-- dump date 20120504_142452 -- class Genbank::misc_feature -- table misc_feature_note -- id note 499177000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 499177000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 499177000003 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 499177000004 Walker A motif; other site 499177000005 ATP binding site [chemical binding]; other site 499177000006 Walker B motif; other site 499177000007 arginine finger; other site 499177000008 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 499177000009 DnaA box-binding interface [nucleotide binding]; other site 499177000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 499177000011 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 499177000012 putative DNA binding surface [nucleotide binding]; other site 499177000013 dimer interface [polypeptide binding]; other site 499177000014 beta-clamp/clamp loader binding surface; other site 499177000015 beta-clamp/translesion DNA polymerase binding surface; other site 499177000016 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 499177000017 recombination protein F; Reviewed; Region: recF; PRK00064 499177000018 RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication...; Region: ABC_RecF; cd03242 499177000019 Walker A/P-loop; other site 499177000020 ATP binding site [chemical binding]; other site 499177000021 Q-loop/lid; other site 499177000022 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000023 ABC transporter signature motif; other site 499177000024 Walker B; other site 499177000025 D-loop; other site 499177000026 H-loop/switch region; other site 499177000027 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 499177000028 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 499177000029 Mg2+ binding site [ion binding]; other site 499177000030 G-X-G motif; other site 499177000031 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 499177000032 anchoring element; other site 499177000033 dimer interface [polypeptide binding]; other site 499177000034 ATP binding site [chemical binding]; other site 499177000035 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 499177000036 active site 499177000037 putative metal-binding site [ion binding]; other site 499177000038 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 499177000039 DNA gyrase subunit A; Validated; Region: PRK05560 499177000040 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 499177000041 CAP-like domain; other site 499177000042 active site 499177000043 primary dimer interface [polypeptide binding]; other site 499177000044 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 499177000045 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 499177000046 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 499177000047 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 499177000048 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 499177000049 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 499177000050 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 499177000051 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 499177000052 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 499177000053 anti sigma factor interaction site; other site 499177000054 regulatory phosphorylation site [posttranslational modification]; other site 499177000055 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 499177000056 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 499177000057 ATP binding site [chemical binding]; other site 499177000058 Mg2+ binding site [ion binding]; other site 499177000059 G-X-G motif; other site 499177000060 RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; Region: SigBFG; TIGR02980 499177000061 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 499177000062 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 499177000063 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 499177000064 DNA binding residues [nucleotide binding] 499177000065 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177000066 metal binding site [ion binding]; metal-binding site 499177000067 active site 499177000068 I-site; other site 499177000069 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 499177000070 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177000071 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 499177000072 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 499177000073 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 499177000074 dimer interface [polypeptide binding]; other site 499177000075 anticodon binding site; other site 499177000076 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 499177000077 homodimer interface [polypeptide binding]; other site 499177000078 motif 1; other site 499177000079 active site 499177000080 motif 2; other site 499177000081 GAD domain; Region: GAD; pfam02938 499177000082 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 499177000083 motif 3; other site 499177000084 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 499177000085 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 499177000086 Amidase; Region: Amidase; cl11426 499177000087 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 499177000088 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 499177000089 GatB domain; Region: GatB_Yqey; cl11497 499177000090 pyruvate carboxylase; Reviewed; Region: PRK12999 499177000091 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 499177000092 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177000093 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 499177000094 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 499177000095 active site 499177000096 catalytic residues [active] 499177000097 metal binding site [ion binding]; metal-binding site 499177000098 homodimer binding site [polypeptide binding]; other site 499177000099 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 499177000100 carboxyltransferase (CT) interaction site; other site 499177000101 biotinylation site [posttranslational modification]; other site 499177000102 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 499177000103 Helix-turn-helix domains; Region: HTH; cl00088 499177000104 Arginine degradation protein (predicted deacylase) [Amino acid transport and metabolism]; Region: RocB; COG4187 499177000105 M20 Peptidase Arginine utilization protein, RocB; Region: M20_ArgE_RocB; cd05654 499177000106 putative metal binding site [ion binding]; other site 499177000107 putative dimer interface [polypeptide binding]; other site 499177000108 CAAX protease self-immunity; Region: Abi; cl00558 499177000109 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 499177000110 active sites [active] 499177000111 tetramer interface [polypeptide binding]; other site 499177000112 urocanate hydratase; Provisional; Region: PRK05414 499177000113 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 499177000114 dimer interface [polypeptide binding]; other site 499177000115 conserved gate region; other site 499177000116 putative PBP binding loops; other site 499177000117 ABC-ATPase subunit interface; other site 499177000118 NMT1-like family; Region: NMT1_2; cl15260 499177000119 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 499177000120 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 499177000121 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000122 Walker A/P-loop; other site 499177000123 ATP binding site [chemical binding]; other site 499177000124 Q-loop/lid; other site 499177000125 ABC transporter signature motif; other site 499177000126 Walker B; other site 499177000127 D-loop; other site 499177000128 H-loop/switch region; other site 499177000129 Cache domain; Region: Cache_1; pfam02743 499177000130 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 499177000131 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177000132 dimer interface [polypeptide binding]; other site 499177000133 putative CheW interface [polypeptide binding]; other site 499177000134 Cache domain; Region: Cache_1; pfam02743 499177000135 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 499177000136 dimerization interface [polypeptide binding]; other site 499177000137 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177000138 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177000139 dimer interface [polypeptide binding]; other site 499177000140 putative CheW interface [polypeptide binding]; other site 499177000141 DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]; Region: DnrI; COG3629 499177000142 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000143 Predicted ATPase [General function prediction only]; Region: COG3899 499177000144 Domain of unknown function (DUF4353); Region: DUF4353; pfam14262 499177000145 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 499177000146 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 499177000147 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 499177000148 OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of...; Region: ABC_OpuCA_Osmoprotection; cd03295 499177000149 Walker A/P-loop; other site 499177000150 ATP binding site [chemical binding]; other site 499177000151 Q-loop/lid; other site 499177000152 ABC transporter signature motif; other site 499177000153 Walker B; other site 499177000154 D-loop; other site 499177000155 H-loop/switch region; other site 499177000156 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; cd02205 499177000157 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 499177000158 dimer interface [polypeptide binding]; other site 499177000159 conserved gate region; other site 499177000160 ABC-ATPase subunit interface; other site 499177000161 NMT1-like family; Region: NMT1_2; cl15260 499177000162 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 499177000163 Arginase family; Region: Arginase; cl00306 499177000164 spermidine synthase; Provisional; Region: PRK00811 499177000165 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; cl15754 499177000166 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 499177000167 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 499177000168 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 499177000169 homodimer interface [polypeptide binding]; other site 499177000170 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177000171 catalytic residue [active] 499177000172 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 499177000173 Predicted amino acid racemase [Amino acid transport and metabolism]; Region: COG3457 499177000174 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; Region: PLPDE_III_AR_like_1; cd06815 499177000175 dimer interface [polypeptide binding]; other site 499177000176 active site 499177000177 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 499177000178 substrate binding site [chemical binding]; other site 499177000179 catalytic residue [active] 499177000180 YibE/F-like protein; Region: YibE_F; cl02259 499177000181 Alkaline phosphatase [Inorganic ion transport and metabolism]; Region: PhoA; COG1785 499177000182 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 499177000183 active site 499177000184 dimer interface [polypeptide binding]; other site 499177000185 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 499177000186 Uncharacterized conserved protein [Function unknown]; Region: COG1615; cl09133 499177000187 Uncharacterized protein family (UPF0182); Region: UPF0182; pfam03699 499177000188 mechanosensitive channel MscS; Provisional; Region: PRK10334 499177000189 Mechanosensitive ion channel; Region: MS_channel; pfam00924 499177000190 Rubrerythrin [Energy production and conversion]; Region: COG1592 499177000191 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 499177000192 binuclear metal center [ion binding]; other site 499177000193 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cl00202 499177000194 iron binding site [ion binding]; other site 499177000195 seryl-tRNA synthetase; Provisional; Region: PRK05431 499177000196 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 499177000197 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound...; Region: SerRS_core; cd00770 499177000198 dimer interface [polypeptide binding]; other site 499177000199 active site 499177000200 motif 1; other site 499177000201 motif 2; other site 499177000202 motif 3; other site 499177000203 cytoplasmic alpha-amylase; Reviewed; Region: PRK09441 499177000204 Alpha amylase catalytic domain found in bacterial and fungal Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac_fung_AmyA; cd11318 499177000205 active site 499177000206 Na/Ca binding site [ion binding]; other site 499177000207 catalytic site [active] 499177000208 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177000209 DNA polymerase IV; Reviewed; Region: PRK03103 499177000210 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 499177000211 active site 499177000212 DNA binding site [nucleotide binding] 499177000213 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 499177000214 inner membrane transporter YjeM; Provisional; Region: PRK15238 499177000215 Protein of unknown function DUF45; Region: DUF45; cl00636 499177000216 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 499177000217 S-adenosylmethionine binding site [chemical binding]; other site 499177000218 Acetyltransferase (GNAT) domain; Region: Acetyltransf_4; pfam13420 499177000219 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177000220 Coenzyme A binding pocket [chemical binding]; other site 499177000221 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 499177000222 ATP binding site [chemical binding]; other site 499177000223 putative Mg++ binding site [ion binding]; other site 499177000224 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 499177000225 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 499177000226 nucleotide binding region [chemical binding]; other site 499177000227 ATP-binding site [chemical binding]; other site 499177000228 potential frameshift: common BLAST hit: gi|134298177|ref|YP_001111673.1| IstB ATP binding domain-containing protein 499177000229 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000230 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000231 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 499177000232 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 499177000233 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 499177000234 Probable transposase; Region: OrfB_IS605; pfam01385 499177000235 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 499177000236 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 499177000237 nucleoside/Zn binding site; other site 499177000238 dimer interface [polypeptide binding]; other site 499177000239 catalytic motif [active] 499177000240 Uncharacterized ArCR, COG2043; Region: DUF169; cl00894 499177000241 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 499177000242 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 499177000243 dimer interface [polypeptide binding]; other site 499177000244 conserved gate region; other site 499177000245 putative PBP binding loops; other site 499177000246 ABC-ATPase subunit interface; other site 499177000247 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 499177000248 NMT1-like family; Region: NMT1_2; cl15260 499177000249 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 499177000250 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000251 Walker A/P-loop; other site 499177000252 ATP binding site [chemical binding]; other site 499177000253 Q-loop/lid; other site 499177000254 ABC transporter signature motif; other site 499177000255 Walker B; other site 499177000256 D-loop; other site 499177000257 H-loop/switch region; other site 499177000258 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 499177000259 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000260 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 499177000261 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 499177000262 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 499177000263 The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four...; Region: URO-D_like; cd03465 499177000264 Predicted cobalamin binding protein [General function prediction only]; Region: COG5012 499177000265 B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or...; Region: corrinoid_protein_B12-BD; cd02070 499177000266 B12 binding site [chemical binding]; other site 499177000267 cobalt ligand [ion binding]; other site 499177000268 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 499177000269 MtaA_CmuA_like family. MtaA/CmuA, also MtsA, or methyltransferase 2 (MT2) MT2-A and MT2-M isozymes, are methylcobamide:Coenzyme M methyltransferases, which play a role in metabolic pathways of methane formation from various substrates, such as methylated...; Region: Mta_CmuA_like; cd03307 499177000270 Uncharacterized metal-binding protein [General function prediction only]; Region: COG3894 499177000271 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 499177000272 catalytic loop [active] 499177000273 iron binding site [ion binding]; other site 499177000274 methyltransferase, MtaA/CmuA family; Region: mtaA_cmuA; TIGR01463 499177000275 The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four...; Region: URO-D_like; cd03465 499177000276 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 499177000277 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 499177000278 dimer interface [polypeptide binding]; other site 499177000279 conserved gate region; other site 499177000280 putative PBP binding loops; other site 499177000281 ABC-ATPase subunit interface; other site 499177000282 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 499177000283 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 499177000284 dimer interface [polypeptide binding]; other site 499177000285 conserved gate region; other site 499177000286 putative PBP binding loops; other site 499177000287 ABC-ATPase subunit interface; other site 499177000288 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 499177000289 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177000290 Walker A/P-loop; other site 499177000291 ATP binding site [chemical binding]; other site 499177000292 Q-loop/lid; other site 499177000293 ABC transporter signature motif; other site 499177000294 Walker B; other site 499177000295 D-loop; other site 499177000296 H-loop/switch region; other site 499177000297 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 499177000298 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 499177000299 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177000300 Walker A/P-loop; other site 499177000301 ATP binding site [chemical binding]; other site 499177000302 Q-loop/lid; other site 499177000303 ABC transporter signature motif; other site 499177000304 Walker B; other site 499177000305 D-loop; other site 499177000306 H-loop/switch region; other site 499177000307 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 499177000308 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 499177000309 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 499177000310 Uncharacterized ArCR, COG2043; Region: DUF169; cl00894 499177000311 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 499177000312 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 499177000313 Walker A/P-loop; other site 499177000314 ATP binding site [chemical binding]; other site 499177000315 Q-loop/lid; other site 499177000316 ABC transporter signature motif; other site 499177000317 Walker B; other site 499177000318 D-loop; other site 499177000319 H-loop/switch region; other site 499177000320 NIL domain; Region: NIL; cl09633 499177000321 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 499177000322 dimer interface [polypeptide binding]; other site 499177000323 conserved gate region; other site 499177000324 ABC-ATPase subunit interface; other site 499177000325 NMT1-like family; Region: NMT1_2; cl15260 499177000326 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 499177000327 The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four...; Region: URO-D_like; cd03465 499177000328 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 499177000329 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 499177000330 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 499177000331 Walker A/P-loop; other site 499177000332 ATP binding site [chemical binding]; other site 499177000333 Q-loop/lid; other site 499177000334 ABC transporter signature motif; other site 499177000335 Walker B; other site 499177000336 D-loop; other site 499177000337 H-loop/switch region; other site 499177000338 Heme NO binding; Region: HNOB; cl15268 499177000339 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177000340 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177000341 dimer interface [polypeptide binding]; other site 499177000342 putative CheW interface [polypeptide binding]; other site 499177000343 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 499177000344 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000345 Walker A/P-loop; other site 499177000346 ATP binding site [chemical binding]; other site 499177000347 Q-loop/lid; other site 499177000348 ABC transporter signature motif; other site 499177000349 Walker B; other site 499177000350 D-loop; other site 499177000351 H-loop/switch region; other site 499177000352 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177000353 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 499177000354 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 499177000355 Peptidase family U32; Region: Peptidase_U32; cl03113 499177000356 Collagenase; Region: DUF3656; pfam12392 499177000357 Peptidase family U32; Region: Peptidase_U32; cl03113 499177000358 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177000359 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177000360 dimer interface [polypeptide binding]; other site 499177000361 putative CheW interface [polypeptide binding]; other site 499177000362 Cache domain; Region: Cache_1; pfam02743 499177000363 Glutamine amidotransferase [Amino acid transport and metabolism]; Region: HisH; COG0118 499177000364 Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis; Region: GATase1_PB; cd01749 499177000365 predicted active site [active] 499177000366 catalytic triad [active] 499177000367 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1; Region: TIGR00343 499177000368 PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some...; Region: pdxS; cd04727 499177000369 active site 499177000370 