-- dump date 20140618_185519 -- class Genbank::misc_feature -- table misc_feature_note -- id note 535289000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 535289000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 535289000003 Probable cobalt transporter subunit (CbtA); Region: CbtA; cl02266 535289000004 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289000005 Walker A motif; other site 535289000006 ATP binding site [chemical binding]; other site 535289000007 Walker B motif; other site 535289000008 arginine finger; other site 535289000009 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 535289000010 DnaA box-binding interface [nucleotide binding]; other site 535289000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 535289000012 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 535289000013 putative DNA binding surface [nucleotide binding]; other site 535289000014 dimer interface [polypeptide binding]; other site 535289000015 beta-clamp/clamp loader binding surface; other site 535289000016 beta-clamp/translesion DNA polymerase binding surface; other site 535289000017 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 535289000018 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 535289000019 ATP binding site [chemical binding]; other site 535289000020 Mg2+ binding site [ion binding]; other site 535289000021 G-X-G motif; other site 535289000022 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 535289000023 anchoring element; other site 535289000024 dimer interface [polypeptide binding]; other site 535289000025 ATP binding site [chemical binding]; other site 535289000026 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 535289000027 active site 535289000028 putative metal-binding site [ion binding]; other site 535289000029 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 535289000030 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 535289000031 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 535289000032 Coenzyme A binding pocket [chemical binding]; other site 535289000033 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 535289000034 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 535289000035 Protein of unknown function DUF72; Region: DUF72; pfam01904 535289000036 Acylphosphatase; Region: Acylphosphatase; pfam00708 535289000037 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 535289000038 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 535289000039 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 535289000040 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 535289000041 Homoserine dehydrogenase [Amino acid transport and metabolism]; Region: ThrA; COG0460 535289000042 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 535289000043 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 535289000044 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 535289000045 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 535289000046 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 535289000047 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 535289000048 active site 535289000049 catalytic site [active] 535289000050 substrate binding site [chemical binding]; other site 535289000051 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 535289000052 transcriptional regulatory protein PtsJ; Provisional; Region: PRK15481 535289000053 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289000054 DNA-binding site [nucleotide binding]; DNA binding site 535289000055 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 535289000056 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289000057 catalytic residue [active] 535289000058 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 535289000059 NlpC/P60 family; Region: NLPC_P60; pfam00877 535289000060 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 535289000061 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 535289000062 PAS domain S-box; Region: sensory_box; TIGR00229 535289000063 PAS domain; Region: PAS; smart00091 535289000064 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 535289000065 GAF domain; Region: GAF; pfam01590 535289000066 PAS domain S-box; Region: sensory_box; TIGR00229 535289000067 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 535289000068 putative active site [active] 535289000069 heme pocket [chemical binding]; other site 535289000070 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289000071 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289000072 metal binding site [ion binding]; metal-binding site 535289000073 active site 535289000074 I-site; other site 535289000075 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 535289000076 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 535289000077 Transcriptional regulator [Transcription]; Region: IclR; COG1414 535289000078 Bacterial transcriptional regulator; Region: IclR; pfam01614 535289000079 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000080 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 535289000081 LTXXQ motif family protein; Region: LTXXQ; pfam07813 535289000082 recombination associated protein; Reviewed; Region: rdgC; PRK00321 535289000083 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 535289000084 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 535289000085 PAS domain; Region: PAS; smart00091 535289000086 PAS fold; Region: PAS_7; pfam12860 535289000087 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289000088 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289000089 dimer interface [polypeptide binding]; other site 535289000090 phosphorylation site [posttranslational modification] 535289000091 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 535289000092 ATP binding site [chemical binding]; other site 535289000093 Mg2+ binding site [ion binding]; other site 535289000094 G-X-G motif; other site 535289000095 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 535289000096 Response regulator receiver domain; Region: Response_reg; pfam00072 535289000097 active site 535289000098 phosphorylation site [posttranslational modification] 535289000099 intermolecular recognition site; other site 535289000100 dimerization interface [polypeptide binding]; other site 535289000101 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 535289000102 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 535289000103 active site 535289000104 phosphorylation site [posttranslational modification] 535289000105 intermolecular recognition site; other site 535289000106 dimerization interface [polypeptide binding]; other site 535289000107 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289000108 DNA binding residues [nucleotide binding] 535289000109 dimerization interface [polypeptide binding]; other site 535289000110 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 535289000111 Uncharacterized membrane protein [Function unknown]; Region: SpmB; cl17667 535289000112 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 535289000113 beta-ketothiolase; Provisional; Region: PRK09051 535289000114 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 535289000115 dimer interface [polypeptide binding]; other site 535289000116 active site 535289000117 Protein of unknown function, DUF488; Region: DUF488; pfam04343 535289000118 Protein of unknown function (DUF2945); Region: DUF2945; pfam11160 535289000119 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 535289000120 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 535289000121 DNA binding residues [nucleotide binding] 535289000122 dimer interface [polypeptide binding]; other site 535289000123 copper binding site [ion binding]; other site 535289000124 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 535289000125 metal-binding site [ion binding] 535289000126 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 535289000127 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 535289000128 metal-binding site [ion binding] 535289000129 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289000130 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 535289000131 motif II; other site 535289000132 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289000133 dimerization interface [polypeptide binding]; other site 535289000134 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289000135 dimer interface [polypeptide binding]; other site 535289000136 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 535289000137 putative CheW interface [polypeptide binding]; other site 535289000138 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 535289000139 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 535289000140 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 535289000141 FMN binding site [chemical binding]; other site 535289000142 active site 535289000143 substrate binding site [chemical binding]; other site 535289000144 catalytic residue [active] 535289000145 glutathionine S-transferase; Provisional; Region: PRK10542 535289000146 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 535289000147 C-terminal domain interface [polypeptide binding]; other site 535289000148 GSH binding site (G-site) [chemical binding]; other site 535289000149 dimer interface [polypeptide binding]; other site 535289000150 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 535289000151 dimer interface [polypeptide binding]; other site 535289000152 N-terminal domain interface [polypeptide binding]; other site 535289000153 substrate binding pocket (H-site) [chemical binding]; other site 535289000154 Flagellin N-methylase; Region: FliB; cl00497 535289000155 Predicted flavoprotein [General function prediction only]; Region: COG0431 535289000156 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 535289000157 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 535289000158 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 535289000159 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 535289000160 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 535289000161 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 535289000162 S-adenosylmethionine binding site [chemical binding]; other site 535289000163 LysE type translocator; Region: LysE; cl00565 535289000164 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 535289000165 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 535289000166 P-loop; other site 535289000167 Magnesium ion binding site [ion binding]; other site 535289000168 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 535289000169 Magnesium ion binding site [ion binding]; other site 535289000170 Serine hydrolase; Region: Ser_hydrolase; pfam06821 535289000171 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 535289000172 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 535289000173 ParB-like nuclease domain; Region: ParB; smart00470 535289000174 Methyltransferase domain; Region: Methyltransf_12; pfam08242 535289000175 Curli production assembly/transport component CsgG; Region: CsgG; cl17434 535289000176 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 535289000177 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 535289000178 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 535289000179 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 535289000180 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 535289000181 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 535289000182 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289000183 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 535289000184 putative substrate translocation pore; other site 535289000185 Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]; Region: ChaC; COG3703 535289000186 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 535289000187 putative active site pocket [active] 535289000188 dimerization interface [polypeptide binding]; other site 535289000189 putative catalytic residue [active] 535289000190 NAD(P)H:quinone oxidoreductase; Provisional; Region: PRK03767 535289000191 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 535289000192 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09638 535289000193 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 535289000194 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]; Region: COG3513 535289000195 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 535289000196 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 535289000197 FAD binding domain; Region: FAD_binding_4; pfam01565 535289000198 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 535289000199 EF-hand domain pair; Region: EF_hand_5; pfam13499 535289000200 Ca2+ binding site [ion binding]; other site 535289000201 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 535289000202 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 535289000203 CoenzymeA binding site [chemical binding]; other site 535289000204 subunit interaction site [polypeptide binding]; other site 535289000205 PHB binding site; other site 535289000206 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 535289000207 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289000208 putative ligand binding site [chemical binding]; other site 535289000209 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 535289000210 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 535289000211 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 535289000212 Transcription factor zinc-finger; Region: zf-TFIIB; pfam13453 535289000213 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 535289000214 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 535289000215 PAS fold; Region: PAS_3; pfam08447 535289000216 putative active site [active] 535289000217 heme pocket [chemical binding]; other site 535289000218 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 535289000219 PAS domain; Region: PAS_9; pfam13426 535289000220 putative active site [active] 535289000221 heme pocket [chemical binding]; other site 535289000222 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289000223 dimer interface [polypeptide binding]; other site 535289000224 putative CheW interface [polypeptide binding]; other site 535289000225 B12 binding domain; Region: B12-binding; pfam02310 535289000226 B12 binding site [chemical binding]; other site 535289000227 Radical SAM superfamily; Region: Radical_SAM; pfam04055 535289000228 GAF domain; Region: GAF_3; pfam13492 535289000229 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289000230 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289000231 metal binding site [ion binding]; metal-binding site 535289000232 active site 535289000233 I-site; other site 535289000234 hypothetical protein; Provisional; Region: PRK09126 535289000235 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 535289000236 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 535289000237 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 535289000238 acyl-activating enzyme (AAE) consensus motif; other site 535289000239 putative AMP binding site [chemical binding]; other site 535289000240 putative active site [active] 535289000241 putative CoA binding site [chemical binding]; other site 535289000242 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289000243 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289000244 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 535289000245 dimerization interface [polypeptide binding]; other site 535289000246 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 535289000247 CoA-transferase family III; Region: CoA_transf_3; pfam02515 535289000248 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289000249 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289000250 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289000251 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289000252 active site 535289000253 enoyl-CoA hydratase; Provisional; Region: PRK09245 535289000254 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 535289000255 substrate binding site [chemical binding]; other site 535289000256 oxyanion hole (OAH) forming residues; other site 535289000257 trimer interface [polypeptide binding]; other site 535289000258 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 535289000259 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 535289000260 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 535289000261 septum formation inhibitor; Reviewed; Region: PRK01973 535289000262 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 535289000263 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 535289000264 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 535289000265 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 535289000266 Switch I; other site 535289000267 Switch II; other site 535289000268 cell division topological specificity factor MinE; Provisional; Region: PRK13989 535289000269 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 535289000270 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 535289000271 TAP-like protein; Region: Abhydrolase_4; pfam08386 535289000272 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289000273 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_2; cd06335 535289000274 putative ligand binding site [chemical binding]; other site 535289000275 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 535289000276 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 535289000277 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 535289000278 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289000279 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 535289000280 dimerization interface [polypeptide binding]; other site 535289000281 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289000282 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289000283 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 535289000284 Ligand Binding Site [chemical binding]; other site 535289000285 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 535289000286 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 535289000287 active site 535289000288 metal binding site [ion binding]; metal-binding site 535289000289 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289000290 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289000291 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 535289000292 substrate binding pocket [chemical binding]; other site 535289000293 dimerization interface [polypeptide binding]; other site 535289000294 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 535289000295 active site 535289000296 substrate-binding site [chemical binding]; other site 535289000297 metal-binding site [ion binding] 535289000298 GTP binding site [chemical binding]; other site 535289000299 threonine dehydratase; Provisional; Region: PRK07334 535289000300 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 535289000301 tetramer interface [polypeptide binding]; other site 535289000302 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289000303 catalytic residue [active] 535289000304 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 535289000305 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289000306 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289000307 active site 535289000308 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 535289000309 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 535289000310 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 535289000311 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 535289000312 ATP binding site [chemical binding]; other site 535289000313 putative Mg++ binding site [ion binding]; other site 535289000314 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 535289000315 nucleotide binding region [chemical binding]; other site 535289000316 ATP-binding site [chemical binding]; other site 535289000317 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 535289000318 HRDC domain; Region: HRDC; pfam00570 535289000319 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 535289000320 FeS/SAM binding site; other site 535289000321 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 535289000322 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 535289000323 ATP cone domain; Region: ATP-cone; pfam03477 535289000324 Class III ribonucleotide reductase; Region: RNR_III; cd01675 535289000325 effector binding site; other site 535289000326 active site 535289000327 Zn binding site [ion binding]; other site 535289000328 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 535289000329 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 535289000330 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 535289000331 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 535289000332 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 535289000333 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289000334 Walker A motif; other site 535289000335 ATP binding site [chemical binding]; other site 535289000336 Walker B motif; other site 535289000337 arginine finger; other site 535289000338 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 535289000339 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 535289000340 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 535289000341 aspartate aminotransferase; Provisional; Region: PRK06108 535289000342 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 535289000343 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289000344 homodimer interface [polypeptide binding]; other site 535289000345 catalytic residue [active] 535289000346 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000347 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 535289000348 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289000349 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 535289000350 acyl-activating enzyme (AAE) consensus motif; other site 535289000351 putative AMP binding site [chemical binding]; other site 535289000352 putative active site [active] 535289000353 putative CoA binding site [chemical binding]; other site 535289000354 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000355 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 535289000356 CoenzymeA binding site [chemical binding]; other site 535289000357 subunit interaction site [polypeptide binding]; other site 535289000358 PHB binding site; other site 535289000359 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000360 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000361 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289000362 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289000363 active site 535289000364 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289000365 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08276 535289000366 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 535289000367 acyl-activating enzyme (AAE) consensus motif; other site 535289000368 acyl-activating enzyme (AAE) consensus motif; other site 535289000369 putative active site [active] 535289000370 putative AMP binding site [chemical binding]; other site 535289000371 putative CoA binding site [chemical binding]; other site 535289000372 CoA binding site [chemical binding]; other site 535289000373 acetyl-CoA acetyltransferase; Provisional; Region: PRK07801 535289000374 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 535289000375 dimer interface [polypeptide binding]; other site 535289000376 active site 535289000377 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 535289000378 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289000379 NAD(P) binding site [chemical binding]; other site 535289000380 active site 535289000381 enoyl-CoA hydratase; Provisional; Region: PRK08252 535289000382 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 535289000383 substrate binding site [chemical binding]; other site 535289000384 oxyanion hole (OAH) forming residues; other site 535289000385 trimer interface [polypeptide binding]; other site 535289000386 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000387 short chain dehydrogenase; Provisional; Region: PRK07576 535289000388 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 535289000389 NAD(P) binding site [chemical binding]; other site 535289000390 substrate binding site [chemical binding]; other site 535289000391 homotetramer interface [polypeptide binding]; other site 535289000392 active site 535289000393 homodimer interface [polypeptide binding]; other site 535289000394 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 535289000395 Transcriptional regulator [Transcription]; Region: IclR; COG1414 535289000396 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 535289000397 CoA-transferase family III; Region: CoA_transf_3; pfam02515 535289000398 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289000399 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 535289000400 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 535289000401 dimer interface [polypeptide binding]; other site 535289000402 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 535289000403 metal binding site [ion binding]; metal-binding site 535289000404 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000405 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 535289000406 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 535289000407 CoA-transferase family III; Region: CoA_transf_3; pfam02515 535289000408 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289000409 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 535289000410 active site 535289000411 Uncharacterized conserved protein [Function unknown]; Region: COG3777 535289000412 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 535289000413 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 535289000414 active site 2 [active] 535289000415 active site 1 [active] 535289000416 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 535289000417 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289000418 NAD(P) binding site [chemical binding]; other site 535289000419 active site 535289000420 enoyl-CoA hydratase; Region: PLN02864 535289000421 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 535289000422 HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit; Region: HDE_HSD; cd03448 535289000423 dimer interaction site [polypeptide binding]; other site 535289000424 substrate-binding tunnel; other site 535289000425 active site 535289000426 catalytic site [active] 535289000427 substrate binding site [chemical binding]; other site 535289000428 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 535289000429 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 535289000430 substrate binding site [chemical binding]; other site 535289000431 oxyanion hole (OAH) forming residues; other site 535289000432 trimer interface [polypeptide binding]; other site 535289000433 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 535289000434 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 535289000435 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 535289000436 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 535289000437 acetyl-CoA acetyltransferase; Provisional; Region: PRK06205 535289000438 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 535289000439 dimer interface [polypeptide binding]; other site 535289000440 active site 535289000441 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000442 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 535289000443 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289000444 acyl-activating enzyme (AAE) consensus motif; other site 535289000445 AMP binding site [chemical binding]; other site 535289000446 active site 535289000447 CoA binding site [chemical binding]; other site 535289000448 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000449 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]; Region: COG1545 535289000450 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 535289000451 DUF35 OB-fold domain; Region: DUF35; pfam01796 535289000452 thiolase; Provisional; Region: PRK06158 535289000453 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...; Region: SCP-x_thiolase; cd00829 535289000454 active site 535289000455 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289000456 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289000457 active site 535289000458 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 535289000459 CoenzymeA binding site [chemical binding]; other site 535289000460 subunit interaction site [polypeptide binding]; other site 535289000461 PHB binding site; other site 535289000462 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289000463 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289000464 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 535289000465 putative dimerization interface [polypeptide binding]; other site 535289000466 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 535289000467 CoA-transferase family III; Region: CoA_transf_3; pfam02515 535289000468 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 535289000469 trimer interface [polypeptide binding]; other site 535289000470 eyelet of channel; other site 535289000471 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 535289000472 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 535289000473 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 535289000474 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 535289000475 NAD(P) binding site [chemical binding]; other site 535289000476 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 535289000477 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289000478 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289000479 LysR substrate binding domain; Region: LysR_substrate; pfam03466 535289000480 dimerization interface [polypeptide binding]; other site 535289000481 Predicted membrane protein [Function unknown]; Region: COG4125 535289000482 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 535289000483 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 535289000484 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 535289000485 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289000486 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 535289000487 dimerization interface [polypeptide binding]; other site 535289000488 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 535289000489 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-derived...; Region: MLE; cd03318 535289000490 octamer interface [polypeptide binding]; other site 535289000491 active site 535289000492 muconolactone delta-isomerase; Region: muco_delta; TIGR03221 535289000493 Catechol 1,2 dioxygenase (1,2-CTD) catalyzes an intradiol cleavage reaction of catechol to form cis,cis-muconate. 1,2-CTDs is homodimers with one catalytic non-heme ferric ion per monomer. They belong to the aromatic dioxygenase family, a family of...; Region: 1,2-CTD; cd03460 535289000494 catechol 1,2-dioxygenase, proteobacterial; Region: catechol_proteo; TIGR02439 535289000495 dimer interface [polypeptide binding]; other site 535289000496 active site 535289000497 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289000498 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 535289000499 4Fe-4S binding domain; Region: Fer4_5; pfam12801 535289000500 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 535289000501 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 535289000502 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 535289000503 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 535289000504 [2Fe-2S] cluster binding site [ion binding]; other site 535289000505 PAS domain; Region: PAS_9; pfam13426 535289000506 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289000507 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 535289000508 Walker A motif; other site 535289000509 ATP binding site [chemical binding]; other site 535289000510 Walker B motif; other site 535289000511 arginine finger; other site 535289000512 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 535289000513 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 535289000514 substrate binding pocket [chemical binding]; other site 535289000515 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 535289000516 B12 binding site [chemical binding]; other site 535289000517 cobalt ligand [ion binding]; other site 535289000518 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 535289000519 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 535289000520 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 535289000521 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 535289000522 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 535289000523 Peptidase M15; Region: Peptidase_M15_3; cl01194 535289000524 shikimate kinase; Reviewed; Region: aroK; PRK00131 535289000525 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 535289000526 ADP binding site [chemical binding]; other site 535289000527 magnesium binding site [ion binding]; other site 535289000528 putative shikimate binding site; other site 535289000529 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 535289000530 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 535289000531 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 535289000532 FAD binding pocket [chemical binding]; other site 535289000533 FAD binding motif [chemical binding]; other site 535289000534 phosphate binding motif [ion binding]; other site 535289000535 beta-alpha-beta structure motif; other site 535289000536 NAD binding pocket [chemical binding]; other site 535289000537 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_Arsenic_SBP_like; cd06330 535289000538 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289000539 putative ligand binding site [chemical binding]; other site 535289000540 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 535289000541 TM-ABC transporter signature motif; other site 535289000542 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 535289000543 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 535289000544 TM-ABC transporter signature motif; other site 535289000545 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 535289000546 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 535289000547 Walker A/P-loop; other site 535289000548 ATP binding site [chemical binding]; other site 535289000549 Q-loop/lid; other site 535289000550 ABC transporter signature motif; other site 535289000551 Walker B; other site 535289000552 D-loop; other site 535289000553 H-loop/switch region; other site 535289000554 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 535289000555 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 535289000556 Walker A/P-loop; other site 535289000557 ATP binding site [chemical binding]; other site 535289000558 Q-loop/lid; other site 535289000559 ABC transporter signature motif; other site 535289000560 Walker B; other site 535289000561 D-loop; other site 535289000562 H-loop/switch region; other site 535289000563 transcriptional regulator; Provisional; Region: PRK10632 535289000564 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289000565 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 535289000566 putative effector binding pocket; other site 535289000567 putative dimerization interface [polypeptide binding]; other site 535289000568 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289000569 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK12825 535289000570 NAD(P) binding site [chemical binding]; other site 535289000571 active site 535289000572 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 535289000573 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 535289000574 dimerization interface [polypeptide binding]; other site 535289000575 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289000576 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289000577 dimer interface [polypeptide binding]; other site 535289000578 putative CheW interface [polypeptide binding]; other site 535289000579 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 535289000580 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 535289000581 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 535289000582 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 535289000583 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 535289000584 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 535289000585 Nitrogen regulatory protein P-II; Region: P-II; smart00938 535289000586 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 535289000587 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 535289000588 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 535289000589 FAD binding domain; Region: FAD_binding_4; pfam01565 535289000590 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 535289000591 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 535289000592 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 535289000593 Cysteine-rich domain; Region: CCG; pfam02754 535289000594 Cysteine-rich domain; Region: CCG; pfam02754 535289000595 ProQ/FINO family; Region: ProQ; smart00945 535289000596 putative RNA binding sites [nucleotide binding]; other site 535289000597 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 535289000598 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 535289000599 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 535289000600 Predicted transcriptional regulator [Transcription]; Region: COG2378 535289000601 HTH domain; Region: HTH_11; pfam08279 535289000602 WYL domain; Region: WYL; pfam13280 535289000603 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 per...; Region: GSH_Peroxidase; cd00340 535289000604 catalytic residues [active] 535289000605 dimer interface [polypeptide binding]; other site 535289000606 EamA-like transporter family; Region: EamA; pfam00892 535289000607 lysophospholipid transporter LplT; Provisional; Region: PRK11195 535289000608 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 535289000609 Protein of unknown function (DUF575); Region: DUF575; pfam04746 535289000610 alanine racemase; Reviewed; Region: dadX; PRK03646 535289000611 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 535289000612 active site 535289000613 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 535289000614 substrate binding site [chemical binding]; other site 535289000615 catalytic residues [active] 535289000616 dimer interface [polypeptide binding]; other site 535289000617 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 535289000618 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 535289000619 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 535289000620 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 535289000621 C-terminal domain interface [polypeptide binding]; other site 535289000622 GSH binding site (G-site) [chemical binding]; other site 535289000623 dimer interface [polypeptide binding]; other site 535289000624 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 535289000625 dimer interface [polypeptide binding]; other site 535289000626 N-terminal domain interface [polypeptide binding]; other site 535289000627 substrate binding pocket (H-site) [chemical binding]; other site 535289000628 DNA repair protein RadA; Provisional; Region: PRK11823 535289000629 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 535289000630 Walker A motif/ATP binding site; other site 535289000631 ATP binding site [chemical binding]; other site 535289000632 Walker B motif; other site 535289000633 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 535289000634 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 535289000635 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 535289000636 homodimer interface [polypeptide binding]; other site 535289000637 substrate-cofactor binding pocket; other site 535289000638 catalytic residue [active] 535289000639 Zinc-finger domain; Region: zf-CHCC; cl01821 535289000640 Capsular polysaccharide synthesis protein; Region: Caps_synth; pfam05704 535289000641 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 535289000642 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 535289000643 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 535289000644 putative ADP-binding pocket [chemical binding]; other site 535289000645 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 535289000646 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 535289000647 O-Antigen ligase; Region: Wzy_C; pfam04932 535289000648 Nitronate monooxygenase; Region: NMO; pfam03060 535289000649 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 535289000650 FMN binding site [chemical binding]; other site 535289000651 substrate binding site [chemical binding]; other site 535289000652 putative catalytic residue [active] 535289000653 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289000654 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 535289000655 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 535289000656 dimerization interface [polypeptide binding]; other site 535289000657 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 535289000658 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 535289000659 MOSC domain; Region: MOSC; pfam03473 535289000660 3-alpha domain; Region: 3-alpha; pfam03475 535289000661 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 535289000662 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 535289000663 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289000664 dimer interface [polypeptide binding]; other site 535289000665 phosphorylation site [posttranslational modification] 535289000666 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 535289000667 ATP binding site [chemical binding]; other site 535289000668 Mg2+ binding site [ion binding]; other site 535289000669 G-X-G motif; other site 535289000670 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 535289000671 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 535289000672 active site 535289000673 phosphorylation site [posttranslational modification] 535289000674 intermolecular recognition site; other site 535289000675 dimerization interface [polypeptide binding]; other site 535289000676 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289000677 DNA binding site [nucleotide binding] 535289000678 AmpG-like permease; Region: 2A0125; TIGR00901 535289000679 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 535289000680 Peptidase family M48; Region: Peptidase_M48; pfam01435 535289000681 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 535289000682 Transposase domain (DUF772); Region: DUF772; pfam05598 535289000683 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 535289000684 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 535289000685 Transcriptional regulators [Transcription]; Region: GntR; COG1802 535289000686 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289000687 DNA-binding site [nucleotide binding]; DNA binding site 535289000688 FCD domain; Region: FCD; pfam07729 535289000689 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289000690 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289000691 active site 535289000692 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 535289000693 classical (c) SDRs; Region: SDR_c; cd05233 535289000694 NAD(P) binding site [chemical binding]; other site 535289000695 active site 535289000696 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 535289000697 putative active site [active] 535289000698 putative substrate binding site [chemical binding]; other site 535289000699 ATP binding site [chemical binding]; other site 535289000700 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 535289000701 putative active site [active] 535289000702 putative catalytic site [active] 535289000703 putative DNA binding site [nucleotide binding]; other site 535289000704 putative phosphate binding site [ion binding]; other site 535289000705 metal binding site A [ion binding]; metal-binding site 535289000706 putative AP binding site [nucleotide binding]; other site 535289000707 putative metal binding site B [ion binding]; other site 535289000708 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 535289000709 active site 535289000710 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 535289000711 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 535289000712 GatB domain; Region: GatB_Yqey; smart00845 535289000713 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 535289000714 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 535289000715 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 535289000716 rod shape-determining protein MreB; Provisional; Region: PRK13927 535289000717 MreB and similar proteins; Region: MreB_like; cd10225 535289000718 nucleotide binding site [chemical binding]; other site 535289000719 Mg binding site [ion binding]; other site 535289000720 putative protofilament interaction site [polypeptide binding]; other site 535289000721 RodZ interaction site [polypeptide binding]; other site 535289000722 rod shape-determining protein MreC; Provisional; Region: PRK13922 535289000723 rod shape-determining protein MreC; Region: MreC; pfam04085 535289000724 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreD; COG2891 535289000725 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 535289000726 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 535289000727 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 535289000728 EamA-like transporter family; Region: EamA; pfam00892 535289000729 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 535289000730 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 535289000731 Walker A/P-loop; other site 535289000732 ATP binding site [chemical binding]; other site 535289000733 Q-loop/lid; other site 535289000734 ABC transporter signature motif; other site 535289000735 Walker B; other site 535289000736 D-loop; other site 535289000737 H-loop/switch region; other site 535289000738 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289000739 dimer interface [polypeptide binding]; other site 535289000740 conserved gate region; other site 535289000741 putative PBP binding loops; other site 535289000742 ABC-ATPase subunit interface; other site 535289000743 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 535289000744 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 535289000745 substrate binding pocket [chemical binding]; other site 535289000746 membrane-bound complex binding site; other site 535289000747 hinge residues; other site 535289000748 Arginase family; Region: Arginase; cd09989 535289000749 agmatinase; Region: agmatinase; TIGR01230 535289000750 active site 535289000751 Mn binding site [ion binding]; other site 535289000752 oligomer interface [polypeptide binding]; other site 535289000753 hypothetical protein; Provisional; Region: PRK10621 535289000754 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 535289000755 choline dehydrogenase; Validated; Region: PRK02106 535289000756 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 535289000757 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 535289000758 Permease; Region: Permease; pfam02405 535289000759 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 535289000760 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 535289000761 Walker A/P-loop; other site 535289000762 ATP binding site [chemical binding]; other site 535289000763 Q-loop/lid; other site 535289000764 ABC transporter signature motif; other site 535289000765 Walker B; other site 535289000766 D-loop; other site 535289000767 H-loop/switch region; other site 535289000768 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 535289000769 mce related protein; Region: MCE; pfam02470 535289000770 hypothetical protein; Provisional; Region: PRK10428 535289000771 Hemerythrin; Region: Hemerythrin; cd12107 535289000772 Fe binding site [ion binding]; other site 535289000773 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 535289000774 PAS fold; Region: PAS_3; pfam08447 535289000775 putative active site [active] 535289000776 heme pocket [chemical binding]; other site 535289000777 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289000778 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289000779 metal binding site [ion binding]; metal-binding site 535289000780 active site 535289000781 I-site; other site 535289000782 MarC family integral membrane protein; Region: MarC; cl00919 535289000783 short chain dehydrogenase; Provisional; Region: PRK06123 535289000784 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289000785 NAD(P) binding site [chemical binding]; other site 535289000786 active site 535289000787 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 535289000788 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 535289000789 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 535289000790 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 535289000791 putative substrate translocation pore; other site 535289000792 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 535289000793 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 535289000794 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 535289000795 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289000796 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 535289000797 MarR family; Region: MarR_2; cl17246 535289000798 Thermotoga maritima CorA-like family; Region: TmCorA-like; cd12822 535289000799 oligomer interface [polypeptide binding]; other site 535289000800 metal binding site [ion binding]; metal-binding site 535289000801 metal binding site [ion binding]; metal-binding site 535289000802 putative Cl binding site [ion binding]; other site 535289000803 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 535289000804 aspartate ring; other site 535289000805 basic sphincter; other site 535289000806 hydrophobic gate; other site 535289000807 periplasmic entrance; other site 535289000808 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 535289000809 dimer interface [polypeptide binding]; other site 535289000810 allosteric magnesium binding site [ion binding]; other site 535289000811 active site 535289000812 aspartate-rich active site metal binding site; other site 535289000813 Schiff base residues; other site 535289000814 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 535289000815 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 535289000816 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 535289000817 dimer interface [polypeptide binding]; other site 535289000818 [2Fe-2S] cluster binding site [ion binding]; other site 535289000819 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 535289000820 Serine hydrolase; Region: Ser_hydrolase; cl17834 535289000821 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 535289000822 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 535289000823 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 535289000824 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 535289000825 S17 interaction site [polypeptide binding]; other site 535289000826 S8 interaction site; other site 535289000827 16S rRNA interaction site [nucleotide binding]; other site 535289000828 streptomycin interaction site [chemical binding]; other site 535289000829 23S rRNA interaction site [nucleotide binding]; other site 535289000830 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 535289000831 30S ribosomal protein S7; Validated; Region: PRK05302 535289000832 elongation factor G; Reviewed; Region: PRK00007 535289000833 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 535289000834 G1 box; other site 535289000835 putative GEF interaction site [polypeptide binding]; other site 535289000836 GTP/Mg2+ binding site [chemical binding]; other site 535289000837 Switch I region; other site 535289000838 G2 box; other site 535289000839 G3 box; other site 535289000840 Switch II region; other site 535289000841 G4 box; other site 535289000842 G5 box; other site 535289000843 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 535289000844 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 535289000845 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 535289000846 elongation factor Tu; Reviewed; Region: PRK00049 535289000847 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 535289000848 G1 box; other site 535289000849 GEF interaction site [polypeptide binding]; other site 535289000850 GTP/Mg2+ binding site [chemical binding]; other site 535289000851 Switch I region; other site 535289000852 G2 box; other site 535289000853 G3 box; other site 535289000854 Switch II region; other site 535289000855 G4 box; other site 535289000856 G5 box; other site 535289000857 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 535289000858 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 535289000859 Antibiotic Binding Site [chemical binding]; other site 535289000860 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 535289000861 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 535289000862 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 535289000863 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 535289000864 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 535289000865 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 535289000866 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 535289000867 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 535289000868 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 535289000869 putative translocon binding site; other site 535289000870 protein-rRNA interface [nucleotide binding]; other site 535289000871 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 535289000872 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 535289000873 G-X-X-G motif; other site 535289000874 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 535289000875 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 535289000876 23S rRNA interface [nucleotide binding]; other site 535289000877 5S rRNA interface [nucleotide binding]; other site 535289000878 putative antibiotic binding site [chemical binding]; other site 535289000879 L25 interface [polypeptide binding]; other site 535289000880 L27 interface [polypeptide binding]; other site 535289000881 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 535289000882 23S rRNA interface [nucleotide binding]; other site 535289000883 putative translocon interaction site; other site 535289000884 signal recognition particle (SRP54) interaction site; other site 535289000885 L23 interface [polypeptide binding]; other site 535289000886 trigger factor interaction site; other site 535289000887 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 535289000888 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 535289000889 catalytic triad [active] 535289000890 dimer interface [polypeptide binding]; other site 535289000891 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 535289000892 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 535289000893 Coenzyme A binding pocket [chemical binding]; other site 535289000894 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 535289000895 Cytochrome C' Region: Cytochrom_C_2; pfam01322 535289000896 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 535289000897 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 535289000898 catalytic residues [active] 535289000899 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 535289000900 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289000901 putative substrate translocation pore; other site 535289000902 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cl00025 535289000903 active pocket/dimerization site; other site 535289000904 active site 535289000905 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 535289000906 dimerization domain swap beta strand [polypeptide binding]; other site 535289000907 regulatory protein interface [polypeptide binding]; other site 535289000908 active site 535289000909 regulatory phosphorylation site [posttranslational modification]; other site 535289000910 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 535289000911 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 535289000912 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 535289000913 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 535289000914 lipoyl synthase; Provisional; Region: PRK05481 535289000915 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 535289000916 FeS/SAM binding site; other site 535289000917 lipoate-protein ligase B; Provisional; Region: PRK14346 535289000918 Protein of unknown function (DUF493); Region: DUF493; cl01102 535289000919 ATP synthase I chain; Region: ATP_synt_I; pfam03899 535289000920 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 535289000921 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 535289000922 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 535289000923 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 535289000924 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 535289000925 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 535289000926 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 535289000927 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 535289000928 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 535289000929 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 535289000930 beta subunit interaction interface [polypeptide binding]; other site 535289000931 Walker A motif; other site 535289000932 ATP binding site [chemical binding]; other site 535289000933 Walker B motif; other site 535289000934 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 535289000935 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 535289000936 core domain interface [polypeptide binding]; other site 535289000937 delta subunit interface [polypeptide binding]; other site 535289000938 epsilon subunit interface [polypeptide binding]; other site 535289000939 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 535289000940 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 535289000941 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 535289000942 alpha subunit interaction interface [polypeptide binding]; other site 535289000943 Walker A motif; other site 535289000944 ATP binding site [chemical binding]; other site 535289000945 Walker B motif; other site 535289000946 inhibitor binding site; inhibition site 535289000947 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 535289000948 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 535289000949 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 535289000950 gamma subunit interface [polypeptide binding]; other site 535289000951 epsilon subunit interface [polypeptide binding]; other site 535289000952 LBP interface [polypeptide binding]; other site 535289000953 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 535289000954 ATP-dependent DNA ligase; Validated; Region: PRK09247 535289000955 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 535289000956 active site 535289000957 DNA binding site [nucleotide binding] 535289000958 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 535289000959 DNA binding site [nucleotide binding] 535289000960 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 535289000961 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 535289000962 ATP binding site [chemical binding]; other site 535289000963 putative Mg++ binding site [ion binding]; other site 535289000964 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 535289000965 nucleotide binding region [chemical binding]; other site 535289000966 ATP-binding site [chemical binding]; other site 535289000967 DEAD/H associated; Region: DEAD_assoc; pfam08494 535289000968 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 535289000969 putative active site [active] 535289000970 putative metal binding site [ion binding]; other site 535289000971 Repair protein; Region: Repair_PSII; pfam04536 535289000972 Repair protein; Region: Repair_PSII; pfam04536 535289000973 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 535289000974 SnoaL-like domain; Region: SnoaL_3; pfam13474 535289000975 SnoaL-like domain; Region: SnoaL_2; pfam12680 535289000976 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 535289000977 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 535289000978 Cytochrome c; Region: Cytochrom_C; cl11414 535289000979 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289000980 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 535289000981 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 535289000982 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289000983 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 535289000984 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289000985 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 535289000986 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 535289000987 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 535289000988 NAD binding site [chemical binding]; other site 535289000989 catalytic Zn binding site [ion binding]; other site 535289000990 structural Zn binding site [ion binding]; other site 535289000991 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 535289000992 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 535289000993 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 535289000994 putative active site [active] 535289000995 putative dimer interface [polypeptide binding]; other site 535289000996 4-oxalocrotonate tautomerase; Provisional; Region: PRK00745 535289000997 active site 1 [active] 535289000998 dimer interface [polypeptide binding]; other site 535289000999 hexamer interface [polypeptide binding]; other site 535289001000 active site 2 [active] 535289001001 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 535289001002 malate synthase G; Provisional; Region: PRK02999 535289001003 active site 535289001004 LysR family transcriptional regulator; Provisional; Region: PRK14997 535289001005 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289001006 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 535289001007 putative effector binding pocket; other site 535289001008 dimerization interface [polypeptide binding]; other site 535289001009 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 535289001010 Predicted membrane protein (DUF2214); Region: DUF2214; pfam09980 535289001011 psiF repeat; Region: PsiF_repeat; pfam07769 535289001012 psiF repeat; Region: PsiF_repeat; pfam07769 535289001013 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 535289001014 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 535289001015 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 535289001016 active site 535289001017 HIGH motif; other site 535289001018 nucleotide binding site [chemical binding]; other site 535289001019 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 535289001020 KMSK motif region; other site 535289001021 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 535289001022 tRNA binding surface [nucleotide binding]; other site 535289001023 anticodon binding site; other site 535289001024 Sporulation related domain; Region: SPOR; pfam05036 535289001025 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 535289001026 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 535289001027 catalytic residues [active] 535289001028 hinge region; other site 535289001029 alpha helical domain; other site 535289001030 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 535289001031 OstA-like protein; Region: OstA; pfam03968 535289001032 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 535289001033 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 535289001034 Walker A/P-loop; other site 535289001035 ATP binding site [chemical binding]; other site 535289001036 Q-loop/lid; other site 535289001037 ABC transporter signature motif; other site 535289001038 Walker B; other site 535289001039 D-loop; other site 535289001040 H-loop/switch region; other site 535289001041 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 535289001042 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 535289001043 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 535289001044 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 535289001045 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 535289001046 active site 535289001047 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 535289001048 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 535289001049 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 535289001050 PIN domain; Region: PIN_3; pfam13470 535289001051 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...; Region: EPT_RTPC-like; cl00288 535289001052 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 535289001053 putative active site [active] 535289001054 Uncharacterized protein family (UPF0149); Region: UPF0149; pfam03695 535289001055 Competence-damaged protein; Region: CinA; pfam02464 535289001056 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 535289001057 tetramer interfaces [polypeptide binding]; other site 535289001058 binuclear metal-binding site [ion binding]; other site 535289001059 thiamine monophosphate kinase; Provisional; Region: PRK05731 535289001060 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 535289001061 ATP binding site [chemical binding]; other site 535289001062 dimerization interface [polypeptide binding]; other site 535289001063 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 535289001064 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 535289001065 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 535289001066 Site-specific recombinase; Region: SpecificRecomb; pfam10136 535289001067 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 535289001068 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 535289001069 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 535289001070 substrate binding site [chemical binding]; other site 535289001071 hexamer interface [polypeptide binding]; other site 535289001072 metal binding site [ion binding]; metal-binding site 535289001073 phosphoglycolate phosphatase; Provisional; Region: PRK13222 535289001074 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 535289001075 motif II; other site 535289001076 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 535289001077 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289001078 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289001079 dimer interface [polypeptide binding]; other site 535289001080 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 535289001081 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 535289001082 dimerization interface [polypeptide binding]; other site 535289001083 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289001084 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289001085 dimer interface [polypeptide binding]; other site 535289001086 putative CheW interface [polypeptide binding]; other site 535289001087 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 535289001088 anthranilate synthase component I; Provisional; Region: PRK13565 535289001089 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 535289001090 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 535289001091 Chorismate mutase type II; Region: CM_2; smart00830 535289001092 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 535289001093 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 535289001094 glutamine binding [chemical binding]; other site 535289001095 catalytic triad [active] 535289001096 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 535289001097 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 535289001098 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 535289001099 heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus and human immunodeficiency virus type 1 (HIV-1); Region: Ebola_HIV-1-like_HR1-HR2; cl02885 535289001100 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 535289001101 active site 535289001102 ribulose/triose binding site [chemical binding]; other site 535289001103 phosphate binding site [ion binding]; other site 535289001104 substrate (anthranilate) binding pocket [chemical binding]; other site 535289001105 product (indole) binding pocket [chemical binding]; other site 535289001106 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 535289001107 PAS fold; Region: PAS_3; pfam08447 535289001108 putative active site [active] 535289001109 heme pocket [chemical binding]; other site 535289001110 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 535289001111 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 535289001112 putative active site [active] 535289001113 heme pocket [chemical binding]; other site 535289001114 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 535289001115 putative active site [active] 535289001116 heme pocket [chemical binding]; other site 535289001117 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289001118 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289001119 metal binding site [ion binding]; metal-binding site 535289001120 active site 535289001121 I-site; other site 535289001122 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 535289001123 ligand binding site [chemical binding]; other site 535289001124 active site 535289001125 UGI interface [polypeptide binding]; other site 535289001126 catalytic site [active] 535289001127 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 535289001128 EamA-like transporter family; Region: EamA; pfam00892 535289001129 Queuosine biosynthesis protein; Region: Queuosine_synth; pfam02547 535289001130 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 535289001131 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 535289001132 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 535289001133 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 535289001134 Zn2+ binding site [ion binding]; other site 535289001135 Mg2+ binding site [ion binding]; other site 535289001136 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 535289001137 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 535289001138 generic binding surface II; other site 535289001139 ssDNA binding site; other site 535289001140 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 535289001141 ATP binding site [chemical binding]; other site 535289001142 putative Mg++ binding site [ion binding]; other site 535289001143 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 535289001144 nucleotide binding region [chemical binding]; other site 535289001145 ATP-binding site [chemical binding]; other site 535289001146 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 535289001147 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289001148 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 535289001149 dimerization interface [polypeptide binding]; other site 535289001150 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 535289001151 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 535289001152 dimerization interface [polypeptide binding]; other site 535289001153 DPS ferroxidase diiron center [ion binding]; other site 535289001154 ion pore; other site 535289001155 CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; Region: CYTH-like_Pase; cl11964 535289001156 putative active site; other site 535289001157 putative triphosphate binding site [ion binding]; other site 535289001158 CHAD domain; Region: CHAD; pfam05235 535289001159 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 535289001160 UbiA prenyltransferase family; Region: UbiA; pfam01040 535289001161 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 535289001162 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 535289001163 glycerol kinase; Provisional; Region: glpK; PRK00047 535289001164 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 535289001165 N- and C-terminal domain interface [polypeptide binding]; other site 535289001166 active site 535289001167 MgATP binding site [chemical binding]; other site 535289001168 catalytic site [active] 535289001169 metal binding site [ion binding]; metal-binding site 535289001170 glycerol binding site [chemical binding]; other site 535289001171 homotetramer interface [polypeptide binding]; other site 535289001172 homodimer interface [polypeptide binding]; other site 535289001173 FBP binding site [chemical binding]; other site 535289001174 protein IIAGlc interface [polypeptide binding]; other site 535289001175 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 535289001176 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 535289001177 putative DNA binding site [nucleotide binding]; other site 535289001178 putative Zn2+ binding site [ion binding]; other site 535289001179 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 535289001180 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 535289001181 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289001182 Walker A/P-loop; other site 535289001183 ATP binding site [chemical binding]; other site 535289001184 Q-loop/lid; other site 535289001185 ABC transporter signature motif; other site 535289001186 Walker B; other site 535289001187 D-loop; other site 535289001188 H-loop/switch region; other site 535289001189 TOBE domain; Region: TOBE_2; pfam08402 535289001190 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 535289001191 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 535289001192 Walker A/P-loop; other site 535289001193 ATP binding site [chemical binding]; other site 535289001194 Q-loop/lid; other site 535289001195 ABC transporter signature motif; other site 535289001196 Walker B; other site 535289001197 D-loop; other site 535289001198 H-loop/switch region; other site 535289001199 TOBE domain; Region: TOBE_2; pfam08402 535289001200 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289001201 putative PBP binding loops; other site 535289001202 dimer interface [polypeptide binding]; other site 535289001203 ABC-ATPase subunit interface; other site 535289001204 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 535289001205 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289001206 dimer interface [polypeptide binding]; other site 535289001207 conserved gate region; other site 535289001208 putative PBP binding loops; other site 535289001209 ABC-ATPase subunit interface; other site 535289001210 Predicted small integral membrane protein (DUF2160); Region: DUF2160; pfam09928 535289001211 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 535289001212 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 535289001213 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 535289001214 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 535289001215 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 535289001216 RNA binding site [nucleotide binding]; other site 535289001217 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 535289001218 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 535289001219 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 535289001220 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 535289001221 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 535289001222 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 535289001223 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 535289001224 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 535289001225 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 535289001226 5S rRNA interface [nucleotide binding]; other site 535289001227 23S rRNA interface [nucleotide binding]; other site 535289001228 L5 interface [polypeptide binding]; other site 535289001229 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 535289001230 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 535289001231 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 535289001232 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 535289001233 23S rRNA binding site [nucleotide binding]; other site 535289001234 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 535289001235 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 535289001236 SecY translocase; Region: SecY; pfam00344 535289001237 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 535289001238 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 535289001239 30S ribosomal protein S13; Region: bact_S13; TIGR03631 535289001240 30S ribosomal protein S11; Validated; Region: PRK05309 535289001241 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 535289001242 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 535289001243 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 535289001244 RNA binding surface [nucleotide binding]; other site 535289001245 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 535289001246 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 535289001247 alphaNTD homodimer interface [polypeptide binding]; other site 535289001248 alphaNTD - beta interaction site [polypeptide binding]; other site 535289001249 alphaNTD - beta' interaction site [polypeptide binding]; other site 535289001250 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 535289001251 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 535289001252 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 535289001253 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 535289001254 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 535289001255 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 535289001256 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 535289001257 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 535289001258 putative NAD(P) binding site [chemical binding]; other site 535289001259 active site 535289001260 putative substrate binding site [chemical binding]; other site 535289001261 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 535289001262 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 535289001263 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 535289001264 Ligand binding site; other site 535289001265 Putative Catalytic site; other site 535289001266 DXD motif; other site 535289001267 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 535289001268 Predicted methyltransferases [General function prediction only]; Region: COG0313 535289001269 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 535289001270 putative SAM binding site [chemical binding]; other site 535289001271 putative homodimer interface [polypeptide binding]; other site 535289001272 hypothetical protein; Provisional; Region: PRK14673 535289001273 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 535289001274 dimer interface [polypeptide binding]; other site 535289001275 active site 535289001276 outer membrane lipoprotein; Provisional; Region: PRK11023 535289001277 BON domain; Region: BON; pfam04972 535289001278 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 535289001279 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 535289001280 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 535289001281 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 535289001282 Walker A motif; other site 535289001283 ATP binding site [chemical binding]; other site 535289001284 Walker B motif; other site 535289001285 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289001286 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 535289001287 ligand binding site [chemical binding]; other site 535289001288 flexible hinge region; other site 535289001289 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 535289001290 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 535289001291 Walker A motif; other site 535289001292 ATP binding site [chemical binding]; other site 535289001293 Walker B motif; other site 535289001294 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 535289001295 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 535289001296 catalytic residue [active] 535289001297 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 535289001298 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289001299 catalytic residue [active] 535289001300 Protein of unknown function (DUF445); Region: DUF445; pfam04286 535289001301 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 535289001302 FAD binding domain; Region: FAD_binding_4; pfam01565 535289001303 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 535289001304 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289001305 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 535289001306 dimerization interface [polypeptide binding]; other site 535289001307 substrate binding pocket [chemical binding]; other site 535289001308 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 535289001309 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 535289001310 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 535289001311 putative active site [active] 535289001312 putative substrate binding site [chemical binding]; other site 535289001313 putative cosubstrate binding site; other site 535289001314 catalytic site [active] 535289001315 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 535289001316 PAS domain; Region: PAS_9; pfam13426 535289001317 putative active site [active] 535289001318 heme pocket [chemical binding]; other site 535289001319 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 535289001320 PAS domain; Region: PAS_9; pfam13426 535289001321 putative active site [active] 535289001322 heme pocket [chemical binding]; other site 535289001323 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289001324 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289001325 metal binding site [ion binding]; metal-binding site 535289001326 active site 535289001327 I-site; other site 535289001328 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 535289001329 Protein of unknown function, DUF399; Region: DUF399; cl01139 535289001330 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 535289001331 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 535289001332 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 535289001333 active site 535289001334 dimer interface [polypeptide binding]; other site 535289001335 effector binding site; other site 535289001336 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 535289001337 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 535289001338 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289001339 dimerization interface [polypeptide binding]; other site 535289001340 GAF domain; Region: GAF; pfam01590 535289001341 Histidine kinase; Region: HisKA_3; pfam07730 535289001342 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 535289001343 ATP binding site [chemical binding]; other site 535289001344 Mg2+ binding site [ion binding]; other site 535289001345 G-X-G motif; other site 535289001346 transcriptional regulator NarL; Provisional; Region: PRK10651 535289001347 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 535289001348 active site 535289001349 phosphorylation site [posttranslational modification] 535289001350 intermolecular recognition site; other site 535289001351 dimerization interface [polypeptide binding]; other site 535289001352 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289001353 DNA binding residues [nucleotide binding] 535289001354 dimerization interface [polypeptide binding]; other site 535289001355 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 535289001356 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 535289001357 