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010485 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561010486 Condensation domain; Region: Condensation; cl09290 643561010487 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 643561010488 Condensation domain; Region: Condensation; cl09290 643561010489 peptide synthase; Provisional; Region: PRK12467 643561010490 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010491 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561010492 Condensation domain; Region: Condensation; cl09290 643561010493 L-aminoadipate-semialdehyde dehydrogenase; Region: alpha_am_amid; TIGR03443 643561010494 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 643561010495 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010496 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010497 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561010498 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 643561010499 Beta-ketoacyl synthase; Region: PKS_KS; smart00825 643561010500 active site 643561010501 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 643561010502 Acyl transferase domain; Region: Acyl_transf_1; cl08282 643561010503 ketoreductase (KR), subgroup 2, complex (x) SDRs; Region: KR_2_SDR_x; cd08953 643561010504 putative NADP binding site [chemical binding]; other site 643561010505 active site 643561010506 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561010507 acyl-CoA synthetase; Validated; Region: PRK05850 643561010508 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010509 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010510 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561010511 Condensation domain; Region: Condensation; cl09290 643561010512 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 643561010513 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010514 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561010515 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561010516 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 643561010517 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 643561010518 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 643561010519 MbtH-like protein; Region: MbtH; cl01279 643561010520 extracytoplasmic-function sigma-70 factor; Validated; Region: PRK07037 643561010521 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561010522 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 643561010523 DNA binding residues [nucleotide binding] 643561010524 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 643561010525 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 643561010526 active site 643561010527 nucleophile elbow; other site 643561010528 Patatin phospholipase; Region: DUF3734; pfam12536 643561010529 Acetoacetate decarboxylase (ADC); Region: ADC; cl01919 643561010530 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK13394 643561010531 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561010532 NAD(P) binding site [chemical binding]; other site 643561010533 active site 643561010534 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 643561010535 trimer interface [polypeptide binding]; other site 643561010536 eyelet of channel; other site 643561010537 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561010538 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561010539 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 643561010540 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 643561010541 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 643561010542 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 643561010543 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 643561010544 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 643561010545 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 643561010546 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561010547 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561010548 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561010549 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 643561010550 putative dimerization interface [polypeptide binding]; other site 643561010551 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 643561010552 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 643561010553 DNA binding residues [nucleotide binding] 643561010554 Domain of unknown function (DUF2760); Region: DUF2760; pfam10816 643561010555 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 643561010556 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 643561010557 DNA-K related protein; Region: DUF3731; pfam12531 643561010558 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561010559 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561010560 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 643561010561 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 643561010562 Cl- selectivity filter; other site 643561010563 Cl- binding residues [ion binding]; other site 643561010564 pore gating glutamate residue; other site 643561010565 dimer interface [polypeptide binding]; other site 643561010566 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561010567 RHS Repeat; Region: RHS_repeat; cl11982 643561010568 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561010569 RHS protein; Region: RHS; pfam03527 643561010570 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561010571 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 643561010572 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 643561010573 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 643561010574 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 643561010575 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 643561010576 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 643561010577 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 643561010578 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 643561010579 dimer interface [polypeptide binding]; other site 643561010580 conserved gate region; other site 643561010581 putative PBP binding loops; other site 643561010582 ABC-ATPase subunit interface; other site 643561010583 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 643561010584 dimer interface [polypeptide binding]; other site 643561010585 conserved gate region; other site 643561010586 putative PBP binding loops; other site 643561010587 ABC-ATPase subunit interface; other site 643561010588 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561010589 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 643561010590 substrate binding pocket [chemical binding]; other site 643561010591 membrane-bound complex binding site; other site 643561010592 hinge residues; other site 643561010593 Predicted amidohydrolase [General function prediction only]; Region: COG0388 643561010594 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 643561010595 active site 643561010596 catalytic triad [active] 643561010597 dimer interface [polypeptide binding]; other site 643561010598 Second nitrilase domain of an uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_1_R2; cd07579 643561010599 Predicted amidohydrolase [General function prediction only]; Region: COG0388 643561010600 putative active site [active] 643561010601 catalytic triad [active] 643561010602 putative dimer interface [polypeptide binding]; other site 643561010603 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 643561010604 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561010605 Walker A/P-loop; other site 643561010606 ATP binding site [chemical binding]; other site 643561010607 Q-loop/lid; other site 643561010608 ABC transporter signature motif; other site 643561010609 Walker B; other site 643561010610 D-loop; other site 643561010611 H-loop/switch region; other site 643561010612 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 643561010613 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561010614 Walker A/P-loop; other site 643561010615 ATP binding site [chemical binding]; other site 643561010616 Q-loop/lid; other site 643561010617 ABC transporter signature motif; other site 643561010618 Walker B; other site 643561010619 D-loop; other site 643561010620 H-loop/switch region; other site 643561010621 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561010622 TM-ABC transporter signature motif; other site 643561010623 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561010624 TM-ABC transporter signature motif; other site 643561010625 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561010626 Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF); Region: PBP1_AmiC_like; cd06331 643561010627 ligand binding site [chemical binding]; other site 643561010628 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 643561010629 ANTAR domain; Region: ANTAR; cl04297 643561010630 Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family; Region: PBP1_AmiC; cd06357 643561010631 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561010632 ligand binding site [chemical binding]; other site 643561010633 regulator interaction site; other site 643561010634 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 643561010635 PAS domain S-box; Region: sensory_box; TIGR00229 643561010636 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 643561010637 putative active site [active] 643561010638 heme pocket [chemical binding]; other site 643561010639 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561010640 metal binding site [ion binding]; metal-binding site 643561010641 active site 643561010642 I-site; other site 643561010643 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561010644 metal binding site [ion binding]; metal-binding site 643561010645 active site 643561010646 I-site; other site 643561010647 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 643561010648 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 643561010649 Domain of unknown function DUF87; Region: DUF87; pfam01935 643561010650 AAA-like domain; Region: AAA_10; pfam12846 643561010651 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 643561010652 IS2 transposase TnpB; Reviewed; Region: PRK09409 643561010653 Integrase core domain; Region: rve; cl01316 643561010654 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561010655 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561010656 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_18; cd08357 643561010657 putative metal binding site [ion binding]; other site 643561010658 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 643561010659 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 643561010660 putative NAD(P) binding site [chemical binding]; other site 643561010661 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561010662 seryl-tRNA synthetase; Provisional; Region: PRK05431 643561010663 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 643561010664 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 643561010665 dimer interface [polypeptide binding]; other site 643561010666 active site 643561010667 motif 1; other site 643561010668 motif 2; other site 643561010669 motif 3; other site 643561010670 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 643561010671 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 643561010672 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561010673 catalytic residue [active] 643561010674 FOG: CBS domain [General function prediction only]; Region: COG0517 643561010675 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; cd02205 643561010676 Domain of unknown function DUF21; Region: DUF21; pfam01595 643561010677 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 643561010678 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 643561010679 Transporter associated domain; Region: CorC_HlyC; cl08393 643561010680 LytB protein; Region: LYTB; cl00507 643561010681 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 643561010682 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 643561010683 hypothetical protein; Reviewed; Region: PRK00024 643561010684 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 643561010685 MPN+ (JAMM) motif; other site 643561010686 Zinc-binding site [ion binding]; other site 643561010687 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4222 643561010688 Cupin domain; Region: Cupin_2; cl09118 643561010689 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561010690 Cupin domain; Region: Cupin_2; cl09118 643561010691 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 643561010692 Smr domain; Region: Smr; cl02619 643561010693 sensor protein PhoQ; Provisional; Region: PRK10815 643561010694 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 643561010695 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561010696 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561010697 active site 643561010698 phosphorylation site [posttranslational modification] 643561010699 intermolecular recognition site; other site 643561010700 dimerization interface [polypeptide binding]; other site 643561010701 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 643561010702 DNA binding site [nucleotide binding] 643561010703 Predicted membrane protein [Function unknown]; Region: COG3212 643561010704 Predicted membrane protein [Function unknown]; Region: COG3212 643561010705 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 643561010706 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 643561010707 active site 643561010708 metal binding site [ion binding]; metal-binding site 643561010709 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 643561010710 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 643561010711 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 643561010712 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 643561010713 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 643561010714 3-oxoacyl-(acyl carrier protein) synthase; Validated; Region: PRK06147 643561010715 RHS Repeat; Region: RHS_repeat; cl11982 643561010716 RHS Repeat; Region: RHS_repeat; cl11982 643561010717 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561010718 RHS Repeat; Region: RHS_repeat; cl11982 643561010719 RHS protein; Region: RHS; pfam03527 643561010720 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561010721 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 643561010722 active site 643561010723 Zn binding site [ion binding]; other site 643561010724 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is...; Region: Trunc_globin; cd00454 643561010725 apolar tunnel; other site 643561010726 heme binding site [chemical binding]; other site 643561010727 dimerization interface [polypeptide binding]; other site 643561010728 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 643561010729 FtsX-like permease family; Region: FtsX; pfam02687 643561010730 chaperone protein DnaJ; Provisional; Region: PRK14280 643561010731 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 643561010732 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 643561010733 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 643561010734 putative molybdopterin cofactor binding site [chemical binding]; other site 643561010735 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT)...; Region: MopB_CT_ydeP; cd02787 643561010736 putative molybdopterin cofactor binding site; other site 643561010737 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 643561010738 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 643561010739 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 643561010740 cell division ATPase MinD, archaeal; Region: minD_arch; TIGR01969 643561010741 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 643561010742 Walker A motif; other site 643561010743 Restriction endonuclease; Region: Mrr_cat; cl00747 643561010744 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 643561010745 active site 643561010746 nucleophile elbow; other site 643561010747 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 643561010748 pyruvate dehydrogenase; Provisional; Region: PRK09124 643561010749 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 643561010750 PYR/PP interface [polypeptide binding]; other site 643561010751 tetramer interface [polypeptide binding]; other site 643561010752 dimer interface [polypeptide binding]; other site 643561010753 TPP binding site [chemical binding]; other site 643561010754 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 643561010755 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX...; Region: TPP_POX; cd02014 643561010756 TPP-binding site [chemical binding]; other site 643561010757 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 643561010758 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 643561010759 active site 643561010760 HIGH motif; other site 643561010761 KMSKS motif; other site 643561010762 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 643561010763 tRNA binding surface [nucleotide binding]; other site 643561010764 anticodon binding site; other site 643561010765 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 643561010766 dimer interface [polypeptide binding]; other site 643561010767 putative tRNA-binding site [nucleotide binding]; other site 643561010768 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 643561010769 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 643561010770 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 643561010771 ScpA/B protein; Region: ScpA_ScpB; cl00598 643561010772 L-aspartate oxidase; Provisional; Region: PRK09077 643561010773 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561010774 domain; Region: Succ_DH_flav_C; pfam02910 643561010775 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 643561010776 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 643561010777 inhibitor-cofactor binding pocket; inhibition site 643561010778 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561010779 catalytic residue [active] 643561010780 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 643561010781 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 643561010782 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 643561010783 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561010784 catalytic residue [active] 643561010785 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 643561010786 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 643561010787 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 643561010788 active site 643561010789 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 643561010790 putative substrate binding pocket [chemical binding]; other site 643561010791 trimer interface [polypeptide binding]; other site 643561010792 aminodeoxychorismate synthase; Provisional; Region: PRK07508 643561010793 chorismate binding enzyme; Region: Chorismate_bind; cl10555 643561010794 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 643561010795 substrate-cofactor binding pocket; other site 643561010796 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561010797 Quinolinate synthetase A protein; Region: NadA; cl00420 643561010798 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 643561010799 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 643561010800 dimerization interface [polypeptide binding]; other site 643561010801 active site 643561010802 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 643561010803 oligomerization interface [polypeptide binding]; other site 643561010804 active site 643561010805 metal binding site [ion binding]; metal-binding site 643561010806 Pantoate-beta-alanine ligase; Region: PanC; cd00560 643561010807 pantoate--beta-alanine ligase; Region: panC; TIGR00018 643561010808 active site 643561010809 ATP-binding site [chemical binding]; other site 643561010810 pantoate-binding site; other site 643561010811 HXXH motif; other site 643561010812 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 643561010813 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561010814 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 643561010815 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 643561010816 SecA binding site; other site 643561010817 Preprotein binding site; other site 643561010818 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 643561010819 GSH binding site [chemical binding]; other site 643561010820 catalytic residues [active] 643561010821 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 643561010822 active site residue [active] 643561010823 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 643561010824 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 643561010825 catalytic core [active] 643561010826 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 643561010827 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 643561010828 C-terminal peptidase (prc); Region: prc; TIGR00225 643561010829 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 643561010830 protein binding site [polypeptide binding]; other site 643561010831 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 643561010832 Catalytic dyad [active] 643561010833 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 643561010834 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 643561010835 ATP binding site [chemical binding]; other site 643561010836 substrate interface [chemical binding]; other site 643561010837 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 643561010838 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561010839 active site 643561010840 phosphorylation site [posttranslational modification] 643561010841 intermolecular recognition site; other site 643561010842 dimerization interface [polypeptide binding]; other site 643561010843 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 643561010844 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561010845 active site 643561010846 phosphorylation site [posttranslational modification] 643561010847 intermolecular recognition site; other site 643561010848 dimerization interface [polypeptide binding]; other site 643561010849 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 643561010850 DNA binding residues [nucleotide binding] 643561010851 dimerization interface [polypeptide binding]; other site 643561010852 CHASE3 domain; Region: CHASE3; cl05000 643561010853 Histidine kinase; Region: HisKA_3; pfam07730 643561010854 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 643561010855 ATP binding site [chemical binding]; other site 643561010856 Mg2+ binding site [ion binding]; other site 643561010857 G-X-G motif; other site 643561010858 Ferritin-like domain; Region: Ferritin; pfam00210 643561010859 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 643561010860 dinuclear metal binding motif [ion binding]; other site 643561010861 BON domain; Region: BON; cl02771 643561010862 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; cl09206 643561010863 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 643561010864 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 643561010865 active site 643561010866 (T/H)XGH motif; other site 643561010867 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 643561010868 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 643561010869 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 643561010870 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 643561010871 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 643561010872 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 643561010873 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 643561010874 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 643561010875 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561010876 human DHRS6-like, classical (c) SDRs; Region: DHRS6_like_SDR_c; cd05368 643561010877 NAD binding site [chemical binding]; other site 643561010878 homotetramer interface [polypeptide binding]; other site 643561010879 homodimer interface [polypeptide binding]; other site 643561010880 active site 643561010881 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl01276 643561010882 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561010883 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 643561010884 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561010885 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 643561010886 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 643561010887 MatE; Region: MatE; cl10513 643561010888 MatE; Region: MatE; cl10513 643561010889 MarC family integral membrane protein; Region: MarC; cl00919 643561010890 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 