multimer interface [polypeptide binding]; other site 499177000371 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177000372 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 499177000373 nucleoside/Zn binding site; other site 499177000374 dimer interface [polypeptide binding]; other site 499177000375 catalytic motif [active] 499177000376 Response regulator receiver domain; Region: Response_reg; pfam00072 499177000377 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 499177000378 active site 499177000379 phosphorylation site [posttranslational modification] 499177000380 intermolecular recognition site; other site 499177000381 dimerization interface [polypeptide binding]; other site 499177000382 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177000383 metal binding site [ion binding]; metal-binding site 499177000384 active site 499177000385 I-site; other site 499177000386 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 499177000387 octamerization interface [polypeptide binding]; other site 499177000388 diferric-oxygen binding site [ion binding]; other site 499177000389 NlpC/P60 family; Region: NLPC_P60; cl11438 499177000390 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 499177000391 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 499177000392 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 499177000393 Walker A motif; other site 499177000394 ATP binding site [chemical binding]; other site 499177000395 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000396 Walker B motif; other site 499177000397 arginine finger; other site 499177000398 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 499177000399 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 499177000400 recombination protein RecR; Reviewed; Region: recR; PRK00076 499177000401 RecR protein; Region: RecR; pfam02132 499177000402 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 499177000403 putative active site [active] 499177000404 putative metal-binding site [ion binding]; other site 499177000405 tetramer interface [polypeptide binding]; other site 499177000406 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 499177000407 Helix-turn-helix domains; Region: HTH; cl00088 499177000408 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 499177000409 dimer interface [polypeptide binding]; other site 499177000410 FMN binding site [chemical binding]; other site 499177000411 Pirin-related protein [General function prediction only]; Region: COG1741 499177000412 Cupin domain; Region: Cupin_2; cl09118 499177000413 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 499177000414 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 499177000415 Protein of unknown function (DUF969); Region: DUF969; cl01573 499177000416 Protein of unknown function (DUF969); Region: DUF969; cl01573 499177000417 Protein of unknown function (DUF979); Region: DUF979; cl01572 499177000418 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 499177000419 putative substrate binding pocket [chemical binding]; other site 499177000420 AC domain interface; other site 499177000421 catalytic triad [active] 499177000422 AB domain interface; other site 499177000423 interchain disulfide; other site 499177000424 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 499177000425 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 499177000426 ligand binding site [chemical binding]; other site 499177000427 flexible hinge region; other site 499177000428 Helix-turn-helix domains; Region: HTH; cl00088 499177000429 Cache domain; Region: Cache_1; pfam02743 499177000430 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 499177000431 PAS fold; Region: PAS_4; pfam08448 499177000432 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177000433 metal binding site [ion binding]; metal-binding site 499177000434 active site 499177000435 I-site; other site 499177000436 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177000437 Zn2+ binding site [ion binding]; other site 499177000438 Mg2+ binding site [ion binding]; other site 499177000439 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 499177000440 MgtE intracellular N domain; Region: MgtE_N; cl15244 499177000441 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 499177000442 Divalent cation transporter; Region: MgtE; cl00786 499177000443 Cache domain; Region: Cache_1; pfam02743 499177000444 two component system sensor kinase SsrA; Provisional; Region: PRK15347 499177000445 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 499177000446 dimerization interface [polypeptide binding]; other site 499177000447 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177000448 metal binding site [ion binding]; metal-binding site 499177000449 active site 499177000450 I-site; other site 499177000451 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 499177000452 Cache domain; Region: Cache_1; pfam02743 499177000453 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 499177000454 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 499177000455 PAS domain; Region: PAS_9; pfam13426 499177000456 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177000457 metal binding site [ion binding]; metal-binding site 499177000458 active site 499177000459 I-site; other site 499177000460 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 499177000461 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177000462 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 499177000463 FeS/SAM binding site; other site 499177000464 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 499177000465 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 499177000466 active site 499177000467 phosphorylation site [posttranslational modification] 499177000468 intermolecular recognition site; other site 499177000469 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 499177000470 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 499177000471 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177000472 Zn2+ binding site [ion binding]; other site 499177000473 Mg2+ binding site [ion binding]; other site 499177000474 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 499177000475 ATP binding site [chemical binding]; other site 499177000476 Mg2+ binding site [ion binding]; other site 499177000477 G-X-G motif; other site 499177000478 Cache domain; Region: Cache_1; pfam02743 499177000479 two component system sensor kinase SsrA; Provisional; Region: PRK15347 499177000480 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 499177000481 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177000482 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177000483 ABC transporter; Region: ABC_tran_2; pfam12848 499177000484 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177000485 helicase 45; Provisional; Region: PTZ00424 499177000486 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 499177000487 ATP binding site [chemical binding]; other site 499177000488 Mg++ binding site [ion binding]; other site 499177000489 motif III; other site 499177000490 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 499177000491 nucleotide binding region [chemical binding]; other site 499177000492 ATP-binding site [chemical binding]; other site 499177000493 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 499177000494 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177000495 acetylornithine aminotransferase; Provisional; Region: PRK02627 499177000496 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 499177000497 inhibitor-cofactor binding pocket; inhibition site 499177000498 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177000499 catalytic residue [active] 499177000500 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 499177000501 feedback inhibition sensing region; other site 499177000502 homohexameric interface [polypeptide binding]; other site 499177000503 nucleotide binding site [chemical binding]; other site 499177000504 N-acetyl-L-glutamate binding site [chemical binding]; other site 499177000505 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 499177000506 heterotetramer interface [polypeptide binding]; other site 499177000507 active site pocket [active] 499177000508 cleavage site 499177000509 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 499177000510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177000511 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 499177000512 argininosuccinate lyase; Provisional; Region: PRK00855 499177000513 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 499177000514 active sites [active] 499177000515 tetramer interface [polypeptide binding]; other site 499177000516 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 499177000517 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 499177000518 ANP binding site [chemical binding]; other site 499177000519 Substrate Binding Site II [chemical binding]; other site 499177000520 Substrate Binding Site I [chemical binding]; other site 499177000521 TfoX N-terminal domain; Region: TfoX_N; cl01167 499177000522 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 499177000523 GIY-YIG motif/motif A; other site 499177000524 putative active site [active] 499177000525 putative metal binding site [ion binding]; other site 499177000526 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 499177000527 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 499177000528 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 499177000529 substrate binding pocket [chemical binding]; other site 499177000530 dimer interface [polypeptide binding]; other site 499177000531 inhibitor binding site; inhibition site 499177000532 Predicted cobalamin binding protein [General function prediction only]; Region: COG5012 499177000533 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 499177000534 B12 binding site [chemical binding]; other site 499177000535 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 499177000536 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 499177000537 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 499177000538 dimerization interface [polypeptide binding]; other site 499177000539 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177000540 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177000541 dimer interface [polypeptide binding]; other site 499177000542 putative CheW interface [polypeptide binding]; other site 499177000543 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 499177000544 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177000545 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 499177000546 active site 499177000547 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 499177000548 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177000549 Zn2+ binding site [ion binding]; other site 499177000550 Mg2+ binding site [ion binding]; other site 499177000551 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 499177000552 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 499177000553 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 499177000554 RNA binding surface [nucleotide binding]; other site 499177000555 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 499177000556 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 499177000557 Ligand Binding Site [chemical binding]; other site 499177000558 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 499177000559 EamA-like transporter family; Region: EamA; cl01037 499177000560 EamA-like transporter family; Region: EamA; cl01037 499177000561 CGGC domain; Region: CGGC; cl02356 499177000562 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 499177000563 Ferritin-like domain; Region: Ferritin; pfam00210 499177000564 dimerization interface [polypeptide binding]; other site 499177000565 DPS ferroxidase diiron center [ion binding]; other site 499177000566 ion pore; other site 499177000567 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 499177000568 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 499177000569 dimer interface [polypeptide binding]; other site 499177000570 active site 499177000571 metal binding site [ion binding]; metal-binding site 499177000572 glutathione binding site [chemical binding]; other site 499177000573 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]; Region: COG3880 499177000574 UvrB/uvrC motif; Region: UVR; pfam02151 499177000575 ATP:guanido phosphotransferase; Provisional; Region: PRK01059 499177000576 Phosphagen (guanidino) kinases found in bacteria; Region: bacterial_phosphagen_kinase; cd07930 499177000577 ADP binding site [chemical binding]; other site 499177000578 phosphagen binding site; other site 499177000579 substrate specificity loop; other site 499177000580 Clp protease ATP binding subunit; Region: clpC; CHL00095 499177000581 Clp amino terminal domain; Region: Clp_N; pfam02861 499177000582 Clp amino terminal domain; Region: Clp_N; pfam02861 499177000583 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 499177000584 Walker A motif; other site 499177000585 ATP binding site [chemical binding]; other site 499177000586 Walker B motif; other site 499177000587 arginine finger; other site 499177000588 UvrB/uvrC motif; Region: UVR; pfam02151 499177000589 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 499177000590 Walker A motif; other site 499177000591 ATP binding site [chemical binding]; other site 499177000592 Walker B motif; other site 499177000593 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 499177000594 DNA repair protein RadA; Provisional; Region: PRK11823 499177000595 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 499177000596 Walker A motif/ATP binding site; other site 499177000597 ATP binding site [chemical binding]; other site 499177000598 Walker B motif; other site 499177000599 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 499177000600 Integral membrane protein (PIN domain superfamily) [General function prediction only]; Region: COG4956 499177000601 PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs; Region: PIN_YacL; cd09877 499177000602 putative active site [active] 499177000603 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 499177000604 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 499177000605 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 499177000606 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 499177000607 ligand binding site [chemical binding]; other site 499177000608 flexible hinge region; other site 499177000609 multifunctional aminopeptidase A; Provisional; Region: PRK00913 499177000610 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 499177000611 interface (dimer of trimers) [polypeptide binding]; other site 499177000612 Substrate-binding/catalytic site; other site 499177000613 Zn-binding sites [ion binding]; other site 499177000614 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 499177000615 5S rRNA interface [nucleotide binding]; other site 499177000616 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 499177000617 CTC domain interface [polypeptide binding]; other site 499177000618 L16 interface [polypeptide binding]; other site 499177000619 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 499177000620 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 499177000621 homodimer interface [polypeptide binding]; other site 499177000622 substrate-cofactor binding pocket; other site 499177000623 catalytic residue [active] 499177000624 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 499177000625 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177000626 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 499177000627 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 499177000628 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 499177000629 Walker A motif; other site 499177000630 ATP binding site [chemical binding]; other site 499177000631 Walker B motif; other site 499177000632 arginine finger; other site 499177000633 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 499177000634 Walker A motif; other site 499177000635 ATP binding site [chemical binding]; other site 499177000636 Walker B motif; other site 499177000637 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 499177000638 trehalose synthase; Region: treS_nterm; TIGR02456 499177000639 Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac2_AmyA; cd11316 499177000640 Ca binding site [ion binding]; other site 499177000641 active site 499177000642 catalytic site [active] 499177000643 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 499177000644 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000645 Walker A/P-loop; other site 499177000646 ATP binding site [chemical binding]; other site 499177000647 Q-loop/lid; other site 499177000648 ABC transporter signature motif; other site 499177000649 Walker B; other site 499177000650 D-loop; other site 499177000651 H-loop/switch region; other site 499177000652 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177000653 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177000654 dimer interface [polypeptide binding]; other site 499177000655 putative CheW interface [polypeptide binding]; other site 499177000656 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 499177000657 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 499177000658 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 499177000659 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 499177000660 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 499177000661 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 499177000662 active site 499177000663 Zn binding site [ion binding]; other site 499177000664 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 499177000665 ApbE family; Region: ApbE; cl00643 499177000666 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 499177000667 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 499177000668 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 499177000669 Walker A motif; other site 499177000670 ATP binding site [chemical binding]; other site 499177000671 Walker B motif; other site 499177000672 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 499177000673 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 499177000674 Walker A motif; other site 499177000675 ATP binding site [chemical binding]; other site 499177000676 Walker B motif; other site 499177000677 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 499177000678 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 499177000679 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 499177000680 PilX N-terminal; Region: PilX_N; pfam14341 499177000681 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 499177000682 metal ion-dependent adhesion site (MIDAS); other site 499177000683 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 499177000684 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 499177000685 Cupin domain; Region: Cupin_2; cl09118 499177000686 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 499177000687 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177000688 NAD(P) binding site [chemical binding]; other site 499177000689 active site 499177000690 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK06130 499177000691 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177000692 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 499177000693 Putative cyclase; Region: Cyclase; cl00814 499177000694 Putative cyclase; Region: Cyclase; cl00814 499177000695 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl15827 499177000696 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 499177000697 PAS domain; Region: PAS_9; pfam13426 499177000698 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 499177000699 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 499177000700 Walker A motif; other site 499177000701 ATP binding site [chemical binding]; other site 499177000702 Walker B motif; other site 499177000703 arginine finger; other site 499177000704 Helix-turn-helix domains; Region: HTH; cl00088 499177000705 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177000706 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 499177000707 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 499177000708 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 499177000709 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 499177000710 dimer interface [polypeptide binding]; other site 499177000711 PYR/PP interface [polypeptide binding]; other site 499177000712 TPP binding site [chemical binding]; other site 499177000713 substrate binding site [chemical binding]; other site 499177000714 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 499177000715 TPP-binding site; other site 499177000716 4Fe-4S binding domain; Region: Fer4; cl02805 499177000717 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 499177000718 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 499177000719 Acetokinase family; Region: Acetate_kinase; cl01029 499177000720 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 499177000721 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000722 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 499177000723 N-acetyl-D-glucosamine binding site [chemical binding]; other site 499177000724 catalytic residue [active] 499177000725 Protein of unknown function (DUF1343); Region: DUF1343; cl01598 499177000726 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 499177000727 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 499177000728 Walker A/P-loop; other site 499177000729 ATP binding site [chemical binding]; other site 499177000730 Q-loop/lid; other site 499177000731 ABC transporter signature motif; other site 499177000732 Walker B; other site 499177000733 D-loop; other site 499177000734 H-loop/switch region; other site 499177000735 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 499177000736 FtsX-like permease family; Region: FtsX; cl15850 499177000737 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 499177000738 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 499177000739 FtsX-like permease family; Region: FtsX; cl15850 499177000740 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 499177000741 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 499177000742 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 499177000743 FtsH Extracellular; Region: FtsH_ext; pfam06480 499177000744 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 499177000745 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 499177000746 Walker A motif; other site 499177000747 ATP