putative substrate translocation pore; other site 535289001358 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 535289001359 CCC1-related family of proteins; Region: CCC1_like; cl00278 535289001360 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 535289001361 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 to...; Region: MopB_Nitrate-R-NarG-like; cd02750 535289001362 [4Fe-4S] binding site [ion binding]; other site 535289001363 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 535289001364 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 535289001365 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 535289001366 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 to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 535289001367 molybdopterin cofactor binding site; other site 535289001368 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 535289001369 4Fe-4S binding domain; Region: Fer4; cl02805 535289001370 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 535289001371 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 535289001372 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 535289001373 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 535289001374 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 535289001375 active site clefts [active] 535289001376 zinc binding site [ion binding]; other site 535289001377 dimer interface [polypeptide binding]; other site 535289001378 NnrS protein; Region: NnrS; pfam05940 535289001379 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 535289001380 putative FMN binding site [chemical binding]; other site 535289001381 Hemerythrin-like domain; Region: Hr-like; cd12108 535289001382 Protein of unknown function (DUF3567); Region: DUF3567; pfam12091 535289001383 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 535289001384 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 535289001385 Transcriptional regulator [Transcription]; Region: IclR; COG1414 535289001386 Bacterial transcriptional regulator; Region: IclR; pfam01614 535289001387 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 535289001388 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 535289001389 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289001390 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 535289001391 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 535289001392 putative [4Fe-4S] binding site [ion binding]; other site 535289001393 putative molybdopterin cofactor binding site [chemical binding]; other site 535289001394 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 535289001395 putative molybdopterin cofactor binding site; other site 535289001396 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289001397 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 535289001398 putative ligand binding site [chemical binding]; other site 535289001399 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 535289001400 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 535289001401 metal binding site [ion binding]; metal-binding site 535289001402 putative dimer interface [polypeptide binding]; other site 535289001403 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_6; cd06233 535289001404 putative active site [active] 535289001405 Zn binding site [ion binding]; other site 535289001406 Acyl CoA binding protein; Region: ACBP; pfam00887 535289001407 acyl-CoA binding pocket [chemical binding]; other site 535289001408 CoA binding site [chemical binding]; other site 535289001409 Predicted aminopeptidase (DUF2265); Region: DUF2265; cl17720 535289001410 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 535289001411 exopolyphosphatase; Region: exo_poly_only; TIGR03706 535289001412 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 535289001413 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 535289001414 S-adenosylmethionine binding site [chemical binding]; other site 535289001415 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 535289001416 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289001417 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289001418 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 535289001419 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289001420 acyl-activating enzyme (AAE) consensus motif; other site 535289001421 active site 535289001422 AMP binding site [chemical binding]; other site 535289001423 CoA binding site [chemical binding]; other site 535289001424 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 535289001425 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 535289001426 Walker A/P-loop; other site 535289001427 ATP binding site [chemical binding]; other site 535289001428 Q-loop/lid; other site 535289001429 ABC transporter signature motif; other site 535289001430 Walker B; other site 535289001431 D-loop; other site 535289001432 H-loop/switch region; other site 535289001433 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 535289001434 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289001435 putative ligand binding site [chemical binding]; other site 535289001436 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 535289001437 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 535289001438 TM-ABC transporter signature motif; other site 535289001439 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 535289001440 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 535289001441 TM-ABC transporter signature motif; other site 535289001442 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 535289001443 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 535289001444 Walker A/P-loop; other site 535289001445 ATP binding site [chemical binding]; other site 535289001446 Q-loop/lid; other site 535289001447 ABC transporter signature motif; other site 535289001448 Walker B; other site 535289001449 D-loop; other site 535289001450 H-loop/switch region; other site 535289001451 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 535289001452 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289001453 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 535289001454 acyl-activating enzyme (AAE) consensus motif; other site 535289001455 putative AMP binding site [chemical binding]; other site 535289001456 putative active site [active] 535289001457 putative CoA binding site [chemical binding]; other site 535289001458 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 535289001459 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289001460 Walker A motif; other site 535289001461 ATP binding site [chemical binding]; other site 535289001462 Walker B motif; other site 535289001463 arginine finger; other site 535289001464 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289001465 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 535289001466 ligand binding site [chemical binding]; other site 535289001467 flexible hinge region; other site 535289001468 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 535289001469 non-specific DNA interactions [nucleotide binding]; other site 535289001470 DNA binding site [nucleotide binding] 535289001471 sequence specific DNA binding site [nucleotide binding]; other site 535289001472 putative cAMP binding site [chemical binding]; other site 535289001473 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 535289001474 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 535289001475 RNA binding surface [nucleotide binding]; other site 535289001476 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 535289001477 active site 535289001478 heat shock protein 90; Provisional; Region: PRK05218 535289001479 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 535289001480 ATP binding site [chemical binding]; other site 535289001481 Mg2+ binding site [ion binding]; other site 535289001482 G-X-G motif; other site 535289001483 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289001484 Predicted membrane protein [Function unknown]; Region: COG4083; cl15694 535289001485 serine/threonine protein kinase; Provisional; Region: PRK11768 535289001486 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 535289001487 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 535289001488 Catalytic domain of Protein Kinases; Region: PKc; cd00180 535289001489 active site 535289001490 ATP binding site [chemical binding]; other site 535289001491 substrate binding site [chemical binding]; other site 535289001492 activation loop (A-loop); other site 535289001493 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 535289001494 Ligand Binding Site [chemical binding]; other site 535289001495 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 535289001496 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 535289001497 active site 535289001498 metal binding site [ion binding]; metal-binding site 535289001499 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 535289001500 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 535289001501 MarR family; Region: MarR; pfam01047 535289001502 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 535289001503 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 535289001504 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 535289001505 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289001506 choline dehydrogenase; Validated; Region: PRK02106 535289001507 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 535289001508 Hemerythrin-like domain of FBXL5-like proteins; Region: Hr_FBXL5; cd12109 535289001509 Fe binding site [ion binding]; other site 535289001510 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 535289001511 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 535289001512 GAF domain; Region: GAF; pfam01590 535289001513 ABC-2 type transporter; Region: ABC2_membrane; cl17235 535289001514 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 535289001515 MgtC family; Region: MgtC; pfam02308 535289001516 Predicted membrane protein [Function unknown]; Region: COG3174 535289001517 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 535289001518 AMP nucleosidase; Provisional; Region: PRK08292 535289001519 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 535289001520 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 535289001521 PAS fold; Region: PAS_4; pfam08448 535289001522 PAS domain S-box; Region: sensory_box; TIGR00229 535289001523 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 535289001524 putative active site [active] 535289001525 heme pocket [chemical binding]; other site 535289001526 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289001527 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289001528 metal binding site [ion binding]; metal-binding site 535289001529 active site 535289001530 I-site; other site 535289001531 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 535289001532 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 535289001533 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 535289001534 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 535289001535 putative active site [active] 535289001536 dimerization interface [polypeptide binding]; other site 535289001537 putative tRNAtyr binding site [nucleotide binding]; other site 535289001538 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 535289001539 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 535289001540 ATP binding site [chemical binding]; other site 535289001541 Mg++ binding site [ion binding]; other site 535289001542 motif III; other site 535289001543 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 535289001544 nucleotide binding region [chemical binding]; other site 535289001545 ATP-binding site [chemical binding]; other site 535289001546 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 535289001547 putative RNA binding site [nucleotide binding]; other site 535289001548 hypothetical protein; Provisional; Region: PRK10621 535289001549 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 535289001550 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 535289001551 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 535289001552 PhoH-like protein; Region: PhoH; pfam02562 535289001553 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 535289001554 RuvA N terminal domain; Region: RuvA_N; pfam01330 535289001555 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 535289001556 Nucleotide-binding domain of the HSP70 family; Region: HSP70_NBD; cd10170 535289001557 nucleotide binding site [chemical binding]; other site 535289001558 putative NEF/HSP70 interaction site [polypeptide binding]; other site 535289001559 SBD interface [polypeptide binding]; other site 535289001560 DNA-K related protein; Region: DUF3731; pfam12531 535289001561 Nucleotide-binding domain of the HSP70 family; Region: HSP70_NBD; cd10170 535289001562 nucleotide binding site [chemical binding]; other site 535289001563 putative NEF/HSP70 interaction site [polypeptide binding]; other site 535289001564 SBD interface [polypeptide binding]; other site 535289001565 Domain of unknown function (DUF2760); Region: DUF2760; pfam10816 535289001566 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 535289001567 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289001568 Walker A motif; other site 535289001569 ATP binding site [chemical binding]; other site 535289001570 Walker B motif; other site 535289001571 arginine finger; other site 535289001572 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 535289001573 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 535289001574 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 535289001575 YhhN-like protein; Region: YhhN; pfam07947 535289001576 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 535289001577 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase; Region: PLPDE_III_LS_D-TA; cd06819 535289001578 dimer interface [polypeptide binding]; other site 535289001579 active site 535289001580 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 535289001581 substrate binding site [chemical binding]; other site 535289001582 catalytic residue [active] 535289001583 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 535289001584 catalytic core [active] 535289001585 hypothetical protein; Provisional; Region: PRK11667 535289001586 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 535289001587 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 535289001588 Ligand Binding Site [chemical binding]; other site 535289001589 Dihydroneopterin aldolase; Region: FolB; smart00905 535289001590 active site 535289001591 Dihydroneopterin aldolase; Region: FolB; smart00905 535289001592 active site 535289001593 Uncharacterized conserved protein [Function unknown]; Region: COG1565 535289001594 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 535289001595 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 oxygenases...; Region: CAS_like; cl00184 535289001596 active site 535289001597 iron coordination sites [ion binding]; other site 535289001598 substrate binding pocket [chemical binding]; other site 535289001599 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 535289001600 NMT1-like family; Region: NMT1_2; pfam13379 535289001601 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 535289001602 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 535289001603 Walker A/P-loop; other site 535289001604 ATP binding site [chemical binding]; other site 535289001605 Q-loop/lid; other site 535289001606 ABC transporter signature motif; other site 535289001607 Walker B; other site 535289001608 D-loop; other site 535289001609 H-loop/switch region; other site 535289001610 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 535289001611 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289001612 dimer interface [polypeptide binding]; other site 535289001613 ABC-ATPase subunit interface; other site 535289001614 putative PBP binding loops; other site 535289001615 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 535289001616 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 535289001617 nucleotide binding site [chemical binding]; other site 535289001618 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 535289001619 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 a...; Region: GT1_TPS; cd03788 535289001620 active site 535289001621 homotetramer interface [polypeptide binding]; other site 535289001622 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 535289001623 Domain of unknown function (DUF4402); Region: DUF4402; pfam14352 535289001624 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 535289001625 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 535289001626 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 535289001627 active site 535289001628 motif I; other site 535289001629 motif II; other site 535289001630 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 535289001631 thioredoxin 2; Provisional; Region: PRK10996 535289001632 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 535289001633 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 535289001634 catalytic residues [active] 535289001635 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 535289001636 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 535289001637 active site 535289001638 NTP binding site [chemical binding]; other site 535289001639 metal binding triad [ion binding]; metal-binding site 535289001640 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 535289001641 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 535289001642 Zn2+ binding site [ion binding]; other site 535289001643 Mg2+ binding site [ion binding]; other site 535289001644 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 535289001645 Microscilla MS158 and related proteins, metallophosphatase domain; Region: MPP_MS158; cd07404 535289001646 putative active site [active] 535289001647 putative metal binding site [ion binding]; other site 535289001648 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) with...; Region: GST_N_1; cd03043 535289001649 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 535289001650 putative C-terminal domain interface [polypeptide binding]; other site 535289001651 putative GSH binding site (G-site) [chemical binding]; other site 535289001652 putative dimer interface [polypeptide binding]; other site 535289001653 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 535289001654 putative dimer interface [polypeptide binding]; other site 535289001655 putative N-terminal domain interface [polypeptide binding]; other site 535289001656 putative substrate binding pocket (H-site) [chemical binding]; other site 535289001657 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 535289001658 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 535289001659 lytic murein transglycosylase; Provisional; Region: PRK11619 535289001660 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 535289001661 N-acetyl-D-glucosamine binding site [chemical binding]; other site 535289001662 catalytic residue [active] 535289001663 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 535289001664 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 535289001665 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 535289001666 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 535289001667 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 535289001668 active site 535289001669 substrate binding site [chemical binding]; other site 535289001670 FMN binding site [chemical binding]; other site 535289001671 putative catalytic residues [active] 535289001672 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 535289001673 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 535289001674 N-terminal plug; other site 535289001675 ligand-binding site [chemical binding]; other site 535289001676 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 535289001677 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 535289001678 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 535289001679 acyl-activating enzyme (AAE) consensus motif; other site 535289001680 putative AMP binding site [chemical binding]; other site 535289001681 putative active site [active] 535289001682 putative CoA binding site [chemical binding]; other site 535289001683 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 535289001684 PGAP1-like protein; Region: PGAP1; pfam07819 535289001685 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 535289001686 cofactor binding site; other site 535289001687 metal binding site [ion binding]; metal-binding site 535289001688 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289001689 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 535289001690 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 535289001691 dimer interface [polypeptide binding]; other site 535289001692 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 535289001693 active site 535289001694 Fe binding site [ion binding]; other site 535289001695 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289001696 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 535289001697 dimerization interface [polypeptide binding]; other site 535289001698 putative DNA binding site [nucleotide binding]; other site 535289001699 putative Zn2+ binding site [ion binding]; other site 535289001700 AsnC family; Region: AsnC_trans_reg; pfam01037 535289001701 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 535289001702 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 535289001703 Coenzyme A binding pocket [chemical binding]; other site 535289001704 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 535289001705 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 535289001706 Transporter associated domain; Region: CorC_HlyC; smart01091 535289001707 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 535289001708 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 535289001709 putative active site [active] 535289001710 catalytic triad [active] 535289001711 putative dimer interface [polypeptide binding]; other site 535289001712 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 535289001713 dimer interface [polypeptide binding]; other site 535289001714 active site 1 [active] 535289001715 active site 2 [active] 535289001716 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 535289001717 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 535289001718 dimer interface [polypeptide binding]; other site 535289001719 active site 535289001720 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 535289001721 dimer interface [polypeptide binding]; other site 535289001722 motif 1; other site 535289001723 active site 535289001724 motif 2; other site 535289001725 motif 3; other site 535289001726 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 535289001727 DALR anticodon binding domain; Region: DALR_1; pfam05746 535289001728 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 535289001729 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 535289001730 active site 535289001731 motif I; other site 535289001732 motif II; other site 535289001733 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 535289001734 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 535289001735 putative acyl-acceptor binding pocket; other site 535289001736 Protein of unknown function DUF45; Region: DUF45; pfam01863 535289001737 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 535289001738 active site residue [active] 535289001739 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 535289001740 BON domain; Region: BON; pfam04972 535289001741 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 535289001742 pantothenate kinase; Reviewed; Region: PRK13329 535289001743 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289001744 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289001745 Bacterial transcriptional repressor; Region: TetR; pfam13972 535289001746 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; pfam05597 535289001747 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 535289001748 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 535289001749 NAD binding site [chemical binding]; other site 535289001750 substrate binding site [chemical binding]; other site 535289001751 homodimer interface [polypeptide binding]; other site 535289001752 active site 535289001753 dTDP-4-dehydrorhamnose reductase; Provisional; Region: PRK09987 535289001754 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 535289001755 NADP binding site [chemical binding]; other site 535289001756 active site 535289001757 putative substrate binding site [chemical binding]; other site 535289001758 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 535289001759 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 535289001760 substrate binding site; other site 535289001761 tetramer interface; other site 535289001762 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 535289001763 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 535289001764 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_4; cd03795 535289001765 putative ADP-binding pocket [chemical binding]; other site 535289001766 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 535289001767 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 535289001768 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 535289001769 active site 535289001770 phosphate binding residues; other site 535289001771 catalytic residues [active] 535289001772 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 535289001773 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289001774 NAD(P) binding site [chemical binding]; other site 535289001775 active site 535289001776 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 535289001777 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 535289001778 NADP-binding site; other site 535289001779 homotetramer interface [polypeptide binding]; other site 535289001780 substrate binding site [chemical binding]; other site 535289001781 homodimer interface [polypeptide binding]; other site 535289001782 active site 535289001783 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 535289001784 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 535289001785 Probable Catalytic site; other site 535289001786 metal-binding site 535289001787 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 535289001788 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 535289001789 Methyltransferase domain; Region: Methyltransf_23; pfam13489 535289001790 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 535289001791 S-adenosylmethionine binding site [chemical binding]; other site 535289001792 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 535289001793 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 535289001794 Walker A/P-loop; other site 535289001795 ATP binding site [chemical binding]; other site 535289001796 Q-loop/lid; other site 535289001797 ABC transporter signature motif; other site 535289001798 Walker B; other site 535289001799 D-loop; other site 535289001800 H-loop/switch region; other site 535289001801 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 535289001802 putative carbohydrate binding site [chemical binding]; other site 535289001803 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 535289001804 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 535289001805 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 535289001806 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 535289001807 Substrate binding site; other site 535289001808 Cupin domain; Region: Cupin_2; cl17218 535289001809 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 535289001810 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, which...; Region: GT_MraY_like; cd06912 535289001811 Mg++ binding site [ion binding]; other site 535289001812 putative catalytic motif [active] 535289001813 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 535289001814 feedback inhibition sensing region; other site 535289001815 homohexameric interface [polypeptide binding]; other site 535289001816 nucleotide binding site [chemical binding]; other site 535289001817 N-acetyl-L-glutamate binding site [chemical binding]; other site 535289001818 division inhibitor protein; Provisional; Region: slmA; PRK09480 535289001819 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289001820 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289001821 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289001822 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 535289001823 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 535289001824 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289001825 active site 535289001826 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 535289001827 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 535289001828 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 535289001829 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 535289001830 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289001831 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289001832 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 535289001833 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 535289001834 substrate binding site [chemical binding]; other site 535289001835 oxyanion hole (OAH) forming residues; other site 535289001836 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 535289001837 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 535289001838 dimer interface [polypeptide binding]; other site 535289001839 active site 535289001840 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 535289001841 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 535289001842 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 535289001843 enoyl-CoA hydratase; Provisional; Region: PRK06688 535289001844 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 535289001845 substrate binding site [chemical binding]; other site 535289001846 oxyanion hole (OAH) forming residues; other site 535289001847 trimer interface [polypeptide binding]; other site 535289001848 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 535289001849 CoenzymeA binding site [chemical binding]; other site 535289001850 subunit interaction site [polypeptide binding]; other site 535289001851 PHB binding site; other site 535289001852 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 535289001853 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 535289001854 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 535289001855 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 535289001856 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 535289001857 Walker A/P-loop; other site 535289001858 ATP binding site [chemical binding]; other site 535289001859 Q-loop/lid; other site 535289001860 ABC transporter signature motif; other site 535289001861 Walker B; other site 535289001862 D-loop; other site 535289001863 H-loop/switch region; other site 535289001864 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 535289001865 homodimer interface [polypeptide binding]; other site 535289001866 chemical substrate binding site [chemical binding]; other site 535289001867 oligomer interface [polypeptide binding]; other site 535289001868 metal binding site [ion binding]; metal-binding site 535289001869 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 535289001870 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 535289001871 DctM-like transporters; Region: DctM; pfam06808 535289001872 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 535289001873 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 535289001874 cell density-dependent motility repressor; Provisional; Region: PRK10082 535289001875 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289001876 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 535289001877 dimerization interface [polypeptide binding]; other site 535289001878 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 535289001879 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 535289001880 substrate binding pocket [chemical binding]; other site 535289001881 membrane-bound complex binding site; other site 535289001882 hinge residues; other site 535289001883 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 535289001884 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 535289001885 substrate binding pocket [chemical binding]; other site 535289001886 membrane-bound complex binding site; other site 535289001887 hinge residues; other site 535289001888 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289001889 dimer interface [polypeptide binding]; other site 535289001890 conserved gate region; other site 535289001891 putative PBP binding loops; other site 535289001892 ABC-ATPase subunit interface; other site 535289001893 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 535289001894 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289001895 dimer interface [polypeptide binding]; other site 535289001896 conserved gate region; other site 535289001897 putative PBP binding loops; other site 535289001898 ABC-ATPase subunit interface; other site 535289001899 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 535289001900 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 535289001901 Walker A/P-loop; other site 535289001902 ATP binding site [chemical binding]; other site 535289001903 Q-loop/lid; other site 535289001904 ABC transporter signature motif; other site 535289001905 Walker B; other site 535289001906 D-loop; other site 535289001907 H-loop/switch region; other site 535289001908 ornithine cyclodeaminase; Validated; Region: PRK07589 535289001909 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 535289001910 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289001911 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 535289001912 AsnC family; Region: AsnC_trans_reg; pfam01037 535289001913 Cytochrome c; Region: Cytochrom_C; cl11414 535289001914 Cytochrome c; Region: Cytochrom_C; cl11414 535289001915 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 535289001916 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 535289001917 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 535289001918 G1 box; other site 535289001919 putative GEF interaction site [polypeptide binding]; other site 535289001920 GTP/Mg2+ binding site [chemical binding]; other site 535289001921 Switch I region; other site 535289001922 G2 box; other site 535289001923 G3 box; other site 535289001924 Switch II region; other site 535289001925 G4 box; other site 535289001926 G5 box; other site 535289001927 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 535289001928 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 535289001929 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 535289001930 homotetramer interface [polypeptide binding]; other site 535289001931 ligand binding site [chemical binding]; other site 535289001932 catalytic site [active] 535289001933 NAD binding site [chemical binding]; other site 535289001934 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 535289001935 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 535289001936 FtsJ-like methyltransferase; Region: FtsJ; cl17430 535289001937 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 535289001938 FAD binding site [chemical binding]; other site 535289001939 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 535289001940 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 535289001941 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 535289001942 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 535289001943 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 535289001944 Catalytic domain of Protein Kinases; Region: PKc; cd00180 535289001945 active site 535289001946 ATP binding site [chemical binding]; other site 535289001947 substrate binding site [chemical binding]; other site 535289001948 activation loop (A-loop); other site 535289001949 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 535289001950 23S rRNA interface [nucleotide binding]; other site 535289001951 L3 interface [polypeptide binding]; other site 535289001952 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 535289001953 Mnd1 family; Region: Mnd1; pfam03962 535289001954 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 535289001955 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 535289001956 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 535289001957 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 535289001958 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 535289001959 Peptidase family M23; Region: Peptidase_M23; pfam01551 535289001960 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 535289001961 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 535289001962 active site 535289001963 HIGH motif; other site 535289001964 dimer interface [polypeptide binding]; other site 535289001965 KMSKS motif; other site 535289001966 Hemerythrin; Region: Hemerythrin; cd12107 535289001967 Fe binding site [ion binding]; other site 535289001968 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289001969 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 535289001970 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 535289001971 dimerization interface [polypeptide binding]; other site 535289001972 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 535289001973 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 535289001974 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 535289001975 Substrate binding site; other site 535289001976 Mg++ binding site; other site 535289001977 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 535289001978 active site 535289001979 substrate binding site [chemical binding]; other site 535289001980 CoA binding site [chemical binding]; other site 535289001981 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289001982 dimer interface [polypeptide binding]; other site 535289001983 phosphorylation site [posttranslational modification] 535289001984 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 535289001985 ATP binding site [chemical binding]; other site 535289001986 Mg2+ binding site [ion binding]; other site 535289001987 G-X-G motif; other site 535289001988 chaperone protein DnaJ; Provisional; Region: PRK14299 535289001989 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 535289001990 HSP70 interaction site [polypeptide binding]; other site 535289001991 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 535289001992 substrate binding site [polypeptide binding]; other site 535289001993 dimer interface [polypeptide binding]; other site 535289001994 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289001995 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 535289001996 AsnC family; Region: AsnC_trans_reg; pfam01037 535289001997 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 535289001998 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 535289001999 glutaminase active site [active] 535289002000 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 535289002001 dimer interface [polypeptide binding]; other site 535289002002 active site 535289002003 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 535289002004 dimer interface [polypeptide binding]; other site 535289002005 active site 535289002006 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 535289002007 NADH(P)-binding; Region: NAD_binding_10; pfam13460 535289002008 NAD binding site [chemical binding]; other site 535289002009 substrate binding site [chemical binding]; other site 535289002010 putative active site [active] 535289002011 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289002012 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289002013 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 535289002014 putative effector binding pocket; other site 535289002015 dimerization interface [polypeptide binding]; other site 535289002016 Protein of unknown function (DUF4256); Region: DUF4256; pfam14066 535289002017 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 535289002018 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 535289002019 putative NAD(P) binding site [chemical binding]; other site 535289002020 putative substrate binding site [chemical binding]; other site 535289002021 catalytic Zn binding site [ion binding]; other site 535289002022 structural Zn binding site [ion binding]; other site 535289002023 dimer interface [polypeptide binding]; other site 535289002024 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 535289002025 rRNA binding site [nucleotide binding]; other site 535289002026 predicted 30S ribosome binding site; other site 535289002027 CHASE3 domain; Region: CHASE3; pfam05227 535289002028 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289002029 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289002030 dimer interface [polypeptide binding]; other site 535289002031 phosphorylation site [posttranslational modification] 535289002032 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 535289002033 ATP binding site [chemical binding]; other site 535289002034 Mg2+ binding site [ion binding]; other site 535289002035 G-X-G motif; other site 535289002036 Response regulator receiver domain; Region: Response_reg; pfam00072 535289002037 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 535289002038 active site 535289002039 phosphorylation site [posttranslational modification] 535289002040 intermolecular recognition site; other site 535289002041 dimerization interface [polypeptide binding]; other site 535289002042 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 535289002043 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 535289002044 active site 535289002045 phosphorylation site [posttranslational modification] 535289002046 intermolecular recognition site; other site 535289002047 dimerization interface [polypeptide binding]; other site 535289002048 Response regulator receiver domain; Region: Response_reg; pfam00072 535289002049 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 535289002050 active site 535289002051 phosphorylation site [posttranslational modification] 535289002052 intermolecular recognition site; other site 535289002053 dimerization interface [polypeptide binding]; other site 535289002054 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 535289002055 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 535289002056 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 535289002057 CheB methylesterase; Region: CheB_methylest; pfam01339 535289002058 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 535289002059 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 535289002060 active site 535289002061 phosphorylation site [posttranslational modification] 535289002062 intermolecular recognition site; other site 535289002063 dimerization interface [polypeptide binding]; other site 535289002064 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289002065 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289002066 dimer interface [polypeptide binding]; other site 535289002067 phosphorylation site [posttranslational modification] 535289002068 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 535289002069 ATP binding site [chemical binding]; other site 535289002070 Mg2+ binding site [ion binding]; other site 535289002071 G-X-G motif; other site 535289002072 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 535289002073 active site 535289002074 phosphorylation site [posttranslational modification] 535289002075 intermolecular recognition site; other site 535289002076 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 535289002077 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 535289002078 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289002079 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 535289002080 acyl-activating enzyme (AAE) consensus motif; other site 535289002081 acyl-activating enzyme (AAE) consensus motif; other site 535289002082 putative AMP binding site [chemical binding]; other site 535289002083 putative active site [active] 535289002084 putative CoA binding site [chemical binding]; other site 535289002085 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 535289002086 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 535289002087 catalytic residues [active] 535289002088 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 535289002089 CreA protein; Region: CreA; pfam05981 535289002090 cyanophycin synthetase; Provisional; Region: PRK14016 535289002091 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 535289002092 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 535289002093 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 535289002094 cyanophycin synthetase; Provisional; Region: PRK14016 535289002095 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 535289002096 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 535289002097 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 535289002098 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 535289002099 Walker A/P-loop; other site 535289002100 ATP binding site [chemical binding]; other site 535289002101 Q-loop/lid; other site 535289002102 ABC transporter signature motif; other site 535289002103 Walker B; other site 535289002104 D-loop; other site 535289002105 H-loop/switch region; other site 535289002106 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 535289002107 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 535289002108 EF-hand domain pair; Region: EF_hand_5; pfam13499 535289002109 Ca2+ binding site [ion binding]; other site 535289002110 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 535289002111 type II secretion system protein F; Region: GspF; TIGR02120 535289002112 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 535289002113 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 535289002114 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 535289002115 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 535289002116 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 535289002117 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 535289002118 type II secretion system protein E; Region: type_II_gspE; TIGR02533 535289002119 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 535289002120 Walker A motif; other site 535289002121 ATP binding site [chemical binding]; other site 535289002122 Walker B motif; other site 535289002123 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 535289002124 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 535289002125 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 535289002126 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 535289002127 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 535289002128 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 535289002129 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 535289002130 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 535289002131 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 535289002132 type II secretion system protein I; Region: gspI; TIGR01707 535289002133 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 535289002134 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 535289002135 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 535289002136 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 535289002137 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 535289002138 cobalamin synthase; Reviewed; Region: cobS; PRK00235 535289002139 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 535289002140 threonine dehydratase; Reviewed; Region: PRK09224 535289002141 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 535289002142 tetramer interface [polypeptide binding]; other site 535289002143 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289002144 catalytic residue [active] 535289002145 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 535289002146 putative Ile/Val binding site [chemical binding]; other site 535289002147 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 535289002148 putative Ile/Val binding site [chemical binding]; other site 535289002149 OsmC-like protein; Region: OsmC; cl00767 535289002150 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 535289002151 diiron binding motif [ion binding]; other site 535289002152 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 535289002153 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 535289002154 trimer interface [polypeptide binding]; other site 535289002155 eyelet of channel; other site 535289002156 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 535289002157 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 535289002158 trimer interface [polypeptide binding]; other site 535289002159 eyelet of channel; other site 535289002160 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 535289002161 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 535289002162 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 535289002163 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289002164 dimer interface [polypeptide binding]; other site 535289002165 conserved gate region; other site 535289002166 putative PBP binding loops; other site 535289002167 ABC-ATPase subunit interface; other site 535289002168 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 535289002169 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 535289002170 metal binding site [ion binding]; metal-binding site 535289002171 putative dimer interface [polypeptide binding]; other site 535289002172 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 535289002173 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 535289002174 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 535289002175 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289002176 dimer interface [polypeptide binding]; other site 535289002177 conserved gate region; other site 535289002178 putative PBP binding loops; other site 535289002179 ABC-ATPase subunit interface; other site 535289002180 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 535289002181 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 535289002182 Walker A/P-loop; other site 535289002183 ATP binding site [chemical binding]; other site 535289002184 Q-loop/lid; other site 535289002185 ABC transporter signature motif; other site 535289002186 Walker B; other site 535289002187 D-loop; other site 535289002188 H-loop/switch region; other site 535289002189 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 535289002190 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 535289002191 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 535289002192 Walker A/P-loop; other site 535289002193 ATP binding site [chemical binding]; other site 535289002194 Q-loop/lid; other site 535289002195 ABC transporter signature motif; other site 535289002196 Walker B; other site 535289002197 D-loop; other site 535289002198 H-loop/switch region; other site 535289002199 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 535289002200 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 535289002201 CD73 ecto-5'-nucleotidase and related proteins, N-terminal metallophosphatase domain; Region: MPP_CD73_N; cd07409 535289002202 active site 535289002203 metal binding site [ion binding]; metal-binding site 535289002204 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 535289002205 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 535289002206 substrate binding site [chemical binding]; other site 535289002207 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 535289002208 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 535289002209 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 535289002210 putative active site [active] 535289002211 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 535289002212 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 535289002213 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 535289002214 transaldolase-like protein; Provisional; Region: PTZ00411 535289002215 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 535289002216 active site 535289002217 dimer interface [polypeptide binding]; other site 535289002218 catalytic residue [active] 535289002219 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 535289002220 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 535289002221 active site 535289002222 dimer interface [polypeptide binding]; other site 535289002223 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 535289002224 dimer interface [polypeptide binding]; other site 535289002225 active site 535289002226 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289002227 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289002228 metal binding site [ion binding]; metal-binding site 535289002229 active site 535289002230 I-site; other site 535289002231 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 535289002232 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 535289002233 ring oligomerisation interface [polypeptide binding]; other site 535289002234 ATP/Mg binding site [chemical binding]; other site 535289002235 stacking interactions; other site 535289002236 hinge regions; other site 535289002237 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 535289002238 oligomerisation interface [polypeptide binding]; other site 535289002239 mobile loop; other site 535289002240 roof hairpin; other site 535289002241 bifunctional nicotinamide mononucleotide adenylyltransferase/ADP-ribose pyrophosphatase; Provisional; Region: PRK05379 535289002242 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 535289002243 active site 535289002244 nucleotide binding site [chemical binding]; other site 535289002245 HIGH motif; other site 535289002246 KMSKS motif; other site 535289002247 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 535289002248 nudix motif; other site 535289002249 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 535289002250 catalytic triad [active] 535289002251 conserved cis-peptide bond; other site 535289002252 hypothetical protein; Provisional; Region: PRK13682 535289002253 S-adenosylmethionine synthetase; Validated; Region: PRK05250 535289002254 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 535289002255 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 535289002256 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 535289002257 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 535289002258 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 535289002259 putative acyl-acceptor binding pocket; other site 535289002260 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 535289002261 putative acyl-acceptor binding pocket; other site 535289002262 Transposase domain (DUF772); Region: DUF772; pfam05598 535289002263 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 535289002264 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 535289002265 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 535289002266 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 535289002267 G1 box; other site 535289002268 GTP/Mg2+ binding site [chemical binding]; other site 535289002269 Switch I region; other site 535289002270 G2 box; other site 535289002271 G3 box; other site 535289002272 Switch II region; other site 535289002273 G4 box; other site 535289002274 G5 box; other site 535289002275 Cytochrome c553 [Energy production and conversion]; Region: COG2863 535289002276 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 535289002277 Cytochrome c; Region: Cytochrom_C; cl11414 535289002278 ResB-like family; Region: ResB; pfam05140 535289002279 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 535289002280 ResB-like family; Region: ResB; pfam05140 535289002281 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 535289002282 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 535289002283 TMAO/DMSO reductase; Reviewed; Region: PRK05363 535289002284 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 535289002285 Moco binding site; other site 535289002286 metal coordination site [ion binding]; other site 535289002287 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 535289002288 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 535289002289 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 535289002290 diaminopimelate decarboxylase; Region: lysA; TIGR01048 535289002291 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 535289002292 active site 535289002293 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 535289002294 substrate binding site [chemical binding]; other site 535289002295 catalytic residues [active] 535289002296 dimer interface [polypeptide binding]; other site 535289002297 Frataxin-like domain; Region: Frataxin_Cyay; pfam01491 535289002298 putative iron binding site [ion binding]; other site 535289002299 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 535289002300 Transglycosylase; Region: Transgly; pfam00912 535289002301 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 535289002302 Competence protein A; Region: Competence_A; pfam11104 535289002303 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 535289002304 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 535289002305 nucleotide binding site [chemical binding]; other site 535289002306 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 535289002307 Pilus assembly protein, PilO; Region: PilO; pfam04350 535289002308 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 535289002309 Pilus assembly protein, PilP; Region: PilP; pfam04351 535289002310 AMIN domain; Region: AMIN; pfam11741 535289002311 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 535289002312 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 535289002313 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 535289002314 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 535289002315 active site 535289002316 dimer interface [polypeptide binding]; other site 535289002317 metal binding site [ion binding]; metal-binding site 535289002318 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 535289002319 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 535289002320 Zn2+ binding site [ion binding]; other site 535289002321 Mg2+ binding site [ion binding]; other site 535289002322 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 535289002323 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 535289002324 Methyltransferase domain; Region: Methyltransf_32; pfam13679 535289002325 Methyltransferase domain; Region: Methyltransf_31; pfam13847 535289002326 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 535289002327 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 535289002328 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 535289002329 active site 535289002330 dimer interface [polypeptide binding]; other site 535289002331 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 535289002332 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 535289002333 active site 535289002334 FMN binding site [chemical binding]; other site 535289002335 substrate binding site [chemical binding]; other site 535289002336 3Fe-4S cluster binding site [ion binding]; other site 535289002337 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 535289002338 domain interface; other site 535289002339 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 535289002340 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 535289002341 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 535289002342 substrate binding pocket [chemical binding]; other site 535289002343 membrane-bound complex binding site; other site 535289002344 hinge residues; other site 535289002345 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 535289002346 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289002347 dimer interface [polypeptide binding]; other site 535289002348 conserved gate region; other site 535289002349 putative PBP binding loops; other site 535289002350 ABC-ATPase subunit interface; other site 535289002351 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 535289002352 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 535289002353 Walker A/P-loop; other site 535289002354 ATP binding site [chemical binding]; other site 535289002355 Q-loop/lid; other site 535289002356 ABC transporter signature motif; other site 535289002357 Walker B; other site 535289002358 D-loop; other site 535289002359 H-loop/switch region; other site 535289002360 spermidine synthase; Provisional; Region: PRK00811 535289002361 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 535289002362 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; pfam02675 535289002363 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 535289002364 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 535289002365 Walker A/P-loop; other site 535289002366 ATP binding site [chemical binding]; other site 535289002367 Q-loop/lid; other site 535289002368 ABC transporter signature motif; other site 535289002369 Walker B; other site 535289002370 D-loop; other site 535289002371 H-loop/switch region; other site 535289002372 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 535289002373 Permease; Region: Permease; pfam02405 535289002374 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 535289002375 mce related protein; Region: MCE; pfam02470 535289002376 VacJ like lipoprotein; Region: VacJ; cl01073 535289002377 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 535289002378 STAS domain; Region: STAS_2; pfam13466 535289002379 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 535289002380 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 535289002381 Walker A/P-loop; other site 535289002382 ATP binding site [chemical binding]; other site 535289002383 Q-loop/lid; other site 535289002384 ABC transporter signature motif; other site 535289002385 Walker B; other site 535289002386 D-loop; other site 535289002387 H-loop/switch region; other site 535289002388 ABC-2 type transporter; Region: ABC2_membrane; cl17235 535289002389 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 535289002390 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 535289002391 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 535289002392 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 535289002393 hinge; other site 535289002394 active site 535289002395 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 535289002396 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 535289002397 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 535289002398 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 535289002399 NAD binding site [chemical binding]; other site 535289002400 dimerization interface [polypeptide binding]; other site 535289002401 product binding site; other site 535289002402 substrate binding site [chemical binding]; other site 535289002403 zinc binding site [ion binding]; other site 535289002404 catalytic residues [active] 535289002405 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 535289002406 putative active site [active] 535289002407 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 535289002408 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 535289002409 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289002410 homodimer interface [polypeptide binding]; other site 535289002411 catalytic residue [active] 535289002412 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 535289002413 putative active site pocket [active] 535289002414 4-fold oligomerization interface [polypeptide binding]; other site 535289002415 metal binding residues [ion binding]; metal-binding site 535289002416 3-fold/trimer interface [polypeptide binding]; other site 535289002417 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 535289002418 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 535289002419 putative active site [active] 535289002420 oxyanion strand; other site 535289002421 catalytic triad [active] 535289002422 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 535289002423 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 535289002424 catalytic residues [active] 535289002425 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289002426 Outer membrane efflux protein; Region: OEP; pfam02321 535289002427 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 535289002428 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 535289002429 DXD motif; other site 535289002430 DNA polymerase II large subunit; Provisional; Region: PRK14714 535289002431 UDP-glucose 4-epimerase; Region: PLN02240 535289002432 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 535289002433 NAD binding site [chemical binding]; other site 535289002434 homodimer interface [polypeptide binding]; other site 535289002435 active site 535289002436 substrate binding site [chemical binding]; other site 535289002437 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 535289002438 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 535289002439 substrate binding site [chemical binding]; other site 535289002440 glutamase interaction surface [polypeptide binding]; other site 535289002441 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 535289002442 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 535289002443 metal binding site [ion binding]; metal-binding site 535289002444 Predicted membrane protein [Function unknown]; Region: COG3671 535289002445 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 535289002446 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 535289002447 active site 535289002448 nucleophile elbow; other site 535289002449 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 535289002450 nucleotide binding site/active site [active] 535289002451 HIT family signature motif; other site 535289002452 catalytic residue [active] 535289002453 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 535289002454 sec-independent translocase; Provisional; Region: tatB; PRK01919 535289002455 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 535289002456 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 535289002457 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 535289002458 protein binding site [polypeptide binding]; other site 535289002459 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 535289002460 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 535289002461 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 535289002462 FAD binding pocket [chemical binding]; other site 535289002463 FAD binding motif [chemical binding]; other site 535289002464 phosphate binding motif [ion binding]; other site 535289002465 beta-alpha-beta structure motif; other site 535289002466 NAD binding pocket [chemical binding]; other site 535289002467 Uncharacterized conserved protein [Function unknown]; Region: COG0327 535289002468 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 535289002469 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 535289002470 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 535289002471 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 535289002472 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 535289002473 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 535289002474 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 535289002475 [2Fe-2S] cluster binding site [ion binding]; other site 535289002476 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 535289002477 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 535289002478 Qi binding site; other site 535289002479 intrachain domain interface; other site 535289002480 interchain domain interface [polypeptide binding]; other site 535289002481 heme bH binding site [chemical binding]; other site 535289002482 heme bL binding site [chemical binding]; other site 535289002483 Qo binding site; other site 535289002484 interchain domain interface [polypeptide binding]; other site 535289002485 intrachain domain interface; other site 535289002486 Qi binding site; other site 535289002487 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 535289002488 Qo binding site; other site 535289002489 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 535289002490 stringent starvation protein A; Provisional; Region: sspA; PRK09481 535289002491 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 535289002492 C-terminal domain interface [polypeptide binding]; other site 535289002493 putative GSH binding site (G-site) [chemical binding]; other site 535289002494 dimer interface [polypeptide binding]; other site 535289002495 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 535289002496 dimer interface [polypeptide binding]; other site 535289002497 N-terminal domain interface [polypeptide binding]; other site 535289002498 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 535289002499 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 535289002500 Peptidase family M23; Region: Peptidase_M23; pfam01551 535289002501 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 535289002502 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 535289002503 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 535289002504 nucleotide binding region [chemical binding]; other site 535289002505 SEC-C motif; Region: SEC-C; pfam02810 535289002506 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 535289002507 heterotetramer interface [polypeptide binding]; other site 535289002508 active site pocket [active] 535289002509 cleavage site 535289002510 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 535289002511 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289002512 Walker A motif; other site 535289002513 ATP binding site [chemical binding]; other site 535289002514 Walker B motif; other site 535289002515 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 535289002516 active site 535289002517 8-oxo-dGMP binding site [chemical binding]; other site 535289002518 nudix motif; other site 535289002519 metal binding site [ion binding]; metal-binding site 535289002520 Domain of unknown function (DUF329); Region: DUF329; pfam03884 535289002521 hypothetical protein; Provisional; Region: PRK05287 535289002522 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 535289002523 dephospho-CoA kinase; Region: TIGR00152 535289002524 CoA-binding site [chemical binding]; other site 535289002525 ATP-binding [chemical binding]; other site 535289002526 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 535289002527 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 535289002528 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 535289002529 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 535289002530 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 535289002531 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 535289002532 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 535289002533 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 535289002534 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 535289002535 Walker A motif; other site 535289002536 ATP binding site [chemical binding]; other site 535289002537 Walker B motif; other site 535289002538 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 535289002539 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 535289002540 substrate binding pocket [chemical binding]; other site 535289002541 chain length determination region; other site 535289002542 substrate-Mg2+ binding site; other site 535289002543 catalytic residues [active] 535289002544 aspartate-rich region 1; other site 535289002545 active site lid residues [active] 535289002546 aspartate-rich region 2; other site 535289002547 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 535289002548 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 535289002549 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 535289002550 GTPase CgtA; Reviewed; Region: obgE; PRK12299 535289002551 GTP1/OBG; Region: GTP1_OBG; pfam01018 535289002552 Obg GTPase; Region: Obg; cd01898 535289002553 G1 box; other site 535289002554 GTP/Mg2+ binding site [chemical binding]; other site 535289002555 Switch I region; other site 535289002556 G2 box; other site 535289002557 G3 box; other site 535289002558 Switch II region; other site 535289002559 G4 box; other site 535289002560 G5 box; other site 535289002561 gamma-glutamyl kinase; Provisional; Region: PRK05429 535289002562 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 535289002563 nucleotide binding site [chemical binding]; other site 535289002564 homotetrameric interface [polypeptide binding]; other site 535289002565 putative phosphate binding site [ion binding]; other site 535289002566 putative allosteric binding site; other site 535289002567 PUA domain; Region: PUA; pfam01472 535289002568 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 535289002569 putative active site [active] 535289002570 Ap4A binding site [chemical binding]; other site 535289002571 nudix motif; other site 535289002572 putative metal binding site [ion binding]; other site 535289002573 prolyl-tRNA synthetase; Provisional; Region: PRK09194 535289002574 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 535289002575 dimer interface [polypeptide binding]; other site 535289002576 motif 1; other site 535289002577 active site 535289002578 motif 2; other site 535289002579 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 535289002580 putative deacylase active site [active] 535289002581 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 535289002582 active site 535289002583 motif 3; other site 535289002584 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 535289002585 anticodon binding site; other site 535289002586 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 535289002587 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 535289002588 N-acetyl-D-glucosamine binding site [chemical binding]; other site 535289002589 catalytic residue [active] 535289002590 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 535289002591 Domain of unknown function DUF21; Region: DUF21; pfam01595 535289002592 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 535289002593 Transporter associated domain; Region: CorC_HlyC; smart01091 535289002594 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 535289002595 putative GSH binding site [chemical binding]; other site 535289002596 catalytic residues [active] 535289002597 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 535289002598 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 535289002599 S-adenosylmethionine binding site [chemical binding]; other site 535289002600 peptide chain release factor 1; Validated; Region: prfA; PRK00591 535289002601 This domain is found in peptide chain release factors; Region: PCRF; smart00937 535289002602 RF-1 domain; Region: RF-1; pfam00472 535289002603 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 535289002604 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 535289002605 tRNA; other site 535289002606 putative tRNA binding site [nucleotide binding]; other site 535289002607 putative NADP binding site [chemical binding]; other site 535289002608 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 535289002609 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 535289002610 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289002611 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 535289002612 dimerization interface [polypeptide binding]; other site 535289002613 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289002614 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 535289002615 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 535289002616 Mechanosensitive ion channel; Region: MS_channel; pfam00924 535289002617 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 535289002618 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 535289002619 putative active site [active] 535289002620 catalytic site [active] 535289002621 putative metal binding site [ion binding]; other site 535289002622 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 535289002623 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 535289002624 Walker A/P-loop; other site 535289002625 ATP binding site [chemical binding]; other site 535289002626 Q-loop/lid; other site 535289002627 ABC transporter signature motif; other site 535289002628 Walker B; other site 535289002629 D-loop; other site 535289002630 H-loop/switch region; other site 535289002631 TOBE domain; Region: TOBE_2; pfam08402 535289002632 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 535289002633 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289002634 dimer interface [polypeptide binding]; other site 535289002635 conserved gate region; other site 535289002636 putative PBP binding loops; other site 535289002637 ABC-ATPase subunit interface; other site 535289002638 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 535289002639 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289002640 dimer interface [polypeptide binding]; other site 535289002641 conserved gate region; other site 535289002642 putative PBP binding loops; other site 535289002643 ABC-ATPase subunit interface; other site 535289002644 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 535289002645 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 535289002646 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 535289002647 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 535289002648 ligand binding site [chemical binding]; other site 535289002649 NAD binding site [chemical binding]; other site 535289002650 tetramer interface [polypeptide binding]; other site 535289002651 catalytic site [active] 535289002652 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 535289002653 L-serine binding site [chemical binding]; other site 535289002654 ACT domain interface; other site 535289002655 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 535289002656 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 535289002657 FAD binding domain; Region: FAD_binding_4; pfam01565 535289002658 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 535289002659 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 535289002660 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 535289002661 Cysteine-rich domain; Region: CCG; pfam02754 535289002662 Cysteine-rich domain; Region: CCG; pfam02754 535289002663 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 535289002664 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 535289002665 HIT family signature motif; other site 535289002666 catalytic residue [active] 535289002667 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 535289002668 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 535289002669 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 535289002670 S-adenosylmethionine binding site [chemical binding]; other site 535289002671 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 535289002672 SCP-2 sterol transfer family; Region: SCP2; pfam02036 535289002673 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 535289002674 ABC1 family; Region: ABC1; pfam03109 535289002675 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 535289002676 active site 535289002677 ATP binding site [chemical binding]; other site 535289002678 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 535289002679 putative transporter; Provisional; Region: PRK10484 535289002680 Na binding site [ion binding]; other site 535289002681 putative glycosylation site [posttranslational modification]; other site 535289002682 putative glycosylation site [posttranslational modification]; other site 535289002683 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 535289002684 Uncharacterized conserved protein [Function unknown]; Region: COG2928 535289002685 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 535289002686 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 535289002687 dimer interface [polypeptide binding]; other site 535289002688 anticodon binding site; other site 535289002689 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 535289002690 homodimer interface [polypeptide binding]; other site 535289002691 motif 1; other site 535289002692 active site 535289002693 motif 2; other site 535289002694 GAD domain; Region: GAD; pfam02938 535289002695 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 535289002696 motif 3; other site 535289002697 Curli production assembly/transport component CsgG; Region: CsgG; cl17434 535289002698 dihydroneopterin triphosphate pyrophosphatase; Provisional; Region: nudB; PRK09438 535289002699 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 535289002700 putative catalytic site [active] 535289002701 putative metal binding site [ion binding]; other site 535289002702 putative phosphate binding site [ion binding]; other site 535289002703 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 535289002704 PLD-like domain; Region: PLDc_2; pfam13091 535289002705 putative active site [active] 535289002706 catalytic site [active] 535289002707 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 535289002708 PLD-like domain; Region: PLDc_2; pfam13091 535289002709 putative active site [active] 535289002710 catalytic site [active] 535289002711 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 535289002712 active site 535289002713 Sensors of blue-light using FAD; Region: BLUF; smart01034 535289002714 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 535289002715 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]; Region: COG4192 535289002716 amidase; Provisional; Region: PRK07042 535289002717 Amidase; Region: Amidase; cl11426 535289002718 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 535289002719 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 535289002720 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 535289002721 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 535289002722 Walker A/P-loop; other site 535289002723 ATP binding site [chemical binding]; other site 535289002724 Q-loop/lid; other site 535289002725 ABC transporter signature motif; other site 535289002726 Walker B; other site 535289002727 D-loop; other site 535289002728 H-loop/switch region; other site 535289002729 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 535289002730 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 535289002731 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 535289002732 Walker A/P-loop; other site 535289002733 ATP binding site [chemical binding]; other site 535289002734 Q-loop/lid; other site 535289002735 ABC transporter signature motif; other site 535289002736 Walker B; other site 535289002737 D-loop; other site 535289002738 H-loop/switch region; other site 535289002739 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 535289002740 glutathione ABC transporter permease GsiD; Provisional; Region: PRK15082 535289002741 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289002742 dimer interface [polypeptide binding]; other site 535289002743 conserved gate region; other site 535289002744 putative PBP binding loops; other site 535289002745 ABC-ATPase subunit interface; other site 535289002746 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 535289002747 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289002748 dimer interface [polypeptide binding]; other site 535289002749 conserved gate region; other site 535289002750 putative PBP binding loops; other site 535289002751 ABC-ATPase subunit interface; other site 535289002752 