643561010891 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561010892 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 643561010893 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561010894 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561010895 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 643561010896 NAD(P) binding site [chemical binding]; other site 643561010897 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 643561010898 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 643561010899 ligand binding site [chemical binding]; other site 643561010900 flexible hinge region; other site 643561010901 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561010902 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 643561010903 Cu(I) binding site [ion binding]; other site 643561010904 UbiA prenyltransferase family; Region: UbiA; cl00337 643561010905 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 643561010906 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 643561010907 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 643561010908 Subunit III/VIIa interface [polypeptide binding]; other site 643561010909 Phospholipid binding site [chemical binding]; other site 643561010910 Subunit I/III interface [polypeptide binding]; other site 643561010911 Subunit III/VIb interface [polypeptide binding]; other site 643561010912 Subunit III/VIa interface; other site 643561010913 Subunit III/Vb interface [polypeptide binding]; other site 643561010914 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 643561010915 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 643561010916 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 643561010917 Subunit I/III interface [polypeptide binding]; other site 643561010918 D-pathway; other site 643561010919 Subunit I/VIIc interface [polypeptide binding]; other site 643561010920 Subunit I/IV interface [polypeptide binding]; other site 643561010921 Subunit I/II interface [polypeptide binding]; other site 643561010922 Low-spin heme (heme a) binding site [chemical binding]; other site 643561010923 Subunit I/VIIa interface [polypeptide binding]; other site 643561010924 Subunit I/VIa interface [polypeptide binding]; other site 643561010925 Dimer interface; other site 643561010926 Putative water exit pathway; other site 643561010927 Binuclear center (heme a3/CuB) [ion binding]; other site 643561010928 K-pathway; other site 643561010929 Subunit I/Vb interface [polypeptide binding]; other site 643561010930 Putative proton exit pathway; other site 643561010931 Subunit I/VIb interface; other site 643561010932 Subunit I/VIc interface [polypeptide binding]; other site 643561010933 Electron transfer pathway; other site 643561010934 Subunit I/VIIIb interface [polypeptide binding]; other site 643561010935 Subunit I/VIIb interface [polypeptide binding]; other site 643561010936 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 643561010937 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 643561010938 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 643561010939 Cytochrome c; Region: Cytochrom_C; cl11414 643561010940 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 643561010941 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 643561010942 DNA utilization protein GntX; Provisional; Region: PRK11595 643561010943 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 643561010944 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 643561010945 transcriptional regulator; Provisional; Region: PRK10632 643561010946 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561010947 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 643561010948 putative effector binding pocket; other site 643561010949 dimerization interface [polypeptide binding]; other site 643561010950 conjugal transfer protein TraK; Provisional; Region: PRK13736; cl05878 643561010951 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 643561010952 putative active site [active] 643561010953 putative catalytic site [active] 643561010954 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 643561010955 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 643561010956 P-loop; other site 643561010957 Magnesium ion binding site [ion binding]; other site 643561010958 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 643561010959 LysE type translocator; Region: LysE; cl00565 643561010960 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 643561010961 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 643561010962 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 643561010963 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561010964 WGR domain of molybdate metabolism regulator and related proteins; Region: WGR_MMR_like; cd07996 643561010965 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 643561010966 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 643561010967 Walker A motif; other site 643561010968 ATP binding site [chemical binding]; other site 643561010969 Walker B motif; other site 643561010970 arginine finger; other site 643561010971 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 643561010972 metal ion-dependent adhesion site (MIDAS); other site 643561010973 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561010974 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 643561010975 Transcriptional regulators [Transcription]; Region: MarR; COG1846 643561010976 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561010977 benzoate transport; Region: 2A0115; TIGR00895 643561010978 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 643561010979 putative substrate translocation pore; other site 643561010980 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 643561010981 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 643561010982 Cytochrome c; Region: Cytochrom_C; cl11414 643561010983 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 643561010984 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 643561010985 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 643561010986 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561010987 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 643561010988 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561010989 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 643561010990 N-carbamoylsarcosine amidohydrolase (CSHase) hydrolyzes N-carbamoylsarcosine to sarcosine, carbon dioxide and ammonia. CSHase is involved in one of the two alternative pathways for creatinine degradation to glycine in microorganisms.This CSHase-...; Region: CSHase; cd01015 643561010991 Isochorismatase family; Region: Isochorismatase; pfam00857 643561010992 substrate binding site [chemical binding]; other site 643561010993 catalytic triad [active] 643561010994 domain interfaces; other site 643561010995 conserved cis-peptide bond; other site 643561010996 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 643561010997 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 643561010998 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 643561010999 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 643561011000 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 643561011001 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 643561011002 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 643561011003 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011004 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 643561011005 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 643561011006 NADP binding site [chemical binding]; other site 643561011007 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 643561011008 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 643561011009 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561011010 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561011011 Muconolactone delta-isomerase; Region: MIase; cl01992 643561011012 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 643561011013 sorbitol-6-phosphate dehydrogenase; Provisional; Region: PRK12384 643561011014 classical (c) SDRs; Region: SDR_c; cd05233 643561011015 NAD(P) binding site [chemical binding]; other site 643561011016 active site 643561011017 YCII-related domain; Region: YCII; cl00999 643561011018 Putative cyclase; Region: Cyclase; cl00814 643561011019 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 643561011020 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 643561011021 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 643561011022 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 643561011023 dimer interface [polypeptide binding]; other site 643561011024 active site 643561011025 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 643561011026 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 643561011027 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 643561011028 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011029 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561011030 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 643561011031 Cache domain; Region: Cache_1; pfam02743 643561011032 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 643561011033 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561011034 metal binding site [ion binding]; metal-binding site 643561011035 active site 643561011036 I-site; other site 643561011037 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 643561011038 Cytochrome c; Region: Cytochrom_C; cl11414 643561011039 Cytochrome c; Region: Cytochrom_C; cl11414 643561011040 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 643561011041 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 643561011042 Walker A motif; other site 643561011043 ATP binding site [chemical binding]; other site 643561011044 Walker B motif; other site 643561011045 arginine finger; other site 643561011046 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 643561011047 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 643561011048 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 643561011049 Surface antigen; Region: Bac_surface_Ag; cl03097 643561011050 Family of unknown function (DUF490); Region: DUF490; pfam04357 643561011051 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 643561011052 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 643561011053 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 643561011054 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 643561011055 aspartate carbamoyltransferase; Provisional; Region: PRK11891 643561011056 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 643561011057 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561011058 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 643561011059 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 643561011060 putative active site [active] 643561011061 catalytic site [active] 643561011062 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 643561011063 putative active site [active] 643561011064 catalytic site [active] 643561011065 sensor protein QseC; Provisional; Region: PRK10337 643561011066 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 643561011067 ATP binding site [chemical binding]; other site 643561011068 Mg2+ binding site [ion binding]; other site 643561011069 G-X-G motif; other site 643561011070 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 643561011071 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561011072 active site 643561011073 phosphorylation site [posttranslational modification] 643561011074 intermolecular recognition site; other site 643561011075 dimerization interface [polypeptide binding]; other site 643561011076 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 643561011077 DNA binding site [nucleotide binding] 643561011078 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 643561011079 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 643561011080 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 643561011081 protein binding site [polypeptide binding]; other site 643561011082 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561011083 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561011084 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561011085 Transposase domain (DUF772); Region: DUF772; cl12084 643561011086 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 643561011087 CRISPR/Cas system-associated protein Cas3''; Region: Cas3''_I; cd09641 643561011088 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 643561011089 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561011090 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 643561011091 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-C; cd09752 643561011092 CRISPR-associated protein Cas8c/Csd1, subtype I-C/DVULG; Region: cas_Csd1; TIGR01863 643561011093 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cd09757 643561011094 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 643561011095 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cd09637 643561011096 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-C; cd09721 643561011097 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 643561011098 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561011099 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 643561011100 N-terminal plug; other site 643561011101 ligand-binding site [chemical binding]; other site 643561011102 putative FMN-dependent luciferase-like monooxygenase, KPN_01858 family; Region: LLM_KPN_01858; TIGR04027 643561011103 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 643561011104 general secretion pathway protein F; Region: GspF; TIGR02120 643561011105 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 643561011106 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 643561011107 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 643561011108 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading...; Region: EFh; cd00051 643561011109 Ca2+ binding site [ion binding]; other site 643561011110 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 643561011111 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 643561011112 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561011113 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 643561011114 Walker A/P-loop; other site 643561011115 ATP binding site [chemical binding]; other site 643561011116 Q-loop/lid; other site 643561011117 ABC transporter signature motif; other site 643561011118 Walker B; other site 643561011119 D-loop; other site 643561011120 H-loop/switch region; other site 643561011121 cyanophycin synthetase; Provisional; Region: PRK14016 643561011122 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561011123 cyanophycin synthetase; Provisional; Region: PRK14016 643561011124 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561011125 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 643561011126 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 643561011127 CreA protein; Region: CreA; cl01154 643561011128 Ulp1 protease family, C-terminal catalytic domain; Region: Peptidase_C48; pfam02902 643561011129 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 643561011130 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 643561011131 catalytic residues [active] 643561011132 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 643561011133 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 643561011134 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 643561011135 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 643561011136 Catalase-like heme-binding proteins and protein domains; Region: catalase_like; cl09506 643561011137 heme binding pocket [chemical binding]; other site 643561011138 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 643561011139 domain interactions; other site 643561011140 Response regulator receiver domain; Region: Response_reg; pfam00072 643561011141 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561011142 active site 643561011143 phosphorylation site [posttranslational modification] 643561011144 intermolecular recognition site; other site 643561011145 dimerization interface [polypeptide binding]; other site 643561011146 Response regulator receiver domain; Region: Response_reg; pfam00072 643561011147 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561011148 active site 643561011149 phosphorylation site [posttranslational modification] 643561011150 intermolecular recognition site; other site 643561011151 dimerization interface [polypeptide binding]; other site 643561011152 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 643561011153 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 643561011154 dimer interface [polypeptide binding]; other site 643561011155 phosphorylation site [posttranslational modification] 643561011156 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 643561011157 ATP binding site [chemical binding]; other site 643561011158 Mg2+ binding site [ion binding]; other site 643561011159 G-X-G motif; other site 643561011160 CheB methylesterase; Region: CheB_methylest; pfam01339 643561011161 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 643561011162 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 643561011163 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 643561011164 CHASE3 domain; Region: CHASE3; cl05000 643561011165 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 643561011166 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 643561011167 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 643561011168 ATP binding site [chemical binding]; other site 643561011169 Mg2+ binding site [ion binding]; other site 643561011170 G-X-G motif; other site 643561011171 Response regulator receiver domain; Region: Response_reg; pfam00072 643561011172 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561011173 active site 643561011174 phosphorylation site [posttranslational modification] 643561011175 intermolecular recognition site; other site 643561011176 dimerization interface [polypeptide binding]; other site 643561011177 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 643561011178 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561011179 active site 643561011180 phosphorylation site [posttranslational modification] 643561011181 intermolecular recognition site; other site 643561011182 dimerization interface [polypeptide binding]; other site 643561011183 Response regulator receiver domain; Region: Response_reg; pfam00072 643561011184 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561011185 active site 643561011186 phosphorylation site [posttranslational modification] 643561011187 intermolecular recognition site; other site 643561011188 dimerization interface [polypeptide binding]; other site 643561011189 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 643561011190 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561011191 metal binding site [ion binding]; metal-binding site 643561011192 active site 643561011193 I-site; other site 643561011194 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561011195 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 643561011196 N-terminal plug; other site 643561011197 ligand-binding site [chemical binding]; other site 643561011198 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 643561011199 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 643561011200 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 643561011201 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 643561011202 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 643561011203 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 643561011204 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 643561011205 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 643561011206 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 643561011207 Walker A/P-loop; other site 643561011208 ATP binding site [chemical binding]; other site 643561011209 Q-loop/lid; other site 643561011210 ABC transporter signature motif; other site 643561011211 Walker B; other site 643561011212 D-loop; other site 643561011213 H-loop/switch region; other site 643561011214 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 643561011215 Walker A/P-loop; other site 643561011216 ATP binding site [chemical binding]; other site 643561011217 Q-loop/lid; other site 643561011218 ABC transporter signature motif; other site 643561011219 Walker B; other site 643561011220 D-loop; other site 643561011221 H-loop/switch region; other site 643561011222 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 643561011223 ATP binding site [chemical binding]; other site 643561011224 putative Mg++ binding site [ion binding]; other site 643561011225 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 643561011226 nucleotide binding region [chemical binding]; other site 643561011227 ATP-binding site [chemical binding]; other site 643561011228 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 643561011229 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 643561011230 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 643561011231 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 643561011232 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 643561011233 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 643561011234 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 643561011235 aldehyde oxidoreductase 2Fe-2S subunit; Provisional; Region: PRK11433 643561011236 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 643561011237 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 643561011238 metal binding site [ion binding]; metal-binding site 643561011239 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 643561011240 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 643561011241 NAD binding site [chemical binding]; other site 643561011242 catalytic Zn binding site [ion binding]; other site 643561011243 structural Zn binding site [ion binding]; other site 643561011244 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 643561011245 dimer interface [polypeptide binding]; other site 643561011246 FMN binding site [chemical binding]; other site 643561011247 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 643561011248 nudix motif; other site 643561011249 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 643561011250 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 643561011251 CD73 ecto-5'-nucleotidase and related proteins, N-terminal metallophosphatase domain; Region: MPP_CD73_N; cd07409 643561011252 active site 643561011253 metal binding site [ion binding]; metal-binding site 643561011254 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 643561011255 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 643561011256 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 643561011257 putative dimerization interface [polypeptide binding]; other site 643561011258 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 643561011259 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 643561011260 C-term; Region: GreA_GreB; pfam01272 643561011261 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 643561011262 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 643561011263 substrate binding pocket [chemical binding]; other site 643561011264 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 643561011265 OsmC-like protein; Region: OsmC; cl00767 643561011266 Cupin domain; Region: Cupin_2; cl09118 643561011267 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561011268 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561011269 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561011270 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 643561011271 putative active site [active] 643561011272 putative metal binding residues [ion binding]; other site 643561011273 signature motif; other site 643561011274 putative triphosphate binding site [ion binding]; other site 643561011275 CHAD domain; Region: CHAD; cl10506 643561011276 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561011277 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011278 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 643561011279 dimerization interface [polypeptide binding]; other site 643561011280 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 643561011281 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 643561011282 dimer interface [polypeptide binding]; other site 643561011283 conserved gate region; other site 643561011284 putative PBP binding loops; other site 643561011285 ABC-ATPase