binding site [chemical binding]; other site 499177000748 Walker B motif; other site 499177000749 arginine finger; other site 499177000750 Peptidase family M41; Region: Peptidase_M41; pfam01434 499177000751 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 499177000752 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 499177000753 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000754 DEAD_2; Region: DEAD_2; pfam06733 499177000755 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000756 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 499177000757 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 499177000758 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 499177000759 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 499177000760 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 499177000761 putative active site [active] 499177000762 putative metal binding site [ion binding]; other site 499177000763 Repair protein; Region: Repair_PSII; cl01535 499177000764 LemA family; Region: LemA; cl00742 499177000765 helicase-exonuclease AddAB, AddB subunit; Region: addB_Gpos; TIGR02773 499177000766 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 499177000767 helicase-exonuclease AddAB, AddA subunit, Firmicutes type; Region: addA_Gpos; TIGR02785 499177000768 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000769 Family description; Region: UvrD_C_2; cl15862 499177000770 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 499177000771 Uncharacterized protein, DegV family COG1307; Region: DegV; cl00577 499177000772 Protein of unknown function (DUF819); Region: DUF819; cl02317 499177000773 Domain of unknown function (DUF3870); Region: DUF3870; pfam12986 499177000774 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 499177000775 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 499177000776 active site 499177000777 hybrid cluster protein; Provisional; Region: PRK05290 499177000778 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 499177000779 ACS interaction site; other site 499177000780 CODH interaction site; other site 499177000781 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 499177000782 hybrid metal cluster; other site 499177000783 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 499177000784 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177000785 Coenzyme A binding pocket [chemical binding]; other site 499177000786 Predicted amidohydrolase [General function prediction only]; Region: COG0388 499177000787 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 499177000788 putative active site [active] 499177000789 catalytic triad [active] 499177000790 putative dimer interface [polypeptide binding]; other site 499177000791 QueT transporter; Region: QueT; cl01932 499177000792 Cache domain; Region: Cache_1; pfam02743 499177000793 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 499177000794 dimerization interface [polypeptide binding]; other site 499177000795 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177000796 dimer interface [polypeptide binding]; other site 499177000797 putative CheW interface [polypeptide binding]; other site 499177000798 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; cl00581 499177000799 Major Facilitator Superfamily; Region: MFS_1; pfam07690 499177000800 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 499177000801 putative substrate translocation pore; other site 499177000802 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 499177000803 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 499177000804 active site 499177000805 phosphorylation site [posttranslational modification] 499177000806 intermolecular recognition site; other site 499177000807 dimerization interface [polypeptide binding]; other site 499177000808 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 499177000809 DNA binding site [nucleotide binding] 499177000810 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 499177000811 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 499177000812 dimerization interface [polypeptide binding]; other site 499177000813 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 499177000814 dimer interface [polypeptide binding]; other site 499177000815 phosphorylation site [posttranslational modification] 499177000816 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 499177000817 ATP binding site [chemical binding]; other site 499177000818 Mg2+ binding site [ion binding]; other site 499177000819 G-X-G motif; other site 499177000820 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduU-EutS; cd07046 499177000821 putative hexamer interface [polypeptide binding]; other site 499177000822 putative hexagonal pore; other site 499177000823 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177000824 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 499177000825 G1 box; other site 499177000826 GTP/Mg2+ binding site [chemical binding]; other site 499177000827 G2 box; other site 499177000828 G3 box; other site 499177000829 Switch II region; other site 499177000830 G4 box; other site 499177000831 G5 box; other site 499177000832 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 499177000833 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 499177000834 active site 499177000835 phosphorylation site [posttranslational modification] 499177000836 intermolecular recognition site; other site 499177000837 dimerization interface [polypeptide binding]; other site 499177000838 ANTAR domain; Region: ANTAR; cl04297 499177000839 Signal transduction histidine kinase; Region: H_kinase_N; pfam12282 499177000840 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 499177000841 Histidine kinase; Region: HisKA_2; cl06527 499177000842 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 499177000843 ATP binding site [chemical binding]; other site 499177000844 Mg2+ binding site [ion binding]; other site 499177000845 G-X-G motif; other site 499177000846 reactivating factor for ethanolamine ammonia lyase; Provisional; Region: eutA; PRK10719 499177000847 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 499177000848 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 499177000849 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 499177000850 ethanolamine utilization protein EutL; Provisional; Region: PRK15405 499177000851 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1; Region: BMC_EutL_repeat1; cd07049 499177000852 putative hexamer interface [polypeptide binding]; other site 499177000853 putative hexagonal pore; other site 499177000854 Bacterial Micro-Compartment (BMC) domain; Region: BMC; cl01982 499177000855 Hexamer interface [polypeptide binding]; other site 499177000856 Hexagonal pore residue; other site 499177000857 Carbon dioxide concentrating mechanism/carboxysome shell protein [Secondary metabolites biosynthesis, transport, and catabolism / Energy production and conversion]; Region: CcmK; COG4577 499177000858 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 499177000859 Hexamer interface [polypeptide binding]; other site 499177000860 Hexagonal pore residue; other site 499177000861 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 499177000862 putative catalytic cysteine [active] 499177000863 1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduA; cd07059 499177000864 Hexamer interface [polypeptide binding]; other site 499177000865 Putative hexagonal pore residue; other site 499177000866 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 499177000867 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 499177000868 Propanediol utilisation protein PduL; Region: PduL; pfam06130 499177000869 Propanediol utilisation protein PduL; Region: PduL; pfam06130 499177000870 ethanolamine utilization protein; Region: eut_hyp; TIGR02536 499177000871 Ethanolamine utilisation protein, EutH; Region: EutH; cl01248 499177000872 Ethanolamine utilisation protein EutQ; Region: EutQ; pfam06249 499177000873 Cupin domain; Region: Cupin_2; cl09118 499177000874 ethanolamine utilization protein EutJ; Provisional; Region: PRK15080 499177000875 Cell division protein FtsA; Region: FtsA; cl11496 499177000876 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 499177000877 Hexamer/Pentamer interface [polypeptide binding]; other site 499177000878 central pore; other site 499177000879 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 499177000880 SLBB domain; Region: SLBB; pfam10531 499177000881 4Fe-4S dicluster domain; Region: Fer4_17; pfam13534 499177000882 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 499177000883 ethanolamine utilization protein, PduT homolog; Region: eut_PduT; TIGR02526 499177000884 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1; Region: BMC_PduT_repeat1; cd07053 499177000885 putative hexamer interface [polypeptide binding]; other site 499177000886 putative hexagonal pore; other site 499177000887 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2; Region: BMC_PduT_repeat2; cd07054 499177000888 putative hexamer interface [polypeptide binding]; other site 499177000889 putative hexagonal pore; other site 499177000890 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 499177000891 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 499177000892 active site 499177000893 HIGH motif; other site 499177000894 dimer interface [polypeptide binding]; other site 499177000895 KMSKS motif; other site 499177000896 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 499177000897 RNA binding surface [nucleotide binding]; other site 499177000898 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 499177000899 Transporter associated domain; Region: CorC_HlyC; cl08393 499177000900 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 499177000901 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 499177000902 G1 box; other site 499177000903 GTP/Mg2+ binding site [chemical binding]; other site 499177000904 Switch I region; other site 499177000905 G2 box; other site 499177000906 G3 box; other site 499177000907 Switch II region; other site 499177000908 G4 box; other site 499177000909 G5 box; other site 499177000910 Nucleoside recognition; Region: Gate; cl00486 499177000911 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 499177000912 Nucleoside recognition; Region: Gate; cl00486 499177000913 FeoA domain; Region: FeoA; cl00838 499177000914 FeoA domain; Region: FeoA; cl00838 499177000915 Cobalt chelatase (CbiK); Region: CbiK; pfam06180 499177000916 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_N; cd03412 499177000917 active site 499177000918 C-terminal domain interface [polypeptide binding]; other site 499177000919 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_C; cd03413 499177000920 active site 499177000921 N-terminal domain interface [polypeptide binding]; other site 499177000922 Cobalt transport protein; Region: CbiQ; cl00463 499177000923 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13638 499177000924 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 499177000925 Walker A/P-loop; other site 499177000926 ATP binding site [chemical binding]; other site 499177000927 Q-loop/lid; other site 499177000928 ABC transporter signature motif; other site 499177000929 Walker B; other site 499177000930 D-loop; other site 499177000931 H-loop/switch region; other site 499177000932 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 499177000933 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 499177000934 Ligand Binding Site [chemical binding]; other site 499177000935 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 499177000936 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 499177000937 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177000938 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 499177000939 dihydroorotase; Validated; Region: pyrC; PRK09357 499177000940 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 499177000941 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 499177000942 active site 499177000943 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 499177000944 active site 499177000945 dimer interface [polypeptide binding]; other site 499177000946 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 499177000947 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 499177000948 FAD binding pocket [chemical binding]; other site 499177000949 FAD binding motif [chemical binding]; other site 499177000950 phosphate binding motif [ion binding]; other site 499177000951 beta-alpha-beta structure motif; other site 499177000952 NAD binding pocket [chemical binding]; other site 499177000953 Iron coordination center [ion binding]; other site 499177000954 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 499177000955 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine...; Region: DHOD_1B_like; cd04740 499177000956 heterodimer interface [polypeptide binding]; other site 499177000957 active site 499177000958 FMN binding site [chemical binding]; other site 499177000959 homodimer interface [polypeptide binding]; other site 499177000960 substrate binding site [chemical binding]; other site 499177000961 orotate phosphoribosyltransferase; Validated; Region: pyrE; PRK00455 499177000962 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177000963 active site 499177000964 Transposase; Region: DEDD_Tnp_IS110; pfam01548 499177000965 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 499177000966 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 499177000967 metal-binding site [ion binding] 499177000968 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 499177000969 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 499177000970 active site 499177000971 metal binding site [ion binding]; metal-binding site 499177000972 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 499177000973 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 499177000974 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 499177000975 putative dimer interface [polypeptide binding]; other site 499177000976 active site pocket [active] 499177000977 putative cataytic base [active] 499177000978 8-oxoguanine DNA glycosylase, N-terminal domain; Region: OGG_N; pfam07934 499177000979 8-oxoguanine DNA-glycosylase (ogg); Region: ogg; TIGR00588 499177000980 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 499177000981 minor groove reading motif; other site 499177000982 helix-hairpin-helix signature motif; other site 499177000983 substrate binding pocket [chemical binding]; other site 499177000984 active site 499177000985 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 499177000986 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 499177000987 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 499177000988 putative active site [active] 499177000989 catalytic site [active] 499177000990 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 499177000991 putative active site [active] 499177000992 catalytic site [active] 499177000993 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 499177000994 oligomerisation interface [polypeptide binding]; other site 499177000995 mobile loop; other site 499177000996 roof hairpin; other site 499177000997 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 499177000998 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 499177000999 ring oligomerisation interface [polypeptide binding]; other site 499177001000 ATP/Mg binding site [chemical binding]; other site 499177001001 stacking interactions; other site 499177001002 hinge regions; other site 499177001003 NCAIR mutase (PurE)-related proteins [General function prediction only]; Region: COG1691 499177001004 AIR carboxylase; Region: AIRC; cl00310 499177001005 Protein of unknown function DUF111; Region: DUF111; cl03398 499177001006 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 499177001007 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 499177001008 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 499177001009 active site 499177001010 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 499177001011 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 499177001012 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and...; Region: ABCC_Glucan_exporter_like; cd03254 499177001013 Walker A/P-loop; other site 499177001014 ATP binding site [chemical binding]; other site 499177001015 Q-loop/lid; other site 499177001016 ABC transporter signature motif; other site 499177001017 Walker B; other site 499177001018 D-loop; other site 499177001019 H-loop/switch region; other site 499177001020 potential frameshift: common BLAST hit: gi|307723928|ref|YP_003903679.1| ABC transporter 499177001021 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177001022 H-loop/switch region; other site 499177001023 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 499177001024 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a...; Region: ABCC_MRP_Like; cd03228 499177001025 Walker A/P-loop; other site 499177001026 ATP binding site [chemical binding]; other site 499177001027 Q-loop/lid; other site 499177001028 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 499177001029 MatE; Region: MatE; cl10513 499177001030 MatE; Region: MatE; cl10513 499177001031 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 499177001032 FeS/SAM binding site; other site 499177001033 Radical SAM superfamily; Region: Radical_SAM; pfam04055 499177001034 B3/4 domain; Region: B3_4; cl11458 499177001035 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 499177001036 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 499177001037 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 499177001038 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 499177001039 active site 499177001040 GMP synthase; Reviewed; Region: guaA; PRK00074 499177001041 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 499177001042 AMP/PPi binding site [chemical binding]; other site 499177001043 candidate oxyanion hole; other site 499177001044 catalytic triad [active] 499177001045 potential glutamine specificity residues [chemical binding]; other site 499177001046 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 499177001047 ATP Binding subdomain [chemical binding]; other site 499177001048 Ligand Binding sites [chemical binding]; other site 499177001049 Dimerization subdomain; other site 499177001050 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 499177001051 non-specific DNA binding site [nucleotide binding]; other site 499177001052 salt bridge; other site 499177001053 sequence-specific DNA binding site [nucleotide binding]; other site 499177001054 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 499177001055 integrase; Provisional; Region: int; PHA02601 499177001056 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 499177001057 Int/Topo IB signature motif; other site 499177001058 Uncharacterized conserved protein [Function unknown]; Region: COG4983 499177001059 Virulence-associated protein E; Region: VirE; pfam05272 499177001060 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 499177001061 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 499177001062 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 499177001063 cofactor binding site; other site 499177001064 DNA binding site [nucleotide binding] 499177001065 substrate interaction site [chemical binding]; other site 499177001066 Restriction endonuclease BpuJI - N terminal; Region: BpuJI_N; pfam11564 499177001067 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 499177001068 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 499177001069 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 499177001070 cofactor binding site; other site 499177001071 DNA binding site [nucleotide binding] 499177001072 substrate interaction site [chemical binding]; other site 499177001073 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 499177001074 Divergent AAA domain; Region: AAA_4; pfam04326 499177001075 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 499177001076 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 499177001077 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 499177001078 MatE; Region: MatE; cl10513 499177001079 MatE; Region: MatE; cl10513 499177001080 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK14869 499177001081 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 499177001082 DRTGG domain; Region: DRTGG; cl12147 499177001083 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 499177001084 DHH family; Region: DHH; pfam01368 499177001085 DHHA2 domain; Region: DHHA2; pfam02833 499177001086 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 499177001087 LemA family; Region: LemA; cl00742 499177001088 Predicted membrane protein (DUF2207); Region: DUF2207; pfam09972 499177001089 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177001090 Coenzyme A binding pocket [chemical binding]; other site 499177001091 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 499177001092 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 499177001093 P-loop; other site 499177001094 Magnesium ion binding site [ion binding]; other site 499177001095 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 499177001096 Magnesium ion binding site [ion binding]; other site 499177001097 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177001098 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177001099 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 499177001100 intracellular protease, PfpI family; Region: PfpI; TIGR01382 499177001101 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 499177001102 proposed catalytic triad [active] 499177001103 conserved cys residue [active] 499177001104 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 499177001105 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 499177001106 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 499177001107 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177001108 dimer interface [polypeptide binding]; other site 499177001109 putative CheW interface [polypeptide binding]; other site 499177001110 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 499177001111 AIR carboxylase; Region: AIRC; cl00310 499177001112 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 499177001113 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 499177001114 ATP binding site [chemical binding]; other site 499177001115 active site 499177001116 substrate binding site [chemical binding]; other site 499177001117 amidophosphoribosyltransferase; Provisional; Region: PRK05793 499177001118 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 