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 535289002753 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 535289002754 putative active site [active] 535289002755 catalytic residue [active] 535289002756 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 535289002757 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 535289002758 5S rRNA interface [nucleotide binding]; other site 535289002759 CTC domain interface [polypeptide binding]; other site 535289002760 L16 interface [polypeptide binding]; other site 535289002761 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 535289002762 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 535289002763 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 535289002764 active site 535289002765 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 535289002766 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 535289002767 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 535289002768 binding surface 535289002769 TPR motif; other site 535289002770 Tetratricopeptide repeat; Region: TPR_16; pfam13432 535289002771 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 535289002772 binding surface 535289002773 TPR motif; other site 535289002774 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 535289002775 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 535289002776 DNA binding site [nucleotide binding] 535289002777 catalytic residue [active] 535289002778 H2TH interface [polypeptide binding]; other site 535289002779 putative catalytic residues [active] 535289002780 turnover-facilitating residue; other site 535289002781 intercalation triad [nucleotide binding]; other site 535289002782 8OG recognition residue [nucleotide binding]; other site 535289002783 putative reading head residues; other site 535289002784 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 535289002785 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 535289002786 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 535289002787 Dynamin family; Region: Dynamin_N; pfam00350 535289002788 G1 box; other site 535289002789 GTP/Mg2+ binding site [chemical binding]; other site 535289002790 G2 box; other site 535289002791 Switch I region; other site 535289002792 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 535289002793 G3 box; other site 535289002794 Switch II region; other site 535289002795 GTP/Mg2+ binding site [chemical binding]; other site 535289002796 G4 box; other site 535289002797 G5 box; other site 535289002798 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 535289002799 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 535289002800 minor groove reading motif; other site 535289002801 helix-hairpin-helix signature motif; other site 535289002802 substrate binding pocket [chemical binding]; other site 535289002803 active site 535289002804 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 535289002805 DNA binding and oxoG recognition site [nucleotide binding] 535289002806 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 535289002807 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 535289002808 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 535289002809 Walker A/P-loop; other site 535289002810 ATP binding site [chemical binding]; other site 535289002811 Q-loop/lid; other site 535289002812 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 535289002813 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 535289002814 ABC transporter signature motif; other site 535289002815 Walker B; other site 535289002816 D-loop; other site 535289002817 H-loop/switch region; other site 535289002818 NAD(+)/NADH kinase family protein; Provisional; Region: ppnK; PRK02155 535289002819 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 535289002820 Phage replication protein CRI; Region: Phage_CRI; pfam05144 535289002821 Protein of unknown function (DUF2523); Region: DUF2523; pfam10734 535289002822 Zonular occludens toxin (Zot); Region: Zot; cl17485 535289002823 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 535289002824 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 535289002825 catalytic residues [active] 535289002826 catalytic nucleophile [active] 535289002827 Presynaptic Site I dimer interface [polypeptide binding]; other site 535289002828 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 535289002829 Synaptic Flat tetramer interface [polypeptide binding]; other site 535289002830 Synaptic Site I dimer interface [polypeptide binding]; other site 535289002831 DNA binding site [nucleotide binding] 535289002832 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 535289002833 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 535289002834 YjgH belongs 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 similarity and no...; Region: YjgH_like; cd02198 535289002835 homotrimer interaction site [polypeptide binding]; other site 535289002836 putative active site [active] 535289002837 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289002838 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289002839 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 535289002840 putative effector binding pocket; other site 535289002841 putative dimerization interface [polypeptide binding]; other site 535289002842 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4430 535289002843 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 535289002844 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 535289002845 catalytic triad [active] 535289002846 Isochorismatase family; Region: Isochorismatase; pfam00857 535289002847 conserved cis-peptide bond; other site 535289002848 Predicted membrane protein [Function unknown]; Region: COG2323 535289002849 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 535289002850 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 535289002851 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 535289002852 FeS/SAM binding site; other site 535289002853 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 535289002854 active site 535289002855 dimerization interface [polypeptide binding]; other site 535289002856 ribonuclease PH; Reviewed; Region: rph; PRK00173 535289002857 Ribonuclease PH; Region: RNase_PH_bact; cd11362 535289002858 hexamer interface [polypeptide binding]; other site 535289002859 active site 535289002860 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 535289002861 Protein phosphatase 2C; Region: PP2C; pfam00481 535289002862 active site 535289002863 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 535289002864 Catalytic domain of Protein Kinases; Region: PKc; cd00180 535289002865 active site 535289002866 ATP binding site [chemical binding]; other site 535289002867 substrate binding site [chemical binding]; other site 535289002868 activation loop (A-loop); other site 535289002869 hypothetical protein; Provisional; Region: PRK11820 535289002870 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 535289002871 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 535289002872 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 535289002873 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 535289002874 catalytic site [active] 535289002875 G-X2-G-X-G-K; other site 535289002876 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 535289002877 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 535289002878 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 535289002879 Zn2+ binding site [ion binding]; other site 535289002880 Mg2+ binding site [ion binding]; other site 535289002881 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 535289002882 synthetase active site [active] 535289002883 NTP binding site [chemical binding]; other site 535289002884 metal binding site [ion binding]; metal-binding site 535289002885 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 535289002886 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 535289002887 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 535289002888 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 535289002889 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 535289002890 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 535289002891 16S/18S rRNA binding site [nucleotide binding]; other site 535289002892 S13e-L30e interaction site [polypeptide binding]; other site 535289002893 25S rRNA binding site [nucleotide binding]; other site 535289002894 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 535289002895 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 535289002896 RNase E interface [polypeptide binding]; other site 535289002897 trimer interface [polypeptide binding]; other site 535289002898 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 535289002899 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 535289002900 RNase E interface [polypeptide binding]; other site 535289002901 trimer interface [polypeptide binding]; other site 535289002902 active site 535289002903 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 535289002904 putative nucleic acid binding region [nucleotide binding]; other site 535289002905 G-X-X-G motif; other site 535289002906 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 535289002907 RNA binding site [nucleotide binding]; other site 535289002908 domain interface; other site 535289002909 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 535289002910 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 535289002911 NAD(P) binding site [chemical binding]; other site 535289002912 triosephosphate isomerase; Provisional; Region: PRK14567 535289002913 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 535289002914 substrate binding site [chemical binding]; other site 535289002915 dimer interface [polypeptide binding]; other site 535289002916 catalytic triad [active] 535289002917 Preprotein translocase SecG subunit; Region: SecG; pfam03840 535289002918 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 535289002919 NADH dehydrogenase subunit B; Validated; Region: PRK06411 535289002920 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 535289002921 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 535289002922 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 535289002923 NADH dehydrogenase subunit D; Validated; Region: PRK06075 535289002924 NADH dehydrogenase subunit E; Validated; Region: PRK07539 535289002925 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 535289002926 putative dimer interface [polypeptide binding]; other site 535289002927 [2Fe-2S] cluster binding site [ion binding]; other site 535289002928 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 535289002929 SLBB domain; Region: SLBB; pfam10531 535289002930 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 535289002931 NADH dehydrogenase subunit G; Validated; Region: PRK09129 535289002932 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 535289002933 catalytic loop [active] 535289002934 iron binding site [ion binding]; other site 535289002935 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 535289002936 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 535289002937 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 535289002938 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 535289002939 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 535289002940 4Fe-4S binding domain; Region: Fer4; pfam00037 535289002941 4Fe-4S binding domain; Region: Fer4; pfam00037 535289002942 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 535289002943 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 535289002944 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 535289002945 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 535289002946 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 535289002947 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 535289002948 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 535289002949 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 535289002950 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 535289002951 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 535289002952 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 535289002953 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 535289002954 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 535289002955 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 535289002956 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289002957 Walker A/P-loop; other site 535289002958 ATP binding site [chemical binding]; other site 535289002959 Q-loop/lid; other site 535289002960 ABC transporter signature motif; other site 535289002961 Walker B; other site 535289002962 D-loop; other site 535289002963 H-loop/switch region; other site 535289002964 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289002965 heme ABC exporter, ATP-binding protein CcmA; Region: ccmA; TIGR01189 535289002966 Walker A/P-loop; other site 535289002967 ATP binding site [chemical binding]; other site 535289002968 Q-loop/lid; other site 535289002969 ABC transporter signature motif; other site 535289002970 Walker B; other site 535289002971 D-loop; other site 535289002972 H-loop/switch region; other site 535289002973 LysE type translocator; Region: LysE; cl00565 535289002974 glutamate dehydrogenase; Provisional; Region: PRK09414 535289002975 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 535289002976 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 535289002977 NAD(P) binding site [chemical binding]; other site 535289002978 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 535289002979 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 535289002980 ATP binding site [chemical binding]; other site 535289002981 Mg2+ binding site [ion binding]; other site 535289002982 G-X-G motif; other site 535289002983 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 535289002984 ATP binding site [chemical binding]; other site 535289002985 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 535289002986 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 535289002987 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 535289002988 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 535289002989 AMIN domain; Region: AMIN; pfam11741 535289002990 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 535289002991 active site 535289002992 metal binding site [ion binding]; metal-binding site 535289002993 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 535289002994 epoxyqueuosine reductase; Region: TIGR00276 535289002995 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 535289002996 Membrane transport protein; Region: Mem_trans; cl09117 535289002997 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289002998 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 535289002999 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 535289003000 active site 535289003001 Int/Topo IB signature motif; other site 535289003002 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 535289003003 EAL domain; Region: EAL; pfam00563 535289003004 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 535289003005 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 535289003006 EAL domain; Region: EAL; pfam00563 535289003007 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 535289003008 dinuclear metal binding motif [ion binding]; other site 535289003009 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 535289003010 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 535289003011 trimer interface [polypeptide binding]; other site 535289003012 putative metal binding site [ion binding]; other site 535289003013 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 535289003014 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 535289003015 dimerization interface [polypeptide binding]; other site 535289003016 domain crossover interface; other site 535289003017 redox-dependent activation switch; other site 535289003018 Septum formation initiator; Region: DivIC; cl17659 535289003019 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 535289003020 enolase; Provisional; Region: eno; PRK00077 535289003021 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 535289003022 dimer interface [polypeptide binding]; other site 535289003023 metal binding site [ion binding]; metal-binding site 535289003024 substrate binding pocket [chemical binding]; other site 535289003025 Uncharacterized conserved protein [Function unknown]; Region: COG5470 535289003026 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 535289003027 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 535289003028 CTP synthetase; Validated; Region: pyrG; PRK05380 535289003029 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 535289003030 Catalytic site [active] 535289003031 active site 535289003032 UTP binding site [chemical binding]; other site 535289003033 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 535289003034 active site 535289003035 putative oxyanion hole; other site 535289003036 catalytic triad [active] 535289003037 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 535289003038 Flavoprotein; Region: Flavoprotein; pfam02441 535289003039 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 535289003040 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 535289003041 trimer interface [polypeptide binding]; other site 535289003042 active site 535289003043 glutamyl-tRNA(Gln) amidotransferase; Region: PLN02751 535289003044 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 535289003045 Uncharacterized conserved protein [Function unknown]; Region: COG2850 535289003046 Cupin-like domain; Region: Cupin_8; pfam13621 535289003047 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 535289003048 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 535289003049 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 535289003050 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 535289003051 dihydrodipicolinate synthase; Region: dapA; TIGR00674 535289003052 dimer interface [polypeptide binding]; other site 535289003053 active site 535289003054 catalytic residue [active] 535289003055 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 535289003056 S-adenosylmethionine binding site [chemical binding]; other site 535289003057 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289003058 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 535289003059 putative substrate translocation pore; other site 535289003060 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 535289003061 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 535289003062 ATP binding site [chemical binding]; other site 535289003063 Mg2+ binding site [ion binding]; other site 535289003064 G-X-G motif; other site 535289003065 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 535289003066 anchoring element; other site 535289003067 dimer interface [polypeptide binding]; other site 535289003068 ATP binding site [chemical binding]; other site 535289003069 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 535289003070 active site 535289003071 metal binding site [ion binding]; metal-binding site 535289003072 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 535289003073 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 535289003074 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 535289003075 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 535289003076 N-acetyl-D-glucosamine binding site [chemical binding]; other site 535289003077 catalytic residue [active] 535289003078 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 535289003079 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 535289003080 CAP-like domain; other site 535289003081 active site 535289003082 primary dimer interface [polypeptide binding]; other site 535289003083 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 535289003084 HAMP domain; Region: HAMP; pfam00672 535289003085 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289003086 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289003087 dimer interface [polypeptide binding]; other site 535289003088 putative CheW interface [polypeptide binding]; other site 535289003089 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 535289003090 homotrimer interaction site [polypeptide binding]; other site 535289003091 putative active site [active] 535289003092 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 535289003093 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 535289003094 Competence protein; Region: Competence; pfam03772 535289003095 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 535289003096 Uncharacterized conserved protein [Function unknown]; Region: COG2308 535289003097 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 535289003098 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 535289003099 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 535289003100 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 535289003101 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289003102 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289003103 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 535289003104 putative effector binding pocket; other site 535289003105 putative dimerization interface [polypeptide binding]; other site 535289003106 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 535289003107 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 535289003108 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289003109 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289003110 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 535289003111 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289003112 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 535289003113 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 535289003114 tetramerization interface [polypeptide binding]; other site 535289003115 NAD(P) binding site [chemical binding]; other site 535289003116 catalytic residues [active] 535289003117 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 535289003118 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 535289003119 N-terminal plug; other site 535289003120 ligand-binding site [chemical binding]; other site 535289003121 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 535289003122 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 535289003123 N-terminal plug; other site 535289003124 ligand-binding site [chemical binding]; other site 535289003125 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 535289003126 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 535289003127 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 535289003128 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 535289003129 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 it...; Region: TST_Repeat_1; cd01448 535289003130 active site residue [active] 535289003131 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 535289003132 active site residue [active] 535289003133 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 535289003134 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 535289003135 [2Fe-2S] cluster binding site [ion binding]; other site 535289003136 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 535289003137 alpha subunit interface [polypeptide binding]; other site 535289003138 active site 535289003139 substrate binding site [chemical binding]; other site 535289003140 Fe binding site [ion binding]; other site 535289003141 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 535289003142 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 535289003143 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 535289003144 substrate binding pocket [chemical binding]; other site 535289003145 chain length determination region; other site 535289003146 substrate-Mg2+ binding site; other site 535289003147 catalytic residues [active] 535289003148 aspartate-rich region 1; other site 535289003149 active site lid residues [active] 535289003150 aspartate-rich region 2; other site 535289003151 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 535289003152 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 535289003153 TPP-binding site; other site 535289003154 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 535289003155 PYR/PP interface [polypeptide binding]; other site 535289003156 dimer interface [polypeptide binding]; other site 535289003157 TPP binding site [chemical binding]; other site 535289003158 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 535289003159 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 535289003160 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 535289003161 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 535289003162 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 535289003163 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 535289003164 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 535289003165 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 535289003166 PAS domain; Region: PAS_9; pfam13426 535289003167 putative active site [active] 535289003168 heme pocket [chemical binding]; other site 535289003169 PAS domain; Region: PAS_9; pfam13426 535289003170 PAS fold; Region: PAS_3; pfam08447 535289003171 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 535289003172 PAS fold; Region: PAS_4; pfam08448 535289003173 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 535289003174 putative active site [active] 535289003175 heme pocket [chemical binding]; other site 535289003176 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289003177 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289003178 dimer interface [polypeptide binding]; other site 535289003179 phosphorylation site [posttranslational modification] 535289003180 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 535289003181 ATP binding site [chemical binding]; other site 535289003182 Mg2+ binding site [ion binding]; other site 535289003183 G-X-G motif; other site 535289003184 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 535289003185 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 535289003186 active site 535289003187 phosphorylation site [posttranslational modification] 535289003188 intermolecular recognition site; other site 535289003189 dimerization interface [polypeptide binding]; other site 535289003190 Response regulator receiver domain; Region: Response_reg; pfam00072 535289003191 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 535289003192 active site 535289003193 phosphorylation site [posttranslational modification] 535289003194 intermolecular recognition site; other site 535289003195 dimerization interface [polypeptide binding]; other site 535289003196 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 535289003197 putative binding surface; other site 535289003198 active site 535289003199 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 535289003200 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 535289003201 active site 535289003202 phosphorylation site [posttranslational modification] 535289003203 intermolecular recognition site; other site 535289003204 dimerization interface [polypeptide binding]; other site 535289003205 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 535289003206 Zn2+ binding site [ion binding]; other site 535289003207 Mg2+ binding site [ion binding]; other site 535289003208 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 535289003209 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 535289003210 active site 535289003211 dimerization interface [polypeptide binding]; other site 535289003212 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 535289003213 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 535289003214 serine O-acetyltransferase; Region: cysE; TIGR01172 535289003215 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 535289003216 trimer interface [polypeptide binding]; other site 535289003217 active site 535289003218 substrate binding site [chemical binding]; other site 535289003219 CoA binding site [chemical binding]; other site 535289003220 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 535289003221 putative FMN binding site [chemical binding]; other site 535289003222 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 535289003223 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 535289003224 tetramer interface [polypeptide binding]; other site 535289003225 catalytic Zn binding site [ion binding]; other site 535289003226 NADP binding site [chemical binding]; other site 535289003227 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 535289003228 Sulfate transporter family; Region: Sulfate_transp; pfam00916 535289003229 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 535289003230 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 535289003231 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 535289003232 MPT binding site; other site 535289003233 trimer interface [polypeptide binding]; other site 535289003234 Protein of unknown function (DUF615); Region: DUF615; pfam04751 535289003235 peptidase PmbA; Provisional; Region: PRK11040 535289003236 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 535289003237 EamA-like transporter family; Region: EamA; pfam00892 535289003238 tellurite resistance protein terB; Region: terB; cd07176 535289003239 putative metal binding site [ion binding]; other site 535289003240 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 535289003241 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 535289003242 Fumarase C-terminus; Region: Fumerase_C; pfam05683 535289003243 fumarate hydratase; Reviewed; Region: fumC; PRK00485 535289003244 Class II fumarases; Region: Fumarase_classII; cd01362 535289003245 active site 535289003246 tetramer interface [polypeptide binding]; other site 535289003247 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289003248 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 535289003249 ligand binding site [chemical binding]; other site 535289003250 flexible hinge region; other site 535289003251 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 535289003252 non-specific DNA interactions [nucleotide binding]; other site 535289003253 DNA binding site [nucleotide binding] 535289003254 sequence specific DNA binding site [nucleotide binding]; other site 535289003255 putative cAMP binding site [chemical binding]; other site 535289003256 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 535289003257 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 535289003258 active site 535289003259 phosphorylation site [posttranslational modification] 535289003260 intermolecular recognition site; other site 535289003261 dimerization interface [polypeptide binding]; other site 535289003262 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289003263 DNA binding site [nucleotide binding] 535289003264 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289003265 dimerization interface [polypeptide binding]; other site 535289003266 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289003267 dimer interface [polypeptide binding]; other site 535289003268 phosphorylation site [posttranslational modification] 535289003269 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 535289003270 ATP binding site [chemical binding]; other site 535289003271 Mg2+ binding site [ion binding]; other site 535289003272 G-X-G motif; other site 535289003273 glycine betaine transporter periplasmic subunit; Provisional; Region: proX; PRK11119 535289003274 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 535289003275 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289003276 dimer interface [polypeptide binding]; other site 535289003277 conserved gate region; other site 535289003278 putative PBP binding loops; other site 535289003279 ABC-ATPase subunit interface; other site 535289003280 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 535289003281 ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system; Region: ABC_Pro_Gly_Betaine; cd03294 535289003282 Walker A/P-loop; other site 535289003283 ATP binding site [chemical binding]; other site 535289003284 Q-loop/lid; other site 535289003285 ABC transporter signature motif; other site 535289003286 Walker B; other site 535289003287 D-loop; other site 535289003288 H-loop/switch region; other site 535289003289 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 535289003290 hypothetical protein; Provisional; Region: PRK05208 535289003291 acetyl-CoA synthetase; Provisional; Region: PRK00174 535289003292 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 535289003293 active site 535289003294 CoA binding site [chemical binding]; other site 535289003295 acyl-activating enzyme (AAE) consensus motif; other site 535289003296 AMP binding site [chemical binding]; other site 535289003297 acetate binding site [chemical binding]; other site 535289003298 Cytochrome c; Region: Cytochrom_C; cl11414 535289003299 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 535289003300 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 535289003301 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 535289003302 CoenzymeA binding site [chemical binding]; other site 535289003303 subunit interaction site [polypeptide binding]; other site 535289003304 PHB binding site; other site 535289003305 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 535289003306 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 535289003307 heme binding site [chemical binding]; other site 535289003308 ferroxidase pore; other site 535289003309 ferroxidase diiron center [ion binding]; other site 535289003310 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 535289003311 Transcriptional regulators [Transcription]; Region: GntR; COG1802 535289003312 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289003313 DNA-binding site [nucleotide binding]; DNA binding site 535289003314 FCD domain; Region: FCD; pfam07729 535289003315 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 535289003316 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289003317 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 535289003318 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 535289003319 substrate binding site [chemical binding]; other site 535289003320 oxyanion hole (OAH) forming residues; other site 535289003321 trimer interface [polypeptide binding]; other site 535289003322 malonyl-CoA synthase; Validated; Region: PRK07514 535289003323 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 535289003324 acyl-activating enzyme (AAE) consensus motif; other site 535289003325 active site 535289003326 AMP binding site [chemical binding]; other site 535289003327 CoA binding site [chemical binding]; other site 535289003328 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 535289003329 Ligand Binding Site [chemical binding]; other site 535289003330 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 535289003331 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 535289003332 metal-binding site [ion binding] 535289003333 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289003334 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 535289003335 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 535289003336 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 535289003337 Low-spin heme binding site [chemical binding]; other site 535289003338 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 535289003339 Putative water exit pathway; other site 535289003340 Binuclear center (active site) [active] 535289003341 Putative proton exit pathway; other site 535289003342 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 535289003343 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 535289003344 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 535289003345 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 535289003346 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 535289003347 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 535289003348 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 535289003349 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 535289003350 FixH; Region: FixH; pfam05751 535289003351 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 535289003352 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 535289003353 ligand binding site [chemical binding]; other site 535289003354 flexible hinge region; other site 535289003355 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 535289003356 putative switch regulator; other site 535289003357 non-specific DNA interactions [nucleotide binding]; other site 535289003358 DNA binding site [nucleotide binding] 535289003359 sequence specific DNA binding site [nucleotide binding]; other site 535289003360 putative cAMP binding site [chemical binding]; other site 535289003361 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 535289003362 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 535289003363 FeS/SAM binding site; other site 535289003364 HemN C-terminal domain; Region: HemN_C; pfam06969 535289003365 Family description; Region: DsbD_2; pfam13386 535289003366 Cell division protein ZapA; Region: ZapA; pfam05164 535289003367 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 535289003368 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 535289003369 N-terminal plug; other site 535289003370 ligand-binding site [chemical binding]; other site 535289003371 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 535289003372 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 535289003373 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 535289003374 catalytic triad [active] 535289003375 Cobinamide kinase / cobinamide phosphate guanyltransferase; Region: CobU; pfam02283 535289003376 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 535289003377 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 535289003378 intersubunit interface [polypeptide binding]; other site 535289003379 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 535289003380 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 535289003381 dimer interface [polypeptide binding]; other site 535289003382 putative PBP binding regions; other site 535289003383 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 535289003384 ABC-ATPase subunit interface; other site 535289003385 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 535289003386 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 535289003387 Walker A/P-loop; other site 535289003388 ATP binding site [chemical binding]; other site 535289003389 Q-loop/lid; other site 535289003390 ABC transporter signature motif; other site 535289003391 Walker B; other site 535289003392 D-loop; other site 535289003393 H-loop/switch region; other site 535289003394 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 535289003395 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 535289003396 homodimer interface [polypeptide binding]; other site 535289003397 Walker A motif; other site 535289003398 ATP binding site [chemical binding]; other site 535289003399 hydroxycobalamin binding site [chemical binding]; other site 535289003400 Walker B motif; other site 535289003401 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 535289003402 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 535289003403 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 535289003404 DNA binding site [nucleotide binding] 535289003405 active site 535289003406 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289003407 Transposase; Region: HTH_Tnp_1; pfam01527 535289003408 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 535289003409 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 535289003410 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 535289003411 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 535289003412 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 535289003413 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 535289003414 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 535289003415 Protein of unknown function (DUF3334); Region: DUF3334; pfam11813 535289003416 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 535289003417 YceI-like domain; Region: YceI; smart00867 535289003418 Uncharacterized conserved protein [Function unknown]; Region: COG2353 535289003419 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 535289003420 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 535289003421 motif II; other site 535289003422 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 535289003423 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 535289003424 putative substrate translocation pore; other site 535289003425 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 535289003426 malic enzyme; Reviewed; Region: PRK12862 535289003427 Malic enzyme, N-terminal domain; Region: malic; pfam00390 535289003428 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 535289003429 putative NAD(P) binding site [chemical binding]; other site 535289003430 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 535289003431 xanthine permease; Region: pbuX; TIGR03173 535289003432 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK08651 535289003433 M20 Zn-peptidases include exopeptidases; Region: M20_like; cd02697 535289003434 putative metal binding site [ion binding]; other site 535289003435 putative bifunctional OHCU decarboxylase/allantoate amidohydrolase; Provisional; Region: PRK13590 535289003436 OHCU decarboxylase; Region: OHCU_decarbox; pfam09349 535289003437 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 535289003438 active site 535289003439 metal binding site [ion binding]; metal-binding site 535289003440 dimer interface [polypeptide binding]; other site 535289003441 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 535289003442 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 535289003443 active site 535289003444 catalytic site [active] 535289003445 tetramer interface [polypeptide binding]; other site 535289003446 Transcriptional regulators [Transcription]; Region: GntR; COG1802 535289003447 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289003448 DNA-binding site [nucleotide binding]; DNA binding site 535289003449 FCD domain; Region: FCD; pfam07729 535289003450 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289003451 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289003452 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 535289003453 putative effector binding pocket; other site 535289003454 putative dimerization interface [polypeptide binding]; other site 535289003455 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 535289003456 tartrate dehydrogenase; Region: TTC; TIGR02089 535289003457 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289003458 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 535289003459 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 535289003460 MOFRL family; Region: MOFRL; pfam05161 535289003461 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 535289003462 active site 535289003463 homotetramer interface [polypeptide binding]; other site 535289003464 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 535289003465 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 535289003466 XdhC Rossmann domain; Region: XdhC_C; pfam13478 535289003467 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 535289003468 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 535289003469 NAD(P) binding site [chemical binding]; other site 535289003470 catalytic residues [active] 535289003471 Transcriptional regulators [Transcription]; Region: GntR; COG1802 535289003472 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl17414 535289003473 FCD domain; Region: FCD; pfam07729 535289003474 Predicted membrane protein [Function unknown]; Region: COG3748 535289003475 Protein of unknown function (DUF989); Region: DUF989; pfam06181 535289003476 Cytochrome c; Region: Cytochrom_C; pfam00034 535289003477 guanine deaminase; Provisional; Region: PRK09228 535289003478 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 535289003479 active site 535289003480 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 535289003481 trimer interface [polypeptide binding]; other site 535289003482 active site 535289003483 Predicted metalloprotease [General function prediction only]; Region: COG2321 535289003484 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 535289003485 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 535289003486 DEAD-like helicases superfamily; Region: DEXDc; smart00487 535289003487 ATP binding site [chemical binding]; other site 535289003488 Mg++ binding site [ion binding]; other site 535289003489 motif III; other site 535289003490 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 535289003491 nucleotide binding region [chemical binding]; other site 535289003492 ATP-binding site [chemical binding]; other site 535289003493 NosL; Region: NosL; cl01769 535289003494 NosL; Region: NosL; pfam05573 535289003495 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 535289003496 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 535289003497 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 535289003498 Walker A/P-loop; other site 535289003499 ATP binding site [chemical binding]; other site 535289003500 Q-loop/lid; other site 535289003501 ABC transporter signature motif; other site 535289003502 Walker B; other site 535289003503 D-loop; other site 535289003504 H-loop/switch region; other site 535289003505 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 535289003506 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 535289003507 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 535289003508 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 535289003509 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 535289003510 4Fe-4S binding domain; Region: Fer4_5; pfam12801 535289003511 4Fe-4S binding domain; Region: Fer4_5; pfam12801 535289003512 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 535289003513 nitrous-oxide reductase; Validated; Region: PRK02888 535289003514 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 535289003515 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 535289003516 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 535289003517 ApbE family; Region: ApbE; pfam02424 535289003518 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 535289003519 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 535289003520 active site 535289003521 metal binding site [ion binding]; metal-binding site 535289003522 H-NS histone family; Region: Histone_HNS; pfam00816 535289003523 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 535289003524 aconitate hydratase; Validated; Region: PRK09277 535289003525 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 535289003526 substrate binding site [chemical binding]; other site 535289003527 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 535289003528 ligand binding site [chemical binding]; other site 535289003529 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 535289003530 substrate binding site [chemical binding]; other site 535289003531 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 535289003532 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 535289003533 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289003534 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 535289003535 putative substrate translocation pore; other site 535289003536 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 535289003537 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 535289003538 active site 535289003539 phosphorylation site [posttranslational modification] 535289003540 intermolecular recognition site; other site 535289003541 dimerization interface [polypeptide binding]; other site 535289003542 LytTr DNA-binding domain; Region: LytTR; smart00850 535289003543 Histidine kinase; Region: His_kinase; pfam06580 535289003544 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 535289003545 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 535289003546 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 535289003547 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289003548 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289003549 metal binding site [ion binding]; metal-binding site 535289003550 active site 535289003551 I-site; other site 535289003552 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 535289003553 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 535289003554 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 535289003555 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 535289003556 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 535289003557 MutS domain I; Region: MutS_I; pfam01624 535289003558 MutS domain II; Region: MutS_II; pfam05188 535289003559 MutS domain III; Region: MutS_III; pfam05192 535289003560 MutS domain V; Region: MutS_V; pfam00488 535289003561 Walker A/P-loop; other site 535289003562 ATP binding site [chemical binding]; other site 535289003563 Q-loop/lid; other site 535289003564 ABC transporter signature motif; other site 535289003565 Walker B; other site 535289003566 D-loop; other site 535289003567 H-loop/switch region; other site 535289003568 PhoD-like phosphatase; Region: PhoD; pfam09423 535289003569 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 535289003570 putative active site [active] 535289003571 putative metal binding site [ion binding]; other site 535289003572 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 535289003573 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289003574 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289003575 metal binding site [ion binding]; metal-binding site 535289003576 active site 535289003577 I-site; other site 535289003578 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 535289003579 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 535289003580 NAD(P) binding site [chemical binding]; other site 535289003581 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 535289003582 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 535289003583 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 535289003584 S-adenosylmethionine binding site [chemical binding]; other site 535289003585 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 535289003586 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 535289003587 Peptidase family M23; Region: Peptidase_M23; pfam01551 535289003588 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 535289003589 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 535289003590 RNA binding surface [nucleotide binding]; other site 535289003591 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 535289003592 active site 535289003593 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 535289003594 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 535289003595 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 535289003596 RNA binding surface [nucleotide binding]; other site 535289003597 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 535289003598 probable active site [active] 535289003599 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 535289003600 active site 535289003601 multimer interface [polypeptide binding]; other site 535289003602 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 535289003603 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 535289003604 FeS/SAM binding site; other site 535289003605 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 535289003606 binding surface 535289003607 TPR motif; other site 535289003608 Tetratricopeptide repeat; Region: TPR_12; pfam13424 535289003609 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 535289003610 binding surface 535289003611 TPR motif; other site 535289003612 TPR repeat; Region: TPR_11; pfam13414 535289003613 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 535289003614 Helix-turn-helix domain; Region: HTH_25; pfam13413 535289003615 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 535289003616 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 535289003617 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 535289003618 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 535289003619 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 535289003620 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 535289003621 dimer interface [polypeptide binding]; other site 535289003622 motif 1; other site 535289003623 active site 535289003624 motif 2; other site 535289003625 motif 3; other site 535289003626 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 535289003627 anticodon binding site; other site 535289003628 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 535289003629 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 535289003630 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 535289003631 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 535289003632 Trp docking motif [polypeptide binding]; other site 535289003633 active site 535289003634 GTP-binding protein Der; Reviewed; Region: PRK00093 535289003635 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 535289003636 G1 box; other site 535289003637 GTP/Mg2+ binding site [chemical binding]; other site 535289003638 Switch I region; other site 535289003639 G2 box; other site 535289003640 Switch II region; other site 535289003641 G3 box; other site 535289003642 G4 box; other site 535289003643 G5 box; other site 535289003644 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 535289003645 G1 box; other site 535289003646 GTP/Mg2+ binding site [chemical binding]; other site 535289003647 Switch I region; other site 535289003648 G2 box; other site 535289003649 G3 box; other site 535289003650 Switch II region; other site 535289003651 G4 box; other site 535289003652 G5 box; other site 535289003653 bacterial Hfq-like; Region: Hfq; cd01716 535289003654 hexamer interface [polypeptide binding]; other site 535289003655 Sm1 motif; other site 535289003656 RNA binding site [nucleotide binding]; other site 535289003657 Sm2 motif; other site 535289003658 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 535289003659 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 535289003660 HflX GTPase family; Region: HflX; cd01878 535289003661 G1 box; other site 535289003662 GTP/Mg2+ binding site [chemical binding]; other site 535289003663 Switch I region; other site 535289003664 G2 box; other site 535289003665 G3 box; other site 535289003666 Switch II region; other site 535289003667 G4 box; other site 535289003668 G5 box; other site 535289003669 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 535289003670 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 535289003671 HflK protein; Region: hflK; TIGR01933 535289003672 HflC protein; Region: hflC; TIGR01932 535289003673 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 535289003674 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 535289003675 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 535289003676 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 535289003677 dimer interface [polypeptide binding]; other site 535289003678 motif 1; other site 535289003679 active site 535289003680 motif 2; other site 535289003681 motif 3; other site 535289003682 adenylosuccinate synthetase; Provisional; Region: PRK01117 535289003683 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 535289003684 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 535289003685 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 535289003686 active site 535289003687 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 535289003688 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 535289003689 active site 535289003690 uracil binding [chemical binding]; other site 535289003691 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 535289003692 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 535289003693 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 535289003694 NodB motif; other site 535289003695 active site 535289003696 catalytic site [active] 535289003697 metal binding site [ion binding]; metal-binding site 535289003698 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 535289003699 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 535289003700 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 535289003701 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 535289003702 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 535289003703 putative MPT binding site; other site 535289003704 glutamine synthetase; Provisional; Region: glnA; PRK09469 535289003705 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 535289003706 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 535289003707 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 535289003708 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289003709 dimer interface [polypeptide binding]; other site 535289003710 phosphorylation site [posttranslational modification] 535289003711 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 535289003712 ATP binding site [chemical binding]; other site 535289003713 Mg2+ binding site [ion binding]; other site 535289003714 G-X-G motif; other site 535289003715 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 535289003716 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 535289003717 active site 535289003718 phosphorylation site [posttranslational modification] 535289003719 intermolecular recognition site; other site 535289003720 dimerization interface [polypeptide binding]; other site 535289003721 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289003722 Walker A motif; other site 535289003723 ATP binding site [chemical binding]; other site 535289003724 Walker B motif; other site 535289003725 arginine finger; other site 535289003726 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 535289003727 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 535289003728 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 535289003729 putative catalytic site [active] 535289003730 putative phosphate binding site [ion binding]; other site 535289003731 active site 535289003732 metal binding site A [ion binding]; metal-binding site 535289003733 DNA binding site [nucleotide binding] 535289003734 putative AP binding site [nucleotide binding]; other site 535289003735 putative metal binding site B [ion binding]; other site 535289003736 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 535289003737 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 535289003738 folate binding site [chemical binding]; other site 535289003739 NADP+ binding site [chemical binding]; other site 535289003740 thymidylate synthase; Reviewed; Region: thyA; PRK01827 535289003741 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 535289003742 dimerization interface [polypeptide binding]; other site 535289003743 active site 535289003744 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 535289003745 FAD binding domain; Region: FAD_binding_4; pfam01565 535289003746 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 535289003747 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 535289003748 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 535289003749 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 535289003750 catalytic residues [active] 535289003751 substrate binding pocket [chemical binding]; other site 535289003752 substrate-Mg2+ binding site; other site 535289003753 aspartate-rich region 1; other site 535289003754 aspartate-rich region 2; other site 535289003755 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 535289003756 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 535289003757 putative active site [active] 535289003758 putative metal binding site [ion binding]; other site 535289003759 Monogalactosyldiacylglycerol (MGDG) synthase; Region: MGDG_synth; pfam06925 535289003760 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 535289003761 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 535289003762 active site lid residues [active] 535289003763 substrate binding pocket [chemical binding]; other site 535289003764 catalytic residues [active] 535289003765 substrate-Mg2+ binding site; other site 535289003766 aspartate-rich region 1; other site 535289003767 aspartate-rich region 2; other site 535289003768 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 535289003769 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289003770 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289003771 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 535289003772 trigger factor; Provisional; Region: tig; PRK01490 535289003773 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 535289003774 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 535289003775 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 535289003776 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 535289003777 oligomer interface [polypeptide binding]; other site 535289003778 active site residues [active] 535289003779 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 535289003780 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 535289003781 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289003782 Walker A motif; other site 535289003783 ATP binding site [chemical binding]; other site 535289003784 Walker B motif; other site 535289003785 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 535289003786 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 535289003787 Found in ATP-dependent protease La (LON); Region: LON; smart00464 535289003788 Found in ATP-dependent protease La (LON); Region: LON; smart00464 535289003789 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289003790 Walker A motif; other site 535289003791 ATP binding site [chemical binding]; other site 535289003792 Walker B motif; other site 535289003793 arginine finger; other site 535289003794 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 535289003795 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 535289003796 metal-binding site [ion binding] 535289003797 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 535289003798 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 535289003799 catalytic loop [active] 535289003800 iron binding site [ion binding]; other site 535289003801 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 535289003802 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 535289003803 DNA binding residues [nucleotide binding] 535289003804 dimer interface [polypeptide binding]; other site 535289003805 copper binding site [ion binding]; other site 535289003806 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 535289003807 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 535289003808 metal-binding site [ion binding] 535289003809 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 535289003810 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 535289003811 metal-binding site [ion binding] 535289003812 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289003813 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 535289003814 motif II; other site 535289003815 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 535289003816 dimerization interface [polypeptide binding]; other site 535289003817 putative DNA binding site [nucleotide binding]; other site 535289003818 putative Zn2+ binding site [ion binding]; other site 535289003819 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 535289003820 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289003821 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 535289003822 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 535289003823 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 535289003824 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289003825 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 535289003826 Alcaligenes xylosoxidans NreA and related domains; this domain family was previously known as part of DUF156; Region: NreA-like_DUF156; cd10154 535289003827 putative homodimer interface [polypeptide binding]; other site 535289003828 putative homotetramer interface [polypeptide binding]; other site 535289003829 putative metal binding site [ion binding]; other site 535289003830 putative homodimer-homodimer interface [polypeptide binding]; other site 535289003831 putative allosteric switch controlling residues; other site 535289003832 H+ Antiporter protein; Region: 2A0121; TIGR00900 535289003833 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 535289003834 putative substrate translocation pore; other site 535289003835 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 535289003836 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 535289003837 dimerization interface [polypeptide binding]; other site 535289003838 putative DNA binding site [nucleotide binding]; other site 535289003839 putative Zn2+ binding site [ion binding]; other site 535289003840 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 535289003841 metal-binding site [ion binding] 535289003842 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 535289003843 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 535289003844 metal-binding site [ion binding] 535289003845 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289003846 Soluble P-type ATPase [General function prediction only]; Region: COG4087 535289003847 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 535289003848 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289003849 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289003850 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 535289003851 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289003852 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 535289003853 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 535289003854 DNA binding residues [nucleotide binding] 535289003855 Sugar (and other) transporter; Region: Sugar_tr; pfam00083 535289003856 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289003857 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289003858 mercuric reductase; Region: MerA; TIGR02053 535289003859 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289003860 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 535289003861 Protein of unknown function (DUF1706); Region: DUF1706; cl01748 535289003862 SnoaL-like domain; Region: SnoaL_2; pfam12680 535289003863 Transcriptional regulators [Transcription]; Region: FadR; COG2186 535289003864 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289003865 DNA-binding site [nucleotide binding]; DNA binding site 535289003866 FCD domain; Region: FCD; pfam07729 535289003867 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 535289003868 ParA/MinD ATPase like; Region: ParA; pfam10609 535289003869 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 535289003870 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 535289003871 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 535289003872 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 535289003873 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 535289003874 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 535289003875 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 535289003876 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 535289003877 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 535289003878 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 535289003879 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 535289003880 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 535289003881 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 535289003882 N-acetyl-D-glucosamine binding site [chemical binding]; other site 535289003883 catalytic residue [active] 535289003884 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 535289003885 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 535289003886 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 535289003887 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 535289003888 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 535289003889 GIY-YIG motif/motif A; other site 535289003890 active site 535289003891 catalytic site [active] 535289003892 putative DNA binding site [nucleotide binding]; other site 535289003893 metal binding site [ion binding]; metal-binding site 535289003894 UvrB/uvrC motif; Region: UVR; pfam02151 535289003895 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 535289003896 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 535289003897 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 535289003898 IHF dimer interface [polypeptide binding]; other site 535289003899 IHF - DNA interface [nucleotide binding]; other site 535289003900 SurA N-terminal domain; Region: SurA_N_3; cl07813 535289003901 periplasmic folding chaperone; Provisional; Region: PRK10788 535289003902 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 535289003903 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 535289003904 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 535289003905 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 535289003906 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 535289003907 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 535289003908 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 535289003909 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289003910 Transposase; Region: HTH_Tnp_1; pfam01527 535289003911 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 535289003912 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 535289003913 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 535289003914 ATP binding site [chemical binding]; other site 535289003915 putative Mg++ binding site [ion binding]; other site 535289003916 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 535289003917 active site 535289003918 Zn binding site [ion binding]; other site 535289003919 helicase 45; Provisional; Region: PTZ00424 535289003920 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 535289003921 ATP binding site [chemical binding]; other site 535289003922 Mg++ binding site [ion binding]; other site 535289003923 motif III; other site 535289003924 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 535289003925 nucleotide binding region [chemical binding]; other site 535289003926 ATP-binding site [chemical binding]; other site 535289003927 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 535289003928 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289003929 Walker A/P-loop; other site 535289003930 ATP binding site [chemical binding]; other site 535289003931 Q-loop/lid; other site 535289003932 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 535289003933 ABC transporter; Region: ABC_tran_2; pfam12848 535289003934 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 535289003935 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 535289003936 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 535289003937 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 535289003938 putative active site pocket [active] 535289003939 cleavage site 535289003940 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 535289003941 Predicted metal-binding protein [General function prediction only]; Region: COG3019 535289003942 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 535289003943 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 535289003944 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 535289003945 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 535289003946 Outer membrane efflux protein; Region: OEP; pfam02321 535289003947 Uncharacterized conserved protein [Function unknown]; Region: COG1284 535289003948 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 535289003949 Protein of unknown function (DUF3703); Region: DUF3703; pfam12487 535289003950 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 535289003951 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289003952 Soluble P-type ATPase [General function prediction only]; Region: COG4087 535289003953 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 535289003954 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 535289003955 DNA binding residues [nucleotide binding] 535289003956 dimer interface [polypeptide binding]; other site 535289003957 putative metal binding site [ion binding]; other site 535289003958 Permease; Region: Permease; pfam02405 535289003959 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 535289003960 mce related protein; Region: MCE; pfam02470 535289003961 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 535289003962 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 535289003963 putative substrate binding site [chemical binding]; other site 535289003964 putative ATP binding site [chemical binding]; other site 535289003965 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 535289003966 hydroxyglutarate oxidase; Provisional; Region: PRK11728 535289003967 amidase; Provisional; Region: PRK07056 535289003968 Amidase; Region: Amidase; cl11426 535289003969 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 535289003970 rRNA interaction site [nucleotide binding]; other site 535289003971 S8 interaction site; other site 535289003972 putative laminin-1 binding site; other site 535289003973 elongation factor Ts; Provisional; Region: tsf; PRK09377 535289003974 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 535289003975 Elongation factor TS; Region: EF_TS; pfam00889 535289003976 Elongation factor TS; Region: EF_TS; pfam00889 535289003977 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 535289003978 putative nucleotide binding site [chemical binding]; other site 535289003979 uridine monophosphate binding site [chemical binding]; other site 535289003980 homohexameric interface [polypeptide binding]; other site 535289003981 ribosome recycling factor; Reviewed; Region: frr; PRK00083 535289003982 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 535289003983 hinge region; other site 535289003984 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 535289003985 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 535289003986 catalytic residue [active] 535289003987 putative FPP diphosphate binding site; other site 535289003988 putative FPP binding hydrophobic cleft; other site 535289003989 dimer interface [polypeptide binding]; other site 535289003990 putative IPP diphosphate binding site; other site 535289003991 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 535289003992 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 535289003993 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 535289003994 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 535289003995 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 535289003996 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 535289003997 zinc metallopeptidase RseP; Provisional; Region: PRK10779 535289003998 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 535289003999 active site 535289004000 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 535289004001 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 535289004002 putative substrate binding region [chemical binding]; other site 535289004003 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 535289004004 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 535289004005 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 535289004006 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 535289004007 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 535289004008 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 535289004009 Surface antigen; Region: Bac_surface_Ag; pfam01103 535289004010 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 535289004011 periplasmic chaperone; Provisional; Region: PRK10780 535289004012 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 535289004013 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 535289004014 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 535289004015 trimer interface [polypeptide binding]; other site 535289004016 active site 535289004017 UDP-GlcNAc binding site [chemical binding]; other site 535289004018 lipid binding site [chemical binding]; lipid-binding site 535289004019 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 535289004020 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 535289004021 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 535289004022 active site 535289004023 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 535289004024 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 535289004025 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 535289004026 RNA/DNA hybrid binding site [nucleotide binding]; other site 535289004027 active site 535289004028 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 535289004029 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 535289004030 ribonuclease R; Region: RNase_R; TIGR02063 535289004031 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 535289004032 RNB domain; Region: RNB; pfam00773 535289004033 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 535289004034 RNA binding site [nucleotide binding]; other site 535289004035 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 535289004036 classical (c) SDRs; Region: SDR_c; cd05233 535289004037 NAD(P) binding site [chemical binding]; other site 535289004038 active site 535289004039 Cytochrome c; Region: Cytochrom_C; cl11414 535289004040 Cytochrome c; Region: Cytochrom_C; cl11414 535289004041 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 535289004042 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 535289004043 Cytochrome c; Region: Cytochrom_C; pfam00034 535289004044 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 535289004045 ribosome maturation protein RimP; Reviewed; Region: PRK00092 535289004046 Sm and related proteins; Region: Sm_like; cl00259 535289004047 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 535289004048 putative oligomer interface [polypeptide binding]; other site 535289004049 putative RNA binding site [nucleotide binding]; other site 535289004050 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 535289004051 NusA N-terminal domain; Region: NusA_N; pfam08529 535289004052 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 535289004053 RNA binding site [nucleotide binding]; other site 535289004054 homodimer interface [polypeptide binding]; other site 535289004055 NusA-like KH domain; Region: KH_5; pfam13184 535289004056 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 535289004057 G-X-X-G motif; other site 535289004058 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 535289004059 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 535289004060 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 535289004061 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 535289004062 translation initiation factor IF-2; Region: IF-2; TIGR00487 535289004063 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 535289004064 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 535289004065 G1 box; other site 535289004066 putative GEF interaction site [polypeptide binding]; other site 535289004067 GTP/Mg2+ binding site [chemical binding]; other site 535289004068 Switch I region; other site 535289004069 G2 box; other site 535289004070 G3 box; other site 535289004071 Switch II region; other site 535289004072 G4 box; other site 535289004073 G5 box; other site 535289004074 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 535289004075 Translation-initiation factor 2; Region: IF-2; pfam11987 535289004076 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 535289004077 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 535289004078 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01851 535289004079 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 535289004080 RNA binding site [nucleotide binding]; other site 535289004081 active site 535289004082 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 535289004083 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 535289004084 G1 box; other site 535289004085 putative GEF interaction site [polypeptide binding]; other site 535289004086 GTP/Mg2+ binding site [chemical binding]; other site 535289004087 Switch I region; other site 535289004088 G2 box; other site 535289004089 G3 box; other site 535289004090 Switch II region; other site 535289004091 G4 box; other site 535289004092 G5 box; other site 535289004093 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 535289004094 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 535289004095 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 535289004096 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 535289004097 substrate binding site [chemical binding]; other site 535289004098 oxyanion hole (OAH) forming residues; other site 535289004099 trimer interface [polypeptide binding]; other site 535289004100 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 535289004101 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 535289004102 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 535289004103 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289004104 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289004105 DNA binding residues [nucleotide binding] 535289004106 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 535289004107 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 535289004108 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 535289004109 SmpB-tmRNA interface; other site 535289004110 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 535289004111 putative coenzyme Q binding site [chemical binding]; other site 535289004112 RnfH family Ubiquitin; Region: Ub-RnfH; cl17382 535289004113 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 535289004114 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 535289004115 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 535289004116 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 535289004117 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 535289004118 active site 535289004119 GMP synthase; Reviewed; Region: guaA; PRK00074 535289004120 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 535289004121 AMP/PPi binding site [chemical binding]; other site 535289004122 candidate oxyanion hole; other site 535289004123 catalytic triad [active] 535289004124 potential glutamine specificity residues [chemical binding]; other site 535289004125 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 535289004126 ATP Binding subdomain [chemical binding]; other site 535289004127 Ligand Binding sites [chemical binding]; other site 535289004128 Dimerization subdomain; other site 535289004129 integrase; Provisional; Region: PRK09692 535289004130 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 535289004131 active site 535289004132 Int/Topo IB signature motif; other site 535289004133 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 535289004134 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 535289004135 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 535289004136 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea; Region: NTP-PPase_u4; cd11541 535289004137 putative metal binding site [ion binding]; other site 535289004138 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_3; cd10035 535289004139 putative uracil binding site [chemical binding]; other site 535289004140 putative active site [active] 535289004141 