subunit interface; other site 643561011286 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 643561011287 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 643561011288 dimer interface [polypeptide binding]; other site 643561011289 conserved gate region; other site 643561011290 putative PBP binding loops; other site 643561011291 ABC-ATPase subunit interface; other site 643561011292 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 643561011293 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 643561011294 Walker A/P-loop; other site 643561011295 ATP binding site [chemical binding]; other site 643561011296 Q-loop/lid; other site 643561011297 ABC transporter signature motif; other site 643561011298 Walker B; other site 643561011299 D-loop; other site 643561011300 H-loop/switch region; other site 643561011301 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561011302 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 643561011303 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 643561011304 Walker A/P-loop; other site 643561011305 ATP binding site [chemical binding]; other site 643561011306 Q-loop/lid; other site 643561011307 ABC transporter signature motif; other site 643561011308 Walker B; other site 643561011309 D-loop; other site 643561011310 H-loop/switch region; other site 643561011311 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 643561011312 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 643561011313 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 643561011314 Predicted acyl esterases [General function prediction only]; Region: COG2936 643561011315 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; cl08482 643561011316 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 643561011317 trimer interface [polypeptide binding]; other site 643561011318 eyelet of channel; other site 643561011319 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 643561011320 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561011321 putative ligand binding site [chemical binding]; other site 643561011322 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561011323 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 643561011324 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 643561011325 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 643561011326 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 643561011327 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 643561011328 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 643561011329 NADH dehydrogenase subunit L; Provisional; Region: PRK08168 643561011330 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 643561011331 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561011332 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011333 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 643561011334 dimerization interface [polypeptide binding]; other site 643561011335 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 643561011336 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 643561011337 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 643561011338 glutaminase active site [active] 643561011339 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 643561011340 dimer interface [polypeptide binding]; other site 643561011341 active site 643561011342 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 643561011343 dimer interface [polypeptide binding]; other site 643561011344 active site 643561011345 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561011346 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011347 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 643561011348 dimer interface [polypeptide binding]; other site 643561011349 phosphorylation site [posttranslational modification] 643561011350 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 643561011351 ATP binding site [chemical binding]; other site 643561011352 Mg2+ binding site [ion binding]; other site 643561011353 G-X-G motif; other site 643561011354 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 643561011355 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 643561011356 Substrate binding site [chemical binding]; other site 643561011357 Mg++ binding site [ion binding]; other site 643561011358 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 643561011359 active site 643561011360 substrate binding site [chemical binding]; other site 643561011361 CoA binding site [chemical binding]; other site 643561011362 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 643561011363 ligand binding site [chemical binding]; other site 643561011364 flexible hinge region; other site 643561011365 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011366 Sensors of blue-light using FAD; Region: BLUF; cl04855 643561011367 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 643561011368 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 643561011369 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011370 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561011371 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 643561011372 dimerization interface [polypeptide binding]; other site 643561011373 substrate binding pocket [chemical binding]; other site 643561011374 oxidase reductase; Provisional; Region: PTZ00273 643561011375 flavanone-3-hydroxylase; Provisional; Region: PLN03176 643561011376 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 643561011377 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 643561011378 active site 643561011379 metal binding site [ion binding]; metal-binding site 643561011380 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 643561011381 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 643561011382 putative ligand binding site [chemical binding]; other site 643561011383 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 643561011384 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 643561011385 Walker A/P-loop; other site 643561011386 ATP binding site [chemical binding]; other site 643561011387 Q-loop/lid; other site 643561011388 ABC transporter signature motif; other site 643561011389 Walker B; other site 643561011390 D-loop; other site 643561011391 H-loop/switch region; other site 643561011392 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 643561011393 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 643561011394 TM-ABC transporter signature motif; other site 643561011395 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 643561011396 TM-ABC transporter signature motif; other site 643561011397 Isochorismatase family; Region: Isochorismatase; pfam00857 643561011398 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 643561011399 catalytic triad [active] 643561011400 conserved cis-peptide bond; other site 643561011401 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 643561011402 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 643561011403 active site 643561011404 HIGH motif; other site 643561011405 dimer interface [polypeptide binding]; other site 643561011406 KMSKS motif; other site 643561011407 putative peptidase; Provisional; Region: PRK11649 643561011408 Peptidase family M23; Region: Peptidase_M23; pfam01551 643561011409 Uncharacterised protein family (UPF0075); Region: UPF0075; cl04217 643561011410 putative transporter; Provisional; Region: PRK10504 643561011411 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 643561011412 putative substrate translocation pore; other site 643561011413 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 643561011414 Polymer-forming cytoskeletal; Region: Bactofilin; cl09137 643561011415 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 643561011416 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 643561011417 23S rRNA interface [nucleotide binding]; other site 643561011418 L3 interface [polypeptide binding]; other site 643561011419 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 643561011420 Catalytic domain of Protein Kinases; Region: PKc; cd00180 643561011421 active site 643561011422 ATP binding site [chemical binding]; other site 643561011423 substrate binding site [chemical binding]; other site 643561011424 activation loop (A-loop); other site 643561011425 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 643561011426 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 643561011427 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 643561011428 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 643561011429 FAD binding site [chemical binding]; other site 643561011430 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 643561011431 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 643561011432 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 643561011433 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 643561011434 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; Region: AdoHcyase; cd00401 643561011435 oligomerization interface [polypeptide binding]; other site 643561011436 active site 643561011437 NAD+ binding site [chemical binding]; other site 643561011438 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 643561011439 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 643561011440 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 643561011441 G1 box; other site 643561011442 putative GEF interaction site [polypeptide binding]; other site 643561011443 GTP/Mg2+ binding site [chemical binding]; other site 643561011444 Switch I region; other site 643561011445 G2 box; other site 643561011446 G3 box; other site 643561011447 Switch II region; other site 643561011448 G4 box; other site 643561011449 G5 box; other site 643561011450 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding...; Region: Translation_Factor_II_like; cl02787 643561011451 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 643561011452 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 643561011453 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 643561011454 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 643561011455 Ligand binding site [chemical binding]; other site 643561011456 Putative Catalytic site [active] 643561011457 DXD motif; other site 643561011458 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 643561011459 sucrose-phosphate phosphatase subfamily; Region: SPP-subfamily; TIGR01482 643561011460 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561011461 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561011462 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 643561011463 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 643561011464 Walker A/P-loop; other site 643561011465 ATP binding site [chemical binding]; other site 643561011466 Q-loop/lid; other site 643561011467 ABC transporter signature motif; other site 643561011468 Walker B; other site 643561011469 D-loop; other site 643561011470 H-loop/switch region; other site 643561011471 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 643561011472 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 643561011473 dimer interface [polypeptide binding]; other site 643561011474 conserved gate region; other site 643561011475 putative PBP binding loops; other site 643561011476 ABC-ATPase subunit interface; other site 643561011477 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 643561011478 dimer interface [polypeptide binding]; other site 643561011479 conserved gate region; other site 643561011480 putative PBP binding loops; other site 643561011481 ABC-ATPase subunit interface; other site 643561011482 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 643561011483 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 643561011484 substrate binding pocket [chemical binding]; other site 643561011485 membrane-bound complex binding site; other site 643561011486 hinge residues; other site 643561011487 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 643561011488 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 643561011489 substrate binding pocket [chemical binding]; other site 643561011490 membrane-bound complex binding site; other site 643561011491 hinge residues; other site 643561011492 cell density-dependent motility repressor; Provisional; Region: PRK10082 643561011493 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011494 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 643561011495 dimerization interface [polypeptide binding]; other site 643561011496 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 643561011497 DctM-like transporters; Region: DctM; pfam06808 643561011498 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 643561011499 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561011500 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 643561011501 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 643561011502 ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to...; Region: ABCC_ATM1_transporter; cd03253 643561011503 Walker A/P-loop; other site 643561011504 ATP binding site [chemical binding]; other site 643561011505 Q-loop/lid; other site 643561011506 ABC transporter signature motif; other site 643561011507 Walker B; other site 643561011508 D-loop; other site 643561011509 H-loop/switch region; other site 643561011510 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 643561011511 Polymer-forming cytoskeletal; Region: Bactofilin; cl09137 643561011512 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561011513 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561011514 enoyl-CoA hydratase; Provisional; Region: PRK06688 643561011515 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 643561011516 substrate binding site [chemical binding]; other site 643561011517 oxyanion hole (OAH) forming residues; other site 643561011518 trimer interface [polypeptide binding]; other site 643561011519 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 643561011520 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 643561011521 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 643561011522 dimer interface [polypeptide binding]; other site 643561011523 active site 643561011524 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 643561011525 CoenzymeA binding site [chemical binding]; other site 643561011526 subunit interaction site [polypeptide binding]; other site 643561011527 PHB binding site; other site 643561011528 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 643561011529 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 643561011530 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561011531 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561011532 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 643561011533 substrate binding site [chemical binding]; other site 643561011534 fatty oxidation complex, alpha subunit FadJ; Region: FadJ; TIGR02440 643561011535 oxyanion hole (OAH) forming residues; other site 643561011536 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 643561011537 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 643561011538 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 643561011539 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561011540 active site 643561011541 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 643561011542 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561011543 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561011544 division inhibitor protein; Provisional; Region: slmA; PRK09480 643561011545 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561011546 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 643561011547 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 643561011548 dimer interface [polypeptide binding]; other site 643561011549 phosphorylation site [posttranslational modification] 643561011550 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 643561011551 ATP binding site [chemical binding]; other site 643561011552 Mg2+ binding site [ion binding]; other site 643561011553 G-X-G motif; other site 643561011554 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561011555 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561011556 active site 643561011557 phosphorylation site [posttranslational modification] 643561011558 intermolecular recognition site; other site 643561011559 dimerization interface [polypeptide binding]; other site 643561011560 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 643561011561 DNA binding site [nucleotide binding] 643561011562 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using...; Region: AAK_NAGK-C; cd04250 643561011563 feedback inhibition sensing region; other site 643561011564 homohexameric interface [polypeptide binding]; other site 643561011565 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 643561011566 nucleotide binding site [chemical binding]; other site 643561011567 N-acetyl-L-glutamate binding site [chemical binding]; other site 643561011568 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 643561011569 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases...; Region: GT_MraY_like; cd06912 643561011570 Mg++ binding site [ion binding]; other site 643561011571 putative catalytic motif [active] 643561011572 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 643561011573 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 643561011574 S-adenosylmethionine binding site [chemical binding]; other site 643561011575 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 643561011576 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 643561011577 Probable Catalytic site [active] 643561011578 metal binding site [ion binding]; metal-binding site 643561011579 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 643561011580 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 643561011581 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 643561011582 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 643561011583 Walker A/P-loop; other site 643561011584 ATP binding site [chemical binding]; other site 643561011585 Q-loop/lid; other site 643561011586 ABC transporter signature motif; other site 643561011587 Walker B; other site 643561011588 D-loop; other site 643561011589 H-loop/switch region; other site 643561011590 ABC-2 type transporter; Region: ABC2_membrane; cl11417 643561011591 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 643561011592 PPIC-type PPIASE domain; Region: Rotamase; cl08278 643561011593 Type II secretory pathway, component PulD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulD; COG1450 643561011594 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 643561011595 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 643561011596 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 643561011597 General secretion pathway protein M; Region: GspM_II; pfam10741 643561011598 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 643561011599 general secretion pathway protein J; Validated; Region: PRK08808 643561011600 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 643561011601 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 643561011602 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 643561011603 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 643561011604 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 643561011605 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 643561011606 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 643561011607 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 643561011608 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 643561011609 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 643561011610 Walker A motif; other site 643561011611 ATP binding site [chemical binding]; other site 643561011612 Walker B motif; other site 643561011613 Cupin domain; Region: Cupin_2; cl09118 643561011614 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 643561011615 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 643561011616 substrate binding site [chemical binding]; other site 643561011617 tetramer interface [polypeptide binding]; other site 643561011618 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 643561011619 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 643561011620 NADP binding site [chemical binding]; other site 643561011621 active site 643561011622 putative substrate binding site [chemical binding]; other site 643561011623 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 643561011624 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 643561011625 NAD binding site [chemical binding]; other site 643561011626 substrate binding site [chemical binding]; other site 643561011627 homodimer interface [polypeptide binding]; other site 643561011628 active site 643561011629 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561011630 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561011631 Bordetella pertussis Bvg accessory factor family; Region: Bvg_acc_factor; cl09130 643561011632 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 643561011633 BON domain; Region: BON; cl02771 643561011634 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 643561011635 putative peptidoglycan binding site; other site 643561011636 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 643561011637 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561011638 DNA-binding site [nucleotide binding]; DNA binding site 643561011639 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 643561011640 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561011641 homodimer interface [polypeptide binding]; other site 643561011642 catalytic residue [active] 643561011643 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 643561011644 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 643561011645 active site residue [active] 643561011646 Protein of unknown function DUF45; Region: DUF45; cl00636 643561011647 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 643561011648 putative acyl-acceptor binding pocket; other site 643561011649 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 643561011650 active site 643561011651 motif I; other site 643561011652 motif II; other site 643561011653 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 643561011654 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 643561011655 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 643561011656 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 643561011657 dimer interface [polypeptide binding]; other site 643561011658 motif 1; other site 643561011659 active site 643561011660 motif 2; other site 643561011661 motif 3; other site 643561011662 Cytochrome c [Energy production and conversion]; Region: COG3258 643561011663 Cytochrome c; Region: Cytochrom_C; cl11414 643561011664 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 643561011665 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 643561011666 dimer interface [polypeptide binding]; other site 643561011667 active site 643561011668 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 643561011669 dimer interface [polypeptide binding]; other site 643561011670 active site 1 [active] 643561011671 active site 2 [active] 643561011672 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; cd00411 643561011673 active site/substrate binding site [active] 643561011674 tetramer interface [polypeptide binding]; other site 643561011675 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561011676 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011677 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 643561011678 dimerization interface [polypeptide binding]; other site 643561011679 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 643561011680 putative active site [active] 643561011681 catalytic triad [active] 643561011682 putative dimer interface [polypeptide binding]; other site 643561011683 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 643561011684 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 643561011685 Transporter associated domain; Region: CorC_HlyC; cl08393 643561011686 Uncharacterized conserved protein [Function unknown]; Region: COG4104 643561011687 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561011688 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 643561011689 RHS Repeat; Region: RHS_repeat; cl11982 643561011690 RHS Repeat; Region: RHS_repeat; cl11982 643561011691 RHS Repeat; Region: RHS_repeat; cl11982 643561011692 RHS Repeat; Region: RHS_repeat; cl11982 643561011693 RHS protein; Region: RHS; pfam03527 643561011694 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 643561011695 