499177001119 active site 499177001120 tetramer interface [polypeptide binding]; other site 499177001121 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177001122 active site 499177001123 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 499177001124 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 499177001125 dimerization interface [polypeptide binding]; other site 499177001126 putative ATP binding site [chemical binding]; other site 499177001127 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 499177001128 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 499177001129 active site 499177001130 substrate binding site [chemical binding]; other site 499177001131 cosubstrate binding site; other site 499177001132 catalytic site [active] 499177001133 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 499177001134 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 499177001135 purine monophosphate binding site [chemical binding]; other site 499177001136 dimer interface [polypeptide binding]; other site 499177001137 putative catalytic residues [active] 499177001138 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 499177001139 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 499177001140 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 499177001141 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177001142 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 499177001143 phosphoribosylformylglycinamidine synthase, clade II; Region: FGAM-synthase; TIGR01857 499177001144 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 499177001145 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 499177001146 dimerization interface [polypeptide binding]; other site 499177001147 ATP binding site [chemical binding]; other site 499177001148 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 499177001149 dimerization interface [polypeptide binding]; other site 499177001150 ATP binding site [chemical binding]; other site 499177001151 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 499177001152 putative active site [active] 499177001153 catalytic triad [active] 499177001154 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177001155 dimer interface [polypeptide binding]; other site 499177001156 putative CheW interface [polypeptide binding]; other site 499177001157 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 499177001158 Cache domain; Region: Cache_1; pfam02743 499177001159 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 499177001160 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 499177001161 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 499177001162 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 499177001163 IHF dimer interface [polypeptide binding]; other site 499177001164 IHF - DNA interface [nucleotide binding]; other site 499177001165 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 499177001166 Septum formation initiator; Region: DivIC; cl11433 499177001167 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 499177001168 Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor...; Region: IPT; cd00102 499177001169 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 499177001170 Interdomain contacts; other site 499177001171 Cytokine receptor motif; other site 499177001172 S-layer homology domain; Region: SLH; pfam00395 499177001173 S-layer homology domain; Region: SLH; pfam00395 499177001174 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 499177001175 C-terminal peptidase (prc); Region: prc; TIGR00225 499177001176 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 499177001177 protein binding site [polypeptide binding]; other site 499177001178 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 499177001179 Catalytic dyad [active] 499177001180 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177001181 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177001182 Outer membrane efflux protein; Region: OEP; pfam02321 499177001183 Chain length determinant protein; Region: Wzz; cl15801 499177001184 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 499177001185 Bacterial sugar transferase; Region: Bac_transf; cl00939 499177001186 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 499177001187 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 499177001188 active site 499177001189 dimer interface [polypeptide binding]; other site 499177001190 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 499177001191 Ligand Binding Site [chemical binding]; other site 499177001192 Molecular Tunnel; other site 499177001193 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 499177001194 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 499177001195 NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family; Region: EDH_00030; TIGR04180 499177001196 NAD binding site [chemical binding]; other site 499177001197 substrate binding site [chemical binding]; other site 499177001198 active site 499177001199 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_III; cd01996 499177001200 Ligand Binding Site [chemical binding]; other site 499177001201 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 499177001202 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 499177001203 inhibitor-cofactor binding pocket; inhibition site 499177001204 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177001205 catalytic residue [active] 499177001206 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 499177001207 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_2; cd06426 499177001208 Substrate binding site; other site 499177001209 metal-binding site 499177001210 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 499177001211 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 499177001212 putative trimer interface [polypeptide binding]; other site 499177001213 putative CoA binding site [chemical binding]; other site 499177001214 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 499177001215 NeuB family; Region: NeuB; cl00496 499177001216 SAF domain; Region: SAF; cl00555 499177001217 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 499177001218 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 499177001219 active site 499177001220 homodimer interface [polypeptide binding]; other site 499177001221 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 499177001222 ligand binding site; other site 499177001223 tetramer interface; other site 499177001224 integral membrane protein MviN; Region: mviN; TIGR01695 499177001225 haloacid dehalogenase-like hydrolase family protein; Region: PLN02919 499177001226 PQQ-like domain; Region: PQQ_2; pfam13360 499177001227 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 499177001228 ligand binding site [chemical binding]; other site 499177001229 flexible hinge region; other site 499177001230 Helix-turn-helix domains; Region: HTH; cl00088 499177001231 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 499177001232 ligand binding site [chemical binding]; other site 499177001233 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 499177001234 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 499177001235 Walker A/P-loop; other site 499177001236 ATP binding site [chemical binding]; other site 499177001237 Q-loop/lid; other site 499177001238 ABC transporter signature motif; other site 499177001239 Walker B; other site 499177001240 D-loop; other site 499177001241 H-loop/switch region; other site 499177001242 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 499177001243 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 499177001244 TM-ABC transporter signature motif; other site 499177001245 potential frameshift: common BLAST hit: gi|158321398|ref|YP_001513905.1| inner-membrane translocator 499177001246 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 499177001247 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 499177001248 TM-ABC transporter signature motif; other site 499177001249 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 499177001250 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177001251 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177001252 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 499177001253 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 499177001254 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 499177001255 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177001256 Hsp70 protein; Region: HSP70; pfam00012 499177001257 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 499177001258 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 499177001259 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 499177001260 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 499177001261 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 499177001262 intersubunit interface [polypeptide binding]; other site 499177001263 active site 499177001264 Zn2+ binding site [ion binding]; other site 499177001265 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 499177001266 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 499177001267 non-specific DNA binding site [nucleotide binding]; other site 499177001268 salt bridge; other site 499177001269 sequence-specific DNA binding site [nucleotide binding]; other site 499177001270 Cupin domain; Region: Cupin_2; cl09118 499177001271 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 499177001272 amino acid/peptide transporter (Peptide:H+ symporter), bacterial; Region: yjdL_sub1_fam; TIGR00924 499177001273 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 499177001274 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 499177001275 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 499177001276 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 499177001277 active site 499177001278 Protein of unknown function (DUF975); Region: DUF975; cl10504 499177001279 threonine dehydratase; Provisional; Region: PRK08198 499177001280 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 499177001281 tetramer interface [polypeptide binding]; other site 499177001282 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177001283 catalytic residue [active] 499177001284 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 499177001285 L-type amino acid transporter; Region: 2A0308; TIGR00911 499177001286 Spore germination protein; Region: Spore_permease; cl15802 499177001287 Spore germination protein; Region: Spore_permease; cl15802 499177001288 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 499177001289 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 499177001290 Predicted cobalamin binding protein [General function prediction only]; Region: COG5012 499177001291 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 499177001292 B12 binding site [chemical binding]; other site 499177001293 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177001294 metal binding site [ion binding]; metal-binding site 499177001295 active site 499177001296 I-site; other site 499177001297 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 499177001298 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage...; Region: Peptidase_C39_like; cl00296 499177001299 putative active site [active] 499177001300 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 499177001301 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177001302 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 499177001303 NAD(P) binding site [chemical binding]; other site 499177001304 homodimer interface [polypeptide binding]; other site 499177001305 substrate binding site [chemical binding]; other site 499177001306 active site 499177001307 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177001308 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 499177001309 Cache domain; Region: Cache_1; pfam02743 499177001310 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 499177001311 dimerization interface [polypeptide binding]; other site 499177001312 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177001313 Zn2+ binding site [ion binding]; other site 499177001314 Mg2+ binding site [ion binding]; other site 499177001315 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 499177001316 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 499177001317 substrate binding pocket [chemical binding]; other site 499177001318 membrane-bound complex binding site; other site 499177001319 hinge residues; other site 499177001320 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177001321 metal binding site [ion binding]; metal-binding site 499177001322 active site 499177001323 I-site; other site 499177001324 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177001325 Zn2+ binding site [ion binding]; other site 499177001326 Mg2+ binding site [ion binding]; other site 499177001327 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 499177001328 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177001329 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177001330 dimer interface [polypeptide binding]; other site 499177001331 putative CheW interface [polypeptide binding]; other site 499177001332 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 499177001333 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177001334 dimer interface [polypeptide binding]; other site 499177001335 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177001336 putative CheW interface [polypeptide binding]; other site 499177001337 CsbD-like; Region: CsbD; cl15799 499177001338 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 499177001339 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 499177001340 substrate binding site; other site 499177001341 tetramer interface; other site 499177001342 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 499177001343 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 499177001344 catalytic motif [active] 499177001345 Zn binding site [ion binding]; other site 499177001346 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 499177001347 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 499177001348 Lumazine binding domain; Region: Lum_binding; pfam00677 499177001349 Lumazine binding domain; Region: Lum_binding; pfam00677 499177001350 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 499177001351 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 499177001352 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 499177001353 dimerization interface [polypeptide binding]; other site 499177001354 active site 499177001355 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 499177001356 homopentamer interface [polypeptide binding]; other site 499177001357 active site 499177001358 2-isopropylmalate synthase; Validated; Region: PRK03739 499177001359 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 499177001360 active site 499177001361 catalytic residues [active] 499177001362 metal binding site [ion binding]; metal-binding site 499177001363 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 499177001364 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 499177001365 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 499177001366 substrate binding site [chemical binding]; other site 499177001367 ligand binding site [chemical binding]; other site 499177001368 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 499177001369 substrate binding site [chemical binding]; other site 499177001370 tartrate dehydrogenase; Provisional; Region: PRK08194 499177001371 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 499177001372 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 499177001373 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 499177001374 dimer interface [polypeptide binding]; other site 499177001375 active site 499177001376 glycine-pyridoxal phosphate binding site [chemical binding]; other site 499177001377 folate binding site [chemical binding]; other site 499177001378 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 499177001379 Helix-turn-helix domains; Region: HTH; cl00088 499177001380 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 499177001381 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 499177001382 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 499177001383 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 499177001384 ABC-2 type transporter; Region: ABC2_membrane; cl11417 499177001385 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 499177001386 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 499177001387 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 499177001388 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 499177001389 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 499177001390 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 499177001391 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 499177001392 lipoyl attachment site [posttranslational modification]; other site 499177001393 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 499177001394 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 499177001395 tetramer interface [polypeptide binding]; other site 499177001396 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177001397 catalytic residue [active] 499177001398 Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG1003 499177001399 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 499177001400 tetramer interface [polypeptide binding]; other site 499177001401 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177001402 catalytic residue [active] 499177001403 aspartate aminotransferase; Provisional; Region: PRK06836 499177001404 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 499177001405 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177001406 homodimer interface [polypeptide binding]; other site 499177001407 catalytic residue [active] 499177001408 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 499177001409 elongation factor G; Reviewed; Region: PRK12740 499177001410 G1 box; other site 499177001411 putative GEF interaction site [polypeptide binding]; other site 499177001412 GTP/Mg2+ binding site [chemical binding]; other site 499177001413 Switch I region; other site 499177001414 G2 box; other site 499177001415 G3 box; other site 499177001416 Switch II region; other site 499177001417 G4 box; other site 499177001418 G5 box; other site 499177001419 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 499177001420 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 499177001421 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 499177001422 alkaline phosphatase isozyme conversion aminopeptidase; Provisional; Region: PRK10199 499177001423 M28 Zn-peptidases include aminopeptidases and carboxypeptidases; Region: M28; cd02690 499177001424 metal binding site [ion binding]; metal-binding site 499177001425 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177001426 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 499177001427 diaminopimelate decarboxylase; Region: lysA; TIGR01048 499177001428 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 499177001429 active site 499177001430 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 499177001431 substrate binding site [chemical binding]; other site 499177001432 catalytic residues [active] 499177001433 dimer interface [polypeptide binding]; other site 499177001434 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 499177001435 dTDP-glucose 4,6-dehydratase; Region: dTDP_gluc_dehyt; TIGR01181 499177001436 NAD binding site [chemical binding]; other site 499177001437 substrate binding site [chemical binding]; other site 499177001438 homodimer interface [polypeptide binding]; other site 499177001439 active site 499177001440 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 499177001441 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177001442 DNA binding residues [nucleotide binding] 499177001443 Herpesvirus latent membrane protein 1 (LMP1); Region: Herpes_LMP1; pfam05297 499177001444 TQXA domain; Region: TQXA_dom; TIGR03934 499177001445 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 499177001446 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 499177001447 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177001448 AAA domain; Region: AAA_21; pfam13304 499177001449 Walker A/P-loop; other site 499177001450 ATP binding site [chemical binding]; other site 499177001451 Q-loop/lid; other site 499177001452 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177001453 ABC transporter signature motif; other site 499177001454 Walker B; other site 499177001455 D-loop; other site 499177001456 H-loop/switch region; other site 499177001457 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 499177001458 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 499177001459 trimer interface [polypeptide binding]; other site 499177001460 active site 499177001461 substrate binding site [chemical binding]; other site 499177001462 CoA binding site [chemical binding]; other site 499177001463 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 499177001464 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 499177001465 Ligand binding site; other site 499177001466 Putative Catalytic site; other site 499177001467 DXD motif; other site 499177001468 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177001469 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 499177001470 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 499177001471 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 499177001472 inhibitor-cofactor binding pocket; inhibition site 499177001473 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177001474 catalytic residue [active] 499177001475 Cupin domain; Region: Cupin_2; cl09118 499177001476 GtrA-like protein; Region: GtrA; cl00971 499177001477 G5 domain; Region: G5; pfam07501 499177001478 NlpC/P60 family; Region: NLPC_P60; cl11438 499177001479 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 499177001480 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 499177001481 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 499177001482 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 499177001483 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 499177001484 Walker A/P-loop; other site 499177001485 ATP binding site [chemical binding]; other site 499177001486 Q-loop/lid; other site 499177001487 ABC transporter signature motif; other site 499177001488 Walker B; other site 499177001489 D-loop; other site 499177001490 H-loop/switch region; other site 499177001491 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 499177001492 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 499177001493 FtsX-like permease family; Region: FtsX; cl15850 499177001494 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177001495 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 499177001496 Helix-turn-helix domains; Region: HTH; cl00088 499177001497 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 499177001498 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 499177001499 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 499177001500 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 499177001501 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 499177001502 Protein of unknown function (DUF1659); Region: DUF1659; pfam07872 499177001503 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 499177001504 active site 499177001505 tetramer interface; other site 499177001506 S-layer homology domain; Region: SLH; pfam00395 499177001507 S-layer homology domain; Region: SLH; pfam00395 499177001508 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 499177001509 active site 499177001510 intersubunit interactions; other site 499177001511 catalytic residue [active] 499177001512 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 499177001513 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. 