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 535289004142 TIR domain; Region: TIR_2; pfam13676 535289004143 hypothetical protein; Reviewed; Region: PRK00024 535289004144 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 535289004145 MPN+ (JAMM) motif; other site 535289004146 Zinc-binding site [ion binding]; other site 535289004147 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 535289004148 Domain of unknown function (DUF932); Region: DUF932; pfam06067 535289004149 ParB-like nuclease domain; Region: ParBc; pfam02195 535289004150 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 535289004151 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 535289004152 sequence-specific DNA binding site [nucleotide binding]; other site 535289004153 salt bridge; other site 535289004154 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 535289004155 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 535289004156 Helix-turn-helix domain; Region: HTH_17; cl17695 535289004157 Replication initiator protein A; Region: RPA; pfam10134 535289004158 ParA-like protein; Provisional; Region: PHA02518 535289004159 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 535289004160 P-loop; other site 535289004161 Magnesium ion binding site [ion binding]; other site 535289004162 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 535289004163 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 535289004164 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 535289004165 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 535289004166 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 535289004167 Phosphoketolase [Carbohydrate transport and metabolism]; Region: COG3957 535289004168 XFP N-terminal domain; Region: XFP_N; pfam09364 535289004169 Acetate kinase [Energy production and conversion]; Region: ackA; COG0282 535289004170 propionate/acetate kinase; Provisional; Region: PRK12379 535289004171 Cytochrome C' Region: Cytochrom_C_2; cl01610 535289004172 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; pfam09982 535289004173 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 535289004174 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 535289004175 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 535289004176 Beta-Casp domain; Region: Beta-Casp; smart01027 535289004177 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 535289004178 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 535289004179 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 535289004180 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 535289004181 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 535289004182 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 535289004183 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 535289004184 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 535289004185 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 535289004186 Walker A/P-loop; other site 535289004187 ATP binding site [chemical binding]; other site 535289004188 Q-loop/lid; other site 535289004189 ABC transporter signature motif; other site 535289004190 Walker B; other site 535289004191 D-loop; other site 535289004192 H-loop/switch region; other site 535289004193 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 535289004194 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 535289004195 Walker A/P-loop; other site 535289004196 ATP binding site [chemical binding]; other site 535289004197 Q-loop/lid; other site 535289004198 ABC transporter signature motif; other site 535289004199 Walker B; other site 535289004200 D-loop; other site 535289004201 H-loop/switch region; other site 535289004202 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 535289004203 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289004204 Glucose dehydrogenase [Carbohydrate transport and metabolism]; Region: Gcd; COG4993 535289004205 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289004206 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289004207 Peptidase C1-like family; Region: Peptidase_C1_2; cl17447 535289004208 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 535289004209 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 535289004210 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 535289004211 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 535289004212 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 535289004213 NAD(P) binding site [chemical binding]; other site 535289004214 homotetramer interface [polypeptide binding]; other site 535289004215 homodimer interface [polypeptide binding]; other site 535289004216 active site 535289004217 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 535289004218 Ligand Binding Site [chemical binding]; other site 535289004219 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 535289004220 phosphate acetyltransferase; Provisional; Region: PRK11890 535289004221 PGAP1-like protein; Region: PGAP1; pfam07819 535289004222 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 535289004223 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289004224 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 535289004225 dimerization interface [polypeptide binding]; other site 535289004226 substrate binding pocket [chemical binding]; other site 535289004227 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 535289004228 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 535289004229 Walker A motif; other site 535289004230 ATP binding site [chemical binding]; other site 535289004231 Walker B motif; other site 535289004232 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 535289004233 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 535289004234 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 535289004235 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 535289004236 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 535289004237 Walker A motif; other site 535289004238 ATP binding site [chemical binding]; other site 535289004239 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 535289004240 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 535289004241 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 535289004242 conjugal transfer protein TrbL; Provisional; Region: PRK13875 535289004243 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 535289004244 conjugal transfer protein TrbF; Provisional; Region: PRK13872 535289004245 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 535289004246 VirB7 interaction site; other site 535289004247 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 535289004248 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 535289004249 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 535289004250 S-adenosylmethionine binding site [chemical binding]; other site 535289004251 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 535289004252 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 535289004253 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 535289004254 non-specific DNA binding site [nucleotide binding]; other site 535289004255 salt bridge; other site 535289004256 sequence-specific DNA binding site [nucleotide binding]; other site 535289004257 Predicted Zn peptidase [Amino acid transport and metabolism]; Region: COG2856 535289004258 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 RNAs; Region: Piwi_piwi-like_ProArk; cd04659 535289004259 5' RNA guide strand anchoring site; other site 535289004260 active site 535289004261 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 535289004262 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 535289004263 putative DNA binding site [nucleotide binding]; other site 535289004264 putative homodimer interface [polypeptide binding]; other site 535289004265 Transposase domain (DUF772); Region: DUF772; pfam05598 535289004266 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 535289004267 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 535289004268 (3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs; Region: hydroxyacyl-CoA-like_DH_SDR_c-like; cd05353 535289004269 homodimer interface [polypeptide binding]; other site 535289004270 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 535289004271 NAD binding site [chemical binding]; other site 535289004272 active site 535289004273 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl17352 535289004274 thiamine pyrophosphate protein; Validated; Region: PRK08199 535289004275 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 535289004276 PYR/PP interface [polypeptide binding]; other site 535289004277 dimer interface [polypeptide binding]; other site 535289004278 TPP binding site [chemical binding]; other site 535289004279 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 535289004280 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 and...; Region: TPP_enzymes; cd00568 535289004281 TPP-binding site [chemical binding]; other site 535289004282 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 535289004283 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289004284 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 535289004285 substrate binding pocket [chemical binding]; other site 535289004286 dimerization interface [polypeptide binding]; other site 535289004287 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 535289004288 putative substrate translocation pore; other site 535289004289 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 535289004290 arsenical-resistance protein; Region: acr3; TIGR00832 535289004291 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 535289004292 Low molecular weight phosphatase family; Region: LMWPc; cd00115 535289004293 active site 535289004294 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_20; cd07254 535289004295 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 535289004296 putative metal binding site [ion binding]; other site 535289004297 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 535289004298 putative DNA binding site [nucleotide binding]; other site 535289004299 putative Zn2+ binding site [ion binding]; other site 535289004300 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 535289004301 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 535289004302 P loop; other site 535289004303 Nucleotide binding site [chemical binding]; other site 535289004304 DTAP/Switch II; other site 535289004305 Switch I; other site 535289004306 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 535289004307 P loop; other site 535289004308 Nucleotide binding site [chemical binding]; other site 535289004309 DTAP/Switch II; other site 535289004310 Switch I; other site 535289004311 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 535289004312 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 535289004313 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 535289004314 GTP/Mg2+ binding site [chemical binding]; other site 535289004315 G4 box; other site 535289004316 G5 box; other site 535289004317 G1 box; other site 535289004318 Switch I region; other site 535289004319 G2 box; other site 535289004320 G3 box; other site 535289004321 Switch II region; other site 535289004322 OsmC-like protein; Region: OsmC; cl00767 535289004323 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 535289004324 MgtC family; Region: MgtC; pfam02308 535289004325 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 535289004326 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 535289004327 active site 535289004328 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 535289004329 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 535289004330 Staphylococcal nuclease homologues; Region: SNc; smart00318 535289004331 Catalytic site; other site 535289004332 Staphylococcal nuclease homologue; Region: SNase; pfam00565 535289004333 Predicted permeases [General function prediction only]; Region: RarD; COG2962 535289004334 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 535289004335 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 535289004336 Sel1-like repeats; Region: SEL1; smart00671 535289004337 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 535289004338 pseudouridine synthase; Region: TIGR00093 535289004339 active site 535289004340 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 535289004341 Peptidase family M23; Region: Peptidase_M23; pfam01551 535289004342 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 535289004343 Aspartase; Region: Aspartase; cd01357 535289004344 active sites [active] 535289004345 tetramer interface [polypeptide binding]; other site 535289004346 Phasin protein; Region: Phasin_2; pfam09361 535289004347 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 535289004348 active site 535289004349 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 535289004350 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 535289004351 active site 535289004352 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 535289004353 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 535289004354 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 535289004355 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 535289004356 dimerization interface [polypeptide binding]; other site 535289004357 ligand binding site [chemical binding]; other site 535289004358 NADP binding site [chemical binding]; other site 535289004359 catalytic site [active] 535289004360 RmuC family; Region: RmuC; pfam02646 535289004361 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 535289004362 putative substrate translocation pore; other site 535289004363 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289004364 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 535289004365 chromosome condensation membrane protein; Provisional; Region: PRK14196 535289004366 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 535289004367 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 535289004368 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 535289004369 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 535289004370 MarR family; Region: MarR_2; cl17246 535289004371 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_5; cd06232 535289004372 putative active site [active] 535289004373 Zn binding site [ion binding]; other site 535289004374 5-oxoprolinase; Region: PLN02666 535289004375 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 535289004376 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 535289004377 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 535289004378 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 535289004379 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK06161 535289004380 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 535289004381 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 535289004382 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 535289004383 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK09094 535289004384 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 535289004385 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 535289004386 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 535289004387 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 535289004388 DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]; Region: ComEA; COG1555 535289004389 tetratricopeptide repeat protein; Provisional; Region: PRK11788 535289004390 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 535289004391 binding surface 535289004392 TPR motif; other site 535289004393 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 535289004394 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 535289004395 IHF - DNA interface [nucleotide binding]; other site 535289004396 IHF dimer interface [polypeptide binding]; other site 535289004397 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 535289004398 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 535289004399 RNA binding site [nucleotide binding]; other site 535289004400 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 535289004401 RNA binding site [nucleotide binding]; other site 535289004402 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 535289004403 RNA binding site [nucleotide binding]; other site 535289004404 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 535289004405 RNA binding site [nucleotide binding]; other site 535289004406 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 535289004407 RNA binding site [nucleotide binding]; other site 535289004408 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 535289004409 RNA binding site [nucleotide binding]; other site 535289004410 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional; Region: PRK11860 535289004411 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 535289004412 hinge; other site 535289004413 active site 535289004414 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 535289004415 CMP-binding site; other site 535289004416 The sites determining sugar specificity; other site 535289004417 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 535289004418 prephenate dehydrogenase; Validated; Region: PRK08507 535289004419 Chorismate mutase type II; Region: CM_2; pfam01817 535289004420 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 535289004421 Prephenate dehydratase; Region: PDT; pfam00800 535289004422 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 535289004423 putative L-Phe binding site [chemical binding]; other site 535289004424 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 535289004425 homodimer interface [polypeptide binding]; other site 535289004426 substrate-cofactor binding pocket; other site 535289004427 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289004428 catalytic residue [active] 535289004429 DNA gyrase subunit A; Validated; Region: PRK05560 535289004430 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 535289004431 CAP-like domain; other site 535289004432 active site 535289004433 primary dimer interface [polypeptide binding]; other site 535289004434 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 535289004435 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 535289004436 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 535289004437 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 535289004438 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 535289004439 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 535289004440 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 535289004441 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 535289004442 ligand binding site [chemical binding]; other site 535289004443 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 535289004444 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 535289004445 S-adenosylmethionine binding site [chemical binding]; other site 535289004446 phosphoglycolate phosphatase; Provisional; Region: PRK13222 535289004447 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 535289004448 motif II; other site 535289004449 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 535289004450 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 535289004451 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 535289004452 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 535289004453 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 535289004454 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 535289004455 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 535289004456 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289004457 Transposase; Region: HTH_Tnp_1; pfam01527 535289004458 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289004459 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289004460 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 535289004461 Predicted transporter component [General function prediction only]; Region: COG2391 535289004462 Sulphur transport; Region: Sulf_transp; pfam04143 535289004463 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 535289004464 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 535289004465 dimerization interface [polypeptide binding]; other site 535289004466 putative DNA binding site [nucleotide binding]; other site 535289004467 putative Zn2+ binding site [ion binding]; other site 535289004468 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 535289004469 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 535289004470 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 535289004471 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 535289004472 catalytic residues [active] 535289004473 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289004474 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 535289004475 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289004476 dimer interface [polypeptide binding]; other site 535289004477 phosphorylation site [posttranslational modification] 535289004478 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 535289004479 ATP binding site [chemical binding]; other site 535289004480 Mg2+ binding site [ion binding]; other site 535289004481 G-X-G motif; other site 535289004482 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 535289004483 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 535289004484 active site 535289004485 phosphorylation site [posttranslational modification] 535289004486 intermolecular recognition site; other site 535289004487 dimerization interface [polypeptide binding]; other site 535289004488 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289004489 DNA binding site [nucleotide binding] 535289004490 This model contains proteins with the VRR-NUC domain; Region: VRR_NUC; smart00990 535289004491 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 535289004492 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 535289004493 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 535289004494 Thermostable Phosphite Dehydrogenase; Region: PTDH; cd12157 535289004495 homodimer interface [polypeptide binding]; other site 535289004496 ligand binding site [chemical binding]; other site 535289004497 NAD binding site [chemical binding]; other site 535289004498 catalytic site [active] 535289004499 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 535289004500 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289004501 dimer interface [polypeptide binding]; other site 535289004502 conserved gate region; other site 535289004503 ABC-ATPase subunit interface; other site 535289004504 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 535289004505 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 535289004506 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 535289004507 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 535289004508 Walker A/P-loop; other site 535289004509 ATP binding site [chemical binding]; other site 535289004510 Q-loop/lid; other site 535289004511 ABC transporter signature motif; other site 535289004512 Walker B; other site 535289004513 D-loop; other site 535289004514 H-loop/switch region; other site 535289004515 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289004516 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 535289004517 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 535289004518 dimerization interface [polypeptide binding]; other site 535289004519 tetrathionate reductase subunit A; Provisional; Region: PRK14991 535289004520 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 535289004521 molybdopterin cofactor binding site; other site 535289004522 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 535289004523 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 535289004524 putative molybdopterin cofactor binding site; other site 535289004525 tetrathionate reductase subunit C; Provisional; Region: PRK14992 535289004526 tetrathionate reductase subunit B; Provisional; Region: PRK14993 535289004527 4Fe-4S binding domain; Region: Fer4; pfam00037 535289004528 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 535289004529 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 535289004530 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 535289004531 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 535289004532 NAD(P) binding site [chemical binding]; other site 535289004533 catalytic residues [active] 535289004534 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 535289004535 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 535289004536 putative DNA binding site [nucleotide binding]; other site 535289004537 putative Zn2+ binding site [ion binding]; other site 535289004538 AsnC family; Region: AsnC_trans_reg; pfam01037 535289004539 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 535289004540 Heavy-metal resistance; Region: Metal_resist; pfam13801 535289004541 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 535289004542 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289004543 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289004544 DNA binding residues [nucleotide binding] 535289004545 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 535289004546 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 535289004547 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 535289004548 YccA-like proteins; Region: YccA_like; cd10433 535289004549 Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only]; Region: GlcG; COG3193 535289004550 Hemin uptake protein hemP; Region: hemP; pfam10636 535289004551 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 535289004552 TolR protein; Region: tolR; TIGR02801 535289004553 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 535289004554 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 535289004555 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 535289004556 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 535289004557 SWIB/MDM2 domain; Region: SWIB; pfam02201 535289004558 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 535289004559 EamA-like transporter family; Region: EamA; pfam00892 535289004560 EamA-like transporter family; Region: EamA; pfam00892 535289004561 isocitrate lyase; Provisional; Region: PRK15063 535289004562 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 535289004563 tetramer interface [polypeptide binding]; other site 535289004564 active site 535289004565 Mg2+/Mn2+ binding site [ion binding]; other site 535289004566 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 535289004567 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 535289004568 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 535289004569 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 535289004570 active site 535289004571 dimer interface [polypeptide binding]; other site 535289004572 motif 1; other site 535289004573 motif 2; other site 535289004574 motif 3; other site 535289004575 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 535289004576 anticodon binding site; other site 535289004577 translation initiation factor IF-3; Region: infC; TIGR00168 535289004578 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 535289004579 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 535289004580 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 535289004581 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 535289004582 23S rRNA binding site [nucleotide binding]; other site 535289004583 L21 binding site [polypeptide binding]; other site 535289004584 L13 binding site [polypeptide binding]; other site 535289004585 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 535289004586 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 535289004587 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 535289004588 dimer interface [polypeptide binding]; other site 535289004589 motif 1; other site 535289004590 active site 535289004591 motif 2; other site 535289004592 motif 3; other site 535289004593 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 535289004594 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 535289004595 putative tRNA-binding site [nucleotide binding]; other site 535289004596 B3/4 domain; Region: B3_4; pfam03483 535289004597 tRNA synthetase B5 domain; Region: B5; smart00874 535289004598 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 535289004599 dimer interface [polypeptide binding]; other site 535289004600 motif 1; other site 535289004601 motif 3; other site 535289004602 motif 2; other site 535289004603 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 535289004604 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 535289004605 IHF - DNA interface [nucleotide binding]; other site 535289004606 IHF dimer interface [polypeptide binding]; other site 535289004607 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 535289004608 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 535289004609 DNA binding residues [nucleotide binding] 535289004610 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 535289004611 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 535289004612 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 535289004613 catalytic site [active] 535289004614 subunit interface [polypeptide binding]; other site 535289004615 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 535289004616 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 535289004617 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 535289004618 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 535289004619 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 535289004620 ATP-grasp domain; Region: ATP-grasp_4; cl17255 535289004621 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 535289004622 IMP binding site; other site 535289004623 dimer interface [polypeptide binding]; other site 535289004624 interdomain contacts; other site 535289004625 partial ornithine binding site; other site 535289004626 glutamate dehydrogenase; Provisional; Region: PRK09414 535289004627 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 535289004628 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 535289004629 NAD(P) binding site [chemical binding]; other site 535289004630 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 535289004631 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 535289004632 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289004633 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 535289004634 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 535289004635 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 535289004636 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289004637 dimer interface [polypeptide binding]; other site 535289004638 phosphorylation site [posttranslational modification] 535289004639 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 535289004640 ATP binding site [chemical binding]; other site 535289004641 Mg2+ binding site [ion binding]; other site 535289004642 G-X-G motif; other site 535289004643 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 535289004644 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 535289004645 active site 535289004646 phosphorylation site [posttranslational modification] 535289004647 intermolecular recognition site; other site 535289004648 dimerization interface [polypeptide binding]; other site 535289004649 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289004650 DNA binding site [nucleotide binding] 535289004651 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 535289004652 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 535289004653 ATP binding site [chemical binding]; other site 535289004654 Mg2+ binding site [ion binding]; other site 535289004655 G-X-G motif; other site 535289004656 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 535289004657 ATP binding site [chemical binding]; other site 535289004658 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 535289004659 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 535289004660 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 535289004661 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 535289004662 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 535289004663 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 535289004664 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 535289004665 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase; Region: Kdo_hydroxy; pfam11004 535289004666 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 535289004667 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 535289004668 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 535289004669 S-adenosylmethionine binding site [chemical binding]; other site 535289004670 FtsH Extracellular; Region: FtsH_ext; pfam06480 535289004671 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 535289004672 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289004673 Walker A motif; other site 535289004674 ATP binding site [chemical binding]; other site 535289004675 Walker B motif; other site 535289004676 arginine finger; other site 535289004677 Peptidase family M41; Region: Peptidase_M41; pfam01434 535289004678 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 535289004679 dihydropteroate synthase; Region: DHPS; TIGR01496 535289004680 substrate binding pocket [chemical binding]; other site 535289004681 dimer interface [polypeptide binding]; other site 535289004682 inhibitor binding site; inhibition site 535289004683 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 535289004684 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 535289004685 active site 535289004686 substrate binding site [chemical binding]; other site 535289004687 metal binding site [ion binding]; metal-binding site 535289004688 PAS domain S-box; Region: sensory_box; TIGR00229 535289004689 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 535289004690 putative active site [active] 535289004691 heme pocket [chemical binding]; other site 535289004692 PAS domain; Region: PAS_8; pfam13188 535289004693 PAS domain; Region: PAS_9; pfam13426 535289004694 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289004695 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289004696 metal binding site [ion binding]; metal-binding site 535289004697 active site 535289004698 I-site; other site 535289004699 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 535289004700 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 535289004701 polyphosphate kinase; Provisional; Region: PRK05443 535289004702 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 535289004703 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 535289004704 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 535289004705 putative active site [active] 535289004706 catalytic site [active] 535289004707 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 535289004708 putative active site [active] 535289004709 catalytic site [active] 535289004710 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 535289004711 catalytic core [active] 535289004712 guanosine pentaphosphate phosphohydrolase; Provisional; Region: PRK11031 535289004713 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 535289004714 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 535289004715 Zn2+ binding site [ion binding]; other site 535289004716 Mg2+ binding site [ion binding]; other site 535289004717 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 535289004718 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 535289004719 Fasciclin domain; Region: Fasciclin; pfam02469 535289004720 PBP superfamily domain; Region: PBP_like_2; cl17296 535289004721 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 535289004722 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289004723 dimer interface [polypeptide binding]; other site 535289004724 conserved gate region; other site 535289004725 putative PBP binding loops; other site 535289004726 ABC-ATPase subunit interface; other site 535289004727 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 535289004728 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289004729 dimer interface [polypeptide binding]; other site 535289004730 conserved gate region; other site 535289004731 putative PBP binding loops; other site 535289004732 ABC-ATPase subunit interface; other site 535289004733 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 535289004734 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 535289004735 Walker A/P-loop; other site 535289004736 ATP binding site [chemical binding]; other site 535289004737 Q-loop/lid; other site 535289004738 ABC transporter signature motif; other site 535289004739 Walker B; other site 535289004740 D-loop; other site 535289004741 H-loop/switch region; other site 535289004742 transcriptional regulator PhoU; Provisional; Region: PRK11115 535289004743 PhoU domain; Region: PhoU; pfam01895 535289004744 PhoU domain; Region: PhoU; pfam01895 535289004745 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 535289004746 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 535289004747 active site 535289004748 phosphorylation site [posttranslational modification] 535289004749 intermolecular recognition site; other site 535289004750 dimerization interface [polypeptide binding]; other site 535289004751 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289004752 DNA binding site [nucleotide binding] 535289004753 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 535289004754 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 535289004755 putative active site [active] 535289004756 heme pocket [chemical binding]; other site 535289004757 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289004758 dimer interface [polypeptide binding]; other site 535289004759 phosphorylation site [posttranslational modification] 535289004760 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 535289004761 ATP binding site [chemical binding]; other site 535289004762 Mg2+ binding site [ion binding]; other site 535289004763 G-X-G motif; other site 535289004764 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 535289004765 putative efflux protein, MATE family; Region: matE; TIGR00797 535289004766 cation binding site [ion binding]; other site 535289004767 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 535289004768 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 535289004769 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 535289004770 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 535289004771 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 535289004772 Walker A/P-loop; other site 535289004773 ATP binding site [chemical binding]; other site 535289004774 Q-loop/lid; other site 535289004775 ABC transporter signature motif; other site 535289004776 Walker B; other site 535289004777 D-loop; other site 535289004778 H-loop/switch region; other site 535289004779 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 535289004780 Walker A/P-loop; other site 535289004781 ATP binding site [chemical binding]; other site 535289004782 Q-loop/lid; other site 535289004783 ABC transporter signature motif; other site 535289004784 Walker B; other site 535289004785 D-loop; other site 535289004786 H-loop/switch region; other site 535289004787 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 535289004788 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 535289004789 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 535289004790 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289004791 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289004792 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289004793 transcription termination factor Rho; Provisional; Region: rho; PRK09376 535289004794 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 535289004795 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 535289004796 RNA binding site [nucleotide binding]; other site 535289004797 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 535289004798 multimer interface [polypeptide binding]; other site 535289004799 Walker A motif; other site 535289004800 ATP binding site [chemical binding]; other site 535289004801 Walker B motif; other site 535289004802 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 535289004803 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 535289004804 catalytic residues [active] 535289004805 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 535289004806 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 535289004807 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 535289004808 putative recombination protein RecB; Provisional; Region: PRK13909 535289004809 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 535289004810 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 535289004811 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 535289004812 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289004813 Walker A motif; other site 535289004814 ATP binding site [chemical binding]; other site 535289004815 Walker B motif; other site 535289004816 arginine finger; other site 535289004817 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 535289004818 hypothetical protein; Validated; Region: PRK00153 535289004819 recombination protein RecR; Reviewed; Region: recR; PRK00076 535289004820 RecR protein; Region: RecR; pfam02132 535289004821 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 535289004822 putative active site [active] 535289004823 putative metal-binding site [ion binding]; other site 535289004824 tetramer interface [polypeptide binding]; other site 535289004825 MAPEG family; Region: MAPEG; cl09190 535289004826 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289004827 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 535289004828 putative substrate translocation pore; other site 535289004829 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 535289004830 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 535289004831 Walker A/P-loop; other site 535289004832 ATP binding site [chemical binding]; other site 535289004833 Q-loop/lid; other site 535289004834 ABC transporter signature motif; other site 535289004835 Walker B; other site 535289004836 D-loop; other site 535289004837 H-loop/switch region; other site 535289004838 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 535289004839 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289004840 dimer interface [polypeptide binding]; other site 535289004841 conserved gate region; other site 535289004842 ABC-ATPase subunit interface; other site 535289004843 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 535289004844 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 535289004845 Predicted flavoprotein [General function prediction only]; Region: COG0431 535289004846 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 535289004847 Acyl carrier protein phosphodiesterase [Lipid metabolism]; Region: AcpD; COG1182 535289004848 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 535289004849 LysR family transcriptional regulator; Provisional; Region: PRK14997 535289004850 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 535289004851 putative effector binding pocket; other site 535289004852 putative dimerization interface [polypeptide binding]; other site 535289004853 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 535289004854 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 535289004855 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 535289004856 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289004857 dimer interface [polypeptide binding]; other site 535289004858 conserved gate region; other site 535289004859 putative PBP binding loops; other site 535289004860 ABC-ATPase subunit interface; other site 535289004861 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289004862 dimer interface [polypeptide binding]; other site 535289004863 conserved gate region; other site 535289004864 putative PBP binding loops; other site 535289004865 ABC-ATPase subunit interface; other site 535289004866 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 535289004867 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 535289004868 Walker A/P-loop; other site 535289004869 ATP binding site [chemical binding]; other site 535289004870 Q-loop/lid; other site 535289004871 ABC transporter signature motif; other site 535289004872 Walker B; other site 535289004873 D-loop; other site 535289004874 H-loop/switch region; other site 535289004875 TOBE-like domain; Region: TOBE_3; pfam12857 535289004876 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 535289004877 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 535289004878 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 535289004879 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 535289004880 putative N-terminal domain interface [polypeptide binding]; other site 535289004881 putative dimer interface [polypeptide binding]; other site 535289004882 putative substrate binding pocket (H-site) [chemical binding]; other site 535289004883 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 535289004884 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 535289004885 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 535289004886 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 535289004887 N-terminal plug; other site 535289004888 ligand-binding site [chemical binding]; other site 535289004889 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 535289004890 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289004891 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 535289004892 dimerization interface [polypeptide binding]; other site 535289004893 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 535289004894 N-acetylglutamate synthase; Validated; Region: PRK05279 535289004895 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 535289004896 putative feedback inhibition sensing region; other site 535289004897 putative nucleotide binding site [chemical binding]; other site 535289004898 putative substrate binding site [chemical binding]; other site 535289004899 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 535289004900 Coenzyme A binding pocket [chemical binding]; other site 535289004901 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 535289004902 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289004903 Transposase; Region: HTH_Tnp_1; pfam01527 535289004904 putative transposase OrfB; Reviewed; Region: PHA02517 535289004905 HTH-like domain; Region: HTH_21; pfam13276 535289004906 Integrase core domain; Region: rve; pfam00665 535289004907 Integrase core domain; Region: rve_2; pfam13333 535289004908 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289004909 Methyltransferase domain; Region: Methyltransf_23; pfam13489 535289004910 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 535289004911 S-adenosylmethionine binding site [chemical binding]; other site 535289004912 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 535289004913 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 535289004914 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 535289004915 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289004916 putative substrate translocation pore; other site 535289004917 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 535289004918 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 535289004919 Walker A/P-loop; other site 535289004920 ATP binding site [chemical binding]; other site 535289004921 Q-loop/lid; other site 535289004922 ABC transporter signature motif; other site 535289004923 Walker B; other site 535289004924 D-loop; other site 535289004925 H-loop/switch region; other site 535289004926 BioY family; Region: BioY; pfam02632 535289004927 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289004928 acyl-CoA synthetase; Validated; Region: PRK07638 535289004929 acyl-activating enzyme (AAE) consensus motif; other site 535289004930 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289004931 AMP binding site [chemical binding]; other site 535289004932 active site 535289004933 acyl-activating enzyme (AAE) consensus motif; other site 535289004934 CoA binding site [chemical binding]; other site 535289004935 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 535289004936 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 535289004937 dimer interface [polypeptide binding]; other site 535289004938 active site 535289004939 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 535289004940 FMN binding site [chemical binding]; other site 535289004941 dimer interface [polypeptide binding]; other site 535289004942 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 535289004943 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 535289004944 putative active site [active] 535289004945 putative metal binding site [ion binding]; other site 535289004946 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]; Region: COG4091 535289004947 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 535289004948 SAF domain of putative dehydrogenases or oxidoreductases; Region: SAF_DH_OX_like; cd11616 535289004949 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 535289004950 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 535289004951 ATP binding site [chemical binding]; other site 535289004952 putative Mg++ binding site [ion binding]; other site 535289004953 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 535289004954 nucleotide binding region [chemical binding]; other site 535289004955 ATP-binding site [chemical binding]; other site 535289004956 Helicase associated domain (HA2); Region: HA2; pfam04408 535289004957 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 535289004958 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 535289004959 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 535289004960 LexA repressor; Validated; Region: PRK00215 535289004961 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 535289004962 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 535289004963 Catalytic site [active] 535289004964 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 535289004965 active site 535289004966 homotetramer interface [polypeptide binding]; other site 535289004967 homodimer interface [polypeptide binding]; other site 535289004968 adenylate kinase; Reviewed; Region: adk; PRK00279 535289004969 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 535289004970 AMP-binding site [chemical binding]; other site 535289004971 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 535289004972 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 535289004973 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 535289004974 Ligand binding site; other site 535289004975 oligomer interface; other site 535289004976 Uncharacterized conserved protein [Function unknown]; Region: COG2835 535289004977 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 535289004978 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 535289004979 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 535289004980 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 535289004981 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 535289004982 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 535289004983 generic binding surface II; other site 535289004984 generic binding surface I; other site 535289004985 superoxide dismutase; Provisional; Region: PRK10543 535289004986 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 535289004987 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 535289004988 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 535289004989 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 535289004990 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 535289004991 isocitrate dehydrogenase; Validated; Region: PRK07362 535289004992 isocitrate dehydrogenase; Reviewed; Region: PRK07006 535289004993 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 535289004994 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 535289004995 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 535289004996 Walker A motif; other site 535289004997 ATP binding site [chemical binding]; other site 535289004998 Walker B motif; other site 535289004999 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 535289005000 TrwC relaxase; Region: TrwC; pfam08751 535289005001 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 535289005002 AAA domain; Region: AAA_30; pfam13604 535289005003 AAA domain; Region: AAA_22; pfam13401 535289005004 Family description; Region: UvrD_C_2; pfam13538 535289005005 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 535289005006 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 535289005007 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 535289005008 Ligand Binding Site [chemical binding]; other site 535289005009 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 535289005010 Ligand Binding Site [chemical binding]; other site 535289005011 integrase; Provisional; Region: PRK09692 535289005012 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 535289005013 active site 535289005014 Int/Topo IB signature motif; other site 535289005015 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 535289005016 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 535289005017 active site 535289005018 catalytic residues [active] 535289005019 metal binding site [ion binding]; metal-binding site 535289005020 PII uridylyl-transferase; Provisional; Region: PRK03059 535289005021 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 535289005022 metal binding triad; other site 535289005023 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 535289005024 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 535289005025 Zn2+ binding site [ion binding]; other site 535289005026 Mg2+ binding site [ion binding]; other site 535289005027 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 535289005028 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 535289005029 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 535289005030 active site 535289005031 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 535289005032 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 535289005033 dimerization interface [polypeptide binding]; other site 535289005034 ATP binding site [chemical binding]; other site 535289005035 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 535289005036 dimerization interface [polypeptide binding]; other site 535289005037 ATP binding site [chemical binding]; other site 535289005038 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 535289005039 putative active site [active] 535289005040 catalytic triad [active] 535289005041 Protein of unknown function (DUF808); Region: DUF808; pfam05661 535289005042 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 535289005043 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 535289005044 Methyltransferase domain; Region: Methyltransf_25; pfam13649 535289005045 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 535289005046 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 535289005047 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 535289005048 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 535289005049 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 535289005050 homodimer interface [polypeptide binding]; other site 535289005051 substrate-cofactor binding pocket; other site 535289005052 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289005053 catalytic residue [active] 535289005054 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 535289005055 Peptidase family U32; Region: Peptidase_U32; pfam01136 535289005056 Collagenase; Region: DUF3656; pfam12392 535289005057 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 535289005058 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 535289005059 nucleoside/Zn binding site; other site 535289005060 dimer interface [polypeptide binding]; other site 535289005061 catalytic motif [active] 535289005062 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 535289005063 dimer interface [polypeptide binding]; other site 535289005064 catalytic triad [active] 535289005065 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 535289005066 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...; Region: Ntn_PGA_like; cd03747 535289005067 active site 535289005068 OsmC-like protein; Region: OsmC; pfam02566 535289005069 Pirin-related protein [General function prediction only]; Region: COG1741 535289005070 Pirin; Region: Pirin; pfam02678 535289005071 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 535289005072 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 535289005073 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 535289005074 P-loop; other site 535289005075 ADP binding residues [chemical binding]; other site 535289005076 Switch I; other site 535289005077 Switch II; other site 535289005078 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289005079 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289005080 metal binding site [ion binding]; metal-binding site 535289005081 active site 535289005082 I-site; other site 535289005083 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 535289005084 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 535289005085 Sulfate transporter family; Region: Sulfate_transp; pfam00916 535289005086 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 535289005087 BON domain; Region: BON; pfam04972 535289005088 cystathionine beta-lyase; Provisional; Region: PRK07050 535289005089 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 535289005090 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289005091 catalytic residue [active] 535289005092 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 535289005093 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 535289005094 active site 535289005095 catalytic triad [active] 535289005096 oxyanion hole [active] 535289005097 switch loop; other site 535289005098 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 535289005099 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 535289005100 Walker A/P-loop; other site 535289005101 ATP binding site [chemical binding]; other site 535289005102 Q-loop/lid; other site 535289005103 ABC transporter signature motif; other site 535289005104 Walker B; other site 535289005105 D-loop; other site 535289005106 H-loop/switch region; other site 535289005107 serine/threonine transporter SstT; Provisional; Region: PRK13628 535289005108 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 535289005109 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 535289005110 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 535289005111 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 535289005112 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 535289005113 dimer interface [polypeptide binding]; other site 535289005114 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 535289005115 putative hydrophobic ligand binding site [chemical binding]; other site 535289005116 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 535289005117 dimer interface [polypeptide binding]; other site 535289005118 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 535289005119 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 535289005120 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289005121 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289005122 WHG domain; Region: WHG; pfam13305 535289005123 NAD-dependent deacetylase; Provisional; Region: PRK00481 535289005124 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 which...; Region: SIRT5_Af1_CobB; cd01412 535289005125 NAD+ binding site [chemical binding]; other site 535289005126 substrate binding site [chemical binding]; other site 535289005127 Zn binding site [ion binding]; other site 535289005128 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 535289005129 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 535289005130 Chromate transporter; Region: Chromate_transp; pfam02417 535289005131 Chromate transporter; Region: Chromate_transp; pfam02417 535289005132 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 535289005133 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 535289005134 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 535289005135 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 535289005136 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 535289005137 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 535289005138 Domain of unknown function (DUF897); Region: DUF897; cl01312 535289005139 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289005140 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289005141 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 535289005142 putative dimerization interface [polypeptide binding]; other site 535289005143 HipA N-terminal domain; Region: Couple_hipA; pfam13657 535289005144 HipA-like N-terminal domain; Region: HipA_N; pfam07805 535289005145 HipA-like C-terminal domain; Region: HipA_C; pfam07804 535289005146 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 535289005147 non-specific DNA binding site [nucleotide binding]; other site 535289005148 salt bridge; other site 535289005149 sequence-specific DNA binding site [nucleotide binding]; other site 535289005150 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 535289005151 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289005152 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 535289005153 dimerization interface [polypeptide binding]; other site 535289005154 D-serine dehydratase; Provisional; Region: PRK02991 535289005155 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 535289005156 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289005157 catalytic residue [active] 535289005158 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289005159 amidase; Provisional; Region: PRK07486 535289005160 Amidase; Region: Amidase; pfam01425 535289005161 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 535289005162 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 535289005163 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289005164 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 535289005165 Uncharacterized conserved protein [Function unknown]; Region: COG1739 535289005166 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 535289005167 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 535289005168 hypothetical protein; Provisional; Region: PRK01254 535289005169 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 535289005170 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 535289005171 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 535289005172 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 535289005173 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 535289005174 putative active site [active] 535289005175 metal binding site [ion binding]; metal-binding site 535289005176 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 535289005177 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 535289005178 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289005179 homodimer interface [polypeptide binding]; other site 535289005180 catalytic residue [active] 535289005181 excinuclease ABC subunit B; Provisional; Region: PRK05298 535289005182 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 535289005183 ATP binding site [chemical binding]; other site 535289005184 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 535289005185 nucleotide binding region [chemical binding]; other site 535289005186 ATP-binding site [chemical binding]; other site 535289005187 Ultra-violet resistance protein B; Region: UvrB; pfam12344 535289005188 UvrB/uvrC motif; Region: UVR; pfam02151 535289005189 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 535289005190 Rrf2 family protein; Region: rrf2_super; TIGR00738 535289005191 cysteine desulfurase; Provisional; Region: PRK14012 535289005192 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 535289005193 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289005194 catalytic residue [active] 535289005195 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 535289005196 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 535289005197 trimerization site [polypeptide binding]; other site 535289005198 active site 535289005199 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 535289005200 co-chaperone HscB; Provisional; Region: hscB; PRK03578 535289005201 DnaJ domain; Region: DnaJ; pfam00226 535289005202 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 535289005203 chaperone protein HscA; Provisional; Region: hscA; PRK05183 535289005204 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 535289005205 nucleotide binding site [chemical binding]; other site 535289005206 putative NEF/HSP70 interaction site [polypeptide binding]; other site 535289005207 SBD interface [polypeptide binding]; other site 535289005208 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 535289005209 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 535289005210 catalytic loop [active] 535289005211 iron binding site [ion binding]; other site 535289005212 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 535289005213 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 535289005214 active site 535289005215 catalytic site [active] 535289005216 substrate binding site [chemical binding]; other site 535289005217 Arginase-like and histone-like hydrolases; Region: Arginase_HDAC; cl17011 535289005218 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 535289005219 Histone deacetylase class IIa; Region: HDAC_classII_APAH; cd10001 535289005220 active site 535289005221 Zn binding site [ion binding]; other site 535289005222 hydroxyglutarate oxidase; Provisional; Region: PRK11728 535289005223 Predicted dehydrogenase [General function prediction only]; Region: COG0579 535289005224 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 535289005225 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 535289005226 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 535289005227 quinone interaction residues [chemical binding]; other site 535289005228 active site 535289005229 catalytic residues [active] 535289005230 FMN binding site [chemical binding]; other site 535289005231 substrate binding site [chemical binding]; other site 535289005232 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 535289005233 tetramer (dimer of dimers) interface [polypeptide binding]; other site 535289005234 active site 535289005235 dimer interface [polypeptide binding]; other site 535289005236 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 reductase...; Region: NrdH; cd02976 535289005237 catalytic residues [active] 535289005238 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 535289005239 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 535289005240 active site 535289005241 Zn binding site [ion binding]; other site 535289005242 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 535289005243 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 535289005244 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 535289005245 homodimer interface [polypeptide binding]; other site 535289005246 NADP binding site [chemical binding]; other site 535289005247 substrate binding site [chemical binding]; other site 535289005248 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 535289005249 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 535289005250 active site 535289005251 phosphorylation site [posttranslational modification] 535289005252 intermolecular recognition site; other site 535289005253 dimerization interface [polypeptide binding]; other site 535289005254 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289005255 DNA binding residues [nucleotide binding] 535289005256 dimerization interface [polypeptide binding]; other site 535289005257 PAS domain S-box; Region: sensory_box; TIGR00229 535289005258 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 535289005259 putative active site [active] 535289005260 heme pocket [chemical binding]; other site 535289005261 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289005262 dimer interface [polypeptide binding]; other site 535289005263 phosphorylation site [posttranslational modification] 535289005264 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 535289005265 ATP binding site [chemical binding]; other site 535289005266 Mg2+ binding site [ion binding]; other site 535289005267 G-X-G motif; other site 535289005268 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 535289005269 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 535289005270 dimer interface [polypeptide binding]; other site 535289005271 TPP-binding site [chemical binding]; other site 535289005272 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 535289005273 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 535289005274 E3 interaction surface; other site 535289005275 lipoyl attachment site [posttranslational modification]; other site 535289005276 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 535289005277 E3 interaction surface; other site 535289005278 lipoyl attachment site [posttranslational modification]; other site 535289005279 e3 binding domain; Region: E3_binding; pfam02817 535289005280 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 535289005281 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 535289005282 E3 interaction surface; other site 535289005283 lipoyl attachment site [posttranslational modification]; other site 535289005284 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 535289005285 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 535289005286 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289005287 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 535289005288 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; pfam10084 535289005289 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 535289005290 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 535289005291 S-adenosylmethionine binding site [chemical binding]; other site 535289005292 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 535289005293 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 535289005294 EVE domain; Region: EVE; cl00728 535289005295 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 535289005296 NlpC/P60 family; Region: NLPC_P60; pfam00877 535289005297 putative transporter; Provisional; Region: PRK10504 535289005298 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 535289005299 putative substrate translocation pore; other site 535289005300 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 535289005301 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 535289005302 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 535289005303 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 535289005304 Walker A/P-loop; other site 535289005305 ATP binding site [chemical binding]; other site 535289005306 Q-loop/lid; other site 535289005307 ABC transporter signature motif; other site 535289005308 Walker B; other site 535289005309 D-loop; other site 535289005310 H-loop/switch region; other site 535289005311 CHASE domain; Region: CHASE; pfam03924 535289005312 PAS domain S-box; Region: sensory_box; TIGR00229 535289005313 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 535289005314 putative active site [active] 535289005315 heme pocket [chemical binding]; other site 535289005316 PAS domain; Region: PAS_8; pfam13188 535289005317 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289005318 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289005319 metal binding site [ion binding]; metal-binding site 535289005320 active site 535289005321 I-site; other site 535289005322 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 535289005323 hypothetical protein; Provisional; Region: PRK02237 535289005324 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 535289005325 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 535289005326 Walker A/P-loop; other site 535289005327 ATP binding site [chemical binding]; other site 535289005328 Q-loop/lid; other site 535289005329 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 535289005330 Q-loop/lid; other site 535289005331 ABC transporter signature motif; other site 535289005332 Walker B; other site 535289005333 D-loop; other site 535289005334 H-loop/switch region; other site 535289005335 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 535289005336 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 535289005337 active site 535289005338 metal binding site [ion binding]; metal-binding site 535289005339 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 535289005340 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 535289005341 nucleotide binding pocket [chemical binding]; other site 535289005342 K-X-D-G motif; other site 535289005343 catalytic site [active] 535289005344 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 535289005345 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 535289005346 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 535289005347 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 535289005348 Dimer interface [polypeptide binding]; other site 535289005349 BRCT sequence motif; other site 535289005350 hypothetical protein; Provisional; Region: PRK10279 535289005351 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 535289005352 nucleophile elbow; other site 535289005353 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 535289005354 Transglycosylase; Region: Transgly; pfam00912 535289005355 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 535289005356 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 535289005357 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289005358 putative substrate translocation pore; other site 535289005359 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 535289005360 nudix motif; other site 535289005361 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 535289005362 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 535289005363 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 535289005364 maleylacetoacetate isomerase; Region: maiA; TIGR01262 535289005365 C-terminal domain interface [polypeptide binding]; other site 535289005366 GSH binding site (G-site) [chemical binding]; other site 535289005367 putative dimer interface [polypeptide binding]; other site 535289005368 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 535289005369 N-terminal domain interface [polypeptide binding]; other site 535289005370 dimer interface [polypeptide binding]; other site 535289005371 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 535289005372 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 535289005373 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 535289005374 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 535289005375 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 535289005376 putative acyltransferase; Provisional; Region: PRK05790 535289005377 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 535289005378 dimer interface [polypeptide binding]; other site 535289005379 active site 535289005380 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289005381 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289005382 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 535289005383 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289005384 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289005385 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 535289005386 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 535289005387 FtsX-like permease family; Region: FtsX; pfam02687 535289005388 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 535289005389 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 535289005390 Walker A/P-loop; other site 535289005391 ATP binding site [chemical binding]; other site 535289005392 Q-loop/lid; other site 535289005393 ABC transporter signature motif; other site 535289005394 Walker B; other site 535289005395 D-loop; other site 535289005396 H-loop/switch region; other site 535289005397 Transglycosylase SLT domain; Region: SLT_2; pfam13406 535289005398 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 535289005399 N-acetyl-D-glucosamine binding site [chemical binding]; other site 535289005400 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 535289005401 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 535289005402 exonuclease I; Provisional; Region: sbcB; PRK11779 535289005403 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 535289005404 active site 535289005405 catalytic site [active] 535289005406 substrate binding site [chemical binding]; other site 535289005407 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 535289005408 NAD-dependent deacetylase; Provisional; Region: PRK05333 535289005409 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 535289005410 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 535289005411 GAF domain; Region: GAF; pfam01590 535289005412 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289005413 Walker A motif; other site 535289005414 ATP binding site [chemical binding]; other site 535289005415 Walker B motif; other site 535289005416 arginine finger; other site 535289005417 HTH domain; Region: HTH_22; pfam13309 535289005418 Protein of unknown function (DUF779); Region: DUF779; pfam05610 535289005419 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 535289005420 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 535289005421 NAD binding site [chemical binding]; other site 535289005422 substrate binding site [chemical binding]; other site 535289005423 catalytic Zn binding site [ion binding]; other site 535289005424 tetramer interface [polypeptide binding]; other site 535289005425 structural Zn binding site [ion binding]; other site 535289005426 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 535289005427 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 535289005428 NAD(P) binding site [chemical binding]; other site 535289005429 catalytic residues [active] 535289005430 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 535289005431 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 535289005432 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 535289005433 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 535289005434 GAF domain; Region: GAF; pfam01590 535289005435 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 535289005436 active site 535289005437 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 535289005438 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 535289005439 tetramer interface [polypeptide binding]; other site 535289005440 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289005441 catalytic residue [active] 535289005442 enoyl-CoA hydratase; Provisional; Region: PRK06142 535289005443 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 535289005444 substrate binding site [chemical binding]; other site 535289005445 oxyanion hole (OAH) forming residues; other site 535289005446 trimer interface [polypeptide binding]; other site 535289005447 hypothetical protein; Provisional; Region: PRK12378 535289005448 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 535289005449 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 sources...; Region: GST_N_Ure2p_like; cd03048 535289005450 C-terminal domain interface [polypeptide binding]; other site 535289005451 GSH binding site (G-site) [chemical binding]; other site 535289005452 dimer interface [polypeptide binding]; other site 535289005453 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 535289005454 N-terminal domain interface [polypeptide binding]; other site 535289005455 putative dimer interface [polypeptide binding]; other site 535289005456 active site 535289005457 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 535289005458 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 535289005459 hypothetical protein; Validated; Region: PRK00110 535289005460 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 535289005461 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 535289005462 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 535289005463 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 535289005464 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 535289005465 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 535289005466 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 535289005467 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 535289005468 Maf-like protein; Region: Maf; pfam02545 535289005469 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 535289005470 active site 535289005471 dimer interface [polypeptide binding]; other site 535289005472 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289005473 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 535289005474 ligand binding site [chemical binding]; other site 535289005475 flexible hinge region; other site 535289005476 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 535289005477 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 535289005478 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 535289005479 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 535289005480 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 from...; Region: WD40; cl02567 535289005481 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 535289005482 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 535289005483 FeS/SAM binding site; other site 535289005484 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 535289005485 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289005486 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 535289005487 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289005488 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289005489 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289005490 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 535289005491 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 535289005492 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 535289005493 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 535289005494 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 535289005495 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 535289005496 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 535289005497 active site 535289005498 SAM binding site [chemical binding]; other site 535289005499 homodimer interface [polypeptide binding]; other site 535289005500 ribonuclease G; Provisional; Region: PRK11712 535289005501 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 535289005502 homodimer interface [polypeptide binding]; other site 535289005503 oligonucleotide binding site [chemical binding]; other site 535289005504 methionine aminotransferase; Validated; Region: PRK09082 535289005505 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 535289005506 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289005507 homodimer interface [polypeptide binding]; other site 535289005508 catalytic residue [active] 535289005509 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 535289005510 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289005511 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 535289005512 substrate binding site [chemical binding]; other site 535289005513 dimerization interface [polypeptide binding]; other site 535289005514 