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561011696 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561011697 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011698 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011699 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 643561011700 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 643561011701 Proteobacterial lipase chaperone protein; Region: Lipase_chap; cl02224 643561011702 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 643561011703 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 643561011704 dimer interface [polypeptide binding]; other site 643561011705 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 643561011706 active site 643561011707 Fe binding site [ion binding]; other site 643561011708 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561011709 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561011710 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 643561011711 cofactor binding site; other site 643561011712 metal binding site [ion binding]; metal-binding site 643561011713 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 643561011714 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 643561011715 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561011716 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 643561011717 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 643561011718 ligand binding site [chemical binding]; other site 643561011719 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 643561011720 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 643561011721 Walker A/P-loop; other site 643561011722 ATP binding site [chemical binding]; other site 643561011723 Q-loop/lid; other site 643561011724 ABC transporter signature motif; other site 643561011725 Walker B; other site 643561011726 D-loop; other site 643561011727 H-loop/switch region; other site 643561011728 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 643561011729 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 643561011730 TM-ABC transporter signature motif; other site 643561011731 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 643561011732 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 643561011733 DNA binding site [nucleotide binding] 643561011734 domain linker motif; other site 643561011735 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 643561011736 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 643561011737 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 643561011738 substrate binding site [chemical binding]; other site 643561011739 dimer interface [polypeptide binding]; other site 643561011740 ATP binding site [chemical binding]; other site 643561011741 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 643561011742 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561011743 lytic murein transglycosylase; Provisional; Region: PRK11619 643561011744 lytic murein transglycosylase; Provisional; Region: PRK11619 643561011745 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 643561011746 N-acetyl-D-glucosamine binding site [chemical binding]; other site 643561011747 catalytic residue [active] 643561011748 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 643561011749 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 643561011750 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 643561011751 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561011752 metal binding site [ion binding]; metal-binding site 643561011753 active site 643561011754 I-site; other site 643561011755 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH)...; Region: GST_N_1; cd03043 643561011756 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 643561011757 putative C-terminal domain interface [polypeptide binding]; other site 643561011758 putative GSH binding site (G-site) [chemical binding]; other site 643561011759 putative dimer interface [polypeptide binding]; other site 643561011760 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 643561011761 putative substrate binding pocket (H-site) [chemical binding]; other site 643561011762 putative N-terminal domain interface [polypeptide binding]; other site 643561011763 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 643561011764 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 643561011765 active site 643561011766 NTP binding site [chemical binding]; other site 643561011767 metal binding triad [ion binding]; metal-binding site 643561011768 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 643561011769 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 643561011770 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 643561011771 catalytic residues [active] 643561011772 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 643561011773 putative bifunctional trehalose-6-phosphate synthase/HAD hydrolase subfamily IIB; Provisional; Region: PRK14501 643561011774 active site 643561011775 motif I; other site 643561011776 motif II; other site 643561011777 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 643561011778 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 643561011779 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is...; Region: GT1_TPS; cd03788 643561011780 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 643561011781 active site 643561011782 homotetramer interface [polypeptide binding]; other site 643561011783 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 643561011784 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 643561011785 Cupin domain; Region: Cupin_2; cl09118 643561011786 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 643561011787 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 643561011788 active site 643561011789 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 643561011790 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561011791 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561011792 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 643561011793 active site 643561011794 metal binding site [ion binding]; metal-binding site 643561011795 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 643561011796 Coenzyme A binding pocket [chemical binding]; other site 643561011797 Bacterial DNA topoisomerase I DNA-binding domain; Region: TOP1Ac; smart00437 643561011798 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 643561011799 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional; Region: PRK06938 643561011800 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 643561011801 inhibitor-cofactor binding pocket; inhibition site 643561011802 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561011803 catalytic residue [active] 643561011804 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 643561011805 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 643561011806 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561011807 catalytic residue [active] 643561011808 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 643561011809 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 643561011810 substrate binding pocket [chemical binding]; other site 643561011811 membrane-bound complex binding site; other site 643561011812 hinge residues; other site 643561011813 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 643561011814 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 643561011815 putative PBP binding loops; other site 643561011816 ABC-ATPase subunit interface; other site 643561011817 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 643561011818 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 643561011819 Walker A/P-loop; other site 643561011820 ATP binding site [chemical binding]; other site 643561011821 Q-loop/lid; other site 643561011822 ABC transporter signature motif; other site 643561011823 Walker B; other site 643561011824 D-loop; other site 643561011825 H-loop/switch region; other site 643561011826 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 643561011827 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 643561011828 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 643561011829 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 643561011830 active site 643561011831 iron coordination sites [ion binding]; other site 643561011832 substrate binding pocket [chemical binding]; other site 643561011833 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 643561011834 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 643561011835 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 643561011836 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 643561011837 dimer interface [polypeptide binding]; other site 643561011838 conserved gate region; other site 643561011839 putative PBP binding loops; other site 643561011840 ABC-ATPase subunit interface; other site 643561011841 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 643561011842 dimer interface [polypeptide binding]; other site 643561011843 conserved gate region; other site 643561011844 putative PBP binding loops; other site 643561011845 ABC-ATPase subunit interface; other site 643561011846 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 643561011847 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 643561011848 Walker A/P-loop; other site 643561011849 ATP binding site [chemical binding]; other site 643561011850 Q-loop/lid; other site 643561011851 ABC transporter signature motif; other site 643561011852 Walker B; other site 643561011853 D-loop; other site 643561011854 H-loop/switch region; other site 643561011855 TOBE domain; Region: TOBE_2; cl01440 643561011856 Uncharacterized conserved protein [Function unknown]; Region: COG1565 643561011857 Uncharacterized ACR, COG1565; Region: DUF185; pfam02636 643561011858 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561011859 NAD(P) binding site [chemical binding]; other site 643561011860 active site 643561011861 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 643561011862 active site 643561011863 Protein of unknown function (DUF466); Region: DUF466; cl01082 643561011864 Carbon starvation protein CstA; Region: CstA; cl00856 643561011865 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 643561011866 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561011867 active site 643561011868 phosphorylation site [posttranslational modification] 643561011869 intermolecular recognition site; other site 643561011870 dimerization interface [polypeptide binding]; other site 643561011871 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 643561011872 DNA binding residues [nucleotide binding] 643561011873 dimerization interface [polypeptide binding]; other site 643561011874 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 643561011875 Cache domain; Region: Cache_2; cl07034 643561011876 Histidine kinase; Region: HisKA_3; pfam07730 643561011877 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 643561011878 ATP binding site [chemical binding]; other site 643561011879 Mg2+ binding site [ion binding]; other site 643561011880 G-X-G motif; other site 643561011881 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 643561011882 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 643561011883 Ligand Binding Site [chemical binding]; other site 643561011884 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 643561011885 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 643561011886 catalytic core [active] 643561011887 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 643561011888 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 643561011889 dimer interface [polypeptide binding]; other site 643561011890 active site 643561011891 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 643561011892 substrate binding site [chemical binding]; other site 643561011893 catalytic residue [active] 643561011894 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 643561011895 Phage Tail Collar Domain; Region: Collar; pfam07484 643561011896 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 643561011897 Phage Tail Collar Domain; Region: Collar; pfam07484 643561011898 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 643561011899 Phage Tail Collar Domain; Region: Collar; pfam07484 643561011900 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 643561011901 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 643561011902 Walker A motif; other site 643561011903 ATP binding site [chemical binding]; other site 643561011904 Walker B motif; other site 643561011905 arginine finger; other site 643561011906 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 643561011907 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 643561011908 RuvA N terminal domain; Region: RuvA_N; pfam01330 643561011909 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 643561011910 PhoH-like protein; Region: PhoH; cl12134 643561011911 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 643561011912 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 643561011913 putative active site [active] 643561011914 dimerization interface [polypeptide binding]; other site 643561011915 putative tRNAtyr binding site [nucleotide binding]; other site 643561011916 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 643561011917 Cation efflux family; Region: Cation_efflux; cl00316 643561011918 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 643561011919 active site 643561011920 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561011921 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 643561011922 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561011923 DNA-binding site [nucleotide binding]; DNA binding site 643561011924 UTRA domain; Region: UTRA; cl01230 643561011925 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 643561011926 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 643561011927 ATP binding site [chemical binding]; other site 643561011928 Mg++ binding site [ion binding]; other site 643561011929 motif III; other site 643561011930 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 643561011931 nucleotide binding region [chemical binding]; other site 643561011932 ATP-binding site [chemical binding]; other site 643561011933 DbpA RNA binding domain; Region: DbpA; pfam03880 643561011934 AMP nucleosidase; Provisional; Region: PRK08292 643561011935 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 643561011936 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 643561011937 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561011938 metal binding site [ion binding]; metal-binding site 643561011939 active site 643561011940 I-site; other site 643561011941 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 643561011942 trimer interface [polypeptide binding]; other site 643561011943 eyelet of channel; other site 643561011944 benzoate transport; Region: 2A0115; TIGR00895 643561011945 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 643561011946 putative substrate translocation pore; other site 643561011947 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 643561011948 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 643561011949 Hydroxyquinol 1,2-dioxygenase (1,2-HQD) catalyzes the ring cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), a intermediate in the degradation of a large variety of aromatic compounds including some polychloro- and nitroaromatic pollutants, to form...; Region: 1,2-HQD; cd03461 643561011950 dimer interface [polypeptide binding]; other site 643561011951 chlorocatechol 1,2-dioxygenase; Region: chlorocat_1_2; TIGR02465 643561011952 active site 643561011953 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 643561011954 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 643561011955 active site 643561011956 dimer interface [polypeptide binding]; other site 643561011957 metal binding site [ion binding]; metal-binding site 643561011958 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 643561011959 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011960 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 643561011961 substrate binding pocket [chemical binding]; other site 643561011962 dimerization interface [polypeptide binding]; other site 643561011963 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561011964 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561011965 Naphthocyclinone hydroxylase; Region: NcnH; cd01159 643561011966 Flavin binding site [chemical binding]; other site 643561011967 Flavin Reductases; Region: FlaRed; cl00801 643561011968 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cl02712 643561011969 amidase catalytic site [active] 643561011970 Zn binding residues [ion binding]; other site 643561011971 substrate binding site [chemical binding]; other site 643561011972 shikimate 5-dehydrogenase; Reviewed; Region: PRK12550 643561011973 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 643561011974 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 643561011975 shikimate binding site; other site 643561011976 NAD(P) binding site [chemical binding]; other site 643561011977 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 643561011978 P-loop; other site 643561011979 active site 643561011980 phosphorylation site [posttranslational modification] 643561011981 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 643561011982 P-loop; other site 643561011983 active site 643561011984 phosphorylation site [posttranslational modification] 643561011985 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 643561011986 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 643561011987 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 643561011988 substrate binding site [chemical binding]; other site 643561011989 ATP binding site [chemical binding]; other site 643561011990 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 643561011991 active site 643561011992 phosphorylation site [posttranslational modification] 643561011993 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 643561011994 dimerization domain swap beta strand [polypeptide binding]; other site 643561011995 regulatory protein interface [polypeptide binding]; other site 643561011996 active site 643561011997 regulatory phosphorylation site [posttranslational modification]; other site 643561011998 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 643561011999 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 643561012000 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 643561012001 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 643561012002 Transcriptional regulators [Transcription]; Region: PurR; COG1609 643561012003 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 643561012004 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 643561012005 Gram-negative bacterial tonB protein; Region: TonB; cl10048 643561012006 Hsp70 protein; Region: HSP70; pfam00012 643561012007 Peptidase domain in the S53 family; Region: Peptidases_S53_like; cd05562 643561012008 putative active site [active] 643561012009 putative catalytic triad [active] 643561012010 Peptidase domain in the S53 family; Region: Peptidases_S53_like; cd05562 643561012011 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 643561012012 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561012013 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561012014 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 643561012015 YCII-related domain; Region: YCII; cl00999 643561012016 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561012017 LysR family transcriptional regulator; Provisional; Region: PRK14997 643561012018 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012019 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 643561012020 dimerization interface [polypeptide binding]; other site 643561012021 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 643561012022 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 643561012023 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561012024 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561012025 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012026 Flavin Reductases; Region: FlaRed; cl00801 643561012027 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561012028 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561012029 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 643561012030 homotrimer interaction site [polypeptide binding]; other site 643561012031 putative active site [active] 643561012032 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 643561012033 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 643561012034 active site 643561012035 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 643561012036 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561012037 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 643561012038 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 643561012039 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 643561012040 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012041 OsmC-like protein; Region: OsmC; cl00767 643561012042 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 643561012043 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 643561012044 active site 643561012045 metal binding site [ion binding]; metal-binding site 643561012046 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 643561012047 Catalytic domain of Protein Kinases; Region: PKc; cd00180 643561012048 active site 643561012049 ATP binding site [chemical binding]; other site 643561012050 substrate binding site [chemical binding]; other site 643561012051 activation loop (A-loop); other site 643561012052 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 643561012053 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 643561012054 Phosphotransferase enzyme family; Region: APH; pfam01636 643561012055 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561012056 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012057 active site 643561012058 phosphorylation site [posttranslational modification] 643561012059 intermolecular recognition site; other site 643561012060 dimerization interface [polypeptide binding]; other site 643561012061 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 643561012062 DNA binding site [nucleotide binding] 643561012063 Domain of unknown function DUF11; Region: DUF11; cl15273 643561012064 Domain of unknown function DUF11; Region: DUF11; cl15273 643561012065 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 643561012066 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 643561012067 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 643561012068 dimer interface [polypeptide binding]; other site 643561012069 phosphorylation site [posttranslational modification] 643561012070 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 643561012071 ATP binding site [chemical binding]; other site 643561012072 Mg2+ binding site [ion binding]; other site 643561012073 G-X-G motif; other site 643561012074 Response regulator receiver domain; Region: Response_reg; pfam00072 643561012075 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012076 active site 643561012077 phosphorylation site [posttranslational modification] 643561012078 intermolecular recognition site; other site 643561012079 dimerization interface [polypeptide binding]; other site 643561012080 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 643561012081 Predicted membrane protein [Function unknown]; Region: COG4083 643561012082 heat shock protein 90; Provisional; Region: PRK05218 643561012083 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 643561012084 PAS fold; Region: PAS_4; pfam08448 643561012085 PAS fold; Region: PAS_3; pfam08447 643561012086 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 643561012087 PAS domain S-box; Region: sensory_box; TIGR00229 643561012088 two-component VirA-like sensor kinase; Provisional; Region: PRK13837 643561012089 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 643561012090 ATP binding site [chemical binding]; other site 643561012091 Mg2+ binding site [ion binding]; other site 643561012092 G-X-G motif; other site 643561012093 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012094 active site 643561012095 phosphorylation site [posttranslational modification] 643561012096 intermolecular recognition site; other site 643561012097 dimerization interface [polypeptide binding]; other site 643561012098 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 643561012099 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 643561012100 RNA binding surface [nucleotide binding]; other site 643561012101 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 643561012102 active site 643561012103 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 643561012104 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 643561012105 dimerization interface [polypeptide binding]; other site 643561012106 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561012107 metal binding site [ion binding]; metal-binding site 643561012108 active site 643561012109 I-site; other site 643561012110 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 643561012111 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 643561012112 dimerization interface [polypeptide binding]; other site 643561012113 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561012114 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 643561012115 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 643561012116 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 643561012117 ligand binding site [chemical binding]; other site 643561012118 flexible hinge region; other site 643561012119 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012120 Glycosyl hydrolase family 98; Region: Glyco_hydro_98M; pfam08306 643561012121 Glycosyl hydrolase family 98 C-terminal domain; Region: Glyco_hydro_98C; pfam08307 643561012122 Carbohydrate Binding Module 6 (CBM6) domains; many are found in association with discoidin domain(s); Region: CBM6_discoidin-like; cd04083 643561012123 putative metal binding site [ion binding]; other site 643561012124 cysteine synthases; Region: cysKM; TIGR01136 643561012125 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 643561012126 dimer interface [polypeptide binding]; other site 643561012127 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561012128 catalytic residue [active] 643561012129 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 643561012130 putative catalytic site [active] 643561012131 putative metal binding site [ion binding]; other site 643561012132 putative phosphate binding site [ion binding]; other site 643561012133 cardiolipin synthase 2; Provisional; Region: PRK11263 643561012134 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 643561012135 putative active site [active] 643561012136 catalytic site [active] 643561012137 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 643561012138 putative active site [active] 643561012139 catalytic site [active] 643561012140 Predicted integral membrane protein [Function unknown]; Region: COG0392 643561012141 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 643561012142 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561012143 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 643561012144 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561012145 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 643561012146 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561012147 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561012148 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 643561012149 intersubunit interface [polypeptide binding]; other site 643561012150 active site 643561012151 Zn2+ binding site [ion binding]; other site 643561012152 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 643561012153 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 643561012154 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 643561012155 Electron transfer flavoprotein, beta subunit [Energy production and conversion]; Region: FixA; COG2086 643561012156 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 643561012157 Ligand binding site [chemical binding]; other site 643561012158 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561012159 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561012160 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561012161 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561012162 CoA-transferase family III; Region: CoA_transf_3; cl00778 643561012163 enoyl-CoA hydratase; Provisional; Region: PRK07511 643561012164 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 643561012165 substrate binding site [chemical binding]; other site 643561012166 oxyanion hole (OAH) forming residues; other site 643561012167 trimer interface [polypeptide binding]; other site 643561012168 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 643561012169 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 643561012170 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 643561012171 active site 643561012172 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 643561012173 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 643561012174 FAD binding site [chemical binding]; other site 643561012175 substrate binding site [chemical binding]; other site 643561012176 catalytic base [active] 643561012177 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 643561012178 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 643561012179 substrate binding site [chemical binding]; other site 643561012180 oxyanion hole (OAH) forming residues; other site 643561012181 trimer interface [polypeptide binding]; other site 643561012182 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 643561012183 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561012184 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 643561012185 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561012186 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012187 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 643561012188 putative effector binding pocket; other site 643561012189 dimerization interface [polypeptide binding]; other site 643561012190 LysE type translocator; Region: LysE; cl00565 643561012191 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561012192 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012193 Peptidase family M48; Region: Peptidase_M48; cl12018 643561012194 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 643561012195 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 643561012196 putative metal binding site [ion binding]; other site 643561012197 LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; Region: LOTUS; cl14879 643561012198 Dihydroorotase [Nucleotide transport and metabolism]; Region: PyrC; COG0418 643561012199 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 643561012200 active site 643561012201 substrate binding pocket [chemical binding]; other site 643561012202 dimer interface [polypeptide binding]; other site 643561012203 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 643561012204 dimerization interface [polypeptide binding]; other site 643561012205 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 643561012206 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 643561012207 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 643561012208 ATP binding site [chemical binding]; other site 643561012209 Mg2+ binding site [ion binding]; other site 643561012210 G-X-G motif; other site 643561012211 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 643561012212 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012213 active site 643561012214 phosphorylation site [posttranslational modification] 643561012215 intermolecular recognition site; other site 643561012216 dimerization interface [polypeptide binding]; other site 643561012217 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 643561012218 DNA binding site [nucleotide binding] 643561012219 NodT family; Region: outer_NodT; TIGR01845 643561012220 Outer membrane efflux protein; Region: OEP; pfam02321 643561012221 DevC protein; Region: devC; TIGR01185 643561012222 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 643561012223 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 643561012224 Walker A/P-loop; other site 643561012225 ATP binding site [chemical binding]; other site 643561012226 Q-loop/lid; other site 643561012227 ABC transporter signature motif; other site 643561012228 Walker B; other site 643561012229 D-loop; other site 643561012230 H-loop/switch region; other site 643561012231 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 643561012232 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 643561012233 Esterase/lipase [General function prediction only]; Region: COG1647 643561012234 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional; Region: PRK12475 643561012235 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 643561012236 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 643561012237 catalytic residue [active] 643561012238 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 643561012239 Arginase family; Region: Arginase; cl00306 643561012240 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 643561012241 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]; Region: GabT; COG0160 643561012242 inhibitor-cofactor binding pocket; inhibition site 643561012243 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561012244 catalytic residue [active] 643561012245 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 643561012246 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 643561012247 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 643561012248 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561012249 Walker A/P-loop; other site 643561012250 ATP binding site [chemical binding]; other site 643561012251 Q-loop/lid; other site 643561012252 ABC transporter signature motif; other site 643561012253 Walker B; other site 643561012254 D-loop; other site 643561012255 H-loop/switch region; other site 643561012256 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 643561012257 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 643561012258 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 643561012259 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 643561012260 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 643561012261 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561012262 putative ligand binding site [chemical binding]; other site 643561012263 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 643561012264 trimer interface [polypeptide binding]; other site 643561012265 eyelet of channel; other site 643561012266 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 643561012267 putative substrate translocation pore; other site 643561012268 metabolite-proton symporter; Region: 2A0106; TIGR00883 643561012269 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 643561012270 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-; Region: DsbA_HCCA_Iso; cd03022 643561012271 putative catalytic residue [active] 643561012272 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 643561012273 This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro)...; Region: ProX_deacylase; cd04333 643561012274 putative deacylase active site [active] 643561012275 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 643561012276 active site 643561012277 catalytic residues [active] 643561012278 metal binding site [ion binding]; metal-binding site 643561012279 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561012280 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 643561012281 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 643561012282 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561012283 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 643561012284 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 643561012285 carboxyltransferase (CT) interaction site; other site 643561012286 biotinylation site [posttranslational modification]; other site 643561012287 enoyl-CoA hydratase; Provisional; Region: PRK05995 643561012288 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 643561012289 substrate binding site [chemical binding]; other site 643561012290 oxyanion hole (OAH) forming residues; other site 643561012291 trimer interface [polypeptide binding]; other site 643561012292 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 643561012293 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561012294 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 643561012295 AMP-binding domain protein; Validated; Region: PRK08315 643561012296 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561012297 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 643561012298 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 643561012299 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 643561012300 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 643561012301 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 643561012302 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 643561012303 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 643561012304 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 643561012305 dimer interface [polypeptide binding]; other site 643561012306 phosphorylation site [posttranslational modification] 643561012307 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 643561012308 ATP binding site [chemical binding]; other site 643561012309 Mg2+ binding site [ion binding]; other site 643561012310 G-X-G motif; other site 643561012311 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012312 Response regulator receiver domain; Region: Response_reg; pfam00072 643561012313 active site 643561012314 phosphorylation site [posttranslational modification] 643561012315 intermolecular recognition site; other site 643561012316 dimerization interface [polypeptide binding]; other site 643561012317 SEC-C motif; Region: SEC-C; cl12132 643561012318 hypothetical protein; Provisional; Region: PRK04233 643561012319 Protein of unknown function (DUF421); Region: DUF421; cl00990 643561012320 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 643561012321 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 643561012322 active site 643561012323 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 643561012324 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 643561012325 NADP binding site [chemical binding]; other site 643561012326 homodimer interface [polypeptide binding]; other site 643561012327 active site 643561012328 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 643561012329 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 643561012330 dimer interface [polypeptide binding]; other site 643561012331 active site 643561012332 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; cl01891 643561012333 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 643561012334 active site clefts [active] 643561012335 zinc binding site [ion binding]; other site 643561012336 dimer interface [polypeptide binding]; other site 643561012337 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 643561012338 isovaleryl-CoA dehydrogenase; Region: PLN02519 643561012339 substrate binding site [chemical binding]; other site 643561012340 FAD binding site [chemical binding]; other site 643561012341 catalytic base [active] 643561012342 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 643561012343 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 643561012344 DNA binding residues [nucleotide binding] 643561012345 putative dimer interface [polypeptide binding]; other site 643561012346 ABC transporter ATPase component; Reviewed; Region: PRK11147 643561012347 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561012348 Walker A/P-loop; other site 643561012349 ATP binding site [chemical binding]; other site 643561012350 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561012351 Q-loop/lid; other site 643561012352 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 643561012353 ABC transporter; Region: ABC_tran_2; pfam12848 643561012354 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 643561012355 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 643561012356 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012357 active site 643561012358 phosphorylation site [posttranslational modification] 643561012359 intermolecular recognition site; other site 643561012360 dimerization interface [polypeptide binding]; other site 643561012361 CheB methylesterase; Region: CheB_methylest; pfam01339 643561012362 CheD chemotactic sensory transduction; Region: CheD; cl00810 643561012363 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 643561012364 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 643561012365 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 643561012366 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 643561012367 putative CheA interaction surface; other site 643561012368 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 643561012369 putative binding surface; other site 643561012370 active site 643561012371 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 643561012372 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 643561012373 ATP binding site [chemical binding]; other site 643561012374 Mg2+ binding site [ion binding]; other site 643561012375 G-X-G motif; other site 643561012376 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 643561012377 Response regulator receiver domain; Region: Response_reg; pfam00072 643561012378 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012379 active site 643561012380 phosphorylation site [posttranslational modification] 643561012381 intermolecular recognition site; other site 643561012382 dimerization interface [polypeptide binding]; other site 643561012383 Response regulator receiver domain; Region: Response_reg; pfam00072 643561012384 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012385 active site 643561012386 phosphorylation site [posttranslational modification] 643561012387 intermolecular recognition site; other site 643561012388 dimerization interface [polypeptide binding]; other site 643561012389 sensory histidine kinase UhpB; Provisional; Region: PRK11644 643561012390 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 643561012391 ATP binding site [chemical binding]; other site 643561012392 Mg2+ binding site [ion binding]; other site 643561012393 G-X-G motif; other site 643561012394 response regulator; Provisional; Region: PRK09483 643561012395 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012396 active site 643561012397 phosphorylation site [posttranslational modification] 643561012398 intermolecular recognition site; other site 643561012399 dimerization interface [polypeptide binding]; other site 643561012400 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 643561012401 DNA binding residues [nucleotide binding] 643561012402 dimerization interface [polypeptide binding]; other site 643561012403 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 643561012404 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 643561012405 FliP family; Region: FliP; cl00593 643561012406 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 643561012407 flagellar motor switch protein; Validated; Region: fliN; PRK05698 643561012408 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 643561012409 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 643561012410 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 643561012411 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 643561012412 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 643561012413 Flagellar FliJ protein; Region: FliJ; cl09161 643561012414 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 643561012415 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 643561012416 Walker A motif/ATP binding site; other site 643561012417 Walker B motif; other site 643561012418 Flagellar assembly protein FliH; Region: FliH; pfam02108 643561012419 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 643561012420 MgtE intracellular N domain; Region: MgtE_N; cl15244 643561012421 FliG C-terminal domain; Region: FliG_C; pfam01706 643561012422 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 643561012423 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 643561012424 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 643561012425 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 643561012426 Flagellar protein FliT; Region: FliT; cl05125 643561012427 Flagellar protein FliS; Region: FliS; cl00654 643561012428 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 643561012429 flagellar capping protein; Reviewed; Region: fliD; PRK08032 643561012430 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 643561012431 flagellin; Provisional; Region: PRK12806 643561012432 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 643561012433 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 643561012434 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 643561012435 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 643561012436 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 643561012437 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 643561012438 inhibitor-cofactor binding pocket; inhibition site 643561012439 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561012440 catalytic residue [active] 643561012441 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 643561012442 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561012443 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 643561012444 S-adenosylmethionine binding site [chemical binding]; other site 643561012445 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 643561012446 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 643561012447 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 643561012448 active site 643561012449 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 643561012450 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 643561012451 Probable Catalytic site [active] 643561012452 metal binding site [ion binding]; metal-binding site 643561012453 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 643561012454 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 643561012455 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 643561012456 flagellar motor protein MotB; Validated; Region: motB; PRK09041 643561012457 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561012458 ligand binding site [chemical binding]; other site 643561012459 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012460 Response regulator receiver domain; Region: Response_reg; pfam00072 643561012461 active site 643561012462 phosphorylation site [posttranslational modification] 643561012463 intermolecular recognition site; other site 643561012464 dimerization interface [polypeptide binding]; other site 643561012465 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 643561012466 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 643561012467 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 643561012468 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 643561012469 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 643561012470 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 643561012471 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 643561012472 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561012473 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 643561012474 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 643561012475 DNA binding residues [nucleotide binding] 643561012476 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 643561012477 SAF domain; Region: SAF; cl00555 643561012478 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 643561012479 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 643561012480 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 643561012481 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 643561012482 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 643561012483 Flagellar hook capping protein; Region: FlgD; cl04347 643561012484 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 643561012485 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 643561012486 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 643561012487 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 643561012488 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 643561012489 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 643561012490 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 643561012491 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 643561012492 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 643561012493 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 643561012494 Flagellar L-ring protein; Region: FlgH; cl00905 643561012495 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 643561012496 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 643561012497 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 