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, reaction...; Region: NAPRTase_A; cd01570 499177001514 active site 499177001515 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 499177001516 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 499177001517 active site 499177001518 HIGH motif; other site 499177001519 KMSKS motif; other site 499177001520 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 499177001521 tRNA binding surface [nucleotide binding]; other site 499177001522 anticodon binding site; other site 499177001523 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 499177001524 dimer interface [polypeptide binding]; other site 499177001525 putative tRNA-binding site [nucleotide binding]; other site 499177001526 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 499177001527 active site 499177001528 ribonuclease M5; Region: 5S_RNA_mat_M5; TIGR00334 499177001529 TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low...; Region: TOPRIM_RNase_M5_like; cd01027 499177001530 putative active site [active] 499177001531 putative metal binding site [ion binding]; other site 499177001532 Domain of unknown function (DUF4093); Region: DUF4093; pfam13331 499177001533 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 499177001534 S-adenosylmethionine binding site [chemical binding]; other site 499177001535 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 499177001536 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 499177001537 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 499177001538 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 499177001539 pur operon repressor; Provisional; Region: PRK09213 499177001540 Bacterial purine repressor, N-terminal; Region: PuR_N; pfam09182 499177001541 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177001542 active site 499177001543 SpoVG; Region: SpoVG; cl00915 499177001544 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14354 499177001545 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 499177001546 Substrate binding site; other site 499177001547 Mg++ binding site; other site 499177001548 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 499177001549 active site 499177001550 substrate binding site [chemical binding]; other site 499177001551 CoA binding site [chemical binding]; other site 499177001552 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 499177001553 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 499177001554 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177001555 active site 499177001556 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 499177001557 putative active site [active] 499177001558 catalytic residue [active] 499177001559 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 499177001560 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 499177001561 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 499177001562 ATP binding site [chemical binding]; other site 499177001563 putative Mg++ binding site [ion binding]; other site 499177001564 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 499177001565 nucleotide binding region [chemical binding]; other site 499177001566 ATP-binding site [chemical binding]; other site 499177001567 TRCF domain; Region: TRCF; cl04088 499177001568 SurA N-terminal domain; Region: SurA_N_3; cl07813 499177001569 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK02998 499177001570 PPIC-type PPIASE domain; Region: Rotamase; cl08278 499177001571 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 499177001572 trimer interface [polypeptide binding]; other site 499177001573 dimer interface [polypeptide binding]; other site 499177001574 putative active site [active] 499177001575 MatE; Region: MatE; cl10513 499177001576 MatE; Region: MatE; cl10513 499177001577 Uncharacterized conserved protein [Function unknown]; Region: COG1624 499177001578 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 499177001579 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4856 499177001580 YbbR-like protein; Region: YbbR; pfam07949 499177001581 Acetokinase family; Region: Acetate_kinase; cl01029 499177001582 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 499177001583 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 499177001584 Acetokinase family; Region: Acetate_kinase; cl01029 499177001585 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 499177001586 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 499177001587 2-ketoisovalerate ferredoxin reductase; Validated; Region: PRK07119 499177001588 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 499177001589 dimer interface [polypeptide binding]; other site 499177001590 PYR/PP interface [polypeptide binding]; other site 499177001591 TPP binding site [chemical binding]; other site 499177001592 substrate binding site [chemical binding]; other site 499177001593 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 499177001594 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; cl01629 499177001595 TPP-binding site [chemical binding]; other site 499177001596 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 499177001597 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 499177001598 Uncharacterized conserved protein [Function unknown]; Region: COG1284 499177001599 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 499177001600 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 499177001601 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 499177001602 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 499177001603 substrate binding pocket [chemical binding]; other site 499177001604 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 499177001605 membrane-bound complex binding site; other site 499177001606 hinge residues; other site 499177001607 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 499177001608 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 499177001609 substrate binding pocket [chemical binding]; other site 499177001610 membrane-bound complex binding site; other site 499177001611 hinge residues; other site 499177001612 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177001613 metal binding site [ion binding]; metal-binding site 499177001614 active site 499177001615 I-site; other site 499177001616 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14316 499177001617 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 499177001618 active site 499177001619 substrate binding site [chemical binding]; other site 499177001620 metal binding site [ion binding]; metal-binding site 499177001621 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 499177001622 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 499177001623 glutaminase active site [active] 499177001624 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 499177001625 dimer interface [polypeptide binding]; other site 499177001626 active site 499177001627 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 499177001628 dimer interface [polypeptide binding]; other site 499177001629 active site 499177001630 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177001631 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 499177001632 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177001633 Zn2+ binding site [ion binding]; other site 499177001634 Mg2+ binding site [ion binding]; other site 499177001635 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 499177001636 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 499177001637 Nitrogen regulatory protein P-II; Region: P-II; cl00412 499177001638 Nitrogen regulatory protein P-II; Region: P-II; smart00938 499177001639 Heat induced stress protein YflT; Region: YflT; pfam11181 499177001640 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 499177001641 FAD dependent oxidoreductase; Region: DAO; pfam01266 499177001642 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177001643 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 499177001644 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 499177001645 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177001646 catalytic residue [active] 499177001647 excinuclease ABC subunit B; Provisional; Region: PRK05298 499177001648 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 499177001649 ATP binding site [chemical binding]; other site 499177001650 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 499177001651 nucleotide binding region [chemical binding]; other site 499177001652 ATP-binding site [chemical binding]; other site 499177001653 Ultra-violet resistance protein B; Region: UvrB; pfam12344 499177001654 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 499177001655 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 499177001656 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 499177001657 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 499177001658 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 499177001659 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 499177001660 active site 499177001661 phosphorylation site [posttranslational modification] 499177001662 intermolecular recognition site; other site 499177001663 dimerization interface [polypeptide binding]; other site 499177001664 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 499177001665 DNA binding residues [nucleotide binding] 499177001666 dimerization interface [polypeptide binding]; other site 499177001667 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 499177001668 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 499177001669 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 499177001670 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177001671 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 499177001672 DNA-binding site [nucleotide binding]; DNA binding site 499177001673 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 499177001674 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 499177001675 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 499177001676 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 499177001677 active site 499177001678 phosphorylation site [posttranslational modification] 499177001679 intermolecular recognition site; other site 499177001680 dimerization interface [polypeptide binding]; other site 499177001681 LytTr DNA-binding domain; Region: LytTR; cl04498 499177001682 S-layer homology domain; Region: SLH; pfam00395 499177001683 S-layer homology domain; Region: SLH; pfam00395 499177001684 S-layer homology domain; Region: SLH; pfam00395 499177001685 Domain of unknown function (DUF4353); Region: DUF4353; pfam14262 499177001686 S-layer homology domain; Region: SLH; pfam00395 499177001687 S-layer homology domain; Region: SLH; pfam00395 499177001688 S-layer homology domain; Region: SLH; pfam00395 499177001689 S-layer homology domain; Region: SLH; pfam00395 499177001690 S-layer homology domain; Region: SLH; pfam00395 499177001691 S-layer homology domain; Region: SLH; pfam00395 499177001692 ATP phosphoribosyltransferase; Region: HisG; cl15266 499177001693 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 499177001694 histidinol dehydrogenase; Region: hisD; TIGR00069 499177001695 NAD binding site [chemical binding]; other site 499177001696 dimerization interface [polypeptide binding]; other site 499177001697 product binding site; other site 499177001698 substrate binding site [chemical binding]; other site 499177001699 zinc binding site [ion binding]; other site 499177001700 catalytic residues [active] 499177001701 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 499177001702 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 499177001703 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177001704 homodimer interface [polypeptide binding]; other site 499177001705 catalytic residue [active] 499177001706 imidazoleglycerol-phosphate dehydratase; Validated; Region: hisB; PRK00951 499177001707 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 499177001708 putative active site pocket [active] 499177001709 4-fold oligomerization interface [polypeptide binding]; other site 499177001710 metal binding residues [ion binding]; metal-binding site 499177001711 3-fold/trimer interface [polypeptide binding]; other site 499177001712 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 499177001713 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 499177001714 putative active site [active] 499177001715 oxyanion strand; other site 499177001716 catalytic triad [active] 499177001717 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 499177001718 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 499177001719 catalytic residues [active] 499177001720 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 499177001721 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 499177001722 substrate binding site [chemical binding]; other site 499177001723 glutamase interaction surface [polypeptide binding]; other site 499177001724 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 499177001725 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 499177001726 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 499177001727 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 499177001728 Catalytic site [active] 499177001729 Uncharacterized protein family (UPF0014); Region: UPF0014; cl00424 499177001730 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177001731 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 499177001732 Walker A/P-loop; other site 499177001733 ATP binding site [chemical binding]; other site 499177001734 Q-loop/lid; other site 499177001735 ABC transporter signature motif; other site 499177001736 Walker B; other site 499177001737 D-loop; other site 499177001738 H-loop/switch region; other site 499177001739 Helix-turn-helix domains; Region: HTH; cl00088 499177001740 EamA-like transporter family; Region: EamA; cl01037 499177001741 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14190 499177001742 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 499177001743 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 499177001744 homodimer interface [polypeptide binding]; other site 499177001745 NADP binding site [chemical binding]; other site 499177001746 substrate binding site [chemical binding]; other site 499177001747 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 499177001748 homotrimer interaction site [polypeptide binding]; other site 499177001749 putative active site [active] 499177001750 putative oxidoreductase; Provisional; Region: PRK11579 499177001751 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177001752 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 499177001753 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 499177001754 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 499177001755 ligand binding site [chemical binding]; other site 499177001756 CHASE3 domain; Region: CHASE3; cl05000 499177001757 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 499177001758 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 499177001759 Histidine kinase; Region: His_kinase; pfam06580 499177001760 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 499177001761 ATP binding site [chemical binding]; other site 499177001762 Mg2+ binding site [ion binding]; other site 499177001763 G-X-G motif; other site 499177001764 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]; Region: COG4753 499177001765 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 499177001766 active site 499177001767 phosphorylation site [posttranslational modification] 499177001768 intermolecular recognition site; other site 499177001769 dimerization interface [polypeptide binding]; other site 499177001770 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 499177001771 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 499177001772 D-xylose ABC transporter, substrate-binding protein; Region: xylF; TIGR02634 499177001773 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 499177001774 putative ligand binding site [chemical binding]; other site 499177001775 ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: XylF; COG4213 499177001776 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 499177001777 putative ligand binding site [chemical binding]; other site 499177001778 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 499177001779 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 499177001780 Walker A/P-loop; other site 499177001781 ATP binding site [chemical binding]; other site 499177001782 Q-loop/lid; other site 499177001783 ABC transporter signature motif; other site 499177001784 Walker B; other site 499177001785 D-loop; other site 499177001786 H-loop/switch region; other site 499177001787 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 499177001788 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 499177001789 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 499177001790 TM-ABC transporter signature motif; other site 499177001791 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 499177001792 Protein of unknown function (DUF554); Region: DUF554; cl00784 499177001793 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 499177001794 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 499177001795 active site 499177001796 catalytic site [active] 499177001797 putative DNA binding site [nucleotide binding]; other site 499177001798 GIY-YIG motif/motif A; other site 499177001799 metal binding site [ion binding]; metal-binding site 499177001800 UvrB/uvrC motif; Region: UVR; pfam02151 499177001801 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 499177001802 HPr kinase/phosphorylase; Provisional; Region: PRK05428 499177001803 DRTGG domain; Region: DRTGG; cl12147 499177001804 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 499177001805 Hpr binding site; other site 499177001806 active site 499177001807 homohexamer subunit interaction site [polypeptide binding]; other site 499177001808 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 499177001809 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 499177001810 Domain of unknown function (DUF3786); Region: DUF3786; pfam12654 499177001811 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 499177001812 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 499177001813 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 499177001814 tRNA CCA-pyrophosphorylase; Provisional; Region: PRK13299 499177001815 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 499177001816 active site 499177001817 NTP binding site [chemical binding]; other site 499177001818 metal binding triad [ion binding]; metal-binding site 499177001819 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 499177001820 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177001821 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177001822 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 499177001823 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 499177001824 active site 499177001825 nucleophile elbow; other site 499177001826 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 499177001827 FMN binding site [chemical binding]; other site 499177001828 dimer interface [polypeptide binding]; other site 499177001829 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 499177001830 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 499177001831 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177001832 Family description; Region: UvrD_C_2; cl15862 499177001833 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 499177001834 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 499177001835 active site 499177001836 metal binding site [ion binding]; metal-binding site 499177001837 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 499177001838 active site 499177001839 metal binding site [ion binding]; metal-binding site 499177001840 DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]; Region: DnrI; COG3629 499177001841 Helix-turn-helix domains; Region: HTH; cl00088 499177001842 Fibronectin type III-like domain; Region: Fn3-like; cl15273 499177001843 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 499177001844 metal ion-dependent adhesion site (MIDAS); other site 499177001845 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 499177001846 Catalytic site [active] 499177001847 Camelysin metallo-endopeptidase; Region: Peptidase_M73; cl13780 499177001848 alternate signal-mediated exported protein, CPF_0494 family; Region: exp_by_SipW_IV; TIGR04090 499177001849 Gram positive anchor; Region: Gram_pos_anchor; cl15427 499177001850 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177001851 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 499177001852 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 499177001853 metal-binding site [ion binding] 499177001854 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 499177001855 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 499177001856 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 499177001857 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 499177001858 dimerization interface [polypeptide binding]; other site 499177001859 putative DNA binding site [nucleotide binding]; other site 499177001860 putative Zn2+ binding site [ion binding]; other site 499177001861 