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 535289005515 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 cobaltochelatase; Region: CbiX_SirB_N; cd03416 535289005516 putative active site [active] 535289005517 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 535289005518 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 535289005519 Predicted permeases [General function prediction only]; Region: COG0795 535289005520 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 535289005521 multifunctional aminopeptidase A; Provisional; Region: PRK00913 535289005522 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 535289005523 interface (dimer of trimers) [polypeptide binding]; other site 535289005524 Substrate-binding/catalytic site; other site 535289005525 Zn-binding sites [ion binding]; other site 535289005526 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 535289005527 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289005528 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 535289005529 dimerization interface [polypeptide binding]; other site 535289005530 ligand binding site [chemical binding]; other site 535289005531 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 535289005532 Putative D-3-Phosphoglycerate Dehydrogenases; Region: PGDH_like_1; cd12169 535289005533 dimerization interface [polypeptide binding]; other site 535289005534 NAD binding site [chemical binding]; other site 535289005535 ligand binding site [chemical binding]; other site 535289005536 catalytic site [active] 535289005537 Biofilm formation and stress response factor; Region: BsmA; pfam10014 535289005538 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 535289005539 Ligand Binding Site [chemical binding]; other site 535289005540 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 535289005541 beta-ketothiolase; Provisional; Region: PRK09051 535289005542 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 535289005543 dimer interface [polypeptide binding]; other site 535289005544 active site 535289005545 short chain dehydrogenase; Provisional; Region: PRK07023 535289005546 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289005547 NAD(P) binding site [chemical binding]; other site 535289005548 active site 535289005549 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 535289005550 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 535289005551 active site 535289005552 PAS domain; Region: PAS; smart00091 535289005553 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 535289005554 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289005555 dimer interface [polypeptide binding]; other site 535289005556 phosphorylation site [posttranslational modification] 535289005557 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 535289005558 ATP binding site [chemical binding]; other site 535289005559 Mg2+ binding site [ion binding]; other site 535289005560 G-X-G motif; other site 535289005561 Response regulator receiver domain; Region: Response_reg; pfam00072 535289005562 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 535289005563 active site 535289005564 phosphorylation site [posttranslational modification] 535289005565 intermolecular recognition site; other site 535289005566 dimerization interface [polypeptide binding]; other site 535289005567 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 535289005568 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 535289005569 glycine dehydrogenase; Provisional; Region: PRK05367 535289005570 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 535289005571 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289005572 catalytic residue [active] 535289005573 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:2.1; Region: GDC-P; cd00613 535289005574 tetramer interface [polypeptide binding]; other site 535289005575 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289005576 catalytic residue [active] 535289005577 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 535289005578 lipoyl attachment site [posttranslational modification]; other site 535289005579 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 535289005580 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 535289005581 DctM-like transporters; Region: DctM; pfam06808 535289005582 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 535289005583 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 535289005584 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 535289005585 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 535289005586 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289005587 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 535289005588 putative DNA binding site [nucleotide binding]; other site 535289005589 putative Zn2+ binding site [ion binding]; other site 535289005590 AsnC family; Region: AsnC_trans_reg; pfam01037 535289005591 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 535289005592 N-terminal plug; other site 535289005593 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 535289005594 ligand-binding site [chemical binding]; other site 535289005595 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 535289005596 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 535289005597 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 535289005598 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289005599 Walker A/P-loop; other site 535289005600 ATP binding site [chemical binding]; other site 535289005601 Q-loop/lid; other site 535289005602 ABC transporter signature motif; other site 535289005603 Walker B; other site 535289005604 D-loop; other site 535289005605 H-loop/switch region; other site 535289005606 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 535289005607 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 535289005608 TM-ABC transporter signature motif; other site 535289005609 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 535289005610 zinc binding site [ion binding]; other site 535289005611 putative ligand binding site [chemical binding]; other site 535289005612 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 535289005613 hydroxyglutarate oxidase; Provisional; Region: PRK11728 535289005614 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 535289005615 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 535289005616 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 535289005617 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 535289005618 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289005619 dimer interface [polypeptide binding]; other site 535289005620 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 535289005621 putative CheW interface [polypeptide binding]; other site 535289005622 sensor protein BasS/PmrB; Provisional; Region: PRK10755 535289005623 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 535289005624 ATP binding site [chemical binding]; other site 535289005625 Mg2+ binding site [ion binding]; other site 535289005626 G-X-G motif; other site 535289005627 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 535289005628 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 535289005629 active site 535289005630 phosphorylation site [posttranslational modification] 535289005631 intermolecular recognition site; other site 535289005632 dimerization interface [polypeptide binding]; other site 535289005633 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289005634 DNA binding site [nucleotide binding] 535289005635 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 535289005636 active site 535289005637 putative metal dependent hydrolase; Provisional; Region: PRK11598 535289005638 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 535289005639 Sulfatase; Region: Sulfatase; pfam00884 535289005640 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 535289005641 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 535289005642 DTW domain; Region: DTW; cl01221 535289005643 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 535289005644 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 535289005645 tetramer interface [polypeptide binding]; other site 535289005646 heme binding pocket [chemical binding]; other site 535289005647 NADPH binding site [chemical binding]; other site 535289005648 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 535289005649 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289005650 PAS domain; Region: PAS_9; pfam13426 535289005651 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 535289005652 putative active site [active] 535289005653 heme pocket [chemical binding]; other site 535289005654 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289005655 DNA binding residues [nucleotide binding] 535289005656 dimerization interface [polypeptide binding]; other site 535289005657 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 535289005658 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 535289005659 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 535289005660 Zn2+ binding site [ion binding]; other site 535289005661 Mg2+ binding site [ion binding]; other site 535289005662 Y-family of DNA polymerases; Region: PolY; cl12025 535289005663 DNA binding site [nucleotide binding] 535289005664 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 535289005665 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 535289005666 putative active site [active] 535289005667 putative PHP Thumb interface [polypeptide binding]; other site 535289005668 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 535289005669 generic binding surface II; other site 535289005670 generic binding surface I; other site 535289005671 Sel1-like repeats; Region: SEL1; smart00671 535289005672 Sel1 repeat; Region: Sel1; pfam08238 535289005673 Domain of unknown function (DUF4384); Region: DUF4384; pfam14326 535289005674 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 535289005675 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 535289005676 active site 535289005677 phosphorylation site [posttranslational modification] 535289005678 intermolecular recognition site; other site 535289005679 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289005680 DNA binding residues [nucleotide binding] 535289005681 dimerization interface [polypeptide binding]; other site 535289005682 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 535289005683 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 535289005684 ATP binding site [chemical binding]; other site 535289005685 Mg2+ binding site [ion binding]; other site 535289005686 G-X-G motif; other site 535289005687 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 535289005688 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 535289005689 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 535289005690 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 535289005691 active site 535289005692 succinic semialdehyde dehydrogenase; Region: PLN02278 535289005693 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 535289005694 tetramerization interface [polypeptide binding]; other site 535289005695 NAD(P) binding site [chemical binding]; other site 535289005696 catalytic residues [active] 535289005697 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 535289005698 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 535289005699 motif 1; other site 535289005700 active site 535289005701 motif 2; other site 535289005702 motif 3; other site 535289005703 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 535289005704 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289005705 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289005706 metal binding site [ion binding]; metal-binding site 535289005707 active site 535289005708 I-site; other site 535289005709 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 535289005710 S-adenosylmethionine binding site [chemical binding]; other site 535289005711 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 535289005712 active site 535289005713 HIGH motif; other site 535289005714 nucleotide binding site [chemical binding]; other site 535289005715 active site 535289005716 KMSKS motif; other site 535289005717 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 535289005718 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 535289005719 DNA-binding transcriptional activator AllS; Provisional; Region: PRK10094 535289005720 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289005721 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 535289005722 dimerization interface [polypeptide binding]; other site 535289005723 Pirin-related protein [General function prediction only]; Region: COG1741 535289005724 Pirin; Region: Pirin; pfam02678 535289005725 DoxX; Region: DoxX; cl17842 535289005726 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 535289005727 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 535289005728 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 535289005729 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 535289005730 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 535289005731 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 535289005732 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 535289005733 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 enzymes; Region: D-glucarate_dehydratase; cd03323 535289005734 active site 535289005735 tetramer interface [polypeptide binding]; other site 535289005736 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 535289005737 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 535289005738 putative ligand binding site [chemical binding]; other site 535289005739 NAD binding site [chemical binding]; other site 535289005740 catalytic site [active] 535289005741 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289005742 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 535289005743 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH); Region: KDGDH; cd00951 535289005744 putative active site [active] 535289005745 catalytic residue [active] 535289005746 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289005747 Transcriptional regulators [Transcription]; Region: FadR; COG2186 535289005748 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289005749 DNA-binding site [nucleotide binding]; DNA binding site 535289005750 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 535289005751 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 535289005752 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 enzymes; Region: D-glucarate_dehydratase; cd03323 535289005753 active site 535289005754 tetramer interface [polypeptide binding]; other site 535289005755 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289005756 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 535289005757 Protein with unknown function (DUF469); Region: DUF469; pfam04320 535289005758 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 535289005759 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 535289005760 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289005761 catalytic residue [active] 535289005762 Chromate resistance exported protein; Region: Chrome_Resist; pfam09828 535289005763 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 535289005764 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 535289005765 Chromate transporter; Region: Chromate_transp; pfam02417 535289005766 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 535289005767 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 535289005768 Alcaligenes xylosoxidans NreA and related domains; this domain family was previously known as part of DUF156; Region: NreA-like_DUF156; cd10154 535289005769 putative homodimer interface [polypeptide binding]; other site 535289005770 putative homotetramer interface [polypeptide binding]; other site 535289005771 putative metal binding site [ion binding]; other site 535289005772 putative homodimer-homodimer interface [polypeptide binding]; other site 535289005773 putative allosteric switch controlling residues; other site 535289005774 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 535289005775 EamA-like transporter family; Region: EamA; pfam00892 535289005776 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 535289005777 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 535289005778 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289005779 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289005780 active site 535289005781 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 535289005782 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 535289005783 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 535289005784 tetrameric interface [polypeptide binding]; other site 535289005785 NAD binding site [chemical binding]; other site 535289005786 catalytic residues [active] 535289005787 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289005788 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289005789 LysR substrate binding domain; Region: LysR_substrate; pfam03466 535289005790 dimerization interface [polypeptide binding]; other site 535289005791 short chain dehydrogenase; Provisional; Region: PRK06701 535289005792 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289005793 NAD(P) binding site [chemical binding]; other site 535289005794 active site 535289005795 FOG: CBS domain [General function prediction only]; Region: COG0517 535289005796 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 535289005797 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 535289005798 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 535289005799 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 535289005800 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 535289005801 Isochorismatase family; Region: Isochorismatase; pfam00857 535289005802 catalytic triad [active] 535289005803 dimer interface [polypeptide binding]; other site 535289005804 conserved cis-peptide bond; other site 535289005805 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 535289005806 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289005807 acyl-activating enzyme (AAE) consensus motif; other site 535289005808 AMP binding site [chemical binding]; other site 535289005809 active site 535289005810 CoA binding site [chemical binding]; other site 535289005811 PAS fold; Region: PAS_3; pfam08447 535289005812 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 535289005813 PAS domain S-box; Region: sensory_box; TIGR00229 535289005814 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 535289005815 putative active site [active] 535289005816 heme pocket [chemical binding]; other site 535289005817 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 535289005818 PAS fold; Region: PAS_3; pfam08447 535289005819 putative active site [active] 535289005820 heme pocket [chemical binding]; other site 535289005821 PAS domain S-box; Region: sensory_box; TIGR00229 535289005822 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 535289005823 putative active site [active] 535289005824 heme pocket [chemical binding]; other site 535289005825 PAS fold; Region: PAS_3; pfam08447 535289005826 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289005827 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289005828 metal binding site [ion binding]; metal-binding site 535289005829 active site 535289005830 I-site; other site 535289005831 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 535289005832 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 535289005833 EamA-like transporter family; Region: EamA; pfam00892 535289005834 EamA-like transporter family; Region: EamA; pfam00892 535289005835 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 535289005836 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 535289005837 DNA binding site [nucleotide binding] 535289005838 active site 535289005839 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 535289005840 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 535289005841 Helix-turn-helix domain; Region: HTH_18; pfam12833 535289005842 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 535289005843 AlkA N-terminal domain; Region: AlkA_N; pfam06029 535289005844 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 535289005845 minor groove reading motif; other site 535289005846 helix-hairpin-helix signature motif; other site 535289005847 active site 535289005848 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 535289005849 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 535289005850 active site 535289005851 substrate binding site [chemical binding]; other site 535289005852 metal binding site [ion binding]; metal-binding site 535289005853 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 535289005854 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 535289005855 CoA binding domain; Region: CoA_binding_2; pfam13380 535289005856 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 535289005857 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 535289005858 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 535289005859 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 535289005860 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 535289005861 hypothetical protein; Provisional; Region: PRK09272 535289005862 RibD C-terminal domain; Region: RibD_C; cl17279 535289005863 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 535289005864 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 535289005865 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 535289005866 active site residue [active] 535289005867 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 535289005868 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 535289005869 S-adenosylmethionine binding site [chemical binding]; other site 535289005870 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289005871 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289005872 methionine sulfoxide reductase A; Provisional; Region: PRK14054 535289005873 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 535289005874 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 535289005875 Protein of unknown function (DUF342); Region: DUF342; pfam03961 535289005876 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 535289005877 Chromate transporter; Region: Chromate_transp; pfam02417 535289005878 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289005879 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 535289005880 AsnC family; Region: AsnC_trans_reg; pfam01037 535289005881 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 535289005882 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289005883 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 535289005884 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 535289005885 acyl-activating enzyme (AAE) consensus motif; other site 535289005886 putative AMP binding site [chemical binding]; other site 535289005887 putative active site [active] 535289005888 putative CoA binding site [chemical binding]; other site 535289005889 Transcriptional regulators [Transcription]; Region: GntR; COG1802 535289005890 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289005891 DNA-binding site [nucleotide binding]; DNA binding site 535289005892 FCD domain; Region: FCD; pfam07729 535289005893 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 535289005894 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 contain...; Region: MM_CoA_mutase_alpha_like; cd03679 535289005895 active site 535289005896 substrate binding site [chemical binding]; other site 535289005897 coenzyme B12 binding site [chemical binding]; other site 535289005898 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 atom...; Region: MM_CoA_mut_B12_BD; cd02071 535289005899 B12 binding site [chemical binding]; other site 535289005900 cobalt ligand [ion binding]; other site 535289005901 membrane ATPase/protein kinase; Provisional; Region: PRK09435 535289005902 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 535289005903 Walker A; other site 535289005904 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 535289005905 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 535289005906 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 535289005907 Domain of unknown function (DUF1200); Region: DUF1200; pfam06713 535289005908 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 535289005909 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 535289005910 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 535289005911 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 535289005912 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 535289005913 carboxyltransferase (CT) interaction site; other site 535289005914 biotinylation site [posttranslational modification]; other site 535289005915 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 535289005916 dimer interface [polypeptide binding]; other site 535289005917 substrate binding site [chemical binding]; other site 535289005918 metal binding site [ion binding]; metal-binding site 535289005919 biotin synthase; Region: bioB; TIGR00433 535289005920 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 535289005921 FeS/SAM binding site; other site 535289005922 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 535289005923 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 535289005924 salt bridge; other site 535289005925 non-specific DNA binding site [nucleotide binding]; other site 535289005926 sequence-specific DNA binding site [nucleotide binding]; other site 535289005927 TniQ; Region: TniQ; pfam06527 535289005928 Integrase core domain; Region: rve; pfam00665 535289005929 Transposase; Region: HTH_Tnp_1; cl17663 535289005930 McrBC 5-methylcytosine restriction system component; Region: McrBC; pfam10117 535289005931 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 535289005932 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 535289005933 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 535289005934 ATP binding site [chemical binding]; other site 535289005935 putative Mg++ binding site [ion binding]; other site 535289005936 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 535289005937 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 535289005938 sequence-specific DNA binding site [nucleotide binding]; other site 535289005939 salt bridge; other site 535289005940 Phage protein; Region: DUF3653; pfam12375 535289005941 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 535289005942 classical (c) SDRs; Region: SDR_c; cd05233 535289005943 NAD(P) binding site [chemical binding]; other site 535289005944 active site 535289005945 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 535289005946 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 535289005947 dimer interface [polypeptide binding]; other site 535289005948 active site 535289005949 metal binding site [ion binding]; metal-binding site 535289005950 glutathione binding site [chemical binding]; other site 535289005951 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 535289005952 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 535289005953 active site 535289005954 intersubunit interface [polypeptide binding]; other site 535289005955 catalytic residue [active] 535289005956 phosphogluconate dehydratase; Validated; Region: PRK09054 535289005957 6-phosphogluconate dehydratase; Region: edd; TIGR01196 535289005958 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 535289005959 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 535289005960 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 535289005961 DctM-like transporters; Region: DctM; pfam06808 535289005962 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 535289005963 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 535289005964 ATP-binding site [chemical binding]; other site 535289005965 Gluconate-6-phosphate binding site [chemical binding]; other site 535289005966 Transcriptional regulators [Transcription]; Region: PurR; COG1609 535289005967 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 535289005968 DNA binding site [nucleotide binding] 535289005969 domain linker motif; other site 535289005970 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 535289005971 putative ligand binding site [chemical binding]; other site 535289005972 putative dimerization interface [polypeptide binding]; other site 535289005973 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 535289005974 ligand binding site [chemical binding]; other site 535289005975 Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]; Region: ChaC; COG3703 535289005976 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 535289005977 putative active site pocket [active] 535289005978 dimerization interface [polypeptide binding]; other site 535289005979 putative catalytic residue [active] 535289005980 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 535289005981 E-class dimer interface [polypeptide binding]; other site 535289005982 P-class dimer interface [polypeptide binding]; other site 535289005983 active site 535289005984 Cu2+ binding site [ion binding]; other site 535289005985 Zn2+ binding site [ion binding]; other site 535289005986 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 535289005987 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 535289005988 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 535289005989 Membrane transport protein; Region: Mem_trans; cl09117 535289005990 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 535289005991 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 535289005992 FMN binding site [chemical binding]; other site 535289005993 active site 535289005994 catalytic residues [active] 535289005995 substrate binding site [chemical binding]; other site 535289005996 CHASE domain; Region: CHASE; pfam03924 535289005997 PAS fold; Region: PAS_4; pfam08448 535289005998 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289005999 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289006000 metal binding site [ion binding]; metal-binding site 535289006001 active site 535289006002 I-site; other site 535289006003 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 535289006004 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 535289006005 synthetase active site [active] 535289006006 NTP binding site [chemical binding]; other site 535289006007 metal binding site [ion binding]; metal-binding site 535289006008 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 535289006009 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 535289006010 ferredoxin; Provisional; Region: PRK08764 535289006011 Putative Fe-S cluster; Region: FeS; cl17515 535289006012 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 535289006013 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289006014 dimerization interface [polypeptide binding]; other site 535289006015 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289006016 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289006017 dimer interface [polypeptide binding]; other site 535289006018 putative CheW interface [polypeptide binding]; other site 535289006019 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 535289006020 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 535289006021 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289006022 homodimer interface [polypeptide binding]; other site 535289006023 catalytic residue [active] 535289006024 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 535289006025 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 535289006026 active site 535289006027 substrate binding site [chemical binding]; other site 535289006028 trimer interface [polypeptide binding]; other site 535289006029 CoA binding site [chemical binding]; other site 535289006030 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 535289006031 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 535289006032 Walker A motif; other site 535289006033 ATP binding site [chemical binding]; other site 535289006034 Walker B motif; other site 535289006035 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 535289006036 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 535289006037 metal binding site [ion binding]; metal-binding site 535289006038 dimer interface [polypeptide binding]; other site 535289006039 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 535289006040 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 535289006041 S-adenosylmethionine binding site [chemical binding]; other site 535289006042 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 535289006043 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 535289006044 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 535289006045 ABC transporter; Region: ABC_tran_2; pfam12848 535289006046 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 535289006047 acetyacetyl-CoA reductase; Provisional; Region: PRK12938 535289006048 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 535289006049 NAD(P) binding site [chemical binding]; other site 535289006050 homotetramer interface [polypeptide binding]; other site 535289006051 homodimer interface [polypeptide binding]; other site 535289006052 active site 535289006053 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 535289006054 Clp amino terminal domain; Region: Clp_N; pfam02861 535289006055 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289006056 Walker A motif; other site 535289006057 ATP binding site [chemical binding]; other site 535289006058 Walker B motif; other site 535289006059 arginine finger; other site 535289006060 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289006061 Walker A motif; other site 535289006062 ATP binding site [chemical binding]; other site 535289006063 Walker B motif; other site 535289006064 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 535289006065 Uncharacterized conserved protein [Function unknown]; Region: COG2127 535289006066 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 535289006067 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 535289006068 putative active site [active] 535289006069 putative PHP Thumb interface [polypeptide binding]; other site 535289006070 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 535289006071 generic binding surface II; other site 535289006072 generic binding surface I; other site 535289006073 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 535289006074 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 535289006075 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 535289006076 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 535289006077 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 535289006078 active site 535289006079 Predicted ATPase [General function prediction only]; Region: COG1485 535289006080 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 535289006081 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289006082 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 535289006083 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 535289006084 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 535289006085 E3 interaction surface; other site 535289006086 lipoyl attachment site [posttranslational modification]; other site 535289006087 e3 binding domain; Region: E3_binding; pfam02817 535289006088 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 535289006089 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 535289006090 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 535289006091 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 535289006092 TPP-binding site [chemical binding]; other site 535289006093 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 535289006094 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 535289006095 Domain of unknown function DUF20; Region: UPF0118; pfam01594 535289006096 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289006097 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 535289006098 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289006099 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289006100 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 535289006101 putative dimerization interface [polypeptide binding]; other site 535289006102 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 535289006103 Ligand Binding Site [chemical binding]; other site 535289006104 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 535289006105 Domain of unknown function (DUF4382); Region: DUF4382; pfam14321 535289006106 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 535289006107 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 535289006108 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 535289006109 Walker A/P-loop; other site 535289006110 ATP binding site [chemical binding]; other site 535289006111 Q-loop/lid; other site 535289006112 ABC transporter signature motif; other site 535289006113 Walker B; other site 535289006114 D-loop; other site 535289006115 H-loop/switch region; other site 535289006116 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 535289006117 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 535289006118 Walker A/P-loop; other site 535289006119 ATP binding site [chemical binding]; other site 535289006120 Q-loop/lid; other site 535289006121 ABC transporter signature motif; other site 535289006122 Walker B; other site 535289006123 D-loop; other site 535289006124 H-loop/switch region; other site 535289006125 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 535289006126 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 535289006127 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289006128 dimer interface [polypeptide binding]; other site 535289006129 conserved gate region; other site 535289006130 putative PBP binding loops; other site 535289006131 ABC-ATPase subunit interface; other site 535289006132 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 535289006133 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289006134 dimer interface [polypeptide binding]; other site 535289006135 conserved gate region; other site 535289006136 putative PBP binding loops; other site 535289006137 ABC-ATPase subunit interface; other site 535289006138 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 535289006139 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 535289006140 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 535289006141 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 535289006142 NAD binding site [chemical binding]; other site 535289006143 homotetramer interface [polypeptide binding]; other site 535289006144 homodimer interface [polypeptide binding]; other site 535289006145 substrate binding site [chemical binding]; other site 535289006146 active site 535289006147 DNA photolyase; Region: DNA_photolyase; pfam00875 535289006148 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 535289006149 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 535289006150 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 involved...; Region: GST_N_GTT1_like; cd03046 535289006151 putative C-terminal domain interface [polypeptide binding]; other site 535289006152 putative GSH binding site (G-site) [chemical binding]; other site 535289006153 putative dimer interface [polypeptide binding]; other site 535289006154 C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases; Region: GST_C_GTT1_like; cd03189 535289006155 putative N-terminal domain interface [polypeptide binding]; other site 535289006156 putative dimer interface [polypeptide binding]; other site 535289006157 putative substrate binding pocket (H-site) [chemical binding]; other site 535289006158 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 535289006159 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 535289006160 substrate binding pocket [chemical binding]; other site 535289006161 membrane-bound complex binding site; other site 535289006162 oxidative damage protection protein; Provisional; Region: PRK05408 535289006163 Predicted membrane protein [Function unknown]; Region: COG2860 535289006164 UPF0126 domain; Region: UPF0126; pfam03458 535289006165 UPF0126 domain; Region: UPF0126; pfam03458 535289006166 Uncharacterized conserved protein [Function unknown]; Region: COG4121 535289006167 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 535289006168 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 535289006169 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 535289006170 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 535289006171 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 535289006172 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 535289006173 Active Sites [active] 535289006174 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 535289006175 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 535289006176 Active Sites [active] 535289006177 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 535289006178 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 535289006179 G1 box; other site 535289006180 GTP/Mg2+ binding site [chemical binding]; other site 535289006181 G2 box; other site 535289006182 Switch I region; other site 535289006183 G3 box; other site 535289006184 Switch II region; other site 535289006185 G4 box; other site 535289006186 G5 box; other site 535289006187 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 535289006188 Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu...; Region: Translation_factor_III; cl02786 535289006189 Ferredoxin [Energy production and conversion]; Region: COG1146 535289006190 4Fe-4S binding domain; Region: Fer4; cl02805 535289006191 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 535289006192 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 535289006193 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 535289006194 Bacterial SH3 domain; Region: SH3_4; pfam06347 535289006195 Bacterial SH3 domain; Region: SH3_3; pfam08239 535289006196 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 535289006197 dimer interface [polypeptide binding]; other site 535289006198 substrate binding site [chemical binding]; other site 535289006199 ATP binding site [chemical binding]; other site 535289006200 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 535289006201 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 535289006202 thiS-thiF/thiG interaction site; other site 535289006203 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 535289006204 ThiS interaction site; other site 535289006205 putative active site [active] 535289006206 tetramer interface [polypeptide binding]; other site 535289006207 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 535289006208 thiamine phosphate binding site [chemical binding]; other site 535289006209 active site 535289006210 pyrophosphate binding site [ion binding]; other site 535289006211 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 535289006212 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 535289006213 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289006214 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289006215 enoyl-CoA hydratase; Provisional; Region: PRK07511 535289006216 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 535289006217 substrate binding site [chemical binding]; other site 535289006218 oxyanion hole (OAH) forming residues; other site 535289006219 trimer interface [polypeptide binding]; other site 535289006220 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289006221 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 535289006222 ligand binding site [chemical binding]; other site 535289006223 flexible hinge region; other site 535289006224 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 535289006225 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 535289006226 putative active site [active] 535289006227 putative substrate binding site [chemical binding]; other site 535289006228 ATP binding site [chemical binding]; other site 535289006229 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289006230 Acyl-CoA dehydrogenases similar to fadE2; Region: ACAD_FadE2; cd01155 535289006231 FAD binding site [chemical binding]; other site 535289006232 substrate binding site [chemical binding]; other site 535289006233 catalytic base [active] 535289006234 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 535289006235 Transcriptional regulator [Transcription]; Region: IclR; COG1414 535289006236 Bacterial transcriptional regulator; Region: IclR; pfam01614 535289006237 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 535289006238 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 535289006239 2-isopropylmalate synthase; Validated; Region: PRK00915 535289006240 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 535289006241 active site 535289006242 catalytic residues [active] 535289006243 metal binding site [ion binding]; metal-binding site 535289006244 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 535289006245 2-isopropylmalate synthase; Validated; Region: PRK03739 535289006246 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 535289006247 active site 535289006248 catalytic residues [active] 535289006249 metal binding site [ion binding]; metal-binding site 535289006250 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 535289006251 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 535289006252 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 535289006253 ketol-acid reductoisomerase; Provisional; Region: PRK05479 535289006254 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 535289006255 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 535289006256 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 535289006257 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 535289006258 putative valine binding site [chemical binding]; other site 535289006259 dimer interface [polypeptide binding]; other site 535289006260 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 535289006261 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 535289006262 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 535289006263 PYR/PP interface [polypeptide binding]; other site 535289006264 dimer interface [polypeptide binding]; other site 535289006265 TPP binding site [chemical binding]; other site 535289006266 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 535289006267 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 535289006268 TPP-binding site [chemical binding]; other site 535289006269 dimer interface [polypeptide binding]; other site 535289006270 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289006271 RNA polymerase factor sigma-70; Validated; Region: PRK09047 535289006272 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289006273 DNA binding residues [nucleotide binding] 535289006274 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 535289006275 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 535289006276 RDD family; Region: RDD; pfam06271 535289006277 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 535289006278 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 535289006279 Nitrogen regulatory protein P-II; Region: P-II; pfam00543 535289006280 Nitrogen regulatory protein P-II; Region: P-II; smart00938 535289006281 NAD synthetase; Provisional; Region: PRK13981 535289006282 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 535289006283 multimer interface [polypeptide binding]; other site 535289006284 active site 535289006285 catalytic triad [active] 535289006286 protein interface 1 [polypeptide binding]; other site 535289006287 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 535289006288 homodimer interface [polypeptide binding]; other site 535289006289 NAD binding pocket [chemical binding]; other site 535289006290 ATP binding pocket [chemical binding]; other site 535289006291 Mg binding site [ion binding]; other site 535289006292 active-site loop [active] 535289006293 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 535289006294 Protein of unknown function, DUF482; Region: DUF482; pfam04339 535289006295 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 535289006296 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 535289006297 dimer interface [polypeptide binding]; other site 535289006298 substrate binding site [chemical binding]; other site 535289006299 metal binding sites [ion binding]; metal-binding site 535289006300 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 535289006301 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 535289006302 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 535289006303 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like; Region: ALDH_AAS00426; cd07109 535289006304 NAD(P) binding site [chemical binding]; other site 535289006305 catalytic residues [active] 535289006306 catalytic residues [active] 535289006307 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 535289006308 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 535289006309 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 535289006310 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 535289006311 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 535289006312 FeS/SAM binding site; other site 535289006313 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 535289006314 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 535289006315 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 535289006316 GTP binding site; other site 535289006317 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 535289006318 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 535289006319 dimer interface [polypeptide binding]; other site 535289006320 putative functional site; other site 535289006321 putative MPT binding site; other site 535289006322 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 535289006323 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 535289006324 catalytic residues [active] 535289006325 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 535289006326 RNA/DNA hybrid binding site [nucleotide binding]; other site 535289006327 active site 535289006328 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 535289006329 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 535289006330 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 535289006331 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 535289006332 N-acetyl-D-glucosamine binding site [chemical binding]; other site 535289006333 catalytic residue [active] 535289006334 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 535289006335 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 535289006336 tol-pal system protein YbgF; Provisional; Region: PRK10803 535289006337 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 535289006338 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 535289006339 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 535289006340 ligand binding site [chemical binding]; other site 535289006341 translocation protein TolB; Provisional; Region: tolB; PRK02889 535289006342 TolB amino-terminal domain; Region: TolB_N; pfam04052 535289006343 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 535289006344 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 535289006345 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 535289006346 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 535289006347 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 535289006348 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289006349 Walker A/P-loop; other site 535289006350 ATP binding site [chemical binding]; other site 535289006351 Q-loop/lid; other site 535289006352 ABC transporter signature motif; other site 535289006353 Walker B; other site 535289006354 D-loop; other site 535289006355 H-loop/switch region; other site 535289006356 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 535289006357 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; cl02529 535289006358 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 535289006359 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 535289006360 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 535289006361 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 535289006362 active site 535289006363 PilZ domain; Region: PilZ; cl01260 535289006364 DNA polymerase III subunit delta'; Validated; Region: PRK06964 535289006365 DNA polymerase III subunit delta'; Validated; Region: PRK08485 535289006366 thymidylate kinase; Validated; Region: tmk; PRK00698 535289006367 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 535289006368 TMP-binding site; other site 535289006369 ATP-binding site [chemical binding]; other site 535289006370 YceG-like family; Region: YceG; pfam02618 535289006371 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 535289006372 dimerization interface [polypeptide binding]; other site 535289006373 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 535289006374 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 535289006375 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 535289006376 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 535289006377 active site 535289006378 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 535289006379 Coenzyme A binding pocket [chemical binding]; other site 535289006380 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; cd00312 535289006381 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 535289006382 substrate binding pocket [chemical binding]; other site 535289006383 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 535289006384 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 535289006385 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 535289006386 putative active site [active] 535289006387 metal binding site [ion binding]; metal-binding site 535289006388 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289006389 dimerization interface [polypeptide binding]; other site 535289006390 PAS fold; Region: PAS; pfam00989 535289006391 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 535289006392 HDOD domain; Region: HDOD; pfam08668 535289006393 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 535289006394 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 535289006395 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 535289006396 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 535289006397 RNA binding site [nucleotide binding]; other site 535289006398 Protein of unknown function DUF72; Region: DUF72; pfam01904 535289006399 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 535289006400 putative substrate translocation pore; other site 535289006401 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 535289006402 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 535289006403 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 535289006404 putative substrate translocation pore; other site 535289006405 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 535289006406 hypothetical protein; Provisional; Region: PRK06194 535289006407 classical (c) SDRs; Region: SDR_c; cd05233 535289006408 NAD(P) binding site [chemical binding]; other site 535289006409 active site 535289006410 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 535289006411 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 535289006412 C-terminal domain interface [polypeptide binding]; other site 535289006413 GSH binding site (G-site) [chemical binding]; other site 535289006414 dimer interface [polypeptide binding]; other site 535289006415 dimer interface [polypeptide binding]; other site 535289006416 N-terminal domain interface [polypeptide binding]; other site 535289006417 substrate binding pocket (H-site) [chemical binding]; other site 535289006418 Glutathione S-transferase, C-terminal domain; Region: GST_C_2; pfam13410 535289006419 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 535289006420 Coenzyme A binding pocket [chemical binding]; other site 535289006421 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 535289006422 Prostaglandin dehydrogenases; Region: PGDH; cd05288 535289006423 NAD(P) binding site [chemical binding]; other site 535289006424 substrate binding site [chemical binding]; other site 535289006425 dimer interface [polypeptide binding]; other site 535289006426 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 535289006427 CoenzymeA binding site [chemical binding]; other site 535289006428 subunit interaction site [polypeptide binding]; other site 535289006429 PHB binding site; other site 535289006430 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 535289006431 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289006432 NAD(P) binding site [chemical binding]; other site 535289006433 active site 535289006434 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 535289006435 nucleoside/Zn binding site; other site 535289006436 dimer interface [polypeptide binding]; other site 535289006437 catalytic motif [active] 535289006438 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289006439 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 535289006440 putative ligand binding site [chemical binding]; other site 535289006441 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 535289006442 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289006443 putative substrate translocation pore; other site 535289006444 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 535289006445 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 535289006446 substrate binding pocket [chemical binding]; other site 535289006447 membrane-bound complex binding site; other site 535289006448 hinge residues; other site 535289006449 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 535289006450 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 535289006451 Walker A/P-loop; other site 535289006452 ATP binding site [chemical binding]; other site 535289006453 Q-loop/lid; other site 535289006454 ABC transporter signature motif; other site 535289006455 Walker B; other site 535289006456 D-loop; other site 535289006457 H-loop/switch region; other site 535289006458 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 535289006459 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 535289006460 Transposase domain (DUF772); Region: DUF772; pfam05598 535289006461 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 535289006462 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 535289006463 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 535289006464 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 535289006465 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 535289006466 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 535289006467 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289006468 active site 535289006469 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 535289006470 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289006471 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289006472 metal binding site [ion binding]; metal-binding site 535289006473 active site 535289006474 I-site; other site 535289006475 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 535289006476 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 535289006477 dimer interface [polypeptide binding]; other site 535289006478 active site 535289006479 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 535289006480 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 535289006481 substrate binding site [chemical binding]; other site 535289006482 oxyanion hole (OAH) forming residues; other site 535289006483 trimer interface [polypeptide binding]; other site 535289006484 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 535289006485 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289006486 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289006487 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 535289006488 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 535289006489 Walker A/P-loop; other site 535289006490 ATP binding site [chemical binding]; other site 535289006491 Q-loop/lid; other site 535289006492 ABC transporter signature motif; other site 535289006493 Walker B; other site 535289006494 D-loop; other site 535289006495 H-loop/switch region; other site 535289006496 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 535289006497 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 535289006498 Walker A/P-loop; other site 535289006499 ATP binding site [chemical binding]; other site 535289006500 Q-loop/lid; other site 535289006501 ABC transporter signature motif; other site 535289006502 Walker B; other site 535289006503 D-loop; other site 535289006504 H-loop/switch region; other site 535289006505 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 535289006506 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 535289006507 TM-ABC transporter signature motif; other site 535289006508 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 535289006509 TM-ABC transporter signature motif; other site 535289006510 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289006511 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 535289006512 putative ligand binding site [chemical binding]; other site 535289006513 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 535289006514 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 535289006515 dimer interface [polypeptide binding]; other site 535289006516 acyl-activating enzyme (AAE) consensus motif; other site 535289006517 putative active site [active] 535289006518 AMP binding site [chemical binding]; other site 535289006519 putative CoA binding site [chemical binding]; other site 535289006520 Uncharacterized conserved protein [Function unknown]; Region: COG0397 535289006521 hypothetical protein; Validated; Region: PRK00029 535289006522 methionine sulfoxide reductase B; Provisional; Region: PRK00222 535289006523 SelR domain; Region: SelR; pfam01641 535289006524 intracellular septation protein A; Reviewed; Region: PRK00259 535289006525 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 535289006526 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 535289006527 Protein of unknown function (DUF1624); Region: DUF1624; pfam07786 535289006528 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 535289006529 rRNA binding site [nucleotide binding]; other site 535289006530 predicted 30S ribosome binding site; other site 535289006531 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 535289006532 HPP family; Region: HPP; pfam04982 535289006533 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 535289006534 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 535289006535 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 535289006536 N-formylglutamate amidohydrolase; Region: FGase; cl01522 535289006537 Transcriptional regulator; Region: Rrf2; cl17282 535289006538 Rrf2 family protein; Region: rrf2_super; TIGR00738 535289006539 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 535289006540 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 535289006541 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 535289006542 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 535289006543 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 535289006544 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 535289006545 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 535289006546 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 535289006547 N-acetyl-D-glucosamine binding site [chemical binding]; other site 535289006548 catalytic residue [active] 535289006549 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 535289006550 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 535289006551 dimer interface [polypeptide binding]; other site 535289006552 active site 535289006553 glycine-pyridoxal phosphate binding site [chemical binding]; other site 535289006554 folate binding site [chemical binding]; other site 535289006555 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 535289006556 ATP cone domain; Region: ATP-cone; pfam03477 535289006557 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 535289006558 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 535289006559 Tetramer interface [polypeptide binding]; other site 535289006560 active site 535289006561 FMN-binding site [chemical binding]; other site 535289006562 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 535289006563 FOG: CBS domain [General function prediction only]; Region: COG0517 535289006564 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK08134 535289006565 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 535289006566 homodimer interface [polypeptide binding]; other site 535289006567 substrate-cofactor binding pocket; other site 535289006568 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289006569 catalytic residue [active] 535289006570 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 535289006571 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 535289006572 nucleophilic elbow; other site 535289006573 catalytic triad; other site 535289006574 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 535289006575 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 535289006576 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289006577 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 535289006578 Soluble P-type ATPase [General function prediction only]; Region: COG4087 535289006579 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 535289006580 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 535289006581 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 535289006582 motif II; other site 535289006583 ferrochelatase; Reviewed; Region: hemH; PRK00035 535289006584 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 535289006585 C-terminal domain interface [polypeptide binding]; other site 535289006586 active site 535289006587 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 535289006588 active site 535289006589 N-terminal domain interface [polypeptide binding]; other site 535289006590 AAA domain; Region: AAA_32; pfam13654 535289006591 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 535289006592 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 535289006593 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 535289006594 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 535289006595 active site residue [active] 535289006596 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 535289006597 active site residue [active] 535289006598 putative inner membrane protein; Provisional; Region: PRK11099 535289006599 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 535289006600 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 535289006601 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289006602 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 535289006603 putative ligand binding site [chemical binding]; other site 535289006604 3HB-oligomer hydrolase (3HBOH); Region: 3HBOH; pfam10605 535289006605 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 535289006606 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 535289006607 TM-ABC transporter signature motif; other site 535289006608 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 535289006609 TM-ABC transporter signature motif; other site 535289006610 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 535289006611 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 535289006612 Walker A/P-loop; other site 535289006613 ATP binding site [chemical binding]; other site 535289006614 Q-loop/lid; other site 535289006615 ABC transporter signature motif; other site 535289006616 Walker B; other site 535289006617 D-loop; other site 535289006618 H-loop/switch region; other site 535289006619 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 535289006620 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 535289006621 Walker A/P-loop; other site 535289006622 ATP binding site [chemical binding]; other site 535289006623 Q-loop/lid; other site 535289006624 ABC transporter signature motif; other site 535289006625 Walker B; other site 535289006626 D-loop; other site 535289006627 H-loop/switch region; other site 535289006628 esterase, PHB depolymerase family; Region: esterase_phb; TIGR01840 535289006629 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 535289006630 Interdomain contacts; other site 535289006631 Cytokine receptor motif; other site 535289006632 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289006633 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria; Region: PBP1_SBP_like_2; cd06328 535289006634 putative ligand binding site [chemical binding]; other site 535289006635 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 535289006636 PAS domain; Region: PAS_9; pfam13426 535289006637 putative active site [active] 535289006638 heme pocket [chemical binding]; other site 535289006639 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 535289006640 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289006641 Walker A motif; other site 535289006642 ATP binding site [chemical binding]; other site 535289006643 Walker B motif; other site 535289006644 arginine finger; other site 535289006645 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 535289006646 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 535289006647 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 535289006648 N-terminal plug; other site 535289006649 ligand-binding site [chemical binding]; other site 535289006650 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 535289006651 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 535289006652 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 535289006653 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 535289006654 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 535289006655 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 535289006656 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 535289006657 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 535289006658 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 535289006659 active site 535289006660 phosphorylation site [posttranslational modification] 535289006661 intermolecular recognition site; other site 535289006662 dimerization interface [polypeptide binding]; other site 535289006663 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289006664 DNA binding site [nucleotide binding] 535289006665 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 535289006666 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289006667 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289006668 dimer interface [polypeptide binding]; other site 535289006669 phosphorylation site [posttranslational modification] 535289006670 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 535289006671 ATP binding site [chemical binding]; other site 535289006672 Mg2+ binding site [ion binding]; other site 535289006673 G-X-G motif; other site 535289006674 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 535289006675 RNA binding surface [nucleotide binding]; other site 535289006676 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 535289006677 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 535289006678 sequence-specific DNA binding site [nucleotide binding]; other site 535289006679 salt bridge; other site 535289006680 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 535289006681 Domain of unknown function (DUF955); Region: DUF955; pfam06114 535289006682 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 535289006683 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 535289006684 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 535289006685 methylcitrate synthase; Provisional; Region: PRK12351 535289006686 oxalacetate binding site [chemical binding]; other site 535289006687 citrylCoA binding site [chemical binding]; other site 535289006688 coenzyme A binding site [chemical binding]; other site 535289006689 catalytic triad [active] 535289006690 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 535289006691 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 535289006692 substrate binding site [chemical binding]; other site 535289006693 ligand binding site [chemical binding]; other site 535289006694 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 535289006695 substrate binding site [chemical binding]; other site 535289006696 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 535289006697 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 535289006698 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 535289006699 tetramer interface [polypeptide binding]; other site 535289006700 active site 535289006701 Mg2+/Mn2+ binding site [ion binding]; other site 535289006702 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 535289006703 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289006704 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 535289006705 putative dimerization interface [polypeptide binding]; other site 535289006706 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 535289006707 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 535289006708 THF binding site; other site 535289006709 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 535289006710 substrate binding site [chemical binding]; other site 535289006711 THF binding site; other site 535289006712 zinc-binding site [ion binding]; other site 535289006713 Predicted integral membrane protein [Function unknown]; Region: COG5615 535289006714 aspartate kinase; Reviewed; Region: PRK06635 535289006715 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 535289006716 putative nucleotide binding site [chemical binding]; other site 535289006717 putative catalytic residues [active] 535289006718 putative Mg ion binding site [ion binding]; other site 535289006719 putative aspartate binding site [chemical binding]; other site 535289006720 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 535289006721 putative allosteric regulatory site; other site 535289006722 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 535289006723 putative allosteric regulatory residue; other site 535289006724 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 535289006725 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 535289006726 Ligand Binding Site [chemical binding]; other site 535289006727 TilS substrate binding domain; Region: TilS; pfam09179 535289006728 Cache domain; Region: Cache_1; pfam02743 535289006729 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289006730 dimerization interface [polypeptide binding]; other site 535289006731 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289006732 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289006733 dimer interface [polypeptide binding]; other site 535289006734 putative CheW interface [polypeptide binding]; other site 535289006735 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 535289006736 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 535289006737 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 535289006738 endonuclease III; Region: ENDO3c; smart00478 535289006739 minor groove reading motif; other site 535289006740 helix-hairpin-helix signature motif; other site 535289006741 substrate binding pocket [chemical binding]; other site 535289006742 active site 535289006743 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 535289006744 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 535289006745 active site 535289006746 HIGH motif; other site 535289006747 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 535289006748 KMSKS motif; other site 535289006749 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 535289006750 tRNA binding surface [nucleotide binding]; other site 535289006751 anticodon binding site; other site 535289006752 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 535289006753 TPR motif; other site 535289006754 TPR repeat; Region: TPR_11; pfam13414 535289006755 binding surface 535289006756 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 535289006757 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 535289006758 substrate binding site [chemical binding]; other site 535289006759 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 535289006760 substrate binding site [chemical binding]; other site 535289006761 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 535289006762 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 535289006763 putative active site [active] 535289006764 putative metal binding site [ion binding]; other site 535289006765 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 535289006766 2-oxoacid dehydrogenase subunit E1; Provisional; Region: PRK13012 535289006767 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 535289006768 dimer interface [polypeptide binding]; other site 535289006769 TPP-binding site [chemical binding]; other site 535289006770 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 535289006771 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 535289006772 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289006773 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 535289006774 putative DNA binding site [nucleotide binding]; other site 535289006775 putative Zn2+ binding site [ion binding]; other site 535289006776 AsnC family; Region: AsnC_trans_reg; pfam01037 535289006777 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 535289006778 Predicted esterase [General function prediction only]; Region: COG0400 535289006779 putative hydrolase; Provisional; Region: PRK11460 535289006780 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 535289006781 putative active site [active] 535289006782 metal binding site [ion binding]; metal-binding site 535289006783 hypothetical protein; Provisional; Region: PRK09256 535289006784 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 535289006785 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 535289006786 Dehydroquinase class II; Region: DHquinase_II; pfam01220 535289006787 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 535289006788 trimer interface [polypeptide binding]; other site 535289006789 active site 535289006790 dimer interface [polypeptide binding]; other site 535289006791 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 535289006792 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 535289006793 active site 535289006794 HIGH motif; other site 535289006795 nucleotide binding site [chemical binding]; other site 535289006796 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 535289006797 active site 535289006798 KMSKS motif; other site 535289006799 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 535289006800 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 535289006801 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 535289006802 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 535289006803 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 535289006804 NAD binding site [chemical binding]; other site 535289006805 homodimer interface [polypeptide binding]; other site 535289006806 homotetramer interface [polypeptide binding]; other site 535289006807 active site 535289006808 TadE-like protein; Region: TadE; pfam07811 535289006809 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 535289006810 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 535289006811 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 535289006812 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 535289006813 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 535289006814 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 535289006815 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 535289006816 phosphopeptide binding site; other site 535289006817 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 535289006818 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 535289006819 ATP binding site [chemical binding]; other site 535289006820 Walker A motif; other site 535289006821 hexamer interface [polypeptide binding]; other site 535289006822 Walker B motif; other site 535289006823 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 535289006824 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 535289006825 TadE-like protein; Region: TadE; pfam07811 535289006826 Transposase, Mutator family; Region: Transposase_mut; pfam00872 535289006827 MULE transposase domain; Region: MULE; pfam10551 535289006828 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 535289006829 Transposase domain (DUF772); Region: DUF772; pfam05598 535289006830 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 535289006831 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 535289006832 IHF dimer interface [polypeptide binding]; other site 535289006833 IHF - DNA interface [nucleotide binding]; other site 535289006834 putative transcriptional regulator MerR; Provisional; Region: PRK13752 535289006835 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 535289006836 DNA binding residues [nucleotide binding] 535289006837 dimer interface [polypeptide binding]; other site 535289006838 mercury binding site [ion binding]; other site 535289006839 putative mercuric transport protein; Provisional; Region: PRK13751 535289006840 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 535289006841 metal-binding site [ion binding] 535289006842 putative mercury transport protein MerC; Provisional; Region: PRK13755 535289006843 putative mercuric reductase; Provisional; Region: PRK13748 535289006844 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 535289006845 metal-binding site [ion binding] 535289006846 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 535289006847 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289006848 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 535289006849 transcriptional regulator MerD; Provisional; Region: PRK13749 535289006850 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 535289006851 DNA binding residues [nucleotide binding] 535289006852 putative mercury resistance protein; Provisional; Region: PRK13747 535289006853 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 535289006854 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 535289006855 Integrase core domain; Region: rve; pfam00665 535289006856 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 535289006857 arsenical pump membrane protein; Provisional; Region: PRK15445 535289006858 transmembrane helices; other site 535289006859 FOG: CBS domain [General function prediction only]; Region: COG0517 535289006860 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection...; Region: CBS_pair_BON_assoc; cd04586 535289006861 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 535289006862 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 535289006863 P loop; other site 535289006864 Nucleotide binding site [chemical binding]; other site 535289006865 DTAP/Switch II; other site 535289006866 Switch I; other site 535289006867 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 535289006868 DTAP/Switch II; other site 535289006869 Switch I; other site 535289006870 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 535289006871 Low molecular weight phosphatase family; Region: LMWPc; cd00115 535289006872 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 535289006873 active site 535289006874 glycerate kinase; Region: TIGR00045 535289006875 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 535289006876 