643561012498 Rod binding protein; Region: Rod-binding; cl01626 643561012499 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 643561012500 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 643561012501 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 643561012502 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 643561012503 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 643561012504 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 643561012505 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 643561012506 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561012507 DNA-binding site [nucleotide binding]; DNA binding site 643561012508 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 643561012509 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561012510 homodimer interface [polypeptide binding]; other site 643561012511 catalytic residue [active] 643561012512 LysE type translocator; Region: LysE; cl00565 643561012513 aspartate aminotransferase; Provisional; Region: PRK08361 643561012514 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 643561012515 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561012516 homodimer interface [polypeptide binding]; other site 643561012517 catalytic residue [active] 643561012518 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 643561012519 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_2; cd03047 643561012520 putative C-terminal domain interface [polypeptide binding]; other site 643561012521 putative GSH binding site (G-site) [chemical binding]; other site 643561012522 putative dimer interface [polypeptide binding]; other site 643561012523 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 643561012524 putative N-terminal domain interface [polypeptide binding]; other site 643561012525 putative dimer interface [polypeptide binding]; other site 643561012526 putative substrate binding pocket (H-site) [chemical binding]; other site 643561012527 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 643561012528 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 643561012529 LysE type translocator; Region: LysE; cl00565 643561012530 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 643561012531 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 643561012532 tetramer interface [polypeptide binding]; other site 643561012533 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561012534 catalytic residue [active] 643561012535 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 643561012536 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 643561012537 catalytic core [active] 643561012538 Creatinine amidohydrolase; Region: Creatininase; cl00618 643561012539 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561012540 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561012541 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 643561012542 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 643561012543 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 643561012544 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561012545 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 643561012546 N-terminal plug; other site 643561012547 ligand-binding site [chemical binding]; other site 643561012548 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 643561012549 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 643561012550 LysR family transcriptional regulator; Provisional; Region: PRK14997 643561012551 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012552 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 643561012553 putative effector binding pocket; other site 643561012554 dimerization interface [polypeptide binding]; other site 643561012555 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 643561012556 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 643561012557 putative NAD(P) binding site [chemical binding]; other site 643561012558 dimer interface [polypeptide binding]; other site 643561012559 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 643561012560 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 643561012561 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 643561012562 Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4233 643561012563 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 643561012564 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 643561012565 DsbD alpha interface [polypeptide binding]; other site 643561012566 catalytic residues [active] 643561012567 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl00556 643561012568 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561012569 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561012570 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 643561012571 Integral membrane protein TerC family; Region: TerC; cl10468 643561012572 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 643561012573 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012574 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 643561012575 dimerization interface [polypeptide binding]; other site 643561012576 Bacterial protein of unknown function (DUF925); Region: DUF925; cl01435 643561012577 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 643561012578 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 643561012579 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 643561012580 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 643561012581 NodT family; Region: outer_NodT; TIGR01845 643561012582 Outer membrane efflux protein; Region: OEP; pfam02321 643561012583 Outer membrane efflux protein; Region: OEP; pfam02321 643561012584 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 643561012585 Sulfatase; Region: Sulfatase; cl10460 643561012586 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561012587 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561012588 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012589 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 643561012590 substrate binding site [chemical binding]; other site 643561012591 active site 643561012592 primosome assembly protein PriA; Validated; Region: PRK05580 643561012593 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 643561012594 ATP binding site [chemical binding]; other site 643561012595 putative Mg++ binding site [ion binding]; other site 643561012596 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561012597 Membrane transport protein; Region: Mem_trans; cl09117 643561012598 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 643561012599 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561012600 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561012601 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among Gram-...; Region: OMPLA; cd00541 643561012602 substrate binding site [chemical binding]; other site 643561012603 dimerization interface [polypeptide binding]; other site 643561012604 active site 643561012605 calcium binding site [ion binding]; other site 643561012606 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 643561012607 Ligand Binding Site [chemical binding]; other site 643561012608 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 643561012609 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 643561012610 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins...; Region: GST_N_GTT1_like; cd03046 643561012611 putative GSH binding site (G-site) [chemical binding]; other site 643561012612 putative C-terminal domain interface [polypeptide binding]; other site 643561012613 C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases; Region: GST_C_GTT1_like; cd03189 643561012614 putative N-terminal domain interface [polypeptide binding]; other site 643561012615 putative dimer interface [polypeptide binding]; other site 643561012616 putative substrate binding pocket (H-site) [chemical binding]; other site 643561012617 short chain dehydrogenase; Provisional; Region: PRK06701 643561012618 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 643561012619 NAD binding site [chemical binding]; other site 643561012620 metal binding site [ion binding]; metal-binding site 643561012621 active site 643561012622 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 643561012623 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 643561012624 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 643561012625 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 643561012626 PAS fold; Region: PAS_3; pfam08447 643561012627 putative active site [active] 643561012628 heme pocket [chemical binding]; other site 643561012629 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 643561012630 PAS fold; Region: PAS_3; pfam08447 643561012631 putative active site [active] 643561012632 heme pocket [chemical binding]; other site 643561012633 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 643561012634 PAS fold; Region: PAS_3; pfam08447 643561012635 putative active site [active] 643561012636 heme pocket [chemical binding]; other site 643561012637 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 643561012638 Double zinc ribbon; Region: DZR; pfam12773 643561012639 Uncharacterized protein conserved in bacteria (DUF2145); Region: DUF2145; pfam09916 643561012640 yiaA/B two helix domain; Region: YiaAB; cl01759 643561012641 yiaA/B two helix domain; Region: YiaAB; cl01759 643561012642 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 643561012643 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561012644 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 643561012645 Aminocyclopropane-1-carboxylate deaminase (ACCD): Pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of 1-aminocyclopropane-L-carboxylate (ACC), a precursor of the plant hormone ethylene, to alpha-ketobutyrate and ammonia; Region: ACCD; cd06449 643561012646 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561012647 catalytic residue [active] 643561012648 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561012649 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561012650 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 643561012651 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561012652 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 643561012653 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 643561012654 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 643561012655 putative acyl-acceptor binding pocket; other site 643561012656 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 643561012657 Curli production assembly/transport component CsgG; Region: CsgG; cl00639 643561012658 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 643561012659 Catalytic site [active] 643561012660 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 643561012661 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561012662 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561012663 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 643561012664 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 643561012665 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 643561012666 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 643561012667 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 643561012668 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 643561012669 FIST N domain; Region: FIST; cl10701 643561012670 FIST C domain; Region: FIST_C; pfam10442 643561012671 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; cl00257 643561012672 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 643561012673 Predicted membrane protein (DUF2254); Region: DUF2254; pfam10011 643561012674 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561012675 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561012676 NAD(P) binding site [chemical binding]; other site 643561012677 active site 643561012678 NMT1/THI5 like; Region: NMT1; pfam09084 643561012679 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561012680 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 643561012681 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 643561012682 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561012683 Walker A/P-loop; other site 643561012684 ATP binding site [chemical binding]; other site 643561012685 Q-loop/lid; other site 643561012686 ABC transporter signature motif; other site 643561012687 Walker B; other site 643561012688 D-loop; other site 643561012689 H-loop/switch region; other site 643561012690 Acyl-CoA reductase LuxC; Region: ALDH_Acyl-CoA-Red_LuxC; cd07080 643561012691 Acyl-CoA reductase (LuxC); Region: LuxC; pfam05893 643561012692 putative catalytic cysteine [active] 643561012693 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561012694 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 643561012695 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 643561012696 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 643561012697 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 643561012698 non-specific DNA binding site [nucleotide binding]; other site 643561012699 salt bridge; other site 643561012700 sequence-specific DNA binding site [nucleotide binding]; other site 643561012701 HipA N-terminal domain; Region: couple_hipA; TIGR03071 643561012702 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 643561012703 HipA-like N-terminal domain; Region: HipA_N; pfam07805 643561012704 HipA-like C-terminal domain; Region: HipA_C; pfam07804 643561012705 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 643561012706 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 643561012707 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 643561012708 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 643561012709 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 643561012710 DNA binding residues [nucleotide binding] 643561012711 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 643561012712 Z1 domain; Region: Z1; pfam10593 643561012713 AIPR protein; Region: AIPR; pfam10592 643561012714 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 643561012715 additional DNA contacts [nucleotide binding]; other site 643561012716 mismatch recognition site; other site 643561012717 active site 643561012718 zinc binding site [ion binding]; other site 643561012719 DNA intercalation site [nucleotide binding]; other site 643561012720 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 643561012721 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 643561012722 DNA binding site [nucleotide binding] 643561012723 substrate interaction site [chemical binding]; other site 643561012724 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 643561012725 Membrane bound L-sorbosone dehydrogenase; Region: SNDH; pfam12303 643561012726 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 643561012727 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 643561012728 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 643561012729 E-class dimer interface [polypeptide binding]; other site 643561012730 P-class dimer interface [polypeptide binding]; other site 643561012731 active site 643561012732 Cu2+ binding site [ion binding]; other site 643561012733 Zn2+ binding site [ion binding]; other site 643561012734 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 643561012735 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 643561012736 putative molybdopterin cofactor binding site [chemical binding]; other site 643561012737 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT)...; Region: MopB_CT_ydeP; cd02787 643561012738 putative molybdopterin cofactor binding site; other site 643561012739 Catalase-like heme-binding proteins similar to the uncharacterized y4iL; Region: y4iL_like; cd08152 643561012740 putative heme binding pocket [chemical binding]; other site 643561012741 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 643561012742 non-specific DNA binding site [nucleotide binding]; other site 643561012743 salt bridge; other site 643561012744 sequence-specific DNA binding site [nucleotide binding]; other site 643561012745 HipA N-terminal domain; Region: couple_hipA; TIGR03071 643561012746 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 643561012747 HipA-like N-terminal domain; Region: HipA_N; pfam07805 643561012748 HipA-like C-terminal domain; Region: HipA_C; pfam07804 643561012749 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 643561012750 Major Facilitator Superfamily; Region: MFS_1; pfam07690 643561012751 putative substrate translocation pore; other site 643561012752 Response regulator receiver domain; Region: Response_reg; pfam00072 643561012753 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012754 active site 643561012755 phosphorylation site [posttranslational modification] 643561012756 intermolecular recognition site; other site 643561012757 dimerization interface [polypeptide binding]; other site 643561012758 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 643561012759 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 643561012760 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 643561012761 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 643561012762 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 643561012763 dimer interface [polypeptide binding]; other site 643561012764 phosphorylation site [posttranslational modification] 643561012765 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 643561012766 ATP binding site [chemical binding]; other site 643561012767 Mg2+ binding site [ion binding]; other site 643561012768 G-X-G motif; other site 643561012769 16S rRNA methyltransferase B; Provisional; Region: PRK10901 643561012770 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 643561012771 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 643561012772 S-adenosylmethionine binding site [chemical binding]; other site 643561012773 LemA family; Region: LemA; cl00742 643561012774 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 643561012775 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 643561012776 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 643561012777 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 643561012778 DNA-directed RNA polymerase, beta'' subunit; Region: rpoC2_cyan; TIGR02388 643561012779 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 643561012780 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 643561012781 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 643561012782 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 643561012783 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 643561012784 DNA binding site [nucleotide binding] 643561012785 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 643561012786 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 643561012787 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 643561012788 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 643561012789 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 643561012790 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 643561012791 RPB11 interaction site [polypeptide binding]; other site 643561012792 RPB12 interaction site [polypeptide binding]; other site 643561012793 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 643561012794 RPB3 interaction site [polypeptide binding]; other site 643561012795 RPB1 interaction site [polypeptide binding]; other site 643561012796 RPB11 interaction site [polypeptide binding]; other site 643561012797 RPB10 interaction site [polypeptide binding]; other site 643561012798 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 643561012799 peripheral dimer interface [polypeptide binding]; other site 643561012800 core dimer interface [polypeptide binding]; other site 643561012801 L10 interface [polypeptide binding]; other site 643561012802 L11 interface [polypeptide binding]; other site 643561012803 putative EF-Tu interaction site [polypeptide binding]; other site 643561012804 putative EF-G interaction site [polypeptide binding]; other site 643561012805 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 643561012806 23S rRNA interface [nucleotide binding]; other site 643561012807 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 643561012808 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 643561012809 mRNA/rRNA interface [nucleotide binding]; other site 643561012810 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 643561012811 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 643561012812 23S rRNA interface [nucleotide binding]; other site 643561012813 L7/L12 interface [polypeptide binding]; other site 643561012814 putative thiostrepton binding site; other site 643561012815 L25 interface [polypeptide binding]; other site 643561012816 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 643561012817 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 643561012818 putative homodimer interface [polypeptide binding]; other site 643561012819 KOW motif; Region: KOW; cl00354 643561012820 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 643561012821 elongation factor Tu; Reviewed; Region: PRK00049 643561012822 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 643561012823 G1 box; other site 643561012824 GEF interaction site [polypeptide binding]; other site 643561012825 GTP/Mg2+ binding site [chemical binding]; other site 643561012826 Switch I region; other site 643561012827 G2 box; other site 643561012828 G3 box; other site 643561012829 Switch II region; other site 643561012830 G4 box; other site 643561012831 G5 box; other site 643561012832 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 643561012833 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 643561012834 Antibiotic Binding Site [chemical binding]; other site 643561012835 glutathione synthetase; Provisional; Region: PRK05246 643561012836 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 643561012837 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561012838 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 643561012839 Sulfate transporter family; Region: Sulfate_transp; cl00967 643561012840 potassium uptake protein; Region: kup; TIGR00794 643561012841 K+ potassium transporter; Region: K_trans; cl01227 643561012842 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 643561012843 Glutamate-cysteine ligase; Region: GshA; pfam08886 643561012844 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 643561012845 Cation transport protein; Region: TrkH; cl10514 643561012846 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 643561012847 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561012848 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 643561012849 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561012850 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 643561012851 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 643561012852 putative catalytic cysteine [active] 643561012853 Predicted amidohydrolase [General function prediction only]; Region: COG0388 643561012854 Nitrilases, cyanide hydratase (CH)s, and similar proteins (class 1 nitrilases); Region: nitrilases_CHs; cd07564 643561012855 putative active site [active] 643561012856 catalytic triad [active] 643561012857 putative dimer interface [polypeptide binding]; other site 643561012858 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561012859 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_2; cd08464 643561012860 putative substrate binding pocket [chemical binding]; other site 643561012861 putative dimerization interface [polypeptide binding]; other site 643561012862 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 643561012863 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 643561012864 Lipopolysaccharide-assembly; Region: LptE; cl01125 643561012865 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 643561012866 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 643561012867 HIGH motif; other site 643561012868 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 643561012869 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 643561012870 active site 643561012871 KMSKS motif; other site 643561012872 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 643561012873 tRNA binding surface [nucleotide binding]; other site 643561012874 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 643561012875 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 643561012876 Catalytic site [active] 643561012877 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 643561012878 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561012879 metal binding site [ion binding]; metal-binding