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 499177001862 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 499177001863 active site 499177001864 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 499177001865 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177001866 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 499177001867 Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar...; Region: RHOD_Pyr_redox; cd01524 499177001868 active site residue [active] 499177001869 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; cl00436 499177001870 CPxP motif; other site 499177001871 DsrE/DsrF-like family; Region: DrsE; cl00672 499177001872 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 499177001873 dimerization interface [polypeptide binding]; other site 499177001874 putative DNA binding site [nucleotide binding]; other site 499177001875 putative Zn2+ binding site [ion binding]; other site 499177001876 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 499177001877 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 499177001878 tetramer interface [polypeptide binding]; other site 499177001879 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177001880 catalytic residue [active] 499177001881 putative lipid kinase; Reviewed; Region: PRK13059 499177001882 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 499177001883 active site 499177001884 ATP binding site [chemical binding]; other site 499177001885 substrate binding site [chemical binding]; other site 499177001886 activation loop (A-loop); other site 499177001887 Predicted ATPase [General function prediction only]; Region: COG3899 499177001888 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177001889 metal binding site [ion binding]; metal-binding site 499177001890 active site 499177001891 I-site; other site 499177001892 Cupin domain; Region: Cupin_2; cl09118 499177001893 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 499177001894 MatE; Region: MatE; cl10513 499177001895 MatE; Region: MatE; cl10513 499177001896 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 499177001897 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177001898 ADP-glucose phosphorylase; Region: PLN02643 499177001899 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 499177001900 nucleotide binding site/active site [active] 499177001901 HIT family signature motif; other site 499177001902 catalytic residue [active] 499177001903 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 499177001904 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 499177001905 nucleotide binding pocket [chemical binding]; other site 499177001906 K-X-D-G motif; other site 499177001907 catalytic site [active] 499177001908 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 499177001909 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 499177001910 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 499177001911 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 499177001912 Dimer interface [polypeptide binding]; other site 499177001913 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177001914 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 499177001915 oligopeptide transporter permease; Reviewed; Region: oppB; PRK09471 499177001916 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 499177001917 dimer interface [polypeptide binding]; other site 499177001918 conserved gate region; other site 499177001919 putative PBP binding loops; other site 499177001920 ABC-ATPase subunit interface; other site 499177001921 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 499177001922 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 499177001923 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 499177001924 dimer interface [polypeptide binding]; other site 499177001925 conserved gate region; other site 499177001926 putative PBP binding loops; other site 499177001927 ABC-ATPase subunit interface; other site 499177001928 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 499177001929 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177001930 Walker A/P-loop; other site 499177001931 ATP binding site [chemical binding]; other site 499177001932 Q-loop/lid; other site 499177001933 ABC transporter signature motif; other site 499177001934 Walker B; other site 499177001935 D-loop; other site 499177001936 H-loop/switch region; other site 499177001937 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 499177001938 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 499177001939 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177001940 Walker A/P-loop; other site 499177001941 ATP binding site [chemical binding]; other site 499177001942 Q-loop/lid; other site 499177001943 ABC transporter signature motif; other site 499177001944 Walker B; other site 499177001945 D-loop; other site 499177001946 H-loop/switch region; other site 499177001947 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 499177001948 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 499177001949 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 499177001950 peptide binding site [polypeptide binding]; other site 499177001951 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypE; COG0309 499177001952 AIR synthase (PurM) related protein, subgroup 1 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two...; Region: PurM-like1; cd06061 499177001953 dimerization interface [polypeptide binding]; other site 499177001954 putative ATP binding site [chemical binding]; other site 499177001955 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177001956 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 499177001957 active site 499177001958 metal binding site [ion binding]; metal-binding site 499177001959 ribonuclease PH; Reviewed; Region: rph; PRK00173 499177001960 Ribonuclease PH; Region: RNase_PH_bact; cd11362 499177001961 hexamer interface [polypeptide binding]; other site 499177001962 active site 499177001963 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 499177001964 active site 499177001965 dimerization interface [polypeptide binding]; other site 499177001966 trigger factor; Provisional; Region: tig; PRK01490 499177001967 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 499177001968 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 499177001969 Clp protease; Region: CLP_protease; pfam00574 499177001970 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 499177001971 oligomer interface [polypeptide binding]; other site 499177001972 active site residues [active] 499177001973 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 499177001974 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 499177001975 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 499177001976 Walker A motif; other site 499177001977 ATP binding site [chemical binding]; other site 499177001978 Walker B motif; other site 499177001979 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 499177001980 Chromate transporter; Region: Chromate_transp; pfam02417 499177001981 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 499177001982 Found in ATP-dependent protease La (LON); Region: LON; smart00464 499177001983 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 499177001984 Walker A motif; other site 499177001985 ATP binding site [chemical binding]; other site 499177001986 Walker B motif; other site 499177001987 arginine finger; other site 499177001988 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 499177001989 Predicted GTPase [General function prediction only]; Region: COG0218 499177001990 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 499177001991 G1 box; other site 499177001992 GTP/Mg2+ binding site [chemical binding]; other site 499177001993 Switch I region; other site 499177001994 G2 box; other site 499177001995 G3 box; other site 499177001996 Switch II region; other site 499177001997 G4 box; other site 499177001998 G5 box; other site 499177001999 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 499177002000 diacylglycerol glucosyltransferase; Provisional; Region: PRK13609 499177002001 Monogalactosyldiacylglycerol (MGDG) synthase; Region: MGDG_synth; pfam06925 499177002002 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 499177002003 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 499177002004 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002005 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 499177002006 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 499177002007 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 499177002008 PhoU domain; Region: PhoU; pfam01895 499177002009 PhoU domain; Region: PhoU; pfam01895 499177002010 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 499177002011 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 499177002012 active site 499177002013 dimer interface [polypeptide binding]; other site 499177002014 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 499177002015 dimer interface [polypeptide binding]; other site 499177002016 active site 499177002017 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; cl01973 499177002018 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 499177002019 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 499177002020 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 499177002021 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 499177002022 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 499177002023 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 499177002024 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 499177002025 ABC-ATPase subunit interface; other site 499177002026 dimer interface [polypeptide binding]; other site 499177002027 putative PBP binding regions; other site 499177002028 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 499177002029 metal binding site 2 [ion binding]; metal-binding site 499177002030 putative DNA binding helix; other site 499177002031 metal binding site 1 [ion binding]; metal-binding site 499177002032 dimer interface [polypeptide binding]; other site 499177002033 structural Zn2+ binding site [ion binding]; other site 499177002034 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177002035 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177002036 dimer interface [polypeptide binding]; other site 499177002037 putative CheW interface [polypeptide binding]; other site 499177002038 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 499177002039 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 499177002040 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177002041 dimer interface [polypeptide binding]; other site 499177002042 putative CheW interface [polypeptide binding]; other site 499177002043 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177002044 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177002045 dimer interface [polypeptide binding]; other site 499177002046 putative CheW interface [polypeptide binding]; other site 499177002047 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 499177002048 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 499177002049 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 499177002050 dimer interface [polypeptide binding]; other site 499177002051 conserved gate region; other site 499177002052 putative PBP binding loops; other site 499177002053 ABC-ATPase subunit interface; other site 499177002054 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 499177002055 dimer interface [polypeptide binding]; other site 499177002056 conserved gate region; other site 499177002057 putative PBP binding loops; other site 499177002058 ABC-ATPase subunit interface; other site 499177002059 phosphate transporter ATP-binding protein; Provisional; Region: PRK14238 499177002060 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 499177002061 Walker A/P-loop; other site 499177002062 ATP binding site [chemical binding]; other site 499177002063 Q-loop/lid; other site 499177002064 ABC transporter signature motif; other site 499177002065 Walker B; other site 499177002066 D-loop; other site 499177002067 H-loop/switch region; other site 499177002068 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 499177002069 PhoU domain; Region: PhoU; pfam01895 499177002070 PhoU domain; Region: PhoU; pfam01895 499177002071 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 499177002072 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 499177002073 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177002074 catalytic residue [active] 499177002075 Uncharacterized protein conserved in archaea [Function unknown]; Region: COG4871 499177002076 Putative Fe-S cluster; Region: FeS; pfam04060 499177002077 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 499177002078 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 499177002079 active site 499177002080 HIGH motif; other site 499177002081 nucleotide binding site [chemical binding]; other site 499177002082 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 499177002083 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 499177002084 active site 499177002085 KMSKS motif; other site 499177002086 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 499177002087 tRNA binding surface [nucleotide binding]; other site 499177002088 anticodon binding site; other site 499177002089 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 499177002090 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 499177002091 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 499177002092 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 499177002093 TSCPD domain; Region: TSCPD; cl14834 499177002094 Domain of unknown function (DUF4364); Region: DUF4364; pfam14277 499177002095 hypothetical protein; Provisional; Region: PRK08317 499177002096 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002097 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177002098 active site 499177002099 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 499177002100 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 499177002101 metal binding site [ion binding]; metal-binding site 499177002102 dimer interface [polypeptide binding]; other site 499177002103 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 499177002104 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 499177002105 ligand binding site [chemical binding]; other site 499177002106 flexible hinge region; other site 499177002107 Helix-turn-helix domains; Region: HTH; cl00088 499177002108 Predicted permease; Region: DUF318; pfam03773 499177002109 Predicted permease; Region: DUF318; pfam03773 499177002110 Cupin domain; Region: Cupin_2; cl09118 499177002111 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 499177002112 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177002113 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]; Region: COG2452 499177002114 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 499177002115 DNA binding residues [nucleotide binding] 499177002116 Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of...; Region: SR_IS607_transposase_like; cd03769 499177002117 catalytic residues [active] 499177002118 catalytic nucleophile [active] 499177002119 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 499177002120 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 499177002121 Probable transposase; Region: OrfB_IS605; pfam01385 499177002122 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 499177002123 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 499177002124 S-adenosylmethionine binding site [chemical binding]; other site 499177002125 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 499177002126 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 499177002127 dimerization interface [polypeptide binding]; other site 499177002128 domain crossover interface; other site 499177002129 redox-dependent activation switch; other site 499177002130 potential frameshift: common BLAST hit: gi|260688373|ref|YP_003219507.1| RNA polymerase sigma-54 factor 499177002131 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 499177002132 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 499177002133 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 499177002134 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 499177002135 Predicted transcriptional regulator [Transcription]; Region: COG3388 499177002136 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 499177002137 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK07729 499177002138 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002139 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 499177002140 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 499177002141 Phosphoglycerate kinase; Region: PGK; pfam00162 499177002142 substrate binding site [chemical binding]; other site 499177002143 hinge regions; other site 499177002144 ADP binding site [chemical binding]; other site 499177002145 catalytic site [active] 499177002146 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 499177002147 substrate binding site [chemical binding]; other site 499177002148 dimer interface [polypeptide binding]; other site 499177002149 catalytic triad [active] 499177002150 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 499177002151 Sulfatase; Region: Sulfatase; cl10460 499177002152 enolase; Provisional; Region: eno; PRK00077 499177002153 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 499177002154 dimer interface [polypeptide binding]; other site 499177002155 metal binding site [ion binding]; metal-binding site 499177002156 substrate binding pocket [chemical binding]; other site 499177002157 Preprotein translocase SecG subunit; Region: SecG; cl09123 499177002158 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 499177002159 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 499177002160 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 499177002161 NeuB family; Region: NeuB; cl00496 499177002162 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002163 Prephenate dehydrogenase; Region: PDH; pfam02153 499177002164 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 499177002165 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 499177002166 hinge; other site 499177002167 active site 499177002168 Chorismate mutase type II; Region: CM_2; cl00693 499177002169 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 499177002170 Prephenate dehydratase; Region: PDT; pfam00800 499177002171 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 499177002172 putative L-Phe binding site [chemical binding]; other site 499177002173 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177002174 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177002175 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 499177002176 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 499177002177 G1 box; other site 499177002178 putative GEF interaction site [polypeptide binding]; other site 499177002179 GTP/Mg2+ binding site [chemical binding]; other site 499177002180 Switch I region; other site 499177002181 G2 box; other site 499177002182 G3 box; other site 499177002183 Switch II region; other site 499177002184 G4 box; other site 499177002185 G5 box; other site 499177002186 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 499177002187 ribonuclease R; Region: RNase_R; TIGR02063 499177002188 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 499177002189 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 499177002190 RNB domain; Region: RNB; pfam00773 499177002191 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 499177002192 RNA binding site [nucleotide binding]; other site 499177002193 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 499177002194 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177002195 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177002196 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 499177002197 SmpB-tmRNA interface; other site 499177002198 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 499177002199 Cache domain; Region: Cache_1; pfam02743 499177002200 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 499177002201 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002202 metal binding site [ion binding]; metal-binding site 499177002203 active site 499177002204 I-site; other site 499177002205 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002206 metal binding site [ion binding]; metal-binding site 499177002207 active site 499177002208 I-site; other site 499177002209 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 499177002210 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 499177002211 Walker A motif; other site 499177002212 ATP binding site [chemical binding]; other site 499177002213 Walker B motif; other site 499177002214 arginine finger; other site 499177002215 potential frameshift: common BLAST hit: gi|269791816|ref|YP_003316720.1| C4-dicarboxylate anaerobic carrier 499177002216 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 499177002217 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 499177002218 isoaspartyl dipeptidase; Provisional; Region: PRK10657 499177002219 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 499177002220 active site 499177002221 CHASE domain; Region: CHASE; cl01369 499177002222 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002223 metal binding site [ion binding]; metal-binding site 499177002224 active site 499177002225 I-site; other site 499177002226 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 499177002227 Phospholipid methyltransferase; Region: PEMT; cl00763 499177002228 DAK2 domain; Region: Dak2; cl03685 499177002229 Uncharacterized protein, DegV family COG1307; Region: DegV; cl00577 499177002230 Predicted membrane protein (DUF2177); Region: DUF2177; cl02014 499177002231 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002232 metal binding site [ion binding]; metal-binding site 499177002233 active site 499177002234 I-site; other site 499177002235 PAS domain; Region: PAS_9; pfam13426 499177002236 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 499177002237 putative active site [active] 499177002238 heme pocket [chemical binding]; other site 499177002239 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 499177002240 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002241 metal binding site [ion binding]; metal-binding site 499177002242 active site 499177002243 I-site; other site 499177002244 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177002245 Zn2+ binding site [ion binding]; other