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 535289006877 active site 535289006878 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 535289006879 metal-binding site [ion binding] 535289006880 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 535289006881 metal-binding site [ion binding] 535289006882 Heavy-metal-associated domain; Region: HMA; pfam00403 535289006883 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 535289006884 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 535289006885 metal-binding site [ion binding] 535289006886 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289006887 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 535289006888 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 535289006889 DNA binding residues [nucleotide binding] 535289006890 dimer interface [polypeptide binding]; other site 535289006891 putative metal binding site [ion binding]; other site 535289006892 Cation efflux family; Region: Cation_efflux; cl00316 535289006893 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 535289006894 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 535289006895 Iron permease FTR1 family; Region: FTR1; cl00475 535289006896 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 535289006897 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289006898 Soluble P-type ATPase [General function prediction only]; Region: COG4087 535289006899 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 535289006900 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 535289006901 DNA binding residues [nucleotide binding] 535289006902 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 535289006903 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 535289006904 putative transposase OrfB; Reviewed; Region: PHA02517 535289006905 HTH-like domain; Region: HTH_21; pfam13276 535289006906 Integrase core domain; Region: rve; pfam00665 535289006907 Integrase core domain; Region: rve_3; pfam13683 535289006908 Transposase; Region: HTH_Tnp_1; pfam01527 535289006909 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289006910 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 535289006911 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 535289006912 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 535289006913 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 535289006914 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289006915 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 535289006916 Trehalase; Region: Trehalase; cl17346 535289006917 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289006918 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 535289006919 Outer membrane efflux protein; Region: OEP; pfam02321 535289006920 Outer membrane efflux protein; Region: OEP; pfam02321 535289006921 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 535289006922 Predicted membrane protein [Function unknown]; Region: COG3174 535289006923 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 535289006924 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 535289006925 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 535289006926 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 535289006927 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 535289006928 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 535289006929 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 535289006930 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 535289006931 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 535289006932 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289006933 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 535289006934 motif II; other site 535289006935 Cytochrome c; Region: Cytochrom_C; pfam00034 535289006936 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 535289006937 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 535289006938 Uncharacterized conserved protein [Function unknown]; Region: COG5569 535289006939 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 535289006940 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 535289006941 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 535289006942 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 535289006943 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 535289006944 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 535289006945 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 535289006946 active site 535289006947 phosphorylation site [posttranslational modification] 535289006948 intermolecular recognition site; other site 535289006949 dimerization interface [polypeptide binding]; other site 535289006950 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289006951 DNA binding site [nucleotide binding] 535289006952 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 535289006953 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289006954 dimerization interface [polypeptide binding]; other site 535289006955 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289006956 dimer interface [polypeptide binding]; other site 535289006957 phosphorylation site [posttranslational modification] 535289006958 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 535289006959 ATP binding site [chemical binding]; other site 535289006960 Mg2+ binding site [ion binding]; other site 535289006961 G-X-G motif; other site 535289006962 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 535289006963 dimerization interface [polypeptide binding]; other site 535289006964 putative DNA binding site [nucleotide binding]; other site 535289006965 putative Zn2+ binding site [ion binding]; other site 535289006966 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 535289006967 active site residue [active] 535289006968 Methyltransferase domain; Region: Methyltransf_23; pfam13489 535289006969 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 535289006970 S-adenosylmethionine binding site [chemical binding]; other site 535289006971 DsrE/DsrF-like family; Region: DrsE; cl00672 535289006972 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 535289006973 S-adenosylmethionine binding site [chemical binding]; other site 535289006974 Outer membrane efflux protein; Region: OEP; pfam02321 535289006975 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 535289006976 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289006977 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 535289006978 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289006979 Nitrogen regulatory protein P-II; Region: P-II; pfam00543 535289006980 Nitrogen regulatory protein P-II; Region: P-II; smart00938 535289006981 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 535289006982 putative metal dependent hydrolase; Provisional; Region: PRK11598 535289006983 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 535289006984 Sulfatase; Region: Sulfatase; pfam00884 535289006985 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 535289006986 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289006987 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 535289006988 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 535289006989 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 535289006990 active site 535289006991 phosphorylation site [posttranslational modification] 535289006992 intermolecular recognition site; other site 535289006993 dimerization interface [polypeptide binding]; other site 535289006994 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289006995 DNA binding site [nucleotide binding] 535289006996 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 535289006997 HAMP domain; Region: HAMP; pfam00672 535289006998 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289006999 dimer interface [polypeptide binding]; other site 535289007000 phosphorylation site [posttranslational modification] 535289007001 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 535289007002 ATP binding site [chemical binding]; other site 535289007003 Mg2+ binding site [ion binding]; other site 535289007004 G-X-G motif; other site 535289007005 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 535289007006 EamA-like transporter family; Region: EamA; pfam00892 535289007007 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 535289007008 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289007009 Transposase; Region: HTH_Tnp_1; pfam01527 535289007010 putative transposase OrfB; Reviewed; Region: PHA02517 535289007011 HTH-like domain; Region: HTH_21; pfam13276 535289007012 Integrase core domain; Region: rve; pfam00665 535289007013 Integrase core domain; Region: rve_2; pfam13333 535289007014 Domain of unknown function (DUF4148); Region: DUF4148; pfam13663 535289007015 Winged helix-turn helix; Region: HTH_29; pfam13551 535289007016 Homeodomain-like domain; Region: HTH_23; pfam13384 535289007017 Homeodomain-like domain; Region: HTH_32; pfam13565 535289007018 DDE superfamily endonuclease; Region: DDE_3; pfam13358 535289007019 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 535289007020 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 535289007021 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 535289007022 active site 535289007023 HIGH motif; other site 535289007024 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 535289007025 active site 535289007026 KMSKS motif; other site 535289007027 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 535289007028 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 535289007029 homodimer interface [polypeptide binding]; other site 535289007030 substrate-cofactor binding pocket; other site 535289007031 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289007032 catalytic residue [active] 535289007033 amidophosphoribosyltransferase; Provisional; Region: PRK09246 535289007034 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 535289007035 active site 535289007036 tetramer interface [polypeptide binding]; other site 535289007037 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 535289007038 active site 535289007039 Colicin V production protein; Region: Colicin_V; pfam02674 535289007040 Sporulation related domain; Region: SPOR; pfam05036 535289007041 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 535289007042 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 535289007043 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 535289007044 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 535289007045 ArsC family; Region: ArsC; pfam03960 535289007046 putative catalytic residues [active] 535289007047 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 535289007048 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 535289007049 argininosuccinate synthase; Validated; Region: PRK05370 535289007050 argininosuccinate synthase; Provisional; Region: PRK13820 535289007051 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 535289007052 Ligand Binding Site [chemical binding]; other site 535289007053 hypothetical protein; Provisional; Region: PRK11212 535289007054 RNA polymerase sigma-70 factor, TIGR02957 family; Region: SigX4 535289007055 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289007056 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 535289007057 DNA binding residues [nucleotide binding] 535289007058 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 535289007059 Uncharacterized conserved protein [Function unknown]; Region: COG2128 535289007060 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 535289007061 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 535289007062 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 535289007063 transmembrane helices; other site 535289007064 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 535289007065 FAD binding domain; Region: FAD_binding_4; pfam01565 535289007066 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 535289007067 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 535289007068 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 535289007069 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 535289007070 catalytic motif [active] 535289007071 Catalytic residue [active] 535289007072 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 535289007073 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 535289007074 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 535289007075 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 535289007076 putative deacylase active site [active] 535289007077 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 535289007078 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 535289007079 active site 535289007080 catalytic tetrad [active] 535289007081 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 535289007082 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 535289007083 PGAP1-like protein; Region: PGAP1; pfam07819 535289007084 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 535289007085 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl17742 535289007086 peptide chain release factor 2; Validated; Region: prfB; PRK00578 535289007087 This domain is found in peptide chain release factors; Region: PCRF; smart00937 535289007088 RF-1 domain; Region: RF-1; pfam00472 535289007089 aminopeptidase N; Provisional; Region: pepN; PRK14015 535289007090 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 535289007091 active site 535289007092 Zn binding site [ion binding]; other site 535289007093 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 535289007094 AMP binding site [chemical binding]; other site 535289007095 metal binding site [ion binding]; metal-binding site 535289007096 active site 535289007097 DNA ligase; Provisional; Region: PRK09125 535289007098 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 535289007099 active site 535289007100 DNA binding site [nucleotide binding] 535289007101 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 535289007102 DNA binding site [nucleotide binding] 535289007103 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 535289007104 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 535289007105 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 535289007106 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289007107 catalytic residue [active] 535289007108 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 535289007109 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 535289007110 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 535289007111 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 535289007112 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 535289007113 catalytic loop [active] 535289007114 iron binding site [ion binding]; other site 535289007115 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 535289007116 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 535289007117 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 535289007118 dimerization interface [polypeptide binding]; other site 535289007119 active site 535289007120 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 535289007121 homopentamer interface [polypeptide binding]; other site 535289007122 active site 535289007123 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 535289007124 putative RNA binding site [nucleotide binding]; other site 535289007125 aminotransferase; Validated; Region: PRK07337 535289007126 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 535289007127 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289007128 homodimer interface [polypeptide binding]; other site 535289007129 catalytic residue [active] 535289007130 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 535289007131 active site 535289007132 TolQ protein; Region: tolQ; TIGR02796 535289007133 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 535289007134 TolR protein; Region: tolR; TIGR02801 535289007135 TolA protein; Region: tolA_full; TIGR02794 535289007136 TonB C terminal; Region: TonB_2; pfam13103 535289007137 metabolite-proton symporter; Region: 2A0106; TIGR00883 535289007138 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 535289007139 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 535289007140 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 535289007141 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 535289007142 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 535289007143 D-pathway; other site 535289007144 Putative ubiquinol binding site [chemical binding]; other site 535289007145 Low-spin heme (heme b) binding site [chemical binding]; other site 535289007146 Putative water exit pathway; other site 535289007147 Binuclear center (heme o3/CuB) [ion binding]; other site 535289007148 K-pathway; other site 535289007149 Putative proton exit pathway; other site 535289007150 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 535289007151 Subunit I/III interface [polypeptide binding]; other site 535289007152 Subunit III/IV interface [polypeptide binding]; other site 535289007153 Heme/copper-type cytochrome/quinol oxidase, subunit 4 [Energy production and conversion]; Region: CyoD; COG3125 535289007154 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 535289007155 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289007156 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289007157 dimer interface [polypeptide binding]; other site 535289007158 phosphorylation site [posttranslational modification] 535289007159 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 535289007160 ATP binding site [chemical binding]; other site 535289007161 Mg2+ binding site [ion binding]; other site 535289007162 G-X-G motif; other site 535289007163 Response regulator receiver domain; Region: Response_reg; pfam00072 535289007164 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 535289007165 active site 535289007166 phosphorylation site [posttranslational modification] 535289007167 intermolecular recognition site; other site 535289007168 dimerization interface [polypeptide binding]; other site 535289007169 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 535289007170 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 535289007171 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 535289007172 C-terminal domain interface [polypeptide binding]; other site 535289007173 GSH binding site (G-site) [chemical binding]; other site 535289007174 dimer interface [polypeptide binding]; other site 535289007175 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 535289007176 N-terminal domain interface [polypeptide binding]; other site 535289007177 dimer interface [polypeptide binding]; other site 535289007178 substrate binding pocket (H-site) [chemical binding]; other site 535289007179 putative protease; Provisional; Region: PRK15452 535289007180 Peptidase family U32; Region: Peptidase_U32; pfam01136 535289007181 Basic region leucine zipper; Region: bZIP_2; pfam07716 535289007182 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 535289007183 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 535289007184 non-specific DNA binding site [nucleotide binding]; other site 535289007185 salt bridge; other site 535289007186 sequence-specific DNA binding site [nucleotide binding]; other site 535289007187 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 535289007188 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 535289007189 substrate binding site [chemical binding]; other site 535289007190 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 535289007191 substrate binding site [chemical binding]; other site 535289007192 ligand binding site [chemical binding]; other site 535289007193 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 535289007194 Trans-aconitate methyltransferase [General function prediction only]; Region: Tam; COG4106 535289007195 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 535289007196 S-adenosylmethionine binding site [chemical binding]; other site 535289007197 malate dehydrogenase; Provisional; Region: PRK05442 535289007198 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 535289007199 NAD(P) binding site [chemical binding]; other site 535289007200 dimer interface [polypeptide binding]; other site 535289007201 malate binding site [chemical binding]; other site 535289007202 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 535289007203 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289007204 DNA-binding site [nucleotide binding]; DNA binding site 535289007205 UTRA domain; Region: UTRA; pfam07702 535289007206 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 535289007207 Iron-sulfur protein interface; other site 535289007208 proximal quinone binding site [chemical binding]; other site 535289007209 SdhD (CybS) interface [polypeptide binding]; other site 535289007210 proximal heme binding site [chemical binding]; other site 535289007211 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 535289007212 SdhC subunit interface [polypeptide binding]; other site 535289007213 proximal heme binding site [chemical binding]; other site 535289007214 cardiolipin binding site; other site 535289007215 Iron-sulfur protein interface; other site 535289007216 proximal quinone binding site [chemical binding]; other site 535289007217 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 535289007218 L-aspartate oxidase; Provisional; Region: PRK06175 535289007219 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 535289007220 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 535289007221 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 535289007222 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 535289007223 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 535289007224 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 535289007225 dimer interface [polypeptide binding]; other site 535289007226 active site 535289007227 citrylCoA binding site [chemical binding]; other site 535289007228 NADH binding [chemical binding]; other site 535289007229 cationic pore residues; other site 535289007230 oxalacetate/citrate binding site [chemical binding]; other site 535289007231 coenzyme A binding site [chemical binding]; other site 535289007232 catalytic triad [active] 535289007233 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 535289007234 putative metal binding site [ion binding]; other site 535289007235 putative homodimer interface [polypeptide binding]; other site 535289007236 putative homotetramer interface [polypeptide binding]; other site 535289007237 putative homodimer-homodimer interface [polypeptide binding]; other site 535289007238 putative allosteric switch controlling residues; other site 535289007239 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 535289007240 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 535289007241 substrate binding site [chemical binding]; other site 535289007242 catalytic Zn binding site [ion binding]; other site 535289007243 NAD binding site [chemical binding]; other site 535289007244 structural Zn binding site [ion binding]; other site 535289007245 dimer interface [polypeptide binding]; other site 535289007246 S-formylglutathione hydrolase; Region: PLN02442 535289007247 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 535289007248 Uncharacterized conserved protein [Function unknown]; Region: COG1359 535289007249 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 535289007250 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 535289007251 FeS/SAM binding site; other site 535289007252 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 535289007253 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 535289007254 WXG100 protein secretion system (Wss), protein YukD; Region: YukD; cl17489 535289007255 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 535289007256 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 535289007257 FMN binding site [chemical binding]; other site 535289007258 substrate binding site [chemical binding]; other site 535289007259 putative catalytic residue [active] 535289007260 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 535289007261 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 535289007262 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289007263 active site 535289007264 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 535289007265 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 535289007266 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 535289007267 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 535289007268 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 535289007269 Ligand binding site [chemical binding]; other site 535289007270 Electron transfer flavoprotein domain; Region: ETF; pfam01012 535289007271 Mechanosensitive ion channel; Region: MS_channel; pfam00924 535289007272 enoyl-CoA hydratase; Validated; Region: PRK08139 535289007273 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 535289007274 substrate binding site [chemical binding]; other site 535289007275 oxyanion hole (OAH) forming residues; other site 535289007276 trimer interface [polypeptide binding]; other site 535289007277 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 535289007278 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 535289007279 putative active site [active] 535289007280 Zn binding site [ion binding]; other site 535289007281 MoxR-like ATPases [General function prediction only]; Region: COG0714 535289007282 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289007283 Walker A motif; other site 535289007284 ATP binding site [chemical binding]; other site 535289007285 Walker B motif; other site 535289007286 arginine finger; other site 535289007287 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 535289007288 Pleckstrin homology-like domain; Region: PH-like; cl17171 535289007289 Protein of unknown function DUF58; Region: DUF58; pfam01882 535289007290 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 535289007291 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 535289007292 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 535289007293 Transglycosylase SLT domain; Region: SLT_2; pfam13406 535289007294 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 535289007295 N-acetyl-D-glucosamine binding site [chemical binding]; other site 535289007296 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 535289007297 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289007298 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 535289007299 putative dimerization interface [polypeptide binding]; other site 535289007300 Conserved hypothetical protein 698; Region: Cons_hypoth698; pfam03601 535289007301 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289007302 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 535289007303 putative ligand binding site [chemical binding]; other site 535289007304 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 535289007305 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 535289007306 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 535289007307 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 535289007308 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 535289007309 FtsX-like permease family; Region: FtsX; pfam02687 535289007310 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 535289007311 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 535289007312 Walker A/P-loop; other site 535289007313 ATP binding site [chemical binding]; other site 535289007314 Q-loop/lid; other site 535289007315 ABC transporter signature motif; other site 535289007316 Walker B; other site 535289007317 D-loop; other site 535289007318 H-loop/switch region; other site 535289007319 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289007320 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289007321 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289007322 UGMP family protein; Validated; Region: PRK09604 535289007323 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 535289007324 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289007325 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 535289007326 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; cl17736 535289007327 active site 535289007328 phosphorylation site [posttranslational modification] 535289007329 intermolecular recognition site; other site 535289007330 dimerization interface [polypeptide binding]; other site 535289007331 ANTAR domain; Region: ANTAR; pfam03861 535289007332 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 535289007333 NMT1-like family; Region: NMT1_2; pfam13379 535289007334 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 535289007335 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289007336 dimer interface [polypeptide binding]; other site 535289007337 conserved gate region; other site 535289007338 putative PBP binding loops; other site 535289007339 ABC-ATPase subunit interface; other site 535289007340 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 535289007341 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 535289007342 Walker A/P-loop; other site 535289007343 ATP binding site [chemical binding]; other site 535289007344 Q-loop/lid; other site 535289007345 ABC transporter signature motif; other site 535289007346 Walker B; other site 535289007347 D-loop; other site 535289007348 H-loop/switch region; other site 535289007349 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 535289007350 FOG: CBS domain [General function prediction only]; Region: COG0517 535289007351 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 535289007352 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 535289007353 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289007354 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289007355 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 535289007356 Protein export membrane protein; Region: SecD_SecF; cl14618 535289007357 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289007358 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 535289007359 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289007360 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 535289007361 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 535289007362 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 535289007363 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 535289007364 [2Fe-2S] cluster binding site [ion binding]; other site 535289007365 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 535289007366 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 535289007367 [4Fe-4S] binding site [ion binding]; other site 535289007368 molybdopterin cofactor binding site; other site 535289007369 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 535289007370 molybdopterin cofactor binding site; other site 535289007371 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 535289007372 glycosyl transferase family protein; Provisional; Region: PRK08136 535289007373 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 535289007374 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 535289007375 active site 535289007376 SAM binding site [chemical binding]; other site 535289007377 homodimer interface [polypeptide binding]; other site 535289007378 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 535289007379 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 535289007380 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289007381 putative ligand binding site [chemical binding]; other site 535289007382 HI0933-like protein; Region: HI0933_like; pfam03486 535289007383 NnrS protein; Region: NnrS; pfam05940 535289007384 Uncharacterized conserved protein (DUF2249); Region: DUF2249; cl17719 535289007385 Domain of unknown function DUF59; Region: DUF59; cl00941 535289007386 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 535289007387 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 535289007388 trimerization site [polypeptide binding]; other site 535289007389 active site 535289007390 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 535289007391 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 535289007392 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289007393 catalytic residue [active] 535289007394 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 535289007395 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 535289007396 FeS assembly ATPase SufC; Region: sufC; TIGR01978 535289007397 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289007398 Walker A/P-loop; other site 535289007399 ATP binding site [chemical binding]; other site 535289007400 Q-loop/lid; other site 535289007401 ABC transporter signature motif; other site 535289007402 Walker B; other site 535289007403 D-loop; other site 535289007404 H-loop/switch region; other site 535289007405 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 535289007406 putative ABC transporter; Region: ycf24; CHL00085 535289007407 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 535289007408 dimerization interface [polypeptide binding]; other site 535289007409 putative DNA binding site [nucleotide binding]; other site 535289007410 putative Zn2+ binding site [ion binding]; other site 535289007411 NIPSNAP; Region: NIPSNAP; pfam07978 535289007412 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 535289007413 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 535289007414 Yqey-like protein; Region: YqeY; pfam09424 535289007415 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 535289007416 tartrate dehydrogenase; Region: TTC; TIGR02089 535289007417 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 535289007418 putative metal binding site [ion binding]; other site 535289007419 putative homodimer interface [polypeptide binding]; other site 535289007420 putative homotetramer interface [polypeptide binding]; other site 535289007421 putative homodimer-homodimer interface [polypeptide binding]; other site 535289007422 putative allosteric switch controlling residues; other site 535289007423 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 535289007424 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 535289007425 S-adenosylmethionine binding site [chemical binding]; other site 535289007426 Uncharacterized conserved protein [Function unknown]; Region: COG3791 535289007427 glutamate racemase; Provisional; Region: PRK00865 535289007428 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 535289007429 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 535289007430 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289007431 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 535289007432 active site 535289007433 catalytic residues [active] 535289007434 metal binding site [ion binding]; metal-binding site 535289007435 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 535289007436 CoA-transferase family III; Region: CoA_transf_3; pfam02515 535289007437 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289007438 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289007439 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 535289007440 putative dimerization interface [polypeptide binding]; other site 535289007441 conserved hypothetical protein, PP_1857 family; Region: efp_adjacent_2; TIGR03837 535289007442 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 535289007443 elongation factor P; Validated; Region: PRK00529 535289007444 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 535289007445 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 535289007446 RNA binding site [nucleotide binding]; other site 535289007447 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 535289007448 RNA binding site [nucleotide binding]; other site 535289007449 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 535289007450 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 535289007451 Domain of unknown function (DUF4212); Region: DUF4212; cl01781 535289007452 phosphoenolpyruvate synthase; Validated; Region: PRK06464 535289007453 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 535289007454 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 535289007455 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 535289007456 PEP synthetase regulatory protein; Provisional; Region: PRK05339 535289007457 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 535289007458 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 535289007459 catalytic residue [active] 535289007460 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 535289007461 catalytic residues [active] 535289007462 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 535289007463 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289007464 alkyl hydroperoxide reductase subunit C; Provisional; Region: PRK10382 535289007465 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 535289007466 dimer interface [polypeptide binding]; other site 535289007467 decamer (pentamer of dimers) interface [polypeptide binding]; other site 535289007468 catalytic triad [active] 535289007469 peroxidatic and resolving cysteines [active] 535289007470 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 535289007471 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 535289007472 heme binding site [chemical binding]; other site 535289007473 ferroxidase pore; other site 535289007474 ferroxidase diiron center [ion binding]; other site 535289007475 Flagellar transcriptional activator (FlhD); Region: FlhD; pfam05247 535289007476 transcriptional activator FlhC; Provisional; Region: PRK12722 535289007477 integral membrane protein, YccS/YhfK family; Region: YCCS_YHJK; TIGR01667 535289007478 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 535289007479 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 535289007480 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 535289007481 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 535289007482 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 535289007483 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 535289007484 domain interfaces; other site 535289007485 active site 535289007486 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 535289007487 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 535289007488 active site 535289007489 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 535289007490 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 535289007491 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 535289007492 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 535289007493 Zn binding site [ion binding]; other site 535289007494 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 535289007495 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 535289007496 HIGH motif; other site 535289007497 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 535289007498 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 535289007499 active site 535289007500 KMSKS motif; other site 535289007501 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 535289007502 tRNA binding surface [nucleotide binding]; other site 535289007503 anticodon binding site; other site 535289007504 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 535289007505 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 535289007506 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 535289007507 active site 535289007508 tetramer interface; other site 535289007509 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 535289007510 CPxP motif; other site 535289007511 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 535289007512 nudix motif; other site 535289007513 cysteine synthase B; Region: cysM; TIGR01138 535289007514 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 535289007515 dimer interface [polypeptide binding]; other site 535289007516 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289007517 catalytic residue [active] 535289007518 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 535289007519 rRNA binding site [nucleotide binding]; other site 535289007520 predicted 30S ribosome binding site; other site 535289007521 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 535289007522 SnoaL-like domain; Region: SnoaL_2; pfam12680 535289007523 short chain dehydrogenase; Provisional; Region: PRK06101 535289007524 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289007525 NAD(P) binding site [chemical binding]; other site 535289007526 active site 535289007527 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 535289007528 MFS/sugar transport protein; Region: MFS_2; pfam13347 535289007529 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289007530 dimer interface [polypeptide binding]; other site 535289007531 putative CheW interface [polypeptide binding]; other site 535289007532 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 535289007533 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 535289007534 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 535289007535 S-adenosylmethionine binding site [chemical binding]; other site 535289007536 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 535289007537 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 535289007538 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 535289007539 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 535289007540 DNA binding residues [nucleotide binding] 535289007541 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 535289007542 B12 binding domain; Region: B12-binding_2; pfam02607 535289007543 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 535289007544 B12 binding site [chemical binding]; other site 535289007545 outer membrane lipoprotein Blc; Provisional; Region: PRK10477 535289007546 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 535289007547 LrgA family; Region: LrgA; pfam03788 535289007548 LrgB-like family; Region: LrgB; pfam04172 535289007549 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 535289007550 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289007551 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 535289007552 dimerization interface [polypeptide binding]; other site 535289007553 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 535289007554 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289007555 FAD binding site [chemical binding]; other site 535289007556 substrate binding pocket [chemical binding]; other site 535289007557 catalytic base [active] 535289007558 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 535289007559 CoA-transferase family III; Region: CoA_transf_3; pfam02515 535289007560 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289007561 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 535289007562 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 535289007563 putative NAD(P) binding site [chemical binding]; other site 535289007564 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 535289007565 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 535289007566 catalytic loop [active] 535289007567 iron binding site [ion binding]; other site 535289007568 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 535289007569 FAD binding pocket [chemical binding]; other site 535289007570 FAD binding motif [chemical binding]; other site 535289007571 phosphate binding motif [ion binding]; other site 535289007572 beta-alpha-beta structure motif; other site 535289007573 NAD binding pocket [chemical binding]; other site 535289007574 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 535289007575 dimerization interface [polypeptide binding]; other site 535289007576 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289007577 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 535289007578 catalytic center binding site [active] 535289007579 ATP binding site [chemical binding]; other site 535289007580 poly(A) polymerase; Region: pcnB; TIGR01942 535289007581 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 535289007582 active site 535289007583 NTP binding site [chemical binding]; other site 535289007584 metal binding triad [ion binding]; metal-binding site 535289007585 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 535289007586 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 535289007587 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 535289007588 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 535289007589 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 535289007590 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 535289007591 Walker A motif; other site 535289007592 ATP binding site [chemical binding]; other site 535289007593 Walker B motif; other site 535289007594 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 535289007595 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 535289007596 dimerization interface [polypeptide binding]; other site 535289007597 putative ATP binding site [chemical binding]; other site 535289007598 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 535289007599 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 535289007600 Ligand Binding Site [chemical binding]; other site 535289007601 metal ion transporter CorA-like divalent cation transporter superfamily; Region: MIT_CorA-like; cl00459 535289007602 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 535289007603 Uncharacterized conserved protein [Function unknown]; Region: COG2912 535289007604 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 535289007605 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 535289007606 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 535289007607 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 535289007608 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 535289007609 acetylornithine aminotransferase; Provisional; Region: PRK02627 535289007610 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 535289007611 inhibitor-cofactor binding pocket; inhibition site 535289007612 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289007613 catalytic residue [active] 535289007614 ornithine carbamoyltransferase; Provisional; Region: PRK00779 535289007615 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 535289007616 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 535289007617 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 535289007618 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 535289007619 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 535289007620 G1 box; other site 535289007621 GTP/Mg2+ binding site [chemical binding]; other site 535289007622 Switch I region; other site 535289007623 G2 box; other site 535289007624 G3 box; other site 535289007625 Switch II region; other site 535289007626 G4 box; other site 535289007627 G5 box; other site 535289007628 Nucleoside recognition; Region: Gate; pfam07670 535289007629 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 535289007630 Nucleoside recognition; Region: Gate; pfam07670 535289007631 FeoA domain; Region: FeoA; pfam04023 535289007632 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 535289007633 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289007634 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 535289007635 putative DNA binding site [nucleotide binding]; other site 535289007636 putative Zn2+ binding site [ion binding]; other site 535289007637 AsnC family; Region: AsnC_trans_reg; pfam01037 535289007638 Putative cyclase; Region: Cyclase; cl00814 535289007639 Kynureninase [Amino acid transport and metabolism]; Region: COG3844 535289007640 kynureninase; Region: kynureninase; TIGR01814 535289007641 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289007642 catalytic residue [active] 535289007643 tryptophan 2,3-dioxygenase; Region: trp_2_3_diox; TIGR03036 535289007644 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 535289007645 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 535289007646 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 535289007647 active site 535289007648 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 535289007649 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 535289007650 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 535289007651 active site 535289007652 purine riboside binding site [chemical binding]; other site 535289007653 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 535289007654 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 535289007655 putative ligand binding site [chemical binding]; other site 535289007656 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 535289007657 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 535289007658 putative ligand binding site [chemical binding]; other site 535289007659 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 535289007660 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 535289007661 TM-ABC transporter signature motif; other site 535289007662 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 535289007663 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 535289007664 TM-ABC transporter signature motif; other site 535289007665 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 535289007666 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 535289007667 Walker A/P-loop; other site 535289007668 ATP binding site [chemical binding]; other site 535289007669 Q-loop/lid; other site 535289007670 ABC transporter signature motif; other site 535289007671 Walker B; other site 535289007672 D-loop; other site 535289007673 H-loop/switch region; other site 535289007674 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 535289007675 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 535289007676 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2; pfam00111 535289007677 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 535289007678 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 535289007679 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 535289007680 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 535289007681 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 535289007682 PAS domain; Region: PAS_9; pfam13426 535289007683 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 535289007684 putative active site [active] 535289007685 heme pocket [chemical binding]; other site 535289007686 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289007687 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289007688 metal binding site [ion binding]; metal-binding site 535289007689 active site 535289007690 I-site; other site 535289007691 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289007692 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 535289007693 ligand binding site [chemical binding]; other site 535289007694 flexible hinge region; other site 535289007695 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 535289007696 putative switch regulator; other site 535289007697 non-specific DNA interactions [nucleotide binding]; other site 535289007698 DNA binding site [nucleotide binding] 535289007699 sequence specific DNA binding site [nucleotide binding]; other site 535289007700 putative cAMP binding site [chemical binding]; other site 535289007701 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 535289007702 trimer interface [polypeptide binding]; other site 535289007703 eyelet of channel; other site 535289007704 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 535289007705 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 535289007706 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 535289007707 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289007708 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289007709 metal binding site [ion binding]; metal-binding site 535289007710 active site 535289007711 I-site; other site 535289007712 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 535289007713 HIT family signature motif; other site 535289007714 catalytic residue [active] 535289007715 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 535289007716 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 535289007717 putative ligand binding site [chemical binding]; other site 535289007718 NAD binding site [chemical binding]; other site 535289007719 catalytic site [active] 535289007720 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 535289007721 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 535289007722 putative substrate translocation pore; other site 535289007723 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 535289007724 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 535289007725 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 535289007726 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 535289007727 Walker A/P-loop; other site 535289007728 ATP binding site [chemical binding]; other site 535289007729 Q-loop/lid; other site 535289007730 ABC transporter signature motif; other site 535289007731 Walker B; other site 535289007732 D-loop; other site 535289007733 H-loop/switch region; other site 535289007734 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 535289007735 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 535289007736 putative dimer interface [polypeptide binding]; other site 535289007737 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 535289007738 FtsX-like permease family; Region: FtsX; pfam02687 535289007739 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 535289007740 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 535289007741 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289007742 catalytic residue [active] 535289007743 Hydroxyneurosporene synthase (CrtC); Region: CrtC; pfam07143 535289007744 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 535289007745 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 535289007746 TM-ABC transporter signature motif; other site 535289007747 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 535289007748 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 535289007749 TM-ABC transporter signature motif; other site 535289007750 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289007751 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 535289007752 putative ligand binding site [chemical binding]; other site 535289007753 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289007754 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 535289007755 putative ligand binding site [chemical binding]; other site 535289007756 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 535289007757 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 535289007758 Walker A/P-loop; other site 535289007759 ATP binding site [chemical binding]; other site 535289007760 Q-loop/lid; other site 535289007761 ABC transporter signature motif; other site 535289007762 Walker B; other site 535289007763 D-loop; other site 535289007764 H-loop/switch region; other site 535289007765 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 535289007766 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 535289007767 Walker A/P-loop; other site 535289007768 ATP binding site [chemical binding]; other site 535289007769 Q-loop/lid; other site 535289007770 ABC transporter signature motif; other site 535289007771 Walker B; other site 535289007772 D-loop; other site 535289007773 H-loop/switch region; other site 535289007774 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 535289007775 TOBE domain; Region: TOBE; cl01440 535289007776 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 535289007777 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 535289007778 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 535289007779 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289007780 putative PBP binding loops; other site 535289007781 dimer interface [polypeptide binding]; other site 535289007782 ABC-ATPase subunit interface; other site 535289007783 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289007784 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 535289007785 Walker A/P-loop; other site 535289007786 ATP binding site [chemical binding]; other site 535289007787 Q-loop/lid; other site 535289007788 ABC transporter signature motif; other site 535289007789 Walker B; other site 535289007790 D-loop; other site 535289007791 H-loop/switch region; other site 535289007792 TOBE domain; Region: TOBE; pfam03459 535289007793 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 535289007794 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 535289007795 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 535289007796 PBP superfamily domain; Region: PBP_like_2; pfam12849 535289007797 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 535289007798 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 535289007799 Walker A/P-loop; other site 535289007800 ATP binding site [chemical binding]; other site 535289007801 Q-loop/lid; other site 535289007802 ABC transporter signature motif; other site 535289007803 Walker B; other site 535289007804 D-loop; other site 535289007805 H-loop/switch region; other site 535289007806 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 535289007807 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; cl17549 535289007808 PBP superfamily domain; Region: PBP_like; pfam12727 535289007809 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 535289007810 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 535289007811 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 535289007812 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 535289007813 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 535289007814 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 535289007815 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 535289007816 acyl-CoA synthetase; Validated; Region: PRK08162 535289007817 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 535289007818 acyl-activating enzyme (AAE) consensus motif; other site 535289007819 putative active site [active] 535289007820 AMP binding site [chemical binding]; other site 535289007821 putative CoA binding site [chemical binding]; other site 535289007822 DNA primase, catalytic core; Region: dnaG; TIGR01391 535289007823 CHC2 zinc finger; Region: zf-CHC2; pfam01807 535289007824 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 535289007825 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 535289007826 active site 535289007827 metal binding site [ion binding]; metal-binding site 535289007828 interdomain interaction site; other site 535289007829 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 535289007830 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 535289007831 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 535289007832 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 535289007833 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 535289007834 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 535289007835 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289007836 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 535289007837 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289007838 DNA binding residues [nucleotide binding] 535289007839 Ketopantoate reductase [Coenzyme metabolism]; Region: ApbA; COG1893 535289007840 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 535289007841 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 535289007842 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 535289007843 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289007844 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 535289007845 CoA-transferase family III; Region: CoA_transf_3; pfam02515 535289007846 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 535289007847 active site 535289007848 catalytic residues [active] 535289007849 metal binding site [ion binding]; metal-binding site 535289007850 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289007851 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289007852 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 535289007853 putative dimerization interface [polypeptide binding]; other site 535289007854 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 535289007855 dimerization interface [polypeptide binding]; other site 535289007856 putative DNA binding site [nucleotide binding]; other site 535289007857 Predicted transcriptional regulators [Transcription]; Region: COG1733 535289007858 putative Zn2+ binding site [ion binding]; other site 535289007859 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 535289007860 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 535289007861 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 535289007862 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 535289007863 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 535289007864 FeS/SAM binding site; other site 535289007865 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 535289007866 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 535289007867 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 535289007868 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 535289007869 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 535289007870 HD domain; Region: HD_4; pfam13328 535289007871 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 535289007872 synthetase active site [active] 535289007873 NTP binding site [chemical binding]; other site 535289007874 metal binding site [ion binding]; metal-binding site 535289007875 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 535289007876 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 535289007877 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 535289007878 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 535289007879 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 535289007880 NAD binding site [chemical binding]; other site 535289007881 homotetramer interface [polypeptide binding]; other site 535289007882 homodimer interface [polypeptide binding]; other site 535289007883 substrate binding site [chemical binding]; other site 535289007884 active site 535289007885 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 535289007886 osmolarity response regulator; Provisional; Region: ompR; PRK09468 535289007887 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 535289007888 active site 535289007889 phosphorylation site [posttranslational modification] 535289007890 intermolecular recognition site; other site 535289007891 dimerization interface [polypeptide binding]; other site 535289007892 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289007893 DNA binding site [nucleotide binding] 535289007894 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 535289007895 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289007896 dimerization interface [polypeptide binding]; other site 535289007897 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289007898 dimer interface [polypeptide binding]; other site 535289007899 phosphorylation site [posttranslational modification] 535289007900 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 535289007901 ATP binding site [chemical binding]; other site 535289007902 Mg2+ binding site [ion binding]; other site 535289007903 G-X-G motif; other site 535289007904 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 535289007905 homotrimer interaction site [polypeptide binding]; other site 535289007906 zinc binding site [ion binding]; other site 535289007907 CDP-binding sites; other site 535289007908 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 535289007909 substrate binding site; other site 535289007910 dimer interface; other site 535289007911 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 535289007912 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 535289007913 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 535289007914 ATP binding site [chemical binding]; other site 535289007915 putative Mg++ binding site [ion binding]; other site 535289007916 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 535289007917 nucleotide binding region [chemical binding]; other site 535289007918 ATP-binding site [chemical binding]; other site 535289007919 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 535289007920 Predicted membrane protein [Function unknown]; Region: COG3235 535289007921 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 535289007922 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 535289007923 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 535289007924 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 535289007925 LysE type translocator; Region: LysE; cl00565 535289007926 chromosome replication initiation inhibitor protein; Provisional; Region: PRK13348 535289007927 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289007928 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 535289007929 dimerization interface [polypeptide binding]; other site 535289007930 Predicted transcriptional regulator [Transcription]; Region: COG1959 535289007931 Transcriptional regulator; Region: Rrf2; cl17282 535289007932 iron-sulfur cluster repair di-iron protein; Provisional; Region: PRK10992 535289007933 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 535289007934 Hemerythrin-like domain; Region: Hr-like; cd12108 535289007935 Fe binding site [ion binding]; other site 535289007936 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 535289007937 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 535289007938 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 535289007939 active site 535289007940 catalytic tetrad [active] 535289007941 SlyX; Region: SlyX; pfam04102 535289007942 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 535289007943 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 535289007944 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289007945 homodimer interface [polypeptide binding]; other site 535289007946 catalytic residue [active] 535289007947 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 535289007948 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 535289007949 minor groove reading motif; other site 535289007950 helix-hairpin-helix signature motif; other site 535289007951 substrate binding pocket [chemical binding]; other site 535289007952 active site 535289007953 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 535289007954 Putative NodB-like catalytic domain of uncharacterized proteins found in bacteria; Region: CE4_COG5298; cd10923 535289007955 Uncharacterized protein conserved in bacteria (DUF2334); Region: DUF2334; pfam10096 535289007956 NodB motif; other site 535289007957 putative active site [active] 535289007958 putative catalytic site [active] 535289007959 putative Zn binding site [ion binding]; other site 535289007960 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289007961 Transposase; Region: HTH_Tnp_1; pfam01527 535289007962 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 535289007963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 535289007964 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 535289007965 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 535289007966 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 535289007967 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 535289007968 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 535289007969 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK11234 535289007970 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 535289007971 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 535289007972 Helix-turn-helix domain; Region: HTH_28; pfam13518 535289007973 Winged helix-turn helix; Region: HTH_29; pfam13551 535289007974 Winged helix-turn helix; Region: HTH_33; pfam13592 535289007975 DDE superfamily endonuclease; Region: DDE_3; pfam13358 535289007976 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 535289007977 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 535289007978 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 535289007979 active site 535289007980 homodimer interface [polypeptide binding]; other site 535289007981 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 535289007982 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 535289007983 putative dimer interface [polypeptide binding]; other site 535289007984 active site pocket [active] 535289007985 putative cataytic base [active] 535289007986 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)...; Region: BluB; cd02145 535289007987 putative FMN binding site [chemical binding]; other site 535289007988 cobyric acid synthase; Provisional; Region: PRK00784 535289007989 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 535289007990 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 535289007991 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 535289007992 catalytic triad [active] 535289007993 Protein of unknown function (DUF3037); Region: DUF3037; pfam11236 535289007994 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 535289007995 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 535289007996 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 535289007997 Type II transport protein GspH; Region: GspH; pfam12019 535289007998 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 535289007999 Type II transport protein GspH; Region: GspH; pfam12019 535289008000 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 535289008001 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 535289008002 Type IV pilus assembly protein PilX C-term; Region: PilX; pfam13681 535289008003 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 535289008004 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 535289008005 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 535289008006 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 535289008007 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 535289008008 putative active site [active] 535289008009 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 535289008010 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 535289008011 catalytic motif [active] 535289008012 Zn binding site [ion binding]; other site 535289008013 RibD C-terminal domain; Region: RibD_C; cl17279 535289008014 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 535289008015 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 535289008016 putative active site [active] 535289008017 catalytic site [active] 535289008018 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 535289008019 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 535289008020 putative active site [active] 535289008021 catalytic site [active] 535289008022 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 535289008023 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 535289008024 FMN binding site [chemical binding]; other site 535289008025 active site 535289008026 catalytic residues [active] 535289008027 substrate binding site [chemical binding]; other site 535289008028 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 535289008029 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 535289008030 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 535289008031 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 535289008032 Coenzyme A binding pocket [chemical binding]; other site 535289008033 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 535289008034 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 535289008035 NAD(P) binding site [chemical binding]; other site 535289008036 catalytic residues [active] 535289008037 Uncharacterized conserved protein [Function unknown]; Region: COG3791 535289008038 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 535289008039 Clp amino terminal domain; Region: Clp_N; pfam02861 535289008040 Clp amino terminal domain; Region: Clp_N; pfam02861 535289008041 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289008042 Walker A motif; other site 535289008043 ATP binding site [chemical binding]; other site 535289008044 Walker B motif; other site 535289008045 arginine finger; other site 535289008046 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289008047 Walker A motif; other site 535289008048 ATP binding site [chemical binding]; other site 535289008049 Walker B motif; other site 535289008050 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 535289008051 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 535289008052 MoaE homodimer interface [polypeptide binding]; other site 535289008053 MoaD interaction [polypeptide binding]; other site 535289008054 active site residues [active] 535289008055 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 535289008056 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 535289008057 MoaE interaction surface [polypeptide binding]; other site 535289008058 MoeB interaction surface [polypeptide binding]; other site 535289008059 thiocarboxylated glycine; other site 535289008060 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 535289008061 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 535289008062 dimer interface [polypeptide binding]; other site 535289008063 putative functional site; other site 535289008064 putative MPT binding site; other site 535289008065 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 535289008066 Walker A motif; other site 535289008067 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 535289008068 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 535289008069 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289008070 catalytic residue [active] 535289008071 homoserine dehydrogenase; Provisional; Region: PRK06349 535289008072 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 535289008073 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 535289008074 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 535289008075 aminotransferase AlaT; Validated; Region: PRK09265 535289008076 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 535289008077 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289008078 homodimer interface [polypeptide binding]; other site 535289008079 catalytic residue [active] 535289008080 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 535289008081 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 535289008082 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 535289008083 catalytic triad [active] 535289008084 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 535289008085 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 535289008086 putative active site [active] 535289008087 PhoH-like protein; Region: PhoH; pfam02562 535289008088 replicative DNA helicase; Region: DnaB; TIGR00665 535289008089 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 535289008090 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 535289008091 Walker A motif; other site 535289008092 ATP binding site [chemical binding]; other site 535289008093 Walker B motif; other site 535289008094 DNA binding loops [nucleotide binding] 535289008095 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 535289008096 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 535289008097 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 535289008098 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 535289008099 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 535289008100 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 535289008101 GrpE; Region: GrpE; pfam01025 535289008102 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 535289008103 dimer interface [polypeptide binding]; other site 535289008104 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 535289008105 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 535289008106 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 535289008107 nucleotide binding site [chemical binding]; other site 535289008108 chaperone protein DnaJ; Provisional; Region: PRK10767 535289008109 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 535289008110 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 535289008111 substrate binding site [polypeptide binding]; other site 535289008112 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 535289008113 Zn binding sites [ion binding]; other site 535289008114 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 535289008115 dimer interface [polypeptide binding]; other site 535289008116 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 535289008117 Peptidase family U32; Region: Peptidase_U32; pfam01136 535289008118 putative protease; Provisional; Region: PRK15447 535289008119 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 535289008120 SCP-2 sterol transfer family; Region: SCP2; cl01225 535289008121 DGC domain; Region: DGC; pfam08859 535289008122 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 535289008123 Flavoprotein; Region: Flavoprotein; pfam02441 535289008124 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 535289008125 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 535289008126 Cytochrome P450; Region: p450; cl12078 535289008127 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 535289008128 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 535289008129 Beta-Casp domain; Region: Beta-Casp; smart01027 535289008130 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 535289008131 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289008132 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289008133 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 535289008134 putative dimerization interface [polypeptide binding]; other site 535289008135 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 535289008136 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 535289008137 substrate binding site [chemical binding]; other site 535289008138 ligand binding site [chemical binding]; other site 535289008139 Entericidin EcnA/B family; Region: Entericidin; pfam08085 535289008140 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 535289008141 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 535289008142 substrate binding site [chemical binding]; other site 535289008143 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 535289008144 tartrate dehydrogenase; Region: TTC; TIGR02089 535289008145 short chain dehydrogenase; Provisional; Region: PRK07478 535289008146 classical (c) SDRs; Region: SDR_c; cd05233 535289008147 NAD(P) binding site [chemical binding]; other site 535289008148 active site 535289008149 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 535289008150 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 535289008151 FimV N-terminal domain; Region: FimV_core; TIGR03505 535289008152 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 535289008153 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 535289008154 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 535289008155 dimerization interface 3.5A [polypeptide binding]; other site 535289008156 active site 535289008157 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 535289008158 active site 535289008159 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 535289008160 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 535289008161 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289008162 catalytic residue [active] 535289008163 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 535289008164 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 535289008165 substrate binding site [chemical binding]; other site 535289008166 active site 535289008167 catalytic residues [active] 535289008168 heterodimer interface [polypeptide binding]; other site 535289008169 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 535289008170 RNA polymerases M/15 Kd subunit; Region: RNA_POL_M_15KD; cl02717 535289008171 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 535289008172 YGGT family; Region: YGGT; pfam02325 535289008173 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 535289008174 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 535289008175 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 535289008176 putative ADP-binding pocket [chemical binding]; other site 535289008177 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 535289008178 Bacterial sugar transferase; Region: Bac_transf; pfam02397 535289008179 Methyltransferase domain; Region: Methyltransf_12; pfam08242 535289008180 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 535289008181 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 535289008182 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 535289008183 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 535289008184 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 535289008185 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 535289008186 dimer interface [polypeptide binding]; other site 535289008187 putative anticodon binding site; other site 535289008188 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 535289008189 motif 1; other site 535289008190 active site 535289008191 motif 2; other site 535289008192 motif 3; other site 535289008193 Response regulator receiver domain; Region: Response_reg; pfam00072 535289008194 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 535289008195 active site 535289008196 phosphorylation site [posttranslational modification] 535289008197 intermolecular recognition site; other site 535289008198 dimerization interface [polypeptide binding]; other site 535289008199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289008200 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289008201 metal binding site [ion binding]; metal-binding site 535289008202 active site 535289008203 I-site; other site 535289008204 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 535289008205 Mechanosensitive ion channel; Region: MS_channel; pfam00924 535289008206 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289008207 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 535289008208 dimerization interface [polypeptide binding]; other site 535289008209 ligand binding site [chemical binding]; other site 535289008210 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 535289008211 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 535289008212 TM-ABC transporter signature motif; other site 535289008213 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 535289008214 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 535289008215 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 535289008216 TM-ABC transporter signature motif; other site 535289008217 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 535289008218 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 535289008219 Walker A/P-loop; other site 535289008220 ATP binding site [chemical binding]; other site 535289008221 Q-loop/lid; other site 535289008222 ABC transporter signature motif; other site 535289008223 Walker B; other site 535289008224 D-loop; other site 535289008225 H-loop/switch region; other site 535289008226 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 535289008227 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 535289008228 Walker A/P-loop; other site 535289008229 ATP binding site [chemical binding]; other site 535289008230 Q-loop/lid; other site 535289008231 ABC transporter signature motif; other site 535289008232 Walker B; other site 535289008233 D-loop; other site 535289008234 H-loop/switch region; other site 535289008235 Uncharacterized conserved protein [Function unknown]; Region: COG2128 535289008236 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 535289008237 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 