site 643561012880 active site 643561012881 I-site; other site 643561012882 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 643561012883 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 643561012884 dihydrodipicolinate reductase; Provisional; Region: PRK00048 643561012885 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561012886 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 643561012887 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 643561012888 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 643561012889 metal binding site 2 [ion binding]; metal-binding site 643561012890 putative DNA binding helix; other site 643561012891 metal binding site 1 [ion binding]; metal-binding site 643561012892 dimer interface [polypeptide binding]; other site 643561012893 structural Zn2+ binding site [ion binding]; other site 643561012894 HPr kinase/phosphorylase; Provisional; Region: PRK05428 643561012895 DRTGG domain; Region: DRTGG; cl12147 643561012896 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-...; Region: HprK_C; cd01918 643561012897 Hpr binding site; other site 643561012898 active site 643561012899 homohexamer subunit interaction site [polypeptide binding]; other site 643561012900 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 643561012901 active site 643561012902 phosphorylation site [posttranslational modification] 643561012903 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 643561012904 30S subunit binding site; other site 643561012905 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 643561012906 ATP binding site [chemical binding]; other site 643561012907 active site 643561012908 substrate binding site [chemical binding]; other site 643561012909 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3126 643561012910 META domain; Region: META; cl01245 643561012911 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 643561012912 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 643561012913 AIR carboxylase; Region: AIRC; cl00310 643561012914 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 643561012915 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561012916 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 643561012917 SUA5 domain; Region: SUA5; pfam03481 643561012918 Triacylglycerol lipase-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: Triacylglycerol_lipase_like; cd01847 643561012919 active site 643561012920 catalytic triad [active] 643561012921 oxyanion hole [active] 643561012922 Surface antigen; Region: Surface_Ag_2; cl01155 643561012923 Triacylglycerol lipase-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: Triacylglycerol_lipase_like; cd01847 643561012924 active site 643561012925 catalytic triad [active] 643561012926 oxyanion hole [active] 643561012927 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl15297 643561012928 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 643561012929 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 643561012930 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 643561012931 Coenzyme A binding pocket [chemical binding]; other site 643561012932 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 643561012933 active site 643561012934 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 643561012935 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 643561012936 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 643561012937 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 643561012938 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561012939 hypothetical protein; Provisional; Region: PRK08185 643561012940 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose...; Region: TBP_aldolase_IIB; cd00947 643561012941 intersubunit interface [polypeptide binding]; other site 643561012942 active site 643561012943 zinc binding site [ion binding]; other site 643561012944 Na+ binding site [ion binding]; other site 643561012945 sensor protein QseC; Provisional; Region: PRK10337 643561012946 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 643561012947 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 643561012948 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 643561012949 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012950 active site 643561012951 phosphorylation site [posttranslational modification] 643561012952 intermolecular recognition site; other site 643561012953 dimerization interface [polypeptide binding]; other site 643561012954 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 643561012955 DNA binding site [nucleotide binding] 643561012956 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 643561012957 active site 643561012958 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 643561012959 active site 643561012960 pyruvate kinase; Provisional; Region: PRK05826 643561012961 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 643561012962 domain interfaces; other site 643561012963 active site 643561012964 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 643561012965 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 643561012966 ATP binding site [chemical binding]; other site 643561012967 Mg2+ binding site [ion binding]; other site 643561012968 G-X-G motif; other site 643561012969 osmolarity response regulator; Provisional; Region: ompR; PRK09468 643561012970 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561012971 active site 643561012972 phosphorylation site [posttranslational modification] 643561012973 intermolecular recognition site; other site 643561012974 dimerization interface [polypeptide binding]; other site 643561012975 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 643561012976 DNA binding site [nucleotide binding] 643561012977 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface...; Region: TroA-like; cl00262 643561012978 intersubunit interface [polypeptide binding]; other site 643561012979 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 643561012980 ABC-ATPase subunit interface; other site 643561012981 dimer interface [polypeptide binding]; other site 643561012982 putative PBP binding regions; other site 643561012983 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 643561012984 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 643561012985 Walker A/P-loop; other site 643561012986 ATP binding site [chemical binding]; other site 643561012987 Q-loop/lid; other site 643561012988 ABC transporter signature motif; other site 643561012989 Walker B; other site 643561012990 D-loop; other site 643561012991 H-loop/switch region; other site 643561012992 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 643561012993 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 643561012994 proline aminopeptidase P II; Provisional; Region: PRK10879 643561012995 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action...; Region: Prolidase; cd01087 643561012996 active site 643561012997 Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]; Region: PspA; COG1842 643561012998 Protein of unknown function (DUF1449); Region: DUF1449; pfam07290 643561012999 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 643561013000 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins...; Region: Band_7_flotillin; cd03399 643561013001 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 643561013002 Substrate binding site [chemical binding]; other site 643561013003 metal binding site [ion binding]; metal-binding site 643561013004 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 643561013005 transketolase; Reviewed; Region: PRK12753 643561013006 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 643561013007 TPP-binding site [chemical binding]; other site 643561013008 dimer interface [polypeptide binding]; other site 643561013009 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 643561013010 PYR/PP interface [polypeptide binding]; other site 643561013011 dimer interface [polypeptide binding]; other site 643561013012 TPP binding site [chemical binding]; other site 643561013013 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 643561013014 Protein of unknown function (DUF1493); Region: DUF1493; pfam07377 643561013015 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 643561013016 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 643561013017 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 643561013018 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013019 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 643561013020 dimerization interface [polypeptide binding]; other site 643561013021 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561013022 ligand binding site [chemical binding]; other site 643561013023 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 643561013024 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 643561013025 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 643561013026 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 643561013027 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 643561013028 Peptidase C26; Region: Peptidase_C26; pfam07722 643561013029 catalytic triad [active] 643561013030 Spore Coat Protein U domain; Region: SCPU; cl02253 643561013031 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 643561013032 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 643561013033 pilin outer membrane usher protein SafC; Provisional; Region: PRK15223; cl14650 643561013034 Spore Coat Protein U domain; Region: SCPU; cl02253 643561013035 Spore Coat Protein U domain; Region: SCPU; cl02253 643561013036 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 643561013037 Cupin domain; Region: Cupin_2; cl09118 643561013038 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 643561013039 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 643561013040 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 643561013041 Mechanosensitive ion channel; Region: MS_channel; pfam00924 643561013042 Sulfatase; Region: Sulfatase; cl10460 643561013043 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 643561013044 classical (c) SDR, subgroup 3; Region: SDR_c3; cd05360 643561013045 putative NAD(P) binding site [chemical binding]; other site 643561013046 active site 643561013047 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 643561013048 Nuclease-related domain; Region: NERD; pfam08378 643561013049 DEAD-like helicases superfamily; Region: DEXDc; smart00487 643561013050 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561013051 UvrD/REP helicase; Region: UvrD-helicase; cl14126 643561013052 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 643561013053 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561013054 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 643561013055 Yersinia/Haemophilus virulence surface antigen; Region: Peptidase_C58; cl04145 643561013056 RDD family; Region: RDD; cl00746 643561013057 Fic family protein [Function unknown]; Region: COG3177 643561013058 Fic/DOC family; Region: Fic; cl00960 643561013059 DNA topoisomerase III; Validated; Region: PRK08173 643561013060 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 643561013061 active site 643561013062 putative interdomain interaction site [polypeptide binding]; other site 643561013063 putative metal-binding site [ion binding]; other site 643561013064 putative nucleotide binding site [chemical binding]; other site 643561013065 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 643561013066 domain I; other site 643561013067 DNA binding groove [nucleotide binding] 643561013068 phosphate binding site [ion binding]; other site 643561013069 domain II; other site 643561013070 domain III; other site 643561013071 nucleotide binding site [chemical binding]; other site 643561013072 catalytic site [active] 643561013073 domain IV; other site 643561013074 SWIB/MDM2 domain; Region: SWIB; cl02489 643561013075 SET domain; Region: SET; cl02566 643561013076 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 643561013077 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 643561013078 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 643561013079 leucine-rich repeat receptor-like protein kinase; Provisional; Region: PLN00113 643561013080 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 643561013081 N-formylglutamate amidohydrolase; Region: FGase; cl01522 643561013082 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561013083 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561013084 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013085 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561013086 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 643561013087 dimerization interface [polypeptide binding]; other site 643561013088 substrate binding pocket [chemical binding]; other site 643561013089 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 643561013090 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 643561013091 ligand binding site [chemical binding]; other site 643561013092 flexible hinge region; other site 643561013093 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 643561013094 catalytic loop [active] 643561013095 iron binding site [ion binding]; other site 643561013096 cyclase homology domain; Region: CHD; cd07302 643561013097 nucleotidyl binding site; other site 643561013098 metal binding site [ion binding]; metal-binding site 643561013099 dimer interface [polypeptide binding]; other site 643561013100 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 643561013101 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 643561013102 dimer interface [polypeptide binding]; other site 643561013103 phosphorylation site [posttranslational modification] 643561013104 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 643561013105 ATP binding site [chemical binding]; other site 643561013106 Mg2+ binding site [ion binding]; other site 643561013107 G-X-G motif; other site 643561013108 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 643561013109 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561013110 active site 643561013111 phosphorylation site [posttranslational modification] 643561013112 intermolecular recognition site; other site 643561013113 dimerization interface [polypeptide binding]; other site 643561013114 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 643561013115 DNA binding site [nucleotide binding] 643561013116 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013117 recombinase A; Provisional; Region: recA; PRK09354 643561013118 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 643561013119 hexamer interface [polypeptide binding]; other site 643561013120 Walker A motif; other site 643561013121 ATP binding site [chemical binding]; other site 643561013122 Walker B motif; other site 643561013123 RecX family; Region: RecX; cl00936 643561013124 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 643561013125 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 643561013126 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 643561013127 Protein export membrane protein; Region: SecD_SecF; cl14618 643561013128 EnvZ/OmpR regulon moderator; Provisional; Region: PRK10629 643561013129 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 643561013130 Protein export membrane protein; Region: SecD_SecF; cl14618 643561013131 Preprotein translocase subunit; Region: YajC; cl00806 643561013132 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 643561013133 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 643561013134 dimer interface [polypeptide binding]; other site 643561013135 PYR/PP interface [polypeptide binding]; other site 643561013136 TPP binding site [chemical binding]; other site 643561013137 substrate binding site [chemical binding]; other site 643561013138 TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the...; Region: TPP_IOR_alpha; cd02008 643561013139 TPP-binding site; other site 643561013140 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 643561013141 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 643561013142 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013143 Bacterial protein of unknown function (DUF894); Region: DUF894; pfam05977 643561013144 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 643561013145 putative substrate translocation pore; other site 643561013146 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 643561013147 MltA specific insert domain; Region: MltA; cl08398 643561013148 3D domain; Region: 3D; cl01439 643561013149 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 643561013150 ligand binding site [chemical binding]; other site 643561013151 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 643561013152 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561013153 active site 643561013154 phosphorylation site [posttranslational modification] 643561013155 intermolecular recognition site; other site 643561013156 dimerization interface [polypeptide binding]; other site 643561013157 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 643561013158 DNA binding residues [nucleotide binding] 643561013159 dimerization interface [polypeptide binding]; other site 643561013160 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 643561013161 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 643561013162 putative active site [active] 643561013163 heme pocket [chemical binding]; other site 643561013164 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 643561013165 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 643561013166 ATP binding site [chemical binding]; other site 643561013167 Mg2+ binding site [ion binding]; other site 643561013168 G-X-G motif; other site 643561013169 Predicted amidohydrolase [General function prediction only]; Region: COG0388 643561013170 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 643561013171 putative active site [active] 643561013172 catalytic triad [active] 643561013173 dimer interface [polypeptide binding]; other site 643561013174 TIGR02099 family protein; Region: TIGR02099 643561013175 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 643561013176 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 643561013177 metal binding triad; other site 643561013178 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 643561013179 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 643561013180 metal binding triad; other site 643561013181 Condensation domain; Region: Condensation; cl09290 643561013182 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 643561013183 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561013184 Phosphopantetheine attachment site; Region: PP-binding; cl09936 643561013185 extended (e) SDRs, subgroup 1; Region: SDR_e1; cd05235 643561013186 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 643561013187 putative NAD(P) binding site [chemical binding]; other site 643561013188 active site 643561013189 putative substrate binding site [chemical binding]; other site 643561013190 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]; Region: COG1819 643561013191 This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the...; Region: GT1_Gtf_like; cd03784 643561013192 active site 643561013193 TDP-binding site; other site 643561013194 acceptor substrate-binding pocket; other site 643561013195 homodimer interface [polypeptide binding]; other site 643561013196 MbtH-like protein; Region: MbtH; cl01279 643561013197 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 643561013198 NodT family; Region: outer_NodT; TIGR01845 643561013199 Outer membrane efflux protein; Region: OEP; pfam02321 643561013200 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 643561013201 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 643561013202 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 643561013203 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue...; Region: GSH_Peroxidase; cd00340 643561013204 catalytic residues [active] 643561013205 dimer interface [polypeptide binding]; other site 643561013206 putative glutathione S-transferase; Provisional; Region: PRK10357 643561013207 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 643561013208 putative C-terminal domain interface [polypeptide binding]; other site 643561013209 putative GSH binding site (G-site) [chemical binding]; other site 643561013210 putative dimer interface [polypeptide binding]; other site 643561013211 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 643561013212 dimer interface [polypeptide binding]; other site 643561013213 N-terminal domain interface [polypeptide binding]; other site 643561013214 putative substrate binding pocket (H-site) [chemical binding]; other site 643561013215 adenylosuccinate lyase; Provisional; Region: PRK09285 643561013216 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 643561013217 tetramer interface [polypeptide binding]; other site 643561013218 active site 643561013219 YaeQ protein; Region: YaeQ; cl01913 643561013220 Protein of unknown function (DUF3717); Region: DUF3717; pfam12512 643561013221 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 643561013222 Integral membrane protein TerC family; Region: TerC; cl10468 643561013223 Membrane protein of unknown function; Region: DUF360; cl00850 643561013224 Peptidase family M48; Region: Peptidase_M48; cl12018 643561013225 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 643561013226 trimer interface [polypeptide binding]; other site 643561013227 dimer interface [polypeptide binding]; other site 643561013228 putative active site [active] 643561013229 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561013230 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561013231 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 643561013232 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 643561013233 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 643561013234 O-Antigen ligase; Region: Wzy_C; cl04850 643561013235 putative major pilin subunit; Provisional; Region: PRK10574 643561013236 Pilin (bacterial filament); Region: Pilin; pfam00114 643561013237 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 643561013238 phosphopeptide binding site; other site 643561013239 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 643561013240 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 643561013241 Active site [active] 643561013242 Integral membrane protein TerC family; Region: TerC; cl10468 643561013243 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 643561013244 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561013245 CoA-ligase; Region: Ligase_CoA; pfam00549 643561013246 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 643561013247 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 643561013248 CoA-ligase; Region: Ligase_CoA; pfam00549 643561013249 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 643561013250 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561013251 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 643561013252 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 643561013253 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 643561013254 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 643561013255 active site 643561013256 catalytic residues [active] 643561013257 metal binding site [ion binding]; metal-binding site 643561013258 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 643561013259 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 643561013260 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 643561013261 putative active site [active] 643561013262 substrate binding site [chemical binding]; other site 643561013263 putative cosubstrate binding site; other site 643561013264 catalytic site [active] 643561013265 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 643561013266 substrate binding site [chemical binding]; other site 643561013267 AzlC protein; Region: AzlC; cl00570 643561013268 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 643561013269 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 643561013270 substrate binding site [chemical binding]; other site 643561013271 hinge regions; other site 643561013272 ADP binding site [chemical binding]; other site 643561013273 catalytic site [active] 643561013274 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 643561013275 active site 643561013276 dimer interface [polypeptide binding]; other site 643561013277 Wilm's tumour protein; Region: WT1; pfam02165 643561013278 cell density-dependent motility repressor; Provisional; Region: PRK10082 643561013279 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013280 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 643561013281 dimerization interface [polypeptide binding]; other site 643561013282 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561013283 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561013284 The M14 family of metallocarboxypeptidases (MCPs) are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key...; Region: Peptidase_M14_like; cl11393 643561013285 active site 643561013286 Zn-binding site [ion binding]; other site 643561013287 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 643561013288 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 643561013289 EamA-like transporter family; Region: EamA; cl01037 643561013290 Nitrate and nitrite sensing; Region: NIT; pfam08376 643561013291 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 643561013292 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 643561013293 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 643561013294 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 643561013295 Protein of unknown function (DUF1501); Region: DUF1501; cl01699 643561013296 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 643561013297 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013298 The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Region: PBP2_GbpR; cd08435 643561013299 putative dimerization interface [polypeptide binding]; other site 643561013300 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561013301 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561013302 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 643561013303 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 643561013304 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 643561013305 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 2. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved...; Region: MR_like_2; cd03327 643561013306 putative active site pocket [active] 643561013307 putative metal binding site [ion binding]; other site 643561013308 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 643561013309 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 643561013310 inhibitor site; inhibition site 643561013311 active site 643561013312 dimer interface [polypeptide binding]; other site 643561013313 catalytic residue [active] 643561013314 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561013315 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 643561013316 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 643561013317 DctM-like transporters; Region: DctM; pfam06808 643561013318 Uncharacterized conserved protein [Function unknown]; Region: COG3391 643561013319 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 643561013320 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 643561013321 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 643561013322 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 643561013323 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 643561013324 DNA binding site [nucleotide binding] 643561013325 domain linker motif; other site 643561013326 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 643561013327 Eukaryotic cytochrome b(561); Region: Cyt_b561; cl14616 643561013328 putative heme binding sites [chemical binding]; other site 643561013329 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 643561013330 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 643561013331 Walker A/P-loop; other site 643561013332 ATP binding site [chemical binding]; other site 643561013333 Q-loop/lid; other site 643561013334 ABC transporter signature motif; other site 643561013335 Walker B; other site 643561013336 D-loop; other site 643561013337 H-loop/switch region; other site 643561013338 TOBE domain; Region: TOBE_2; cl01440 643561013339 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 643561013340 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 643561013341 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 643561013342 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 643561013343 dimer interface [polypeptide binding]; other site 643561013344 conserved gate region; other site 643561013345 putative PBP binding loops; other site 643561013346 ABC-ATPase subunit interface; other site 643561013347 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 643561013348 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 643561013349 dimer interface [polypeptide binding]; other site 643561013350 conserved gate region; other site 643561013351 putative PBP binding loops; other site 643561013352 ABC-ATPase subunit interface; other site 643561013353 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 643561013354 Uncharacterized conserved protein [Function unknown]; Region: COG3391 643561013355 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 643561013356 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 643561013357 dimer interface [polypeptide binding]; other site 643561013358 NADP binding site [chemical binding]; other site 643561013359 catalytic residues [active] 643561013360 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 643561013361 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 643561013362 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 643561013363 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 643561013364 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 643561013365 ligand-binding site [chemical binding]; other site 643561013366 Ubiquitin; Region: Ubiquitin; cd01803 643561013367 Ubiquitin homologues; Region: UBQ; smart00213 643561013368 Ubq - E2 interaction site; other site 643561013369 Ubq - UCH interaction site; other site 643561013370 Ubq - CUE interaction site; other site 643561013371 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 643561013372 putative substrate translocation pore; other site 643561013373 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 643561013374 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 643561013375 putative ion selectivity filter; other site 643561013376 putative pore gating glutamate residue; other site 643561013377 putative H+/Cl- coupling transport residue; other site 643561013378 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 643561013379 dimer interface [polypeptide binding]; other site 643561013380 ssDNA binding site [nucleotide binding]; other site 643561013381 tetramer (dimer of dimers) interface [polypeptide binding]; other site 643561013382 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 643561013383 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 643561013384 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 643561013385 ATP binding site [chemical binding]; other site 643561013386 putative Mg++ binding site [ion binding]; other site 643561013387 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 643561013388 Fic family protein [Function unknown]; Region: COG3177 643561013389 Fic/DOC family; Region: Fic; cl00960 643561013390 Phosphoinositide 3-kinase (PI3K)-like family, catalytic domain; The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (...; Region: PI3Kc_like; cl00119 643561013391 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 643561013392 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 643561013393 HsdM N-terminal domain; Region: HsdM_N; pfam12161 643561013394 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 643561013395 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561013396 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013397 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 643561013398 putative dimerization interface [polypeptide binding]; other site 643561013399 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 643561013400 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561013401 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013402 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 643561013403 GAF domain; Region: GAF; cl00853 643561013404 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 643561013405 LysR family transcriptional regulator; Provisional; Region: PRK14997 643561013406 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013407 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 643561013408 putative effector binding pocket; other site 643561013409 dimerization interface [polypeptide binding]; other site 643561013410 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 643561013411 EamA-like transporter family; Region: EamA; cl01037 643561013412 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 643561013413 dimerization interface [polypeptide binding]; other site 643561013414 putative DNA binding site [nucleotide binding]; other site 643561013415 putative Zn2+ binding site [ion binding]; other site 643561013416 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 643561013417 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561013418 metal binding site [ion binding]; metal-binding site 643561013419 active site 643561013420 I-site; other site 643561013421 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561013422 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 643561013423 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA)...; Region: CCL_ACL-C; cd06100 643561013424 active site 643561013425 oxalacetate binding site [chemical binding]; other site 643561013426 citrylCoA binding site [chemical binding]; other site 643561013427 coenzyme A binding site [chemical binding]; other site 643561013428 catalytic triad [active] 643561013429 acyl-CoA synthetase; Validated; Region: PRK06188 643561013430 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 643561013431 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 643561013432 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 643561013433 Transcriptional regulator [Transcription]; Region: IclR; COG1414 643561013434 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013435 Bacterial transcriptional regulator; Region: IclR; pfam01614 643561013436 glycolate transporter; Provisional; Region: PRK09695 643561013437 L-lactate permease; Region: Lactate_perm; cl00701 643561013438 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 643561013439 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 643561013440 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 643561013441 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 643561013442 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 643561013443 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 643561013444 Putative Ig domain; Region: He_PIG; pfam05345 643561013445 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 643561013446 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 643561013447 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 643561013448 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 643561013449 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 643561013450 Ligand Binding Site [chemical binding]; other site 643561013451 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X...; Region: Nudix_Hydrolase_2; cd03675 643561013452 nudix motif; other site 643561013453 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 643561013454 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013455 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 643561013456 dimerization interface [polypeptide binding]; other site 643561013457 substrate binding pocket [chemical binding]; other site 643561013458 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 643561013459 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561013460 metal binding site [ion binding]; metal-binding site 643561013461 active site 643561013462 I-site; other site 643561013463 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 643561013464 Lumazine binding domain; Region: Lum_binding; pfam00677 643561013465 Lumazine binding domain; Region: Lum_binding; pfam00677 643561013466 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 643561013467 putative active site [active] 643561013468 PAS fold; Region: PAS_3; pfam08447 643561013469 heme pocket [chemical binding]; other site 643561013470 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 643561013471 GAF domain; Region: GAF; cl00853 643561013472 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 643561013473 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 643561013474 dimer interface [polypeptide binding]; other site 643561013475 phosphorylation site [posttranslational modification] 643561013476 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 643561013477 ATP binding site [chemical binding]; other site 643561013478 Mg2+ binding site [ion binding]; other site 643561013479 G-X-G motif; other site 643561013480 Response regulator receiver domain; Region: Response_reg; pfam00072 643561013481 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cd00156 643561013482 active site 643561013483 phosphorylation site [posttranslational modification] 643561013484 intermolecular recognition site; other site 643561013485 dimerization interface [polypeptide binding]; other site 643561013486 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4222 643561013487 Predicted membrane protein (DUF2127); Region: DUF2127; cl01785 643561013488 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 643561013489 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 643561013490 FAD binding pocket [chemical binding]; other site 643561013491 FAD binding motif [chemical binding]; other site 643561013492 phosphate binding motif [ion binding]; other site 643561013493 NAD binding pocket [chemical binding]; other site 643561013494 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013495 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 643561013496 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 643561013497 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]; Region: COG4262 643561013498 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 643561013499 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 643561013500 N-terminal plug; other site 643561013501 ligand-binding site [chemical binding]; other site 643561013502 Gram-negative bacterial tonB protein; Region: TonB; cl10048 643561013503 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 643561013504 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 643561013505 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 643561013506 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 643561013507 Transcriptional regulator [Transcription]; Region: LysR; COG0583 643561013508 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 643561013509 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 643561013510 dimerization interface [polypeptide binding]; other site 643561013511 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 643561013512 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 643561013513 inhibitor-cofactor binding pocket; inhibition site 643561013514 pyridoxal 5'-phosphate binding site [chemical binding]; other site 643561013515 catalytic residue [active] 643561013516 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 643561013517 conserved cys residue [active] 643561013518 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 643561013519 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 643561013520 tetrameric interface [polypeptide binding]; other site 643561013521 NAD binding site [chemical binding]; other site 643561013522 catalytic residues [active] 643561013523 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 643561013524 MASE2 domain; Region: MASE2; pfam05230 643561013525 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561013526 metal binding site [ion binding]; metal-binding site 643561013527 active site 643561013528 I-site; other site 643561013529 Transcriptional regulators [Transcription]; Region: FadR; COG2186 643561013530 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 643561013531 DNA-binding site [nucleotide binding]; DNA binding site 643561013532 FCD domain; Region: FCD; cl11656 643561013533 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 643561013534 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 643561013535 putative ligand binding site [chemical binding]; other site 643561013536 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 643561013537 TM-ABC transporter signature motif; other site 643561013538 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 643561013539 TM-ABC transporter signature motif; other site 643561013540 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 643561013541 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 643561013542 Walker A/P-loop; other site 643561013543 ATP binding site [chemical binding]; other site 643561013544 Q-loop/lid; other site 643561013545 ABC transporter signature motif; other site 643561013546 Walker B; other site 643561013547 D-loop; other site 643561013548 H-loop/switch region; other site 643561013549 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 643561013550 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 643561013551 Walker A/P-loop; other site 643561013552 ATP binding site [chemical binding]; other site 643561013553 Q-loop/lid; other site 643561013554 ABC transporter signature motif; other site 643561013555 Walker B; other site 643561013556 D-loop; other site 643561013557 H-loop/switch region; other site 643561013558 allantoate amidohydrolase; Reviewed; Region: PRK12893 643561013559 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 643561013560 active site 643561013561 metal binding site [ion binding]; metal-binding site 643561013562 dimer interface [polypeptide binding]; other site 643561013563 Uncharacterized conserved protein [Function unknown]; Region: COG5476 643561013564 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 643561013565 MlrC C-terminus; Region: MlrC_C; pfam07171 643561013566 malic enzyme; Reviewed; Region: PRK12862 643561013567 Malic enzyme, N-terminal domain; Region: malic; pfam00390 643561013568 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 643561013569 putative NAD(P) binding site [chemical binding]; other site 643561013570 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 643561013571 RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a...; Region: RNase_Sa; cd00607 643561013572 active site 643561013573 barstar interaction site; other site 643561013574 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 643561013575 putative RNAase interaction site [polypeptide binding]; other site 643561013576 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 643561013577 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 643561013578 SurA N-terminal domain; Region: SurA_N; pfam09312 643561013579 PPIC-type PPIASE domain; Region: Rotamase; cl08278 643561013580 PPIC-type PPIASE domain; Region: Rotamase; cl08278 643561013581 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 643561013582 Organic solvent tolerance protein; Region: OstA_C; pfam04453 643561013583 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 643561013584 Phosphotransferase enzyme family; Region: APH; pfam01636 643561013585 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 643561013586 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 643561013587 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561013588 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561013589 Walker A/P-loop; other site 643561013590 Walker A/P-loop; other site 643561013591 ATP binding site [chemical binding]; other site 643561013592 ATP binding site [chemical binding]; other site 643561013593 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 643561013594 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 643561013595 ABC transporter signature motif; other site 643561013596 Walker B; other site 643561013597 D-loop; other site 643561013598 H-loop/switch region; other site 643561013599 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561013600 metal binding site [ion binding]; metal-binding site 643561013601 active site 643561013602 I-site; other site 643561013603 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 643561013604 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 643561013605 metal binding site [ion binding]; metal-binding site 643561013606 putative dimer interface [polypeptide binding]; other site 643561013607 ethanolamine permease; Region: 2A0305; TIGR00908 643561013608 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 643561013609 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 643561013610 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; cl09205 643561013611 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 643561013612 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 643561013613 metal binding site [ion binding]; metal-binding site 643561013614 active site 643561013615 I-site; other site 643561013616 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 643561013617 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 643561013618 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 643561013619 Predicted membrane protein [Function unknown]; Region: COG2119 643561013620 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 643561013621 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 643561013622 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 643561013623 RNA/DNA binding site [nucleotide binding]; other site 643561013624 RRM dimerization site [polypeptide binding]; other site 643561013625 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 643561013626 RNA/DNA binding site [nucleotide binding]; other site 643561013627 RRM dimerization site [polypeptide binding]; other site 643561013628 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 643561013629 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561013630 NAD(P) binding site [chemical binding]; other site 643561013631 active site 643561013632 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 643561013633 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 643561013634 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 643561013635 KpsF/GutQ family protein; Region: kpsF; TIGR00393 643561013636 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 643561013637 putative active site [active] 643561013638 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 643561013639 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 643561013640 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 643561013641 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 643561013642 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 643561013643 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 643561013644 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 643561013645 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 643561013646 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 643561013647 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 643561013648 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR_like1; cd06200 643561013649 FAD binding pocket [chemical binding]; other site 643561013650 FAD binding motif [chemical binding]; other site 643561013651 catalytic residues [active] 643561013652 NAD binding pocket [chemical binding]; other site 643561013653 phosphate binding motif [ion binding]; other site 643561013654 beta-alpha-beta structure motif; other site 643561013655 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 643561013656 ligand binding site [chemical binding]; other site 643561013657 flexible hinge region; other site 643561013658 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 643561013659 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 643561013660 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 643561013661 G1 box; other site 643561013662 GTP/Mg2+ binding site [chemical binding]; other site 643561013663 Switch I region; other site 643561013664 G2 box; other site 643561013665 Switch II region; other site 643561013666 G3 box; other site 643561013667 G4 box; other site 643561013668 G5 box; other site 643561013669 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 643561013670 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 643561013671 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 643561013672 N-terminal domain; Region: yidC_nterm; TIGR03593 643561013673 membrane protein insertase; Provisional; Region: PRK01318 643561013674 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 643561013675 Domain of unknown function DUF37; Region: DUF37; cl00506 643561013676 Ribonuclease P; Region: Ribonuclease_P; cl00457 643561013677 Ribosomal protein L34; Region: Ribosomal_L34; cl00370