site 499177002246 Mg2+ binding site [ion binding]; other site 499177002247 M20 Peptidase T like enzymes specifically cleave tripeptides; Region: M20_peptT_like; cd05683 499177002248 peptidase T-like protein; Region: PepT-like; TIGR01883 499177002249 metal binding site [ion binding]; metal-binding site 499177002250 putative dimer interface [polypeptide binding]; other site 499177002251 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 499177002252 Helix-turn-helix domains; Region: HTH; cl00088 499177002253 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 499177002254 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 499177002255 intersubunit interface [polypeptide binding]; other site 499177002256 active site 499177002257 Zn2+ binding site [ion binding]; other site 499177002258 Ethanolamine utilization protein EutE-like; Region: ALDH_EutE; cd07121 499177002259 putative catalytic cysteine [active] 499177002260 Bacterial Micro-Compartment (BMC) domain; Region: BMC; cd06169 499177002261 Hexamer interface [polypeptide binding]; other site 499177002262 Hexagonal pore residue; other site 499177002263 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 499177002264 Hexamer interface [polypeptide binding]; other site 499177002265 Hexagonal pore residue; other site 499177002266 Bacterial Micro-Compartment (BMC) domain; Region: BMC; cd06169 499177002267 Hexamer interface [polypeptide binding]; other site 499177002268 Hexagonal pore residue; other site 499177002269 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 499177002270 Hexamer interface [polypeptide binding]; other site 499177002271 Hexagonal pore residue; other site 499177002272 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 499177002273 Propanediol utilisation protein PduL; Region: PduL; pfam06130 499177002274 Propanediol utilisation protein PduL; Region: PduL; pfam06130 499177002275 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 499177002276 Hexamer/Pentamer interface [polypeptide binding]; other site 499177002277 central pore; other site 499177002278 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 499177002279 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 499177002280 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 499177002281 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177002282 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 499177002283 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 499177002284 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 499177002285 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 499177002286 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 499177002287 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 499177002288 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 499177002289 Walker A/P-loop; other site 499177002290 ATP binding site [chemical binding]; other site 499177002291 Q-loop/lid; other site 499177002292 ABC transporter signature motif; other site 499177002293 Walker B; other site 499177002294 D-loop; other site 499177002295 H-loop/switch region; other site 499177002296 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 499177002297 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 499177002298 TM-ABC transporter signature motif; other site 499177002299 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 499177002300 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 499177002301 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 499177002302 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 499177002303 PAS domain S-box; Region: sensory_box; TIGR00229 499177002304 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 499177002305 PAS domain; Region: PAS_9; pfam13426 499177002306 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 499177002307 putative active site [active] 499177002308 heme pocket [chemical binding]; other site 499177002309 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002310 metal binding site [ion binding]; metal-binding site 499177002311 active site 499177002312 I-site; other site 499177002313 Protein of unknown function (DUF523); Region: DUF523; cl00733 499177002314 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 499177002315 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 499177002316 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 499177002317 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 499177002318 EamA-like transporter family; Region: EamA; cl01037 499177002319 EamA-like transporter family; Region: EamA; cl01037 499177002320 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 499177002321 B12 binding site [chemical binding]; other site 499177002322 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177002323 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 499177002324 FeS/SAM binding site; other site 499177002325 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 499177002326 S-adenosylmethionine binding site [chemical binding]; other site 499177002327 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 499177002328 B12 binding site [chemical binding]; other site 499177002329 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177002330 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 499177002331 FeS/SAM binding site; other site 499177002332 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 499177002333 B12 binding site [chemical binding]; other site 499177002334 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177002335 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 499177002336 FeS/SAM binding site; other site 499177002337 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 499177002338 B12 binding site [chemical binding]; other site 499177002339 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177002340 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 499177002341 FeS/SAM binding site; other site 499177002342 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 499177002343 S-adenosylmethionine binding site [chemical binding]; other site 499177002344 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 499177002345 Pirin-related protein [General function prediction only]; Region: COG1741 499177002346 Cupin domain; Region: Cupin_2; cl09118 499177002347 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 499177002348 Protein of unknown function (DUF1475); Region: DUF1475; pfam07343 499177002349 Predicted membrane protein (DUF2254); Region: DUF2254; pfam10011 499177002350 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177002351 Protein of unknown function DUF89; Region: DUF89; cl15397 499177002352 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB2; cd01048 499177002353 diiron binding motif [ion binding]; other site 499177002354 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 499177002355 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 499177002356 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 499177002357 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 499177002358 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 499177002359 active site 499177002360 dimer interface [polypeptide binding]; other site 499177002361 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 499177002362 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 499177002363 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 499177002364 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 499177002365 S-adenosylmethionine binding site [chemical binding]; other site 499177002366 Rrf2 family protein; Region: rrf2_super; TIGR00738 499177002367 Helix-turn-helix domains; Region: HTH; cl00088 499177002368 Uncharacterized conserved protein (DUF2196); Region: DUF2196; cl02044 499177002369 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177002370 Sterol carrier protein domain; Region: SCP2_2; pfam13530 499177002371 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 499177002372 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 499177002373 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 499177002374 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 499177002375 Protein export membrane protein; Region: SecD_SecF; cl14618 499177002376 Protein export membrane protein; Region: SecD_SecF; cl14618 499177002377 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 499177002378 synthetase active site [active] 499177002379 NTP binding site [chemical binding]; other site 499177002380 metal binding site [ion binding]; metal-binding site 499177002381 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 499177002382 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 499177002383 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 499177002384 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 499177002385 active site 499177002386 catalytic site [active] 499177002387 putative DNA binding site [nucleotide binding]; other site 499177002388 GIY-YIG motif/motif A; other site 499177002389 metal binding site [ion binding]; metal-binding site 499177002390 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 499177002391 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 499177002392 Protein of unknown function (DUF541); Region: SIMPL; cl01077 499177002393 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177002394 Zn2+ binding site [ion binding]; other site 499177002395 Mg2+ binding site [ion binding]; other site 499177002396 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 499177002397 Serpentine type 7TM GPCR receptor class ab chemoreceptor; Region: 7TM_GPCR_Srab; cl11607 499177002398 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 499177002399 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 499177002400 FeS/SAM binding site; other site 499177002401 Protein of unknown function DUF262; Region: DUF262; cl14890 499177002402 Protein of unknown function DUF262; Region: DUF262; cl14890 499177002403 Peptidase C26; Region: Peptidase_C26; pfam07722 499177002404 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 499177002405 catalytic triad [active] 499177002406 Amino acid permease; Region: AA_permease_2; pfam13520 499177002407 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 499177002408 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 499177002409 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 499177002410 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 499177002411 Walker A motif; other site 499177002412 ATP binding site [chemical binding]; other site 499177002413 Walker B motif; other site 499177002414 arginine finger; other site 499177002415 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 499177002416 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 499177002417 active site 499177002418 metal binding site [ion binding]; metal-binding site 499177002419 DNA binding site [nucleotide binding] 499177002420 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 499177002421 exonuclease SbcC; Region: sbcc; TIGR00618 499177002422 SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini; Region: ABC_sbcCD; cd03279 499177002423 Walker A/P-loop; other site 499177002424 ATP binding site [chemical binding]; other site 499177002425 Q-loop/lid; other site 499177002426 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177002427 ABC transporter signature motif; other site 499177002428 Walker B; other site 499177002429 D-loop; other site 499177002430 H-loop/switch region; other site 499177002431 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 499177002432 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002433 NAD(P) binding site [chemical binding]; other site 499177002434 active site 499177002435 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional; Region: PRK11921 499177002436 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177002437 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177002438 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 499177002439 catalytic residues [active] 499177002440 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 499177002441 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002442 metal binding site [ion binding]; metal-binding site 499177002443 active site 499177002444 I-site; other site 499177002445 Transcriptional regulator [Transcription]; Region: IclR; COG1414 499177002446 Helix-turn-helix domains; Region: HTH; cl00088 499177002447 Bacterial transcriptional regulator; Region: IclR; pfam01614 499177002448 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 499177002449 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 499177002450 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 499177002451 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 499177002452 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 499177002453 pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK08367 499177002454 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 499177002455 dimer interface [polypeptide binding]; other site 499177002456 PYR/PP interface [polypeptide binding]; other site 499177002457 TPP binding site [chemical binding]; other site 499177002458 substrate binding site [chemical binding]; other site 499177002459 2-ketoisovalerate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11864 499177002460 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 499177002461 TPP-binding site [chemical binding]; other site 499177002462 putative dimer interface [polypeptide binding]; other site 499177002463 Acetokinase family; Region: Acetate_kinase; cl01029 499177002464 L-asparaginase II; Region: Asparaginase_II; cl01842 499177002465 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 499177002466 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 499177002467 dimerization interface [polypeptide binding]; other site 499177002468 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177002469 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177002470 dimer interface [polypeptide binding]; other site 499177002471 putative CheW interface [polypeptide binding]; other site 499177002472 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 499177002473 Predicted permeases [General function prediction only]; Region: COG0701 499177002474 Predicted permease; Region: DUF318; pfam03773 499177002475 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 499177002476 dimerization interface [polypeptide binding]; other site 499177002477 putative DNA binding site [nucleotide binding]; other site 499177002478 putative Zn2+ binding site [ion binding]; other site 499177002479 Predicted permease; Region: DUF318; pfam03773 499177002480 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 499177002481 dimerization interface [polypeptide binding]; other site 499177002482 putative DNA binding site [nucleotide binding]; other site 499177002483 putative Zn2+ binding site [ion binding]; other site 499177002484 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 499177002485 Membrane transport protein; Region: Mem_trans; cl09117 499177002486 PAS domain S-box; Region: sensory_box; TIGR00229 499177002487 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 499177002488 putative active site [active] 499177002489 heme pocket [chemical binding]; other site 499177002490 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002491 metal binding site [ion binding]; metal-binding site 499177002492 active site 499177002493 I-site; other site 499177002494 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 499177002495 Transcriptional regulators [Transcription]; Region: PurR; COG1609 499177002496 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 499177002497 DNA binding site [nucleotide binding] 499177002498 domain linker motif; other site 499177002499 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 499177002500 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 499177002501 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177002502 Walker A/P-loop; other site 499177002503 ATP binding site [chemical binding]; other site 499177002504 Q-loop/lid; other site 499177002505 ABC transporter signature motif; other site 499177002506 Walker B; other site 499177002507 D-loop; other site 499177002508 H-loop/switch region; other site 499177002509 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 499177002510 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 499177002511 TM-ABC transporter signature motif; other site 499177002512 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 499177002513 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 499177002514 ligand binding site [chemical binding]; other site 499177002515 L-idonate 5-dehydrogenase; Region: PLN02702 499177002516 Sorbitol dehydrogenase; Region: sorbitol_DH; cd05285 499177002517 inhibitor binding site; inhibition site 499177002518 catalytic Zn binding site [ion binding]; other site 499177002519 structural Zn binding site [ion binding]; other site 499177002520 NADP binding site [chemical binding]; other site 499177002521 tetramer interface [polypeptide binding]; other site 499177002522 D-xylulose kinases, Escherichia coli xylulokinase-like subgroup; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_EcXK-like; cd07808 499177002523 N- and C-terminal domain interface [polypeptide binding]; other site 499177002524 D-xylulose kinase; Region: XylB; TIGR01312 499177002525 active site 499177002526 catalytic site [active] 499177002527 metal binding site [ion binding]; metal-binding site 499177002528 xylulose binding site [chemical binding]; other site 499177002529 putative ATP binding site [chemical binding]; other site 499177002530 homodimer interface [polypeptide binding]; other site 499177002531 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 499177002532 Cysteine-rich domain; Region: CCG; pfam02754 499177002533 Cysteine-rich domain; Region: CCG; pfam02754 499177002534 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 499177002535 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 499177002536 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 499177002537 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 499177002538 dimer interface [polypeptide binding]; other site 499177002539 conserved gate region; other site 499177002540 putative PBP binding loops; other site 499177002541 ABC-ATPase subunit interface; other site 499177002542 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 499177002543 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 499177002544 Walker A/P-loop; other site 499177002545 ATP binding site [chemical binding]; other site 499177002546 Q-loop/lid; other site 499177002547 ABC transporter signature motif; other site 499177002548 Walker B; other site 499177002549 D-loop; other site 499177002550 H-loop/switch region; other site 499177002551 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 499177002552 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 499177002553 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 499177002554 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 499177002555 Domain of unknown function (DUF4418); Region: DUF4418; pfam14387 499177002556 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 499177002557 FtsX-like permease family; Region: FtsX; cl15850 499177002558 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 499177002559 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 499177002560 Walker A/P-loop; other site 499177002561 ATP binding site [chemical binding]; other site 499177002562 Q-loop/lid; other site 499177002563 ABC transporter signature motif; other site 499177002564 Walker B; other site 499177002565 D-loop; other site 499177002566 H-loop/switch region; other site 499177002567 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177002568 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177002569 Helix-turn-helix domains; Region: HTH; cl00088 499177002570 Transcriptional regulators [Transcription]; Region: MarR; COG1846 499177002571 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 499177002572 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 499177002573 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177002574 Walker A/P-loop; other site 499177002575 ATP binding site [chemical binding]; other site 499177002576 Q-loop/lid; other site 499177002577 ABC transporter signature motif; other site 499177002578 Walker B; other site 499177002579 D-loop; other site 499177002580 H-loop/switch region; other site 499177002581 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 499177002582 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 499177002583 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and...; Region: ABCC_Glucan_exporter_like; cd03254 499177002584 Walker A/P-loop; other site 499177002585 ATP binding site [chemical binding]; other site 499177002586 Q-loop/lid; other site 499177002587 ABC transporter signature motif; other site 499177002588 Walker B; other site 499177002589 D-loop; other site 499177002590 H-loop/switch region; other site 499177002591 threonine synthase; Validated; Region: PRK05638 499177002592 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 499177002593 catalytic residue [active] 499177002594 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177002595 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 499177002596 active site residue [active] 499177002597 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 499177002598 putative active site [active] 499177002599 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 499177002600 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002601 metal binding site [ion binding]; metal-binding site 499177002602 active site 499177002603 I-site; other site 499177002604 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 499177002605 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 499177002606 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 499177002607 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 499177002608 Predicted Permease Membrane Region; Region: Asp-Al_Ex; cl06061 499177002609 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 499177002610 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 499177002611 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 499177002612 active site 499177002613 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 499177002614 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 499177002615 active site 499177002616 Uncharacterized protein, DegV family COG1307; Region: DegV; cl00577 499177002617 Beta propeller domain; Region: Beta_propel; pfam09826 499177002618 Divergent AAA domain; Region: AAA_4; pfam04326 