535289008238 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 535289008239 active site 535289008240 ADP/pyrophosphate binding site [chemical binding]; other site 535289008241 dimerization interface [polypeptide binding]; other site 535289008242 allosteric effector site; other site 535289008243 fructose-1,6-bisphosphate binding site; other site 535289008244 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 535289008245 beta-hexosaminidase; Provisional; Region: PRK05337 535289008246 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 535289008247 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 535289008248 active site 535289008249 hydrophilic channel; other site 535289008250 dimerization interface [polypeptide binding]; other site 535289008251 catalytic residues [active] 535289008252 active site lid [active] 535289008253 Domain of unknown function (DUF4153); Region: DUF4153; pfam13687 535289008254 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 535289008255 Recombination protein O N terminal; Region: RecO_N; pfam11967 535289008256 GTPase Era; Reviewed; Region: era; PRK00089 535289008257 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 535289008258 G1 box; other site 535289008259 GTP/Mg2+ binding site [chemical binding]; other site 535289008260 Switch I region; other site 535289008261 G2 box; other site 535289008262 Switch II region; other site 535289008263 G3 box; other site 535289008264 G4 box; other site 535289008265 G5 box; other site 535289008266 KH domain; Region: KH_2; pfam07650 535289008267 ribonuclease III; Reviewed; Region: rnc; PRK00102 535289008268 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 535289008269 dimerization interface [polypeptide binding]; other site 535289008270 active site 535289008271 metal binding site [ion binding]; metal-binding site 535289008272 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 535289008273 signal peptidase I; Provisional; Region: PRK10861 535289008274 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 535289008275 Catalytic site [active] 535289008276 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 535289008277 GTP-binding protein LepA; Provisional; Region: PRK05433 535289008278 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 535289008279 G1 box; other site 535289008280 putative GEF interaction site [polypeptide binding]; other site 535289008281 GTP/Mg2+ binding site [chemical binding]; other site 535289008282 Switch I region; other site 535289008283 G2 box; other site 535289008284 G3 box; other site 535289008285 Switch II region; other site 535289008286 G4 box; other site 535289008287 G5 box; other site 535289008288 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 535289008289 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 535289008290 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 535289008291 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 535289008292 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 535289008293 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 535289008294 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 535289008295 protein binding site [polypeptide binding]; other site 535289008296 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 535289008297 anti-sigma E factor; Provisional; Region: rseB; PRK09455 535289008298 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 535289008299 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 535289008300 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289008301 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289008302 DNA binding residues [nucleotide binding] 535289008303 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 535289008304 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 535289008305 dimer interface [polypeptide binding]; other site 535289008306 active site 535289008307 acyl carrier protein; Provisional; Region: acpP; PRK00982 535289008308 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289008309 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 535289008310 NAD(P) binding site [chemical binding]; other site 535289008311 active site 535289008312 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 535289008313 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 535289008314 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 535289008315 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 535289008316 dimer interface [polypeptide binding]; other site 535289008317 active site 535289008318 CoA binding pocket [chemical binding]; other site 535289008319 putative phosphate acyltransferase; Provisional; Region: PRK05331 535289008320 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 535289008321 Predicted metal-binding, possibly nucleic acid-binding protein [General function prediction only]; Region: COG1399 535289008322 Maf-like protein; Region: Maf; pfam02545 535289008323 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 535289008324 active site 535289008325 dimer interface [polypeptide binding]; other site 535289008326 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 535289008327 putative SAM binding site [chemical binding]; other site 535289008328 homodimer interface [polypeptide binding]; other site 535289008329 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 535289008330 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 535289008331 tandem repeat interface [polypeptide binding]; other site 535289008332 oligomer interface [polypeptide binding]; other site 535289008333 active site residues [active] 535289008334 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) complexes; Region: Rieske; cl00938 535289008335 iron-sulfur cluster [ion binding]; other site 535289008336 [2Fe-2S] cluster binding site [ion binding]; other site 535289008337 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 535289008338 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 535289008339 motif II; other site 535289008340 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 535289008341 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 535289008342 RNA binding surface [nucleotide binding]; other site 535289008343 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 535289008344 active site 535289008345 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 535289008346 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 535289008347 homodimer interface [polypeptide binding]; other site 535289008348 oligonucleotide binding site [chemical binding]; other site 535289008349 hypothetical protein; Validated; Region: PRK02101 535289008350 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 535289008351 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 535289008352 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 535289008353 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 535289008354 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 535289008355 PAS domain; Region: PAS_9; pfam13426 535289008356 putative active site [active] 535289008357 heme pocket [chemical binding]; other site 535289008358 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289008359 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289008360 dimer interface [polypeptide binding]; other site 535289008361 putative CheW interface [polypeptide binding]; other site 535289008362 DNA polymerase IV; Validated; Region: PRK03352 535289008363 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 535289008364 active site 535289008365 DNA binding site [nucleotide binding] 535289008366 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 535289008367 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 535289008368 phosphate binding site [ion binding]; other site 535289008369 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 535289008370 Transglycosylase; Region: Transgly; pfam00912 535289008371 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 535289008372 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 535289008373 MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate...; Region: MGS-like; cl00245 535289008374 substrate binding site [chemical binding]; other site 535289008375 Uncharacterized conserved protein [Function unknown]; Region: COG3339 535289008376 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 535289008377 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 535289008378 putative catalytic site [active] 535289008379 putative metal binding site [ion binding]; other site 535289008380 putative phosphate binding site [ion binding]; other site 535289008381 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 535289008382 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289008383 dimer interface [polypeptide binding]; other site 535289008384 conserved gate region; other site 535289008385 putative PBP binding loops; other site 535289008386 ABC-ATPase subunit interface; other site 535289008387 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289008388 dimer interface [polypeptide binding]; other site 535289008389 conserved gate region; other site 535289008390 putative PBP binding loops; other site 535289008391 ABC-ATPase subunit interface; other site 535289008392 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 535289008393 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 535289008394 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 535289008395 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289008396 Walker A/P-loop; other site 535289008397 ATP binding site [chemical binding]; other site 535289008398 Q-loop/lid; other site 535289008399 ABC transporter signature motif; other site 535289008400 Walker B; other site 535289008401 D-loop; other site 535289008402 H-loop/switch region; other site 535289008403 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 535289008404 MG2 domain; Region: A2M_N; pfam01835 535289008405 Alpha-2-macroglobulin family; Region: A2M; pfam00207 535289008406 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 535289008407 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 535289008408 tetramer interface [polypeptide binding]; other site 535289008409 heme binding pocket [chemical binding]; other site 535289008410 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 535289008411 domain interactions; other site 535289008412 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289008413 argininosuccinate lyase; Provisional; Region: PRK00855 535289008414 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 535289008415 active sites [active] 535289008416 tetramer interface [polypeptide binding]; other site 535289008417 Histidine kinase; Region: His_kinase; pfam06580 535289008418 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 535289008419 Mg2+ binding site [ion binding]; other site 535289008420 G-X-G motif; other site 535289008421 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 535289008422 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 535289008423 active site 535289008424 phosphorylation site [posttranslational modification] 535289008425 intermolecular recognition site; other site 535289008426 dimerization interface [polypeptide binding]; other site 535289008427 LytTr DNA-binding domain; Region: LytTR; smart00850 535289008428 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 535289008429 Dienelactone hydrolase family; Region: DLH; pfam01738 535289008430 DNA polymerase I; Provisional; Region: PRK05755 535289008431 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 535289008432 active site 535289008433 metal binding site 1 [ion binding]; metal-binding site 535289008434 putative 5' ssDNA interaction site; other site 535289008435 metal binding site 3; metal-binding site 535289008436 metal binding site 2 [ion binding]; metal-binding site 535289008437 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 535289008438 putative DNA binding site [nucleotide binding]; other site 535289008439 putative metal binding site [ion binding]; other site 535289008440 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 535289008441 active site 535289008442 catalytic site [active] 535289008443 substrate binding site [chemical binding]; other site 535289008444 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 535289008445 active site 535289008446 DNA binding site [nucleotide binding] 535289008447 catalytic site [active] 535289008448 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 535289008449 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 535289008450 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 535289008451 putative active site [active] 535289008452 putative substrate binding site [chemical binding]; other site 535289008453 ATP binding site [chemical binding]; other site 535289008454 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 535289008455 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 535289008456 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 535289008457 ligand binding site [chemical binding]; other site 535289008458 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 535289008459 Part of AAA domain; Region: AAA_19; pfam13245 535289008460 Family description; Region: UvrD_C_2; pfam13538 535289008461 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 535289008462 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 535289008463 active site 535289008464 NnrS protein; Region: NnrS; pfam05940 535289008465 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 535289008466 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289008467 Walker A/P-loop; other site 535289008468 ATP binding site [chemical binding]; other site 535289008469 Q-loop/lid; other site 535289008470 ABC transporter signature motif; other site 535289008471 Walker B; other site 535289008472 D-loop; other site 535289008473 H-loop/switch region; other site 535289008474 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 535289008475 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 535289008476 Uncharacterized conserved protein (DUF2149); Region: DUF2149; pfam09919 535289008477 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 535289008478 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 535289008479 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 535289008480 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 535289008481 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 535289008482 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 535289008483 N-terminal plug; other site 535289008484 ligand-binding site [chemical binding]; other site 535289008485 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 535289008486 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 535289008487 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 535289008488 N-terminal plug; other site 535289008489 ligand-binding site [chemical binding]; other site 535289008490 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289008491 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 535289008492 ligand binding site [chemical binding]; other site 535289008493 flexible hinge region; other site 535289008494 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 535289008495 Protein of unknown function (DUF461); Region: DUF461; pfam04314 535289008496 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 535289008497 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 535289008498 putative substrate translocation pore; other site 535289008499 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 535289008500 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 535289008501 ATP binding site [chemical binding]; other site 535289008502 Mg++ binding site [ion binding]; other site 535289008503 motif III; other site 535289008504 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 535289008505 nucleotide binding region [chemical binding]; other site 535289008506 ATP-binding site [chemical binding]; other site 535289008507 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 535289008508 catalytic site [active] 535289008509 putative active site [active] 535289008510 putative substrate binding site [chemical binding]; other site 535289008511 dimer interface [polypeptide binding]; other site 535289008512 Peptidase family M48; Region: Peptidase_M48; pfam01435 535289008513 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cd00488 535289008514 aromatic arch; other site 535289008515 DCoH dimer interaction site [polypeptide binding]; other site 535289008516 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 535289008517 DCoH tetramer interaction site [polypeptide binding]; other site 535289008518 substrate binding site [chemical binding]; other site 535289008519 GTPase RsgA; Reviewed; Region: PRK00098 535289008520 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 535289008521 RNA binding site [nucleotide binding]; other site 535289008522 homodimer interface [polypeptide binding]; other site 535289008523 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 535289008524 GTPase/Zn-binding domain interface [polypeptide binding]; other site 535289008525 GTP/Mg2+ binding site [chemical binding]; other site 535289008526 G4 box; other site 535289008527 G5 box; other site 535289008528 G1 box; other site 535289008529 Switch I region; other site 535289008530 G2 box; other site 535289008531 G3 box; other site 535289008532 Switch II region; other site 535289008533 CobD/Cbib protein; Region: CobD_Cbib; cl00561 535289008534 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 535289008535 putative active site [active] 535289008536 putative CoA binding site [chemical binding]; other site 535289008537 nudix motif; other site 535289008538 metal binding site [ion binding]; metal-binding site 535289008539 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 535289008540 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 535289008541 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 535289008542 RimM N-terminal domain; Region: RimM; pfam01782 535289008543 PRC-barrel domain; Region: PRC; pfam05239 535289008544 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 535289008545 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 535289008546 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 535289008547 Coenzyme A binding pocket [chemical binding]; other site 535289008548 TM2 domain; Region: TM2; pfam05154 535289008549 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 535289008550 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 535289008551 Protein of unknown function, DUF486; Region: DUF486; pfam04342 535289008552 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 535289008553 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 535289008554 Walker A/P-loop; other site 535289008555 ATP binding site [chemical binding]; other site 535289008556 Q-loop/lid; other site 535289008557 ABC transporter signature motif; other site 535289008558 Walker B; other site 535289008559 D-loop; other site 535289008560 H-loop/switch region; other site 535289008561 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 535289008562 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 535289008563 Walker A/P-loop; other site 535289008564 ATP binding site [chemical binding]; other site 535289008565 Q-loop/lid; other site 535289008566 ABC transporter signature motif; other site 535289008567 Walker B; other site 535289008568 D-loop; other site 535289008569 H-loop/switch region; other site 535289008570 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 535289008571 TM-ABC transporter signature motif; other site 535289008572 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 535289008573 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 535289008574 TM-ABC transporter signature motif; other site 535289008575 recombination factor protein RarA; Reviewed; Region: PRK13342 535289008576 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289008577 Walker A motif; other site 535289008578 ATP binding site [chemical binding]; other site 535289008579 Walker B motif; other site 535289008580 arginine finger; other site 535289008581 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 535289008582 integron integrase; Region: integrase_gron; TIGR02249 535289008583 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 535289008584 Int/Topo IB signature motif; other site 535289008585 Protein of unknown function (DUF1010); Region: DUF1010; pfam06231 535289008586 Protein of unknown function, DUF488; Region: DUF488; cl01246 535289008587 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 535289008588 putative uracil binding site [chemical binding]; other site 535289008589 putative active site [active] 535289008590 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 535289008591 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 535289008592 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 535289008593 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 535289008594 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 535289008595 thioredoxin reductase; Provisional; Region: PRK10262 535289008596 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 535289008597 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289008598 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 535289008599 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 535289008600 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 535289008601 Fatty acid desaturase; Region: FA_desaturase; pfam00487 535289008602 Di-iron ligands [ion binding]; other site 535289008603 Transposase; Region: DDE_Tnp_ISL3; pfam01610 535289008604 16S rRNA methyltransferase B; Provisional; Region: PRK14902 535289008605 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 535289008606 S-adenosylmethionine binding site [chemical binding]; other site 535289008607 Peptidase family M48; Region: Peptidase_M48; cl12018 535289008608 Protein of unknown function (DUF1653); Region: DUF1653; pfam07866 535289008609 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 535289008610 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 535289008611 active site 535289008612 substrate binding site [chemical binding]; other site 535289008613 cosubstrate binding site; other site 535289008614 catalytic site [active] 535289008615 hypothetical protein; Provisional; Region: PRK11239 535289008616 Protein of unknown function, DUF480; Region: DUF480; pfam04337 535289008617 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 535289008618 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289008619 active site 535289008620 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 535289008621 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 535289008622 active site 535289008623 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 535289008624 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 535289008625 active site 535289008626 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 535289008627 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 535289008628 active site 535289008629 Riboflavin kinase; Region: Flavokinase; smart00904 535289008630 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 535289008631 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 535289008632 active site 535289008633 HIGH motif; other site 535289008634 nucleotide binding site [chemical binding]; other site 535289008635 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 535289008636 active site 535289008637 KMSKS motif; other site 535289008638 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 535289008639 tRNA binding surface [nucleotide binding]; other site 535289008640 anticodon binding site; other site 535289008641 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 535289008642 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 535289008643 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 535289008644 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 535289008645 PhoU domain; Region: PhoU; pfam01895 535289008646 PhoU domain; Region: PhoU; pfam01895 535289008647 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 535289008648 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 535289008649 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 535289008650 nudix motif; other site 535289008651 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 535289008652 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 535289008653 NADP binding site [chemical binding]; other site 535289008654 dimer interface [polypeptide binding]; other site 535289008655 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 535289008656 EamA-like transporter family; Region: EamA; pfam00892 535289008657 EamA-like transporter family; Region: EamA; pfam00892 535289008658 PAS fold; Region: PAS_7; pfam12860 535289008659 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289008660 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289008661 metal binding site [ion binding]; metal-binding site 535289008662 active site 535289008663 I-site; other site 535289008664 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 535289008665 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 535289008666 short chain dehydrogenase; Provisional; Region: PRK08339 535289008667 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 535289008668 putative NAD(P) binding site [chemical binding]; other site 535289008669 putative active site [active] 535289008670 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 535289008671 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 535289008672 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 535289008673 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 535289008674 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 535289008675 Walker A motif; other site 535289008676 ATP binding site [chemical binding]; other site 535289008677 Walker B motif; other site 535289008678 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 535289008679 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 535289008680 putative active site [active] 535289008681 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 535289008682 active site 535289008683 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 535289008684 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 535289008685 dimerization interface [polypeptide binding]; other site 535289008686 putative DNA binding site [nucleotide binding]; other site 535289008687 putative Zn2+ binding site [ion binding]; other site 535289008688 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 535289008689 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 535289008690 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 535289008691 Walker A/P-loop; other site 535289008692 ATP binding site [chemical binding]; other site 535289008693 Q-loop/lid; other site 535289008694 ABC transporter signature motif; other site 535289008695 Walker B; other site 535289008696 D-loop; other site 535289008697 H-loop/switch region; other site 535289008698 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 535289008699 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 535289008700 FtsX-like permease family; Region: FtsX; pfam02687 535289008701 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 535289008702 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 535289008703 putative active site [active] 535289008704 catalytic site [active] 535289008705 putative metal binding site [ion binding]; other site 535289008706 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 535289008707 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 535289008708 DHH family; Region: DHH; pfam01368 535289008709 DHHA1 domain; Region: DHHA1; pfam02272 535289008710 Curli production assembly/transport component CsgG; Region: CsgG; pfam03783 535289008711 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4259 535289008712 Putative bacterial lipoprotein (DUF799); Region: DUF799; cl01813 535289008713 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289008714 dimerization interface [polypeptide binding]; other site 535289008715 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289008716 dimer interface [polypeptide binding]; other site 535289008717 putative CheW interface [polypeptide binding]; other site 535289008718 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 535289008719 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 535289008720 active site 535289008721 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 535289008722 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 535289008723 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 535289008724 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 535289008725 metal ion-dependent adhesion site (MIDAS); other site 535289008726 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289008727 MoxR-like ATPases [General function prediction only]; Region: COG0714 535289008728 Walker A motif; other site 535289008729 ATP binding site [chemical binding]; other site 535289008730 Walker B motif; other site 535289008731 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 535289008732 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 535289008733 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 535289008734 D-pathway; other site 535289008735 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 535289008736 Cytochrome c; Region: Cytochrom_C; pfam00034 535289008737 Cytochrome c; Region: Cytochrom_C; pfam00034 535289008738 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 535289008739 Peptidase family M50; Region: Peptidase_M50; pfam02163 535289008740 active site 535289008741 putative substrate binding region [chemical binding]; other site 535289008742 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 535289008743 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 535289008744 active site 535289008745 HIGH motif; other site 535289008746 dimer interface [polypeptide binding]; other site 535289008747 KMSKS motif; other site 535289008748 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 535289008749 seryl-tRNA synthetase; Provisional; Region: PRK05431 535289008750 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 535289008751 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 535289008752 dimer interface [polypeptide binding]; other site 535289008753 active site 535289008754 motif 1; other site 535289008755 motif 2; other site 535289008756 motif 3; other site 535289008757 FOG: CBS domain [General function prediction only]; Region: COG0517 535289008758 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 535289008759 Domain of unknown function DUF21; Region: DUF21; pfam01595 535289008760 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 535289008761 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 535289008762 Transporter associated domain; Region: CorC_HlyC; smart01091 535289008763 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 535289008764 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 535289008765 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 535289008766 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 535289008767 hypothetical protein; Reviewed; Region: PRK00024 535289008768 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 535289008769 MPN+ (JAMM) motif; other site 535289008770 Zinc-binding site [ion binding]; other site 535289008771 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 535289008772 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 535289008773 Smr domain; Region: Smr; pfam01713 535289008774 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 535289008775 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 535289008776 active site 535289008777 metal binding site [ion binding]; metal-binding site 535289008778 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 535289008779 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 535289008780 apolar tunnel; other site 535289008781 heme binding site [chemical binding]; other site 535289008782 dimerization interface [polypeptide binding]; other site 535289008783 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 535289008784 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 535289008785 AAA domain; Region: AAA_33; pfam13671 535289008786 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 535289008787 active site 535289008788 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 535289008789 FtsX-like permease family; Region: FtsX; pfam02687 535289008790 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 535289008791 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 535289008792 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 535289008793 Protein of unknown function (DUF1498); Region: DUF1498; cl17840 535289008794 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 535289008795 Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]; Region: FwdB; COG1029 535289008796 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 535289008797 [4Fe-4S] binding site [ion binding]; other site 535289008798 molybdopterin cofactor binding site; other site 535289008799 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 535289008800 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 535289008801 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 535289008802 molybdopterin cofactor binding site; other site 535289008803 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 535289008804 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 535289008805 4Fe-4S binding domain; Region: Fer4; pfam00037 535289008806 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 535289008807 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 535289008808 4Fe-4S binding domain; Region: Fer4; pfam00037 535289008809 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 535289008810 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 535289008811 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 535289008812 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 535289008813 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 535289008814 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 535289008815 catalytic loop [active] 535289008816 iron binding site [ion binding]; other site 535289008817 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 535289008818 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 535289008819 [4Fe-4S] binding site [ion binding]; other site 535289008820 molybdopterin cofactor binding site; other site 535289008821 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 535289008822 molybdopterin cofactor binding site; other site 535289008823 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 535289008824 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH...; Region: TRX_Fd_NuoE_W_FDH_beta; cd03082 535289008825 putative dimer interface [polypeptide binding]; other site 535289008826 [2Fe-2S] cluster binding site [ion binding]; other site 535289008827 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 535289008828 SLBB domain; Region: SLBB; pfam10531 535289008829 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 535289008830 PBP superfamily domain; Region: PBP_like_2; cl17296 535289008831 antiporter inner membrane protein; Provisional; Region: PRK11670 535289008832 Domain of unknown function DUF59; Region: DUF59; pfam01883 535289008833 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 535289008834 Walker A motif; other site 535289008835 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_like_1; cd09319 535289008836 gating phenylalanine in ion channel; other site 535289008837 selenophosphate synthetase; Provisional; Region: PRK00943 535289008838 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 535289008839 dimerization interface [polypeptide binding]; other site 535289008840 putative ATP binding site [chemical binding]; other site 535289008841 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 535289008842 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 535289008843 active site residue [active] 535289008844 Restriction endonuclease; Region: Mrr_cat; pfam04471 535289008845 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 535289008846 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 535289008847 active site 535289008848 nucleophile elbow; other site 535289008849 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 535289008850 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 535289008851 active site 535289008852 HIGH motif; other site 535289008853 KMSKS motif; other site 535289008854 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 535289008855 tRNA binding surface [nucleotide binding]; other site 535289008856 anticodon binding site; other site 535289008857 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 535289008858 dimer interface [polypeptide binding]; other site 535289008859 putative tRNA-binding site [nucleotide binding]; other site 535289008860 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 535289008861 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 535289008862 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 535289008863 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 535289008864 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 535289008865 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 535289008866 phosphate binding site [ion binding]; other site 535289008867 hypothetical protein; Validated; Region: PRK07586 535289008868 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 535289008869 PYR/PP interface [polypeptide binding]; other site 535289008870 dimer interface [polypeptide binding]; other site 535289008871 TPP binding site [chemical binding]; other site 535289008872 Thiamine pyrophosphate (TPP) family, BFDC subfamily, 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...; Region: TPP_BFDC; cd02002 535289008873 TPP-binding site [chemical binding]; other site 535289008874 dimer interface [polypeptide binding]; other site 535289008875 Uncharacterized conserved protein [Function unknown]; Region: COG1284 535289008876 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 535289008877 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 535289008878 Domain of unknown function (DUF4309); Region: DUF4309; pfam14172 535289008879 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 535289008880 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 535289008881 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 535289008882 L-aspartate oxidase; Provisional; Region: PRK09077 535289008883 L-aspartate oxidase; Provisional; Region: PRK06175 535289008884 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 535289008885 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 535289008886 tetramerization interface [polypeptide binding]; other site 535289008887 active site 535289008888 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 535289008889 putative substrate binding pocket [chemical binding]; other site 535289008890 trimer interface [polypeptide binding]; other site 535289008891 aminodeoxychorismate synthase; Provisional; Region: PRK07508 535289008892 chorismate binding enzyme; Region: Chorismate_bind; cl10555 535289008893 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...; Region: PLPDE_IV; cl00224 535289008894 substrate-cofactor binding pocket; other site 535289008895 homodimer interface [polypeptide binding]; other site 535289008896 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 535289008897 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289008898 catalytic residue [active] 535289008899 quinolinate synthetase; Provisional; Region: PRK09375 535289008900 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 535289008901 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 535289008902 dimerization interface [polypeptide binding]; other site 535289008903 active site 535289008904 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 535289008905 oligomerization interface [polypeptide binding]; other site 535289008906 active site 535289008907 metal binding site [ion binding]; metal-binding site 535289008908 pantoate--beta-alanine ligase; Reviewed; Region: panC; PRK00380 535289008909 active site 535289008910 nucleotide binding site [chemical binding]; other site 535289008911 HIGH motif; other site 535289008912 KMSKS motif; other site 535289008913 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 535289008914 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 535289008915 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 535289008916 preprotein translocase subunit SecB; Validated; Region: PRK05751 535289008917 SecA binding site; other site 535289008918 Preprotein binding site; other site 535289008919 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 535289008920 GSH binding site [chemical binding]; other site 535289008921 catalytic residues [active] 535289008922 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 535289008923 active site residue [active] 535289008924 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 535289008925 catalytic core [active] 535289008926 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 535289008927 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 535289008928 C-terminal peptidase (prc); Region: prc; TIGR00225 535289008929 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 535289008930 protein binding site [polypeptide binding]; other site 535289008931 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 535289008932 Catalytic dyad [active] 535289008933 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 535289008934 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 535289008935 ATP binding site [chemical binding]; other site 535289008936 substrate interface [chemical binding]; other site 535289008937 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 535289008938 Response regulator receiver domain; Region: Response_reg; pfam00072 535289008939 active site 535289008940 phosphorylation site [posttranslational modification] 535289008941 intermolecular recognition site; other site 535289008942 dimerization interface [polypeptide binding]; other site 535289008943 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 535289008944 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 535289008945 active site 535289008946 phosphorylation site [posttranslational modification] 535289008947 intermolecular recognition site; other site 535289008948 dimerization interface [polypeptide binding]; other site 535289008949 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289008950 DNA binding residues [nucleotide binding] 535289008951 dimerization interface [polypeptide binding]; other site 535289008952 CHASE3 domain; Region: CHASE3; pfam05227 535289008953 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 535289008954 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 535289008955 ATP binding site [chemical binding]; other site 535289008956 Mg2+ binding site [ion binding]; other site 535289008957 G-X-G motif; other site 535289008958 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 535289008959 dinuclear metal binding motif [ion binding]; other site 535289008960 BON domain; Region: BON; pfam04972 535289008961 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4307 535289008962 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 535289008963 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 535289008964 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 535289008965 active site 535289008966 (T/H)XGH motif; other site 535289008967 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 535289008968 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 535289008969 S-adenosylmethionine binding site [chemical binding]; other site 535289008970 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 535289008971 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 535289008972 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 535289008973 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 535289008974 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 535289008975 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 535289008976 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 535289008977 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 535289008978 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 535289008979 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 535289008980 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289008981 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289008982 DNA binding residues [nucleotide binding] 535289008983 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289008984 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289008985 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 535289008986 ligand binding site [chemical binding]; other site 535289008987 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 535289008988 PAS domain S-box; Region: sensory_box; TIGR00229 535289008989 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 535289008990 putative active site [active] 535289008991 heme pocket [chemical binding]; other site 535289008992 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289008993 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289008994 metal binding site [ion binding]; metal-binding site 535289008995 active site 535289008996 I-site; other site 535289008997 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 535289008998 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 535289008999 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 535289009000 Cu(I) binding site [ion binding]; other site 535289009001 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 535289009002 UbiA prenyltransferase family; Region: UbiA; pfam01040 535289009003 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 535289009004 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 535289009005 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 535289009006 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 535289009007 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 535289009008 Subunit III/VIIa interface [polypeptide binding]; other site 535289009009 Phospholipid binding site [chemical binding]; other site 535289009010 Subunit I/III interface [polypeptide binding]; other site 535289009011 Subunit III/VIb interface [polypeptide binding]; other site 535289009012 Subunit III/VIa interface; other site 535289009013 Subunit III/Vb interface [polypeptide binding]; other site 535289009014 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 535289009015 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 535289009016 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 535289009017 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 535289009018 Subunit I/III interface [polypeptide binding]; other site 535289009019 D-pathway; other site 535289009020 Subunit I/VIIc interface [polypeptide binding]; other site 535289009021 Subunit I/IV interface [polypeptide binding]; other site 535289009022 Subunit I/II interface [polypeptide binding]; other site 535289009023 Low-spin heme (heme a) binding site [chemical binding]; other site 535289009024 Subunit I/VIIa interface [polypeptide binding]; other site 535289009025 Subunit I/VIa interface [polypeptide binding]; other site 535289009026 Dimer interface; other site 535289009027 Putative water exit pathway; other site 535289009028 Binuclear center (heme a3/CuB) [ion binding]; other site 535289009029 K-pathway; other site 535289009030 Subunit I/Vb interface [polypeptide binding]; other site 535289009031 Putative proton exit pathway; other site 535289009032 Subunit I/VIb interface; other site 535289009033 Subunit I/VIc interface [polypeptide binding]; other site 535289009034 Electron transfer pathway; other site 535289009035 Subunit I/VIIIb interface [polypeptide binding]; other site 535289009036 Subunit I/VIIb interface [polypeptide binding]; other site 535289009037 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 535289009038 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 535289009039 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 535289009040 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 535289009041 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 535289009042 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 535289009043 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 535289009044 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 535289009045 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 535289009046 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 535289009047 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 535289009048 putative active site [active] 535289009049 putative catalytic site [active] 535289009050 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 535289009051 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 535289009052 P-loop; other site 535289009053 Magnesium ion binding site [ion binding]; other site 535289009054 LysE type translocator; Region: LysE; cl00565 535289009055 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 535289009056 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 535289009057 TrkA-N domain; Region: TrkA_N; pfam02254 535289009058 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289009059 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 535289009060 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 535289009061 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 535289009062 dimer interface [polypeptide binding]; other site 535289009063 active site 535289009064 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 535289009065 Coenzyme A transferase; Region: CoA_trans; cl17247 535289009066 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 535289009067 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 535289009068 Bacterial transcriptional regulator; Region: IclR; pfam01614 535289009069 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 535289009070 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 535289009071 Ligand Binding Site [chemical binding]; other site 535289009072 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 535289009073 Ligand Binding Site [chemical binding]; other site 535289009074 Cytochrome c553 [Energy production and conversion]; Region: COG2863 535289009075 Cytochrome c; Region: Cytochrom_C; cl11414 535289009076 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289009077 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 535289009078 Walker A motif; other site 535289009079 ATP binding site [chemical binding]; other site 535289009080 Walker B motif; other site 535289009081 arginine finger; other site 535289009082 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 535289009083 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 535289009084 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 535289009085 Surface antigen; Region: Bac_surface_Ag; pfam01103 535289009086 Family of unknown function (DUF490); Region: DUF490; pfam04357 535289009087 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 535289009088 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 535289009089 putative active site [active] 535289009090 catalytic site [active] 535289009091 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 535289009092 putative active site [active] 535289009093 catalytic site [active] 535289009094 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 535289009095 ArsC family; Region: ArsC; pfam03960 535289009096 catalytic residues [active] 535289009097 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 535289009098 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289009099 dimer interface [polypeptide binding]; other site 535289009100 conserved gate region; other site 535289009101 putative PBP binding loops; other site 535289009102 ABC-ATPase subunit interface; other site 535289009103 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 535289009104 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 535289009105 Walker A/P-loop; other site 535289009106 ATP binding site [chemical binding]; other site 535289009107 Q-loop/lid; other site 535289009108 ABC transporter signature motif; other site 535289009109 Walker B; other site 535289009110 D-loop; other site 535289009111 H-loop/switch region; other site 535289009112 TOBE domain; Region: TOBE_2; pfam08402 535289009113 Yip1 domain; Region: Yip1; pfam04893 535289009114 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 535289009115 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 535289009116 putative acyl-acceptor binding pocket; other site 535289009117 dihydroorotase; Provisional; Region: PRK07627 535289009118 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 535289009119 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 535289009120 active site 535289009121 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 535289009122 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 535289009123 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 535289009124 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 535289009125 active site 535289009126 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 535289009127 hypothetical protein; Validated; Region: PRK00228 535289009128 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 535289009129 putative binding surface; other site 535289009130 active site 535289009131 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 535289009132 putative binding surface; other site 535289009133 active site 535289009134 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 535289009135 putative binding surface; other site 535289009136 active site 535289009137 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 535289009138 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 535289009139 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 535289009140 ATP binding site [chemical binding]; other site 535289009141 Mg2+ binding site [ion binding]; other site 535289009142 G-X-G motif; other site 535289009143 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 535289009144 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 535289009145 Response regulator receiver domain; Region: Response_reg; pfam00072 535289009146 active site 535289009147 phosphorylation site [posttranslational modification] 535289009148 intermolecular recognition site; other site 535289009149 dimerization interface [polypeptide binding]; other site 535289009150 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 535289009151 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289009152 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289009153 dimer interface [polypeptide binding]; other site 535289009154 putative CheW interface [polypeptide binding]; other site 535289009155 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 535289009156 Response regulator receiver domain; Region: Response_reg; pfam00072 535289009157 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 535289009158 active site 535289009159 phosphorylation site [posttranslational modification] 535289009160 intermolecular recognition site; other site 535289009161 dimerization interface [polypeptide binding]; other site 535289009162 Response regulator receiver domain; Region: Response_reg; pfam00072 535289009163 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 535289009164 active site 535289009165 phosphorylation site [posttranslational modification] 535289009166 intermolecular recognition site; other site 535289009167 dimerization interface [polypeptide binding]; other site 535289009168 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 535289009169 Rubredoxin; Region: Rubredoxin; pfam00301 535289009170 iron binding site [ion binding]; other site 535289009171 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 535289009172 substrate binding site [chemical binding]; other site 535289009173 ATP binding site [chemical binding]; other site 535289009174 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 535289009175 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 535289009176 inhibitor-cofactor binding pocket; inhibition site 535289009177 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289009178 catalytic residue [active] 535289009179 PhoD-like phosphatase; Region: PhoD; pfam09423 535289009180 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 535289009181 putative active site [active] 535289009182 putative metal binding site [ion binding]; other site 535289009183 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 535289009184 Cytochrome c; Region: Cytochrom_C; cl11414 535289009185 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 535289009186 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 535289009187 purine monophosphate binding site [chemical binding]; other site 535289009188 dimer interface [polypeptide binding]; other site 535289009189 putative catalytic residues [active] 535289009190 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 535289009191 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 535289009192 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 535289009193 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 535289009194 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 535289009195 FMN binding site [chemical binding]; other site 535289009196 active site 535289009197 catalytic residues [active] 535289009198 substrate binding site [chemical binding]; other site 535289009199 Predicted membrane protein [Function unknown]; Region: COG1238 535289009200 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289009201 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 535289009202 dimerization interface [polypeptide binding]; other site 535289009203 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 535289009204 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 535289009205 M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily; Region: M20_Acy1L2_AbgB; cd05673 535289009206 putative metal binding site [ion binding]; other site 535289009207 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 535289009208 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 535289009209 dimer interface [polypeptide binding]; other site 535289009210 conserved gate region; other site 535289009211 ABC-ATPase subunit interface; other site 535289009212 phosphonate ABC transporter, periplasmic phosphonate binding protein; Region: PhnD; TIGR03431 535289009213 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 535289009214 substrate binding pocket [chemical binding]; other site 535289009215 membrane-bound complex binding site; other site 535289009216 hinge residues; other site 535289009217 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 535289009218 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 535289009219 Walker A/P-loop; other site 535289009220 ATP binding site [chemical binding]; other site 535289009221 Q-loop/lid; other site 535289009222 ABC transporter signature motif; other site 535289009223 Walker B; other site 535289009224 D-loop; other site 535289009225 H-loop/switch region; other site 535289009226 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 535289009227 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 535289009228 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 535289009229 active site 535289009230 phosphonate C-P lyase system protein PhnL; Region: CP_lyasePhnL; TIGR02324 535289009231 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289009232 Walker A/P-loop; other site 535289009233 ATP binding site [chemical binding]; other site 535289009234 Q-loop/lid; other site 535289009235 ABC transporter signature motif; other site 535289009236 Walker B; other site 535289009237 D-loop; other site 535289009238 H-loop/switch region; other site 535289009239 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 535289009240 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 535289009241 Walker A/P-loop; other site 535289009242 ATP binding site [chemical binding]; other site 535289009243 Q-loop/lid; other site 535289009244 ABC transporter signature motif; other site 535289009245 Walker B; other site 535289009246 D-loop; other site 535289009247 H-loop/switch region; other site 535289009248 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 535289009249 putative acetyltransferase; Provisional; Region: PRK03624 535289009250 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 535289009251 Coenzyme A binding pocket [chemical binding]; other site 535289009252 Phosphonate metabolism protein PhnJ; Region: PhnJ; pfam06007 535289009253 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; pfam05861 535289009254 Bacterial phosphonate metabolism protein (PhnH); Region: PhnH; pfam05845 535289009255 Phosphonate metabolism protein PhnG; Region: PhnG; pfam06754 535289009256 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 535289009257 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289009258 DNA-binding site [nucleotide binding]; DNA binding site 535289009259 UTRA domain; Region: UTRA; pfam07702 535289009260 putative phosphonate metabolism protein; Region: Phn_opern_protn; TIGR03223 535289009261 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 535289009262 active site 535289009263 GTP-binding protein YchF; Reviewed; Region: PRK09601 535289009264 YchF GTPase; Region: YchF; cd01900 535289009265 G1 box; other site 535289009266 GTP/Mg2+ binding site [chemical binding]; other site 535289009267 Switch I region; other site 535289009268 G2 box; other site 535289009269 Switch II region; other site 535289009270 G3 box; other site 535289009271 G4 box; other site 535289009272 G5 box; other site 535289009273 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 535289009274 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 535289009275 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 535289009276 MOSC domain; Region: MOSC; pfam03473 535289009277 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 535289009278 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 535289009279 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 535289009280 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 535289009281 dimerization domain [polypeptide binding]; other site 535289009282 dimer interface [polypeptide binding]; other site 535289009283 catalytic residues [active] 535289009284 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 535289009285 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 535289009286 enoyl-CoA hydratase; Provisional; Region: PRK05862 535289009287 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 535289009288 substrate binding site [chemical binding]; other site 535289009289 oxyanion hole (OAH) forming residues; other site 535289009290 trimer interface [polypeptide binding]; other site 535289009291 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 535289009292 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 535289009293 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 535289009294 FeS/SAM binding site; other site 535289009295 TRAM domain; Region: TRAM; pfam01938 535289009296 signal recognition particle protein; Provisional; Region: PRK10867 535289009297 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 535289009298 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 535289009299 GTP binding site [chemical binding]; other site 535289009300 Signal peptide binding domain; Region: SRP_SPB; pfam02978 535289009301 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 535289009302 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 535289009303 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 535289009304 putative active site [active] 535289009305 heme pocket [chemical binding]; other site 535289009306 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289009307 dimer interface [polypeptide binding]; other site 535289009308 phosphorylation site [posttranslational modification] 535289009309 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 535289009310 ATP binding site [chemical binding]; other site 535289009311 Mg2+ binding site [ion binding]; other site 535289009312 G-X-G motif; other site 535289009313 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 535289009314 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 535289009315 active site 535289009316 phosphorylation site [posttranslational modification] 535289009317 intermolecular recognition site; other site 535289009318 dimerization interface [polypeptide binding]; other site 535289009319 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289009320 Walker A motif; other site 535289009321 ATP binding site [chemical binding]; other site 535289009322 Walker B motif; other site 535289009323 arginine finger; other site 535289009324 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 535289009325 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 535289009326 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 535289009327 amidase catalytic site [active] 535289009328 Zn binding residues [ion binding]; other site 535289009329 substrate binding site [chemical binding]; other site 535289009330 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 535289009331 ATP cone domain; Region: ATP-cone; pfam03477 535289009332 Class I ribonucleotide reductase; Region: RNR_I; cd01679 535289009333 active site 535289009334 dimer interface [polypeptide binding]; other site 535289009335 catalytic residues [active] 535289009336 effector binding site; other site 535289009337 R2 peptide binding site; other site 535289009338 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 535289009339 dimer interface [polypeptide binding]; other site 535289009340 putative radical transfer pathway; other site 535289009341 diiron center [ion binding]; other site 535289009342 tyrosyl radical; other site 535289009343 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 535289009344 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 535289009345 substrate binding site [chemical binding]; other site 535289009346 ATP binding site [chemical binding]; other site 535289009347 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 535289009348 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 535289009349 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 535289009350 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 535289009351 S-adenosylmethionine binding site [chemical binding]; other site 535289009352 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 535289009353 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 535289009354 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 535289009355 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 535289009356 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 535289009357 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 535289009358 carboxyltransferase (CT) interaction site; other site 535289009359 biotinylation site [posttranslational modification]; other site 535289009360 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 535289009361 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 535289009362 catalytic residues [active] 535289009363 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 535289009364 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 535289009365 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 535289009366 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 535289009367 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 535289009368 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 535289009369 protease TldD; Provisional; Region: tldD; PRK10735 535289009370 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 535289009371 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 535289009372 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 535289009373 O-Antigen ligase; Region: Wzy_C; pfam04932 535289009374 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 535289009375 Cytochrome c; Region: Cytochrom_C; cl11414 535289009376 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 535289009377 dinuclear metal binding motif [ion binding]; other site 535289009378 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 535289009379 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289009380 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289009381 DNA binding residues [nucleotide binding] 535289009382 RNB domain; Region: RNB; pfam00773 535289009383 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 535289009384 Gram-negative bacterial tonB protein; Region: TonB; cl10048 535289009385 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 535289009386 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 535289009387 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 535289009388 shikimate binding site; other site 535289009389 NAD(P) binding site [chemical binding]; other site 535289009390 Transglycosylase; Region: Transgly; cl17702 535289009391 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 535289009392 active site 535289009393 putative DNA-binding cleft [nucleotide binding]; other site 535289009394 dimer interface [polypeptide binding]; other site 535289009395 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 535289009396 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289009397 dimerization interface [polypeptide binding]; other site 535289009398 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289009399 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289009400 dimer interface [polypeptide binding]; other site 535289009401 putative CheW interface [polypeptide binding]; other site 535289009402 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 535289009403 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 535289009404 dimerization interface [polypeptide binding]; other site 535289009405 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289009406 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289009407 dimer interface [polypeptide binding]; other site 535289009408 putative CheW interface [polypeptide binding]; other site 535289009409 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 535289009410 ThiC-associated domain; Region: ThiC-associated; pfam13667 535289009411 ThiC family; Region: ThiC; pfam01964 535289009412 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 535289009413 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 535289009414 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 535289009415 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289009416 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289009417 dimer interface [polypeptide binding]; other site 535289009418 putative CheW interface [polypeptide binding]; other site 535289009419 cell division protein FtsZ; Validated; Region: PRK09330 535289009420 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 535289009421 nucleotide binding site [chemical binding]; other site 535289009422 SulA interaction site; other site 535289009423 cell division protein FtsA; Region: ftsA; TIGR01174 535289009424 Cell division protein FtsA; Region: FtsA; smart00842 535289009425 Cell division protein FtsA; Region: FtsA; pfam14450 535289009426 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 535289009427 Cell division protein FtsQ; Region: FtsQ; pfam03799 535289009428 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 535289009429 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 535289009430 ATP-grasp domain; Region: ATP-grasp_4; cl17255 535289009431 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 535289009432 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 535289009433 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 535289009434 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 535289009435 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 535289009436 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 535289009437 active site 535289009438 homodimer interface [polypeptide binding]; other site 535289009439 cell division protein FtsW; Region: ftsW; TIGR02614 535289009440 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 535289009441 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 535289009442 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 535289009443 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 535289009444 Mg++ binding site [ion binding]; other site 535289009445 putative catalytic motif [active] 535289009446 putative substrate binding site [chemical binding]; other site 535289009447 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 535289009448 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 535289009449 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 535289009450 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 535289009451 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 535289009452 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 535289009453 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 535289009454 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 535289009455 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 535289009456 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 535289009457 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 535289009458 Cell division protein FtsL; Region: FtsL; pfam04999 535289009459 MraW methylase family; Region: Methyltransf_5; cl17771 535289009460 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 535289009461 cell division protein MraZ; Reviewed; Region: PRK00326 535289009462 MraZ protein; Region: MraZ; pfam02381 535289009463 MraZ protein; Region: MraZ; pfam02381 535289009464 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 535289009465 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289009466 Walker A motif; other site 535289009467 ATP binding site [chemical binding]; other site 535289009468 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 535289009469 Walker B motif; other site 535289009470 arginine finger; other site 535289009471 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 535289009472 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 535289009473 active site 535289009474 HslU subunit interaction site [polypeptide binding]; other site 535289009475 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 535289009476 STAS domain; Region: STAS_2; pfam13466 535289009477 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 535289009478 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 535289009479 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 535289009480 P-loop, Walker A motif; other site 535289009481 Base recognition motif; other site 535289009482 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 535289009483 PUA domain; Region: PUA; cl00607 535289009484 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 535289009485 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 535289009486 putative RNA binding site [nucleotide binding]; other site 535289009487 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 535289009488 S-adenosylmethionine binding site [chemical binding]; other site 535289009489 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 535289009490 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 535289009491 active site 535289009492 DNA binding site [nucleotide binding] 535289009493 Int/Topo IB signature motif; other site 535289009494 Protein of unknown function, DUF484; Region: DUF484; cl17449 535289009495 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 535289009496 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 535289009497 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 535289009498 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 535289009499 nudix motif; other site 535289009500 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 535289009501 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 535289009502 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 535289009503 RNA binding surface [nucleotide binding]; other site 535289009504 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 535289009505 active site 535289009506 Bacterial protein of unknown function (DUF898); Region: DUF898; pfam05987 535289009507 Peptidase family M48; Region: Peptidase_M48; cl12018 535289009508 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 535289009509 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 535289009510 dimer interface [polypeptide binding]; other site 535289009511 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289009512 catalytic residue [active] 535289009513 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 535289009514 putative catalytic site [active] 535289009515 putative metal binding site [ion binding]; other site 535289009516 putative phosphate binding site [ion binding]; other site 535289009517 cardiolipin synthase 2; Provisional; Region: PRK11263 535289009518 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 535289009519 putative active site [active] 535289009520 catalytic site [active] 535289009521 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 535289009522 putative active site [active] 535289009523 catalytic site [active] 535289009524 Predicted integral membrane protein [Function unknown]; Region: COG0392 535289009525 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 535289009526 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 535289009527 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 535289009528 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 535289009529 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 535289009530 Ligand binding site [chemical binding]; other site 535289009531 Electron transfer flavoprotein domain; Region: ETF; pfam01012 535289009532 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 535289009533 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 535289009534 FMN binding site [chemical binding]; other site 535289009535 substrate binding site [chemical binding]; other site 535289009536 putative catalytic residue [active] 535289009537 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289009538 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 535289009539 CoA-transferase family III; Region: CoA_transf_3; pfam02515 535289009540 enoyl-CoA hydratase; Provisional; Region: PRK07511 535289009541 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 535289009542 substrate binding site [chemical binding]; other site 535289009543 oxyanion hole (OAH) forming residues; other site 535289009544 trimer interface [polypeptide binding]; other site 535289009545 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 535289009546 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 535289009547 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 535289009548 active site 535289009549 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 535289009550 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289009551 active site 535289009552 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 535289009553 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 535289009554 dimer interface [polypeptide binding]; other site 535289009555 active site 535289009556 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 535289009557 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 535289009558 substrate binding site [chemical binding]; other site 535289009559 oxyanion hole (OAH) forming residues; other site 535289009560 trimer interface [polypeptide binding]; other site 535289009561 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 535289009562 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289009563 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 535289009564 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289009565 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289009566 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 535289009567 putative effector binding pocket; other site 535289009568 dimerization interface [polypeptide binding]; other site 535289009569 heat shock protein HtpX; Provisional; Region: PRK05457 535289009570 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 535289009571 Uncharacterized conserved protein [Function unknown]; Region: COG1432 535289009572 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 535289009573 putative metal binding site [ion binding]; other site 535289009574 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 535289009575 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 535289009576 active site 535289009577 substrate binding pocket [chemical binding]; other site 535289009578 dimer interface [polypeptide binding]; other site 535289009579 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 535289009580 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 535289009581 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 535289009582 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 535289009583 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289009584 Walker A/P-loop; other site 535289009585 ATP binding site [chemical binding]; other site 535289009586 Q-loop/lid; other site 535289009587 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 535289009588 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 535289009589 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289009590 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 535289009591 putative ligand binding site [chemical binding]; other site 535289009592 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 535289009593 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 535289009594 putative ligand binding site [chemical binding]; other site 535289009595 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 535289009596 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 535289009597 trimer interface [polypeptide binding]; other site 535289009598 eyelet of channel; other site 535289009599 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 535289009600 putative substrate translocation pore; other site 535289009601 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 535289009602 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; Region: DsbA_HCCA_Iso; cd03022 535289009603 putative catalytic residue [active] 535289009604 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 535289009605 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 535289009606 putative deacylase active site [active] 535289009607 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 535289009608 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 535289009609 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289009610 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289009611 metal binding site [ion binding]; metal-binding site 535289009612 active site 535289009613 I-site; other site 535289009614 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 535289009615 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 535289009616 active site 535289009617 catalytic residues [active] 535289009618 metal binding site [ion binding]; metal-binding site 535289009619 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 535289009620 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; Region: GDH_like_2; cd12164 535289009621 putative ligand binding site [chemical binding]; other site 535289009622 NAD binding site [chemical binding]; other site 535289009623 dimerization interface [polypeptide binding]; other site 535289009624 catalytic site [active] 535289009625 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 535289009626 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 535289009627 ATP-grasp domain; Region: ATP-grasp_4; cl17255 535289009628 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 535289009629 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 535289009630 carboxyltransferase (CT) interaction site; other site 535289009631 biotinylation site [posttranslational modification]; other site 535289009632 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 535289009633 enoyl-CoA hydratase; Provisional; Region: PRK05995 535289009634 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 535289009635 substrate binding site [chemical binding]; other site 535289009636 oxyanion hole (OAH) forming residues; other site 535289009637 trimer interface [polypeptide binding]; other site 535289009638 DinB family; Region: DinB; cl17821 535289009639 DinB superfamily; Region: DinB_2; pfam12867 535289009640 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 535289009641 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 535289009642 AMP-binding domain protein; Validated; Region: PRK08315 535289009643 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289009644 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 535289009645 acyl-activating enzyme (AAE) consensus motif; other site 535289009646 putative AMP binding site [chemical binding]; other site 535289009647 putative active site [active] 535289009648 putative CoA binding site [chemical binding]; other site 535289009649 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 535289009650 Helix-turn-helix domain; Region: HTH_18; pfam12833 535289009651 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 535289009652 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 535289009653 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 535289009654 putative active site [active] 535289009655 heme pocket [chemical binding]; other site 535289009656 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289009657 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289009658 metal binding site [ion binding]; metal-binding site 535289009659 active site 535289009660 I-site; other site 535289009661 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 535289009662 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 535289009663 hypothetical protein; Provisional; Region: PRK04233 535289009664 Predicted membrane protein [Function unknown]; Region: COG2323 535289009665 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 535289009666 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 535289009667 active site 535289009668 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 535289009669 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 535289009670 NADP binding site [chemical binding]; other site 535289009671 homodimer interface [polypeptide binding]; other site 535289009672 active site 535289009673 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 535289009674 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 535289009675 dimer interface [polypeptide binding]; other site 535289009676 active site 535289009677 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 535289009678 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 535289009679 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 535289009680 active site clefts [active] 535289009681 zinc binding site [ion binding]; other site 535289009682 dimer interface [polypeptide binding]; other site 535289009683 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 535289009684 isovaleryl-CoA dehydrogenase; Region: PLN02519 535289009685 substrate binding site [chemical binding]; other site 535289009686 FAD binding site [chemical binding]; other site 535289009687 catalytic base [active] 535289009688 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 535289009689 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 535289009690 DNA binding residues [nucleotide binding] 535289009691 putative dimer interface [polypeptide binding]; other site 535289009692 ABC transporter ATPase component; Reviewed; Region: PRK11147 535289009693 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289009694 Walker A/P-loop; other site 535289009695 ATP binding site [chemical binding]; other site 535289009696 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 535289009697 ABC transporter signature motif; other site 535289009698 Walker B; other site 535289009699 ABC transporter; Region: ABC_tran_2; pfam12848 535289009700 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 535289009701 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 535289009702 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 535289009703 active site 535289009704 phosphorylation site [posttranslational modification] 535289009705 intermolecular recognition site; other site 535289009706 dimerization interface [polypeptide binding]; other site 535289009707 CheB methylesterase; Region: CheB_methylest; pfam01339 535289009708 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 535289009709 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 535289009710 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 535289009711 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 535289009712 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 535289009713 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 535289009714 putative binding surface; other site 535289009715 active site 535289009716 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 535289009717 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 535289009718 ATP binding site [chemical binding]; other site 535289009719 Mg2+ binding site [ion binding]; other site 535289009720 G-X-G motif; other site 535289009721 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 535289009722 Response regulator receiver domain; Region: Response_reg; pfam00072 535289009723 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 535289009724 active site 535289009725 phosphorylation site [posttranslational modification] 535289009726 intermolecular recognition site; other site 535289009727 dimerization interface [polypeptide binding]; other site 535289009728 Response regulator receiver domain; Region: Response_reg; pfam00072 535289009729 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 535289009730 active site 535289009731 phosphorylation site [posttranslational modification] 535289009732 intermolecular recognition site; other site 535289009733 dimerization interface [polypeptide binding]; other site 535289009734 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 535289009735 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 535289009736 ATP binding site [chemical binding]; other site 535289009737 Mg2+ binding site [ion binding]; other site 535289009738 G-X-G motif; other site 535289009739 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 535289009740 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 535289009741 active site 535289009742 phosphorylation site [posttranslational modification] 535289009743 intermolecular recognition site; other site 535289009744 dimerization interface [polypeptide binding]; other site 535289009745 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289009746 DNA binding residues [nucleotide binding] 535289009747 dimerization interface [polypeptide binding]; other site 535289009748 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 535289009749 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 535289009750 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 535289009751 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 535289009752 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 535289009753 flagellar motor switch protein; Validated; Region: fliN; PRK05698 535289009754 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 535289009755 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 535289009756 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 535289009757 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 535289009758 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 535289009759 Flagellar FliJ protein; Region: FliJ; pfam02050 535289009760 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 535289009761 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 535289009762 Walker A motif/ATP binding site; other site 535289009763 Walker B motif; other site 535289009764 Flagellar assembly protein FliH; Region: FliH; pfam02108 535289009765 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 535289009766 FliG C-terminal domain; Region: FliG_C; pfam01706 535289009767 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 535289009768 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 535289009769 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 535289009770 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 535289009771 Flagellar protein FliT; Region: FliT; pfam05400 535289009772 Flagellar protein FliS; Region: FliS; cl00654 535289009773 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 535289009774 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 535289009775 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 535289009776 flagellin; Provisional; Region: PRK12806 535289009777 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 535289009778 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 535289009779 flagellin; Provisional; Region: PRK12806 535289009780 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 535289009781 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 535289009782 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 535289009783 flagellar motor stator protein MotA; Region: MotA1; TIGR03818 535289009784 flagellar motor protein MotB; Validated; Region: motB; PRK09041 535289009785 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 535289009786 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 535289009787 ligand binding site [chemical binding]; other site 535289009788 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 535289009789 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 535289009790 active site 535289009791 phosphorylation site [posttranslational modification] 535289009792 intermolecular recognition site; other site 535289009793 dimerization interface [polypeptide binding]; other site 535289009794 Chemotaxis phosphatase, CheZ; Region: CheZ; pfam04344 535289009795 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 535289009796 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 535289009797 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 535289009798 FHIPEP family; Region: FHIPEP; pfam00771 535289009799 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 535289009800 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 535289009801 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 535289009802 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 535289009803 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 535289009804 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 535289009805 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289009806 DNA binding residues [nucleotide binding] 535289009807 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 535289009808 SAF-like; Region: SAF_2; pfam13144 535289009809 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 535289009810 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 535289009811 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 535289009812 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 535289009813 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 535289009814 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 535289009815 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 535289009816 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 535289009817 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 535289009818 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 535289009819 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 535289009820 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 535289009821 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 535289009822 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 535289009823 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 535289009824 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 535289009825 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 535289009826 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 535289009827 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 535289009828 Flagellar L-ring protein; Region: FlgH; pfam02107 535289009829 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 535289009830 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 535289009831 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 535289009832 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 535289009833 Rod binding protein; Region: Rod-binding; cl01626 535289009834 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 535289009835 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 535289009836 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 535289009837 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 535289009838 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 535289009839 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 535289009840 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 535289009841 Na2 binding site [ion binding]; other site 535289009842 putative substrate binding site 1 [chemical binding]; other site 535289009843 Na binding site 1 [ion binding]; other site 535289009844 putative substrate binding site 2 [chemical binding]; other site 535289009845 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 535289009846 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 535289009847 FMN binding site [chemical binding]; other site 535289009848 substrate binding site [chemical binding]; other site 535289009849 putative catalytic residue [active] 535289009850 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 535289009851 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289009852 DNA-binding site [nucleotide binding]; DNA binding site 535289009853 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 535289009854 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289009855 homodimer interface [polypeptide binding]; other site 535289009856 catalytic residue [active] 535289009857 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 535289009858 EamA-like transporter family; Region: EamA; pfam00892 535289009859 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 535289009860 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 535289009861 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289009862 homodimer interface [polypeptide binding]; other site 535289009863 catalytic residue [active] 535289009864 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 535289009865 hypothetical protein; Provisional; Region: PRK06110 535289009866 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 535289009867 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 535289009868 catalytic residue [active] 535289009869 Putative cyclase; Region: Cyclase; cl00814 535289009870 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289009871 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 535289009872 putative ligand binding site [chemical binding]; other site 535289009873 progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs; Region: 5beta-POR_like_SDR_a; cd08948 535289009874 NAD(P) binding site [chemical binding]; other site 535289009875 active site 535289009876 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 535289009877 catalytic core [active] 535289009878 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 535289009879 Creatinine amidohydrolase; Region: Creatininase; pfam02633 535289009880 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 535289009881 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 535289009882 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 535289009883 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 535289009884 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 535289009885 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 535289009886 DsbD alpha interface [polypeptide binding]; other site 535289009887 catalytic residues [active] 535289009888 Uncharacterized conserved protein [Function unknown]; Region: COG1262 535289009889 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 535289009890 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 535289009891 CoA binding domain; Region: CoA_binding; cl17356 535289009892 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 535289009893 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 535289009894 homodimer interface [polypeptide binding]; other site 535289009895 substrate-cofactor binding pocket; other site 535289009896 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289009897 catalytic residue [active] 535289009898 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 535289009899 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 535289009900 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289009901 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 535289009902 dimerization interface [polypeptide binding]; other site 535289009903 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 535289009904 substrate binding site [chemical binding]; other site 535289009905 active site 535289009906 primosome assembly protein PriA; Validated; Region: PRK05580 535289009907 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 535289009908 ATP binding site [chemical binding]; other site 535289009909 putative Mg++ binding site [ion binding]; other site 535289009910 helicase superfamily c-terminal domain; Region: HELICc; smart00490 535289009911 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 535289009912 active site 535289009913 homodimer interface [polypeptide binding]; other site 535289009914 Predicted permeases [General function prediction only]; Region: COG0679 535289009915 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 535289009916 Part of AAA domain; Region: AAA_19; pfam13245 535289009917 Family description; Region: UvrD_C_2; pfam13538 535289009918 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 535289009919 substrate binding site [chemical binding]; other site 535289009920 dimerization interface [polypeptide binding]; other site 535289009921 active site 535289009922 calcium binding site [ion binding]; other site 535289009923 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 535289009924 Ligand Binding Site [chemical binding]; other site 535289009925 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 535289009926 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 535289009927 Protein of unknown function DUF72; Region: DUF72; pfam01904 535289009928 Putative zinc ribbon domain; Region: DUF164; pfam02591 535289009929 Double zinc ribbon; Region: DZR; pfam12773 535289009930 Uncharacterized protein conserved in bacteria (DUF2145); Region: DUF2145; pfam09916 535289009931 yiaA/B two helix domain; Region: YiaAB; cl01759 535289009932 yiaA/B two helix domain; Region: YiaAB; cl01759 535289009933 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 535289009934 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 535289009935 putative DNA binding site [nucleotide binding]; other site 535289009936 putative Zn2+ binding site [ion binding]; other site 535289009937 AsnC family; Region: AsnC_trans_reg; pfam01037 535289009938 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 535289009939 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 535289009940 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289009941 catalytic residue [active] 535289009942 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 535289009943 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 535289009944 putative acyl-acceptor binding pocket; other site 535289009945 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 535289009946 non-specific DNA binding site [nucleotide binding]; other site 535289009947 salt bridge; other site 535289009948 sequence-specific DNA binding site [nucleotide binding]; other site 535289009949 Protein required for attachment to host cells; Region: Host_attach; cl02398 535289009950 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289009951 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 535289009952 FAD-NAD(P)-binding; Region: NAD_binding_9; pfam13454 535289009953 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 535289009954 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 535289009955 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 535289009956 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 535289009957 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 535289009958 FIST N domain; Region: FIST; pfam08495 535289009959 FIST C domain; Region: FIST_C; pfam10442 535289009960 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 535289009961 IHF dimer interface [polypeptide binding]; other site 535289009962 IHF - DNA interface [nucleotide binding]; other site 535289009963 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 535289009964 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 535289009965 integrase; Provisional; Region: PRK09692 535289009966 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 535289009967 active site 535289009968 Int/Topo IB signature motif; other site 535289009969 Transposase, Mutator family; Region: Transposase_mut; pfam00872 535289009970 MULE transposase domain; Region: MULE; pfam10551 535289009971 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 535289009972 TIGR04255 family protein; Region: sporadTIGR04255 535289009973 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 535289009974 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 535289009975 catalytic residues [active] 535289009976 catalytic nucleophile [active] 535289009977 Recombinase; Region: Recombinase; pfam07508 535289009978 ParB-like nuclease domain; Region: ParB; smart00470 535289009979 RepB plasmid partitioning protein; Region: RepB; pfam07506 535289009980 ParB-like nuclease domain; Region: ParBc; pfam02195 535289009981 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 535289009982 RepB plasmid partitioning protein; Region: RepB; pfam07506 535289009983 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 535289009984 WYL domain; Region: WYL; pfam13280 535289009985 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_a; cd09179 535289009986 PLD-like domain; Region: PLDc_2; pfam13091 535289009987 putative active site [active] 535289009988 catalytic site [active] 535289009989 putative transposase OrfB; Reviewed; Region: PHA02517 535289009990 HTH-like domain; Region: HTH_21; pfam13276 535289009991 Integrase core domain; Region: rve; pfam00665 535289009992 Integrase core domain; Region: rve_2; pfam13333 535289009993 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289009994 Transposase; Region: HTH_Tnp_1; pfam01527 535289009995 DNA sulfur modification protein DndD; Region: DNA_S_dndD; TIGR03185 535289009996 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 535289009997 DNA binding residues [nucleotide binding] 535289009998 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289009999 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 535289010000 Walker A motif; other site 535289010001 ATP binding site [chemical binding]; other site 535289010002 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 535289010003 DNA methylase; Region: N6_N4_Mtase; pfam01555 535289010004 HNH endonuclease; Region: HNH_2; pfam13391 535289010005 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 535289010006 catalytic residues [active] 535289010007 Phage-related minor tail protein [Function unknown]; Region: COG5281 535289010008 tape measure domain; Region: tape_meas_nterm; TIGR02675 535289010009 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 535289010010 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 535289010011 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 535289010012 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 535289010013 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 535289010014 tandem repeat interface [polypeptide binding]; other site 535289010015 oligomer interface [polypeptide binding]; other site 535289010016 active site residues [active] 535289010017 Bacteriophage capsid protein [General function prediction only]; Region: COG5511 535289010018 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 535289010019 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 535289010020 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 535289010021 ParB-like nuclease domain; Region: ParBc; pfam02195 535289010022 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 535289010023 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 535289010024 DNA methylase; Region: N6_N4_Mtase; pfam01555 535289010025 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 535289010026 ParB-like nuclease domain; Region: ParBc; pfam02195 535289010027 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 535289010028 DNA methylase; Region: N6_N4_Mtase; pfam01555 535289010029 hypothetical protein; Validated; Region: PRK07078 535289010030 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 535289010031 active site 535289010032 metal binding site [ion binding]; metal-binding site 535289010033 interdomain interaction site; other site 535289010034 D5 N terminal like; Region: D5_N; smart00885 535289010035 Helix-turn-helix domain; Region: HTH_17; cl17695 535289010036 AAA domain; Region: AAA_24; pfam13479 535289010037 phage nucleotide-binding protein; Region: phage_P_loop; TIGR01618 535289010038 Prophage antirepressor [Transcription]; Region: COG3617 535289010039 BRO family, N-terminal domain; Region: Bro-N; smart01040 535289010040 Helix-turn-helix domain; Region: HTH_17; pfam12728 535289010041 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 535289010042 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 535289010043 catalytic residues [active] 535289010044 catalytic nucleophile [active] 535289010045 Presynaptic Site I dimer interface [polypeptide binding]; other site 535289010046 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 535289010047 Synaptic Flat tetramer interface [polypeptide binding]; other site 535289010048 Synaptic Site I dimer interface [polypeptide binding]; other site 535289010049 DNA binding site [nucleotide binding] 535289010050 Recombinase; Region: Recombinase; pfam07508 535289010051 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 535289010052 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 535289010053 Protein of unknown function DUF262; Region: DUF262; pfam03235 535289010054 Domain of unknown function (DUF955); Region: DUF955; pfam06114 535289010055 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 535289010056 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 535289010057 non-specific DNA binding site [nucleotide binding]; other site 535289010058 salt bridge; other site 535289010059 sequence-specific DNA binding site [nucleotide binding]; other site 535289010060 Uncharacterized protein conserved in bacteria (DUF2188); Region: DUF2188; pfam09954 535289010061 Response regulator receiver domain; Region: Response_reg; pfam00072 535289010062 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 535289010063 active site 535289010064 phosphorylation site [posttranslational modification] 535289010065 intermolecular recognition site; other site 535289010066 dimerization interface [polypeptide binding]; other site 535289010067 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 535289010068 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289010069 dimerization interface [polypeptide binding]; other site 535289010070 PAS domain; Region: PAS; smart00091 535289010071 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 535289010072 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289010073 dimer interface [polypeptide binding]; other site 535289010074 phosphorylation site [posttranslational modification] 535289010075 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 535289010076 ATP binding site [chemical binding]; other site 535289010077 Mg2+ binding site [ion binding]; other site 535289010078 G-X-G motif; other site 535289010079 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 535289010080 16S rRNA methyltransferase B; Provisional; Region: PRK10901 535289010081 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 535289010082 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 535289010083 S-adenosylmethionine binding site [chemical binding]; other site 535289010084 LemA family; Region: LemA; cl00742 535289010085 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 535289010086 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 535289010087 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 535289010088 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 535289010089 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 535289010090 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 535289010091 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 535289010092 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 535289010093 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 535289010094 DNA binding site [nucleotide binding] 535289010095 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 535289010096 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 535289010097 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 535289010098 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 535289010099 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 535289010100 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 535289010101 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 535289010102 RPB3 interaction site [polypeptide binding]; other site 535289010103 RPB1 interaction site [polypeptide binding]; other site 535289010104 RPB11 interaction site [polypeptide binding]; other site 535289010105 RPB10 interaction site [polypeptide binding]; other site 535289010106 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 535289010107 peripheral dimer interface [polypeptide binding]; other site 535289010108 core dimer interface [polypeptide binding]; other site 535289010109 L10 interface [polypeptide binding]; other site 535289010110 L11 interface [polypeptide binding]; other site 535289010111 putative EF-Tu interaction site [polypeptide binding]; other site 535289010112 putative EF-G interaction site [polypeptide binding]; other site 535289010113 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 535289010114 23S rRNA interface [nucleotide binding]; other site 535289010115 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 535289010116 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 535289010117 mRNA/rRNA interface [nucleotide binding]; other site 535289010118 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 535289010119 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 535289010120 23S rRNA interface [nucleotide binding]; other site 535289010121 L7/L12 interface [polypeptide binding]; other site 535289010122 putative thiostrepton binding site; other site 535289010123 L25 interface [polypeptide binding]; other site 535289010124 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 535289010125 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 535289010126 putative homodimer interface [polypeptide binding]; other site 535289010127 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 535289010128 heterodimer interface [polypeptide binding]; other site 535289010129 homodimer interface [polypeptide binding]; other site 535289010130 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 535289010131 elongation factor Tu; Reviewed; Region: PRK00049 535289010132 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 535289010133 G1 box; other site 535289010134 GEF interaction site [polypeptide binding]; other site 535289010135 GTP/Mg2+ binding site [chemical binding]; other site 535289010136 Switch I region; other site 535289010137 G2 box; other site 535289010138 G3 box; other site 535289010139 Switch II region; other site 535289010140 G4 box; other site 535289010141 G5 box; other site 535289010142 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 535289010143 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 535289010144 Antibiotic Binding Site [chemical binding]; other site 535289010145 Transposase; Region: HTH_Tnp_1; cl17663 535289010146 putative transposase OrfB; Reviewed; Region: PHA02517 535289010147 HTH-like domain; Region: HTH_21; pfam13276 535289010148 Integrase core domain; Region: rve; pfam00665 535289010149 Integrase core domain; Region: rve_3; pfam13683 535289010150 glutathione synthetase; Provisional; Region: PRK05246 535289010151 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 535289010152 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 535289010153 benzoate transporter; Region: benE; TIGR00843 535289010154 Benzoate membrane transport protein; Region: BenE; pfam03594 535289010155 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 535289010156 potassium uptake protein; Region: kup; TIGR00794 535289010157 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 535289010158 Glutamate-cysteine ligase; Region: GshA; pfam08886 535289010159 Cation transport protein; Region: TrkH; cl17365 535289010160 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 535289010161 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 535289010162 TrkA-N domain; Region: TrkA_N; pfam02254 535289010163 TrkA-C domain; Region: TrkA_C; pfam02080 535289010164 TrkA-N domain; Region: TrkA_N; pfam02254 535289010165 TrkA-C domain; Region: TrkA_C; pfam02080 535289010166 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 535289010167 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 535289010168 putative catalytic cysteine [active] 535289010169 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 535289010170 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 535289010171 Lipopolysaccharide-assembly; Region: LptE; pfam04390 535289010172 leucyl-tRNA synthetase, eubacterial and mitochondrial family; Region: leuS_bact; TIGR00396 535289010173 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 535289010174 HIGH motif; other site 535289010175 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 535289010176 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 535289010177 active site 535289010178 KMSKS motif; other site 535289010179 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 535289010180 tRNA binding surface [nucleotide binding]; other site 535289010181 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 535289010182 Mechanosensitive ion channel; Region: MS_channel; pfam00924 535289010183 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 535289010184 TolR protein; Region: tolR; TIGR02801 535289010185 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 535289010186 dihydrodipicolinate reductase; Provisional; Region: PRK00048 535289010187 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 535289010188 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 535289010189 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 535289010190 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 535289010191 ferric uptake regulator; Provisional; Region: fur; PRK09462 535289010192 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 535289010193 metal binding site 2 [ion binding]; metal-binding site 535289010194 putative DNA binding helix; other site 535289010195 metal binding site 1 [ion binding]; metal-binding site 535289010196 dimer interface [polypeptide binding]; other site 535289010197 structural Zn2+ binding site [ion binding]; other site 535289010198 HPr kinase/phosphorylase; Provisional; Region: PRK05428 535289010199 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 535289010200 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 535289010201 Hpr binding site; other site 535289010202 active site 535289010203 homohexamer subunit interaction site [polypeptide binding]; other site 535289010204 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 535289010205 active site 535289010206 phosphorylation site [posttranslational modification] 535289010207 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 535289010208 30S subunit binding site; other site 535289010209 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 535289010210 active site 535289010211 ATP binding site [chemical binding]; other site 535289010212 substrate binding site [chemical binding]; other site 535289010213 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 535289010214 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 535289010215 N-terminal plug; other site 535289010216 ligand-binding site [chemical binding]; other site 535289010217 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 535289010218 META domain; Region: META; pfam03724 535289010219 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 535289010220 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 535289010221 intracellular protease, PfpI family; Region: PfpI; TIGR01382 535289010222 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 535289010223 conserved cys residue [active] 535289010224 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 535289010225 AIR carboxylase; Region: AIRC; cl00310 535289010226 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 535289010227 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 535289010228 ATP-grasp domain; Region: ATP-grasp; pfam02222 535289010229 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 535289010230 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 535289010231 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 535289010232 active site 535289010233 catalytic triad [active] 535289010234 oxyanion hole [active] 535289010235 OmpW family; Region: OmpW; cl17427 535289010236 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 535289010237 active site 535289010238 catalytic triad [active] 535289010239 oxyanion hole [active] 535289010240 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 535289010241 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 535289010242 Glycoprotease family; Region: Peptidase_M22; pfam00814 535289010243 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 535289010244 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 535289010245 Coenzyme A binding pocket [chemical binding]; other site 535289010246 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 535289010247 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 535289010248 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 535289010249 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 535289010250 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 535289010251 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 535289010252 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 535289010253 ThiS family; Region: ThiS; pfam02597 535289010254 charged pocket; other site 535289010255 hydrophobic patch; other site 535289010256 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 535289010257 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 535289010258 Cl binding site [ion binding]; other site 535289010259 oligomer interface [polypeptide binding]; other site 535289010260 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 535289010261 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 535289010262 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 535289010263 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 535289010264 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 535289010265 acyl-activating enzyme (AAE) consensus motif; other site 535289010266 putative AMP binding site [chemical binding]; other site 535289010267 putative active site [active] 535289010268 putative CoA binding site [chemical binding]; other site 535289010269 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 535289010270 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 535289010271 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 535289010272 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 535289010273 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 535289010274 ligand binding site [chemical binding]; other site 535289010275 homodimer interface [polypeptide binding]; other site 535289010276 NAD(P) binding site [chemical binding]; other site 535289010277 trimer interface B [polypeptide binding]; other site 535289010278 trimer interface A [polypeptide binding]; other site 535289010279 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 535289010280 intersubunit interface [polypeptide binding]; other site 535289010281 active site 535289010282 zinc binding site [ion binding]; other site 535289010283 Na+ binding site [ion binding]; other site 535289010284 pyruvate kinase; Provisional; Region: PRK05826 535289010285 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 535289010286 domain interfaces; other site 535289010287 active site 535289010288 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 535289010289 proline aminopeptidase P II; Provisional; Region: PRK10879 535289010290 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 535289010291 active site 535289010292 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 535289010293 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 535289010294 Substrate binding site; other site 535289010295 metal-binding site 535289010296 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 535289010297 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 535289010298 TPP-binding site [chemical binding]; other site 535289010299 dimer interface [polypeptide binding]; other site 535289010300 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 535289010301 PYR/PP interface [polypeptide binding]; other site 535289010302 dimer interface [polypeptide binding]; other site 535289010303 TPP binding site [chemical binding]; other site 535289010304 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 535289010305 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 535289010306 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 535289010307 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 535289010308 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 535289010309 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 535289010310 Peptidase C26; Region: Peptidase_C26; pfam07722 535289010311 catalytic triad [active] 535289010312 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 535289010313 Pirin-related protein [General function prediction only]; Region: COG1741 535289010314 Pirin; Region: Pirin; pfam02678 535289010315 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 535289010316 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 535289010317 dimer interface [polypeptide binding]; other site 535289010318 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 535289010319 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 535289010320 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289010321 NAD(P) binding site [chemical binding]; other site 535289010322 active site 535289010323 Uncharacterized conserved protein [Function unknown]; Region: COG3148 535289010324 Transcriptional regulator [Transcription]; Region: IclR; COG1414 535289010325 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 535289010326 Bacterial transcriptional regulator; Region: IclR; pfam01614 535289010327 thiolase; Provisional; Region: PRK06158 535289010328 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...; Region: SCP-x_thiolase; cd00829 535289010329 active site 535289010330 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]; Region: COG1545 535289010331 DUF35 OB-fold domain; Region: DUF35; pfam01796 535289010332 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289010333 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 535289010334 CoA binding domain; Region: CoA_binding_2; pfam13380 535289010335 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 535289010336 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 535289010337 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 sources...; Region: GST_N_Ure2p_like; cd03048 535289010338 dimer interface [polypeptide binding]; other site 535289010339 GSH binding site (G-site) [chemical binding]; other site 535289010340 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 535289010341 dimer interface [polypeptide binding]; other site 535289010342 N-terminal domain interface [polypeptide binding]; other site 535289010343 putative transposase OrfB; Reviewed; Region: PHA02517 535289010344 HTH-like domain; Region: HTH_21; pfam13276 535289010345 Integrase core domain; Region: rve; pfam00665 535289010346 Integrase core domain; Region: rve_3; pfam13683 535289010347 Transposase; Region: HTH_Tnp_1; pfam01527 535289010348 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 535289010349 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 535289010350 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08642 535289010351 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289010352 NAD(P) binding site [chemical binding]; other site 535289010353 active site 535289010354 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 535289010355 Protein of unknown function (DUF1010); Region: DUF1010; pfam06231 535289010356 Transposase, Mutator family; Region: Transposase_mut; pfam00872 535289010357 MULE transposase domain; Region: MULE; pfam10551 535289010358 DNA topoisomerase III; Provisional; Region: PRK14724 535289010359 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 535289010360 active site 535289010361 putative interdomain interaction site [polypeptide binding]; other site 535289010362 putative metal-binding site [ion binding]; other site 535289010363 putative nucleotide binding site [chemical binding]; other site 535289010364 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 535289010365 domain I; other site 535289010366 DNA binding groove [nucleotide binding] 535289010367 phosphate binding site [ion binding]; other site 535289010368 domain II; other site 535289010369 domain III; other site 535289010370 nucleotide binding site [chemical binding]; other site 535289010371 catalytic site [active] 535289010372 domain IV; other site 535289010373 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 535289010374 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 535289010375 SWI complex, BAF60b domains; Region: SWIB; smart00151 535289010376 Proteins containing SET domain [General function prediction only]; Region: COG2940 535289010377 SET domain; Region: SET; pfam00856 535289010378 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 535289010379 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 535289010380 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 535289010381 Sporulation related domain; Region: SPOR; cl10051 535289010382 Transposase domain (DUF772); Region: DUF772; pfam05598 535289010383 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 535289010384 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 535289010385 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 535289010386 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 535289010387 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 535289010388 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289010389 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 535289010390 dimerization interface [polypeptide binding]; other site 535289010391 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 535289010392 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289010393 dimer interface [polypeptide binding]; other site 535289010394 phosphorylation site [posttranslational modification] 535289010395 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 535289010396 ATP binding site [chemical binding]; other site 535289010397 Mg2+ binding site [ion binding]; other site 535289010398 G-X-G motif; other site 535289010399 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 535289010400 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 535289010401 active site 535289010402 phosphorylation site [posttranslational modification] 535289010403 intermolecular recognition site; other site 535289010404 dimerization interface [polypeptide binding]; other site 535289010405 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289010406 DNA binding site [nucleotide binding] 535289010407 Transcriptional regulators [Transcription]; Region: MarR; COG1846 535289010408 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 535289010409 recombinase A; Provisional; Region: recA; PRK09354 535289010410 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 535289010411 hexamer interface [polypeptide binding]; other site 535289010412 Walker A motif; other site 535289010413 ATP binding site [chemical binding]; other site 535289010414 Walker B motif; other site 535289010415 RecX family; Region: RecX; cl00936 535289010416 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 535289010417 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 535289010418 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 535289010419 Protein export membrane protein; Region: SecD_SecF; pfam02355 535289010420 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 535289010421 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 535289010422 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 535289010423 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 535289010424 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 535289010425 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 535289010426 Mechanosensitive ion channel; Region: MS_channel; pfam00924 535289010427 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 535289010428 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 535289010429 dimer interface [polypeptide binding]; other site 535289010430 PYR/PP interface [polypeptide binding]; other site 535289010431 TPP binding site [chemical binding]; other site 535289010432 substrate binding site [chemical binding]; other site 535289010433 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 535289010434 TPP-binding site; other site 535289010435 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 535289010436 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 535289010437 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 535289010438 putative DNA binding site [nucleotide binding]; other site 535289010439 putative Zn2+ binding site [ion binding]; other site 535289010440 AsnC family; Region: AsnC_trans_reg; pfam01037 535289010441 Transmembrane secretion effector; Region: MFS_3; pfam05977 535289010442 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 535289010443 putative substrate translocation pore; other site 535289010444 MltA specific insert domain; Region: MltA; smart00925 535289010445 3D domain; Region: 3D; pfam06725 535289010446 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 535289010447 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 535289010448 ligand binding site [chemical binding]; other site 535289010449 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 535289010450 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 535289010451 active site 535289010452 phosphorylation site [posttranslational modification] 535289010453 intermolecular recognition site; other site 535289010454 dimerization interface [polypeptide binding]; other site 535289010455 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289010456 DNA binding residues [nucleotide binding] 535289010457 dimerization interface [polypeptide binding]; other site 535289010458 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 535289010459 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 535289010460 putative active site [active] 535289010461 heme pocket [chemical binding]; other site 535289010462 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289010463 dimer interface [polypeptide binding]; other site 535289010464 phosphorylation site [posttranslational modification] 535289010465 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 535289010466 ATP binding site [chemical binding]; other site 535289010467 Mg2+ binding site [ion binding]; other site 535289010468 G-X-G motif; other site 535289010469 nitrilase; Region: PLN02798 535289010470 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 535289010471 putative active site [active] 535289010472 catalytic triad [active] 535289010473 dimer interface [polypeptide binding]; other site 535289010474 TIGR02099 family protein; Region: TIGR02099 535289010475 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 535289010476 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 535289010477 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 535289010478 metal binding triad; other site 535289010479 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 535289010480 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 535289010481 metal binding triad; other site 535289010482 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 535289010483 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 535289010484 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 535289010485 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 535289010486 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289010487 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 535289010488 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289010489 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289010490 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 535289010491 Protein export membrane protein; Region: SecD_SecF; cl14618 535289010492 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 per...; Region: GSH_Peroxidase; cd00340 535289010493 catalytic residues [active] 535289010494 dimer interface [polypeptide binding]; other site 535289010495 putative glutathione S-transferase; Provisional; Region: PRK10357 535289010496 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 535289010497 putative C-terminal domain interface [polypeptide binding]; other site 535289010498 putative GSH binding site (G-site) [chemical binding]; other site 535289010499 putative dimer interface [polypeptide binding]; other site 535289010500 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 535289010501 dimer interface [polypeptide binding]; other site 535289010502 N-terminal domain interface [polypeptide binding]; other site 535289010503 adenylosuccinate lyase; Provisional; Region: PRK09285 535289010504 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 535289010505 tetramer interface [polypeptide binding]; other site 535289010506 active site 535289010507 YaeQ protein; Region: YaeQ; pfam07152 535289010508 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 535289010509 Protein of unknown function (DUF3717); Region: DUF3717; pfam12512 535289010510 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 535289010511 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 535289010512 Predicted membrane protein [Function unknown]; Region: COG1950 535289010513 Peptidase family M48; Region: Peptidase_M48; pfam01435 535289010514 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 535289010515 trimer interface [polypeptide binding]; other site 535289010516 dimer interface [polypeptide binding]; other site 535289010517 putative active site [active] 535289010518 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 535289010519 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 535289010520 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 535289010521 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 535289010522 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 535289010523 phosphopeptide binding site; other site 535289010524 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 535289010525 active site 535289010526 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 535289010527 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 535289010528 CoA binding domain; Region: CoA_binding; smart00881 535289010529 CoA-ligase; Region: Ligase_CoA; pfam00549 535289010530 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 535289010531 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 535289010532 CoA-ligase; Region: Ligase_CoA; pfam00549 535289010533 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 535289010534 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 535289010535 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 535289010536 DNA protecting protein DprA; Region: dprA; TIGR00732 535289010537 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 535289010538 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 535289010539 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 535289010540 active site 535289010541 catalytic residues [active] 535289010542 metal binding site [ion binding]; metal-binding site 535289010543 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 535289010544 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 535289010545 putative active site [active] 535289010546 substrate binding site [chemical binding]; other site 535289010547 putative cosubstrate binding site; other site 535289010548 catalytic site [active] 535289010549 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 535289010550 substrate binding site [chemical binding]; other site 535289010551 AzlC protein; Region: AzlC; pfam03591 535289010552 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 535289010553 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 535289010554 Phosphoglycerate kinase; Region: PGK; pfam00162 535289010555 substrate binding site [chemical binding]; other site 535289010556 hinge regions; other site 535289010557 ADP binding site [chemical binding]; other site 535289010558 catalytic site [active] 535289010559 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 535289010560 EamA-like transporter family; Region: EamA; pfam00892 535289010561 EamA-like transporter family; Region: EamA; pfam00892 535289010562 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 535289010563 active site 535289010564 dimer interface [polypeptide binding]; other site 535289010565 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289010566 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289010567 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 535289010568 dimerization interface [polypeptide binding]; other site 535289010569 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289010570 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 535289010571 active site 535289010572 Zn binding site [ion binding]; other site 535289010573 Nitrate and nitrite sensing; Region: NIT; pfam08376 535289010574 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289010575 dimerization interface [polypeptide binding]; other site 535289010576 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289010577 dimer interface [polypeptide binding]; other site 535289010578 putative CheW interface [polypeptide binding]; other site 535289010579 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 535289010580 Na binding site [ion binding]; other site 535289010581 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 535289010582 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 535289010583 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 535289010584 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 535289010585 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 535289010586 Major Facilitator Superfamily; Region: MFS_1; pfam07690 535289010587 putative substrate translocation pore; other site 535289010588 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 535289010589 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 535289010590 dimer interface [polypeptide binding]; other site 535289010591 ssDNA binding site [nucleotide binding]; other site 535289010592 tetramer (dimer of dimers) interface [polypeptide binding]; other site 535289010593 L-lactate permease; Region: Lactate_perm; cl00701 535289010594 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 535289010595 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 535289010596 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 535289010597 Ligand Binding Site [chemical binding]; other site 535289010598 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 535289010599 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289010600 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 535289010601 putative dimerization interface [polypeptide binding]; other site 535289010602 tricarballylate dehydrogenase; Validated; Region: PRK08274 535289010603 tricarballylate utilization protein B; Provisional; Region: PRK15033 535289010604 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289010605 PAS domain; Region: PAS_9; pfam13426 535289010606 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 535289010607 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 535289010608 Walker A motif; other site 535289010609 ATP binding site [chemical binding]; other site 535289010610 Walker B motif; other site 535289010611 arginine finger; other site 535289010612 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 535289010613 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 535289010614 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 535289010615 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 535289010616 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 535289010617 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 535289010618 CoA binding domain; Region: CoA_binding_2; pfam13380 535289010619 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 535289010620 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 535289010621 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 535289010622 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK06111 535289010623 ATP-grasp domain; Region: ATP-grasp_4; cl17255 535289010624 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 535289010625 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 535289010626 carboxyltransferase (CT) interaction site; other site 535289010627 biotinylation site [posttranslational modification]; other site 535289010628 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 535289010629 CoenzymeA binding site [chemical binding]; other site 535289010630 subunit interaction site [polypeptide binding]; other site 535289010631 PHB binding site; other site 535289010632 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 535289010633 nudix motif; other site 535289010634 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 535289010635 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 535289010636 N-terminal plug; other site 535289010637 ligand-binding site [chemical binding]; other site 535289010638 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 535289010639 Lumazine binding domain; Region: Lum_binding; pfam00677 535289010640 Lumazine binding domain; Region: Lum_binding; pfam00677 535289010641 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289010642 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 535289010643 ATP binding site [chemical binding]; other site 535289010644 Mg2+ binding site [ion binding]; other site 535289010645 G-X-G motif; other site 535289010646 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 535289010647 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 535289010648 active site 535289010649 phosphorylation site [posttranslational modification] 535289010650 intermolecular recognition site; other site 535289010651 dimerization interface [polypeptide binding]; other site 535289010652 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 535289010653 DNA binding site [nucleotide binding] 535289010654 Predicted membrane protein [Function unknown]; Region: COG3212 535289010655 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 535289010656 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 535289010657 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 535289010658 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 535289010659 FAD binding pocket [chemical binding]; other site 535289010660 FAD binding motif [chemical binding]; other site 535289010661 phosphate binding motif [ion binding]; other site 535289010662 beta-alpha-beta structure motif; other site 535289010663 NAD binding pocket [chemical binding]; other site 535289010664 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 535289010665 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 535289010666 Flavodoxin; Region: Flavodoxin_1; pfam00258 535289010667 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_like2; cd06201 535289010668 ferredoxin--NADP+ reductase; Provisional; Region: PLN03116 535289010669 FAD binding pocket [chemical binding]; other site 535289010670 FAD binding motif [chemical binding]; other site 535289010671 catalytic residues [active] 535289010672 NAD binding pocket [chemical binding]; other site 535289010673 phosphate binding motif [ion binding]; other site 535289010674 beta-alpha-beta structure motif; other site 535289010675 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 535289010676 ApbE family; Region: ApbE; pfam02424 535289010677 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cd06462 535289010678 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 535289010679 Catalytic site [active] 535289010680 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289010681 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 535289010682 ligand binding site [chemical binding]; other site 535289010683 flexible hinge region; other site 535289010684 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 535289010685 putative switch regulator; other site 535289010686 non-specific DNA interactions [nucleotide binding]; other site 535289010687 DNA binding site [nucleotide binding] 535289010688 sequence specific DNA binding site [nucleotide binding]; other site 535289010689 putative cAMP binding site [chemical binding]; other site 535289010690 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 535289010691 ATPase, P-type (transporting), HAD superfamily, subfamily IC; Region: ATPase_P-type; TIGR01494 535289010692 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289010693 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 535289010694 motif II; other site 535289010695 spermidine synthase; Provisional; Region: PRK03612 535289010696 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 535289010697 S-adenosylmethionine binding site [chemical binding]; other site 535289010698 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 535289010699 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 535289010700 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 535289010701 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 535289010702 Short C-terminal domain; Region: SHOCT; pfam09851 535289010703 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 535289010704 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 535289010705 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289010706 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289010707 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 535289010708 dimerization interface [polypeptide binding]; other site 535289010709 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 535289010710 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 535289010711 inhibitor-cofactor binding pocket; inhibition site 535289010712 pyridoxal 5'-phosphate binding site [chemical binding]; other site 535289010713 catalytic residue [active] 535289010714 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 535289010715 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 535289010716 tetrameric interface [polypeptide binding]; other site 535289010717 NAD binding site [chemical binding]; other site 535289010718 catalytic residues [active] 535289010719 Transcriptional regulators [Transcription]; Region: FadR; COG2186 535289010720 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 535289010721 DNA-binding site [nucleotide binding]; DNA binding site 535289010722 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 535289010723 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 535289010724 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 535289010725 putative ligand binding site [chemical binding]; other site 535289010726 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 535289010727 TM-ABC transporter signature motif; other site 535289010728 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 535289010729 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 535289010730 TM-ABC transporter signature motif; other site 535289010731 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 535289010732 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 535289010733 Walker A/P-loop; other site 535289010734 ATP binding site [chemical binding]; other site 535289010735 Q-loop/lid; other site 535289010736 ABC transporter signature motif; other site 535289010737 Walker B; other site 535289010738 D-loop; other site 535289010739 H-loop/switch region; other site 535289010740 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 535289010741 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 535289010742 Walker A/P-loop; other site 535289010743 ATP binding site [chemical binding]; other site 535289010744 Q-loop/lid; other site 535289010745 ABC transporter signature motif; other site 535289010746 Walker B; other site 535289010747 D-loop; other site 535289010748 H-loop/switch region; other site 535289010749 allantoate amidohydrolase; Reviewed; Region: PRK12893 535289010750 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 535289010751 active site 535289010752 metal binding site [ion binding]; metal-binding site 535289010753 dimer interface [polypeptide binding]; other site 535289010754 Uncharacterized conserved protein [Function unknown]; Region: COG5476 535289010755 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 535289010756 MlrC C-terminus; Region: MlrC_C; pfam07171 535289010757 Malate dehydrogenase enzyme; Region: Malate_DH; pfam12434 535289010758 malic enzyme; Reviewed; Region: PRK12862 535289010759 Malic enzyme, N-terminal domain; Region: malic; pfam00390 535289010760 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 535289010761 putative NAD(P) binding site [chemical binding]; other site 535289010762 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 535289010763 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 guanylate...; Region: RNase_Sa; cd00607 535289010764 active site 535289010765 barstar interaction site; other site 535289010766 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 535289010767 putative RNAase interaction site [polypeptide binding]; other site 535289010768 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 535289010769 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 535289010770 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 535289010771 SurA N-terminal domain; Region: SurA_N; pfam09312 535289010772 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 535289010773 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 535289010774 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 535289010775 OstA-like protein; Region: OstA; cl00844 535289010776 Organic solvent tolerance protein; Region: OstA_C; pfam04453 535289010777 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 535289010778 Phosphotransferase enzyme family; Region: APH; pfam01636 535289010779 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 535289010780 RNA methyltransferase, RsmE family; Region: TIGR00046 535289010781 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 535289010782 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289010783 Walker A/P-loop; other site 535289010784 ATP binding site [chemical binding]; other site 535289010785 Q-loop/lid; other site 535289010786 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 535289010787 ABC transporter signature motif; other site 535289010788 Walker B; other site 535289010789 D-loop; other site 535289010790 H-loop/switch region; other site 535289010791 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289010792 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289010793 metal binding site [ion binding]; metal-binding site 535289010794 active site 535289010795 I-site; other site 535289010796 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 535289010797 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 535289010798 PGAP1-like protein; Region: PGAP1; pfam07819 535289010799 hypothetical protein; Provisional; Region: PRK07907 535289010800 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_5; cd05682 535289010801 metal binding site [ion binding]; metal-binding site 535289010802 putative dimer interface [polypeptide binding]; other site 535289010803 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 535289010804 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 535289010805 metal binding site [ion binding]; metal-binding site 535289010806 active site 535289010807 I-site; other site 535289010808 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 535289010809 dimerization interface [polypeptide binding]; other site 535289010810 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 535289010811 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 535289010812 dimer interface [polypeptide binding]; other site 535289010813 putative CheW interface [polypeptide binding]; other site 535289010814 Methyltransferase domain; Region: Methyltransf_23; pfam13489 535289010815 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 535289010816 S-adenosylmethionine binding site [chemical binding]; other site 535289010817 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 535289010818 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 535289010819 Predicted membrane protein [Function unknown]; Region: COG2119 535289010820 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 535289010821 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 535289010822 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 535289010823 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 535289010824 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 535289010825 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 535289010826 short chain dehydrogenase; Provisional; Region: PRK07024 535289010827 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 535289010828 NAD(P) binding site [chemical binding]; other site 535289010829 active site 535289010830 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 535289010831 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 535289010832 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 535289010833 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 535289010834 active site 535289010835 motif I; other site 535289010836 motif II; other site 535289010837 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 535289010838 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 535289010839 putative active site [active] 535289010840 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 535289010841 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 535289010842 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 535289010843 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 535289010844 TrkA-N domain; Region: TrkA_N; pfam02254 535289010845 TrkA-C domain; Region: TrkA_C; pfam02080 535289010846 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 535289010847 active site 535289010848 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 535289010849 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 535289010850 ligand binding site [chemical binding]; other site 535289010851 flexible hinge region; other site 535289010852 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 535289010853 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 535289010854 trmE is a tRNA modification GTPase; Region: trmE; cd04164 535289010855 G1 box; other site 535289010856 GTP/Mg2+ binding site [chemical binding]; other site 535289010857 Switch I region; other site 535289010858 G2 box; other site 535289010859 Switch II region; other site 535289010860 G3 box; other site 535289010861 G4 box; other site 535289010862 G5 box; other site 535289010863 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 535289010864 Uncharacterized conserved small protein [Function unknown]; Region: COG5639 535289010865 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 535289010866 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 535289010867 VirB7 interaction site; other site 535289010868 conjugal transfer protein TrbF; Provisional; Region: PRK13872 535289010869 conjugal transfer protein TrbL; Provisional; Region: PRK13875 535289010870 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 535289010871 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 535289010872 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 535289010873 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 535289010874 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 535289010875 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 535289010876 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 535289010877 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 535289010878 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 535289010879 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 535289010880 ATP binding site [chemical binding]; other site 535289010881 Walker A motif; other site 535289010882 hexamer interface [polypeptide binding]; other site 535289010883 Walker B motif; other site 535289010884 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 535289010885 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 535289010886 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 535289010887 Walker A motif; other site 535289010888 ATP binding site [chemical binding]; other site 535289010889 Walker B motif; other site 535289010890 Transcriptional regulator [Transcription]; Region: LysR; COG0583 535289010891 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 535289010892 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 535289010893 dimerization interface [polypeptide binding]; other site 535289010894 substrate binding pocket [chemical binding]; other site 535289010895 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 535289010896 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 535289010897 active site 535289010898 phosphorylation site [posttranslational modification] 535289010899 intermolecular recognition site; other site 535289010900 dimerization interface [polypeptide binding]; other site 535289010901 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 535289010902 DNA binding residues [nucleotide binding] 535289010903 dimerization interface [polypeptide binding]; other site 535289010904 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 535289010905 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 535289010906 dimer interface [polypeptide binding]; other site 535289010907 phosphorylation site [posttranslational modification] 535289010908 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 535289010909 ATP binding site [chemical binding]; other site 535289010910 Mg2+ binding site [ion binding]; other site 535289010911 G-X-G motif; other site 535289010912 Alcaligenes xylosoxidans NreA and related domains; this domain family was previously known as part of DUF156; Region: NreA-like_DUF156; cd10154 535289010913 putative homodimer interface [polypeptide binding]; other site 535289010914 putative homotetramer interface [polypeptide binding]; other site 535289010915 putative metal binding site [ion binding]; other site 535289010916 putative homodimer-homodimer interface [polypeptide binding]; other site 535289010917 putative allosteric switch controlling residues; other site 535289010918 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 535289010919 MgtC family; Region: MgtC; pfam02308 535289010920 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 535289010921 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 535289010922 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 535289010923 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 535289010924 Soluble P-type ATPase [General function prediction only]; Region: COG4087 535289010925 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 535289010926 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 535289010927 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 535289010928 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 535289010929 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 535289010930 HlyD family secretion protein; Region: HlyD_3; pfam13437 535289010931 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 535289010932 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 535289010933 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 535289010934 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 535289010935 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 535289010936 ParA-like protein; Provisional; Region: PHA02518 535289010937 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 535289010938 P-loop; other site 535289010939 Magnesium ion binding site [ion binding]; other site 535289010940 Replication initiator protein A; Region: RPA; pfam10134 535289010941 Helix-turn-helix domain; Region: HTH_17; cl17695 535289010942 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 535289010943 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 535289010944 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 535289010945 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 535289010946 non-specific DNA binding site [nucleotide binding]; other site 535289010947 salt bridge; other site 535289010948 sequence-specific DNA binding site [nucleotide binding]; other site 535289010949 Uncharacterized conserved protein [Function unknown]; Region: COG5489 535289010950 ParB-like nuclease domain; Region: ParBc; pfam02195 535289010951 Domain of unknown function (DUF932); Region: DUF932; pfam06067 535289010952 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 535289010953 hypothetical protein; Reviewed; Region: PRK00024 535289010954 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 535289010955 MPN+ (JAMM) motif; other site 535289010956 Zinc-binding site [ion binding]; other site 535289010957 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 535289010958 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 535289010959 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 535289010960 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 535289010961 active site 535289010962 Int/Topo IB signature motif; other site 535289010963 DNA binding site [nucleotide binding] 535289010964 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 535289010965 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 535289010966 membrane protein insertase; Provisional; Region: PRK01318 535289010967 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 535289010968 hypothetical protein; Provisional; Region: PRK14389 535289010969 Ribonuclease P; Region: Ribonuclease_P; pfam00825 535289010970 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399