499177002619 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 499177002620 catalytic residues [active] 499177002621 potential frameshift: common BLAST hit: gi|110800293|ref|YP_695463.1| DNA-cytosine methyltransferase 499177002622 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; cl15754 499177002623 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; cl15754 499177002624 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 499177002625 potential frameshift: common BLAST hit: gi|304317150|ref|YP_003852295.1| IstB domain protein ATP-binding protein 499177002626 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177002627 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177002628 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177002629 YCII-related domain; Region: YCII; cl00999 499177002630 Protein of unknown function (DUF4001); Region: DUF4001; cl14848 499177002631 SCIFF radical SAM maturase; Region: rSAM_six_Cys; TIGR03974 499177002632 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 499177002633 FeS/SAM binding site; other site 499177002634 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 499177002635 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 499177002636 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 499177002637 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177002638 catalytic residue [active] 499177002639 DNA topoisomerase III, bacteria and conjugative plasmid; Region: topB; TIGR01056 499177002640 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 499177002641 active site 499177002642 metal binding site [ion binding]; metal-binding site 499177002643 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 499177002644 domain I; other site 499177002645 DNA binding groove [nucleotide binding] 499177002646 phosphate binding site [ion binding]; other site 499177002647 domain II; other site 499177002648 domain III; other site 499177002649 nucleotide binding site [chemical binding]; other site 499177002650 catalytic site [active] 499177002651 domain IV; other site 499177002652 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 499177002653 MoaE interaction surface [polypeptide binding]; other site 499177002654 MoeB interaction surface [polypeptide binding]; other site 499177002655 thiocarboxylated glycine; other site 499177002656 Ubiquitin-like proteins; Region: UBQ; cl00155 499177002657 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 499177002658 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; cl08354 499177002659 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 499177002660 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 499177002661 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 499177002662 [4Fe-4S] binding site [ion binding]; other site 499177002663 molybdopterin cofactor binding site; other site 499177002664 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 499177002665 molybdopterin cofactor binding site; other site 499177002666 putative oxidoreductase Fe-S binding subunit; Reviewed; Region: PRK12769 499177002667 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 499177002668 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177002669 metal binding site [ion binding]; metal-binding site 499177002670 active site 499177002671 I-site; other site 499177002672 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 499177002673 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4868 499177002674 hypothetical protein; Provisional; Region: PRK13663 499177002675 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 499177002676 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002677 Mpv17 / PMP22 family; Region: Mpv17_PMP22; pfam04117 499177002678 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 499177002679 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 499177002680 dimer interface [polypeptide binding]; other site 499177002681 putative functional site; other site 499177002682 putative MPT binding site; other site 499177002683 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 499177002684 putative oxidoreductase Fe-S binding subunit; Reviewed; Region: PRK12769 499177002685 4Fe-4S binding domain; Region: Fer4; cl02805 499177002686 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 499177002687 4Fe-4S binding domain; Region: Fer4; cl02805 499177002688 4Fe-4S binding domain; Region: Fer4; cl02805 499177002689 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 499177002690 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; cl03503 499177002691 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 499177002692 TOBE domain; Region: TOBE_2; cl01440 499177002693 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 499177002694 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 499177002695 GTP binding site; other site 499177002696 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 499177002697 hypothetical protein; Provisional; Region: PRK05590 499177002698 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 499177002699 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 499177002700 G1 box; other site 499177002701 GTP/Mg2+ binding site [chemical binding]; other site 499177002702 Switch I region; other site 499177002703 G2 box; other site 499177002704 Switch II region; other site 499177002705 G3 box; other site 499177002706 G4 box; other site 499177002707 G5 box; other site 499177002708 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09613 499177002709 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 499177002710 FeS/SAM binding site; other site 499177002711 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 499177002712 [FeFe] hydrogenase H-cluster radical SAM maturase HydE; Region: rSAM_HydE; TIGR03956 499177002713 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 499177002714 FeS/SAM binding site; other site 499177002715 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 499177002716 putative iron-only hydrogenase system regulator; Region: hyd_TM1266; TIGR03959 499177002717 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 499177002718 catalytic residues [active] 499177002719 MoxR-like ATPases [General function prediction only]; Region: COG0714 499177002720 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 499177002721 Walker A motif; other site 499177002722 ATP binding site [chemical binding]; other site 499177002723 Walker B motif; other site 499177002724 arginine finger; other site 499177002725 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 499177002726 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 499177002727 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 499177002728 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 499177002729 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 499177002730 active site 499177002731 trimer interface [polypeptide binding]; other site 499177002732 allosteric site; other site 499177002733 active site lid [active] 499177002734 hexamer (dimer of trimers) interface [polypeptide binding]; other site 499177002735 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 499177002736 S-adenosylmethionine binding site [chemical binding]; other site 499177002737 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 499177002738 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177002739 Zn2+ binding site [ion binding]; other site 499177002740 Mg2+ binding site [ion binding]; other site 499177002741 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 499177002742 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 499177002743 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 499177002744 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177002745 Walker A motif; other site 499177002746 ATP binding site [chemical binding]; other site 499177002747 Walker B motif; other site 499177002748 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 499177002749 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 499177002750 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 499177002751 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 499177002752 DNA-binding site [nucleotide binding]; DNA binding site 499177002753 RNA-binding motif; other site 499177002754 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 499177002755 PPIC-type PPIASE domain; Region: Rotamase; cl08278 499177002756 RecX family; Region: RecX; cl00936 499177002757 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 499177002758 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 499177002759 G1 box; other site 499177002760 putative GEF interaction site [polypeptide binding]; other site 499177002761 GTP/Mg2+ binding site [chemical binding]; other site 499177002762 Switch I region; other site 499177002763 G2 box; other site 499177002764 G3 box; other site 499177002765 Switch II region; other site 499177002766 G4 box; other site 499177002767 G5 box; other site 499177002768 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 499177002769 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 499177002770 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 499177002771 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 499177002772 active site 499177002773 phosphorylation site [posttranslational modification] 499177002774 intermolecular recognition site; other site 499177002775 dimerization interface [polypeptide binding]; other site 499177002776 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 499177002777 DNA binding site [nucleotide binding] 499177002778 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 499177002779 dimer interface [polypeptide binding]; other site 499177002780 phosphorylation site [posttranslational modification] 499177002781 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 499177002782 ATP binding site [chemical binding]; other site 499177002783 Mg2+ binding site [ion binding]; other site 499177002784 G-X-G motif; other site 499177002785 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 499177002786 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 499177002787 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 499177002788 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 499177002789 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 499177002790 dimer interface [polypeptide binding]; other site 499177002791 conserved gate region; other site 499177002792 putative PBP binding loops; other site 499177002793 ABC-ATPase subunit interface; other site 499177002794 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 499177002795 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177002796 Walker A/P-loop; other site 499177002797 ATP binding site [chemical binding]; other site 499177002798 Q-loop/lid; other site 499177002799 ABC transporter signature motif; other site 499177002800 Walker B; other site 499177002801 D-loop; other site 499177002802 H-loop/switch region; other site 499177002803 Flagellin N-methylase; Region: FliB; cl00497 499177002804 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_HprK; cl00270 499177002805 active site 499177002806 metal-binding site [ion binding] 499177002807 nucleotide-binding site [chemical binding]; other site 499177002808 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_19; cd08518 499177002809 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 499177002810 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 499177002811 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 499177002812 dimer interface [polypeptide binding]; other site 499177002813 conserved gate region; other site 499177002814 putative PBP binding loops; other site 499177002815 ABC-ATPase subunit interface; other site 499177002816 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 499177002817 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 499177002818 dimer interface [polypeptide binding]; other site 499177002819 conserved gate region; other site 499177002820 putative PBP binding loops; other site 499177002821 ABC-ATPase subunit interface; other site 499177002822 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 499177002823 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177002824 Walker A/P-loop; other site 499177002825 ATP binding site [chemical binding]; other site 499177002826 Q-loop/lid; other site 499177002827 ABC transporter signature motif; other site 499177002828 Walker B; other site 499177002829 D-loop; other site 499177002830 H-loop/switch region; other site 499177002831 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 499177002832 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177002833 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 499177002834 Walker A/P-loop; other site 499177002835 ATP binding site [chemical binding]; other site 499177002836 Q-loop/lid; other site 499177002837 ABC transporter signature motif; other site 499177002838 Walker B; other site 499177002839 D-loop; other site 499177002840 H-loop/switch region; other site 499177002841 Response regulator receiver domain; Region: Response_reg; pfam00072 499177002842 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 499177002843 active site 499177002844 phosphorylation site [posttranslational modification] 499177002845 intermolecular recognition site; other site 499177002846 dimerization interface [polypeptide binding]; other site 499177002847 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 499177002848 Peptidase family M23; Region: Peptidase_M23; pfam01551 499177002849 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 499177002850 GAF domain; Region: GAF; cl15785 499177002851 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 499177002852 sensory histidine kinase AtoS; Provisional; Region: PRK11360 499177002853 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 499177002854 ATP binding site [chemical binding]; other site 499177002855 Mg2+ binding site [ion binding]; other site 499177002856 G-X-G motif; other site 499177002857 Response regulator receiver domain; Region: Response_reg; pfam00072 499177002858 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 499177002859 active site 499177002860 phosphorylation site [posttranslational modification] 499177002861 intermolecular recognition site; other site 499177002862 dimerization interface [polypeptide binding]; other site 499177002863 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 499177002864 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002865 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002866 MOSC domain; Region: MOSC; pfam03473 499177002867 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 499177002868 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 499177002869 ATP binding site [chemical binding]; other site 499177002870 substrate interface [chemical binding]; other site 499177002871 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 499177002872 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 499177002873 carboxyltransferase (CT) interaction site; other site 499177002874 biotinylation site [posttranslational modification]; other site 499177002875 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 499177002876 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 499177002877 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177002878 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 499177002879 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 499177002880 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 499177002881 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 499177002882 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 499177002883 Helix-turn-helix domains; Region: HTH; cl00088 499177002884 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 499177002885 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 499177002886 dimer interface [polypeptide binding]; other site 499177002887 active site 499177002888 CoA binding pocket [chemical binding]; other site 499177002889 Phosphopantetheine attachment site; Region: PP-binding; cl09936 499177002890 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 499177002891 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 499177002892 FMN binding site [chemical binding]; other site 499177002893 substrate binding site [chemical binding]; other site 499177002894 putative catalytic residue [active] 499177002895 Acyl transferase domain; Region: Acyl_transf_1; cl08282 499177002896 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 499177002897 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 499177002898 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 499177002899 NAD(P) binding site [chemical binding]; other site 499177002900 homotetramer interface [polypeptide binding]; other site 499177002901 homodimer interface [polypeptide binding]; other site 499177002902 active site 499177002903 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 499177002904 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 499177002905 dimer interface [polypeptide binding]; other site 499177002906 active site 499177002907 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 499177002908 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002909 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 499177002910 Glycosyl hydrolase family 26; Region: Glyco_hydro_26; cl09200 499177002911 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 499177002912 Methylomonas sp. 4,4'-diapolycopene-dialdehyde dehydrogenase-like; Region: ALDH_DDALDH; cd07099 499177002913 NAD(P) binding site [chemical binding]; other site 499177002914 catalytic residues [active] 499177002915 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 499177002916 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 499177002917 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 499177002918 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177002919 polyphosphate kinase; Provisional; Region: PRK05443 499177002920 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 499177002921 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 499177002922 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 499177002923 putative domain interface [polypeptide binding]; other site 499177002924 putative active site [active] 499177002925 catalytic site [active] 499177002926 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 499177002927 putative domain interface [polypeptide binding]; other site 499177002928 putative active site [active] 499177002929 catalytic site [active] 499177002930 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 499177002931 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 499177002932 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 499177002933 4Fe-4S binding domain; Region: Fer4; cl02805 499177002934 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 499177002935 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; cl03503 499177002936 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 499177002937 dimer interface [polypeptide binding]; other site 499177002938 [2Fe-2S] cluster binding site [ion binding]; other site 499177002939 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 499177002940 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 499177002941 SLBB domain; Region: SLBB; pfam10531 499177002942 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 499177002943 4Fe-4S binding domain; Region: Fer4; cl02805 499177002944 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 499177002945 4Fe-4S binding domain; Region: Fer4; cl02805 499177002946 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 499177002947 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 499177002948 putative dimer interface [polypeptide binding]; other site 499177002949 [2Fe-2S] cluster binding site [ion binding]; other site 499177002950 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 499177002951 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177002952 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 499177002953 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 499177002954 S-adenosylmethionine binding site [chemical binding]; other site 499177002955 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 499177002956 active site 499177002957 Predicted membrane protein [Function unknown]; Region: COG2119 499177002958 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 499177002959 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 499177002960 UPF0489 domain; Region: UPF0489; pfam12640 499177002961 Bacitracin resistance protein BacA; Region: BacA; cl00858 499177002962 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 499177002963 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 499177002964 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177002965 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 499177002966 synthetase active site [active] 499177002967 NTP binding site [chemical binding]; other site 499177002968 metal binding site [ion binding]; metal-binding site 499177002969 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 499177002970 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 499177002971 active site 499177002972 metal binding site [ion binding]; metal-binding site 499177002973 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 499177002974 active site 499177002975 ADP/pyrophosphate binding site [chemical binding]; other site 499177002976 allosteric effector site; other site 499177002977 dimerization interface [polypeptide binding]; other site 499177002978 fructose-1,6-bisphosphate binding site; other site 499177002979 Indigoidine synthase A like protein; Region: Indigoidine_A; cl00983 499177002980 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 499177002981 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 499177002982 putative substrate translocation pore; other site 499177002983 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 499177002984 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 499177002985 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 499177002986 DNA binding residues [nucleotide binding] 499177002987 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 499177002988 Amidinotransferase; Region: Amidinotransf; cl12043 499177002989 ornithine carbamoyltransferase; Validated; Region: PRK02102 499177002990 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 499177002991 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177002992 carbamate kinase; Reviewed; Region: PRK12686 499177002993 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 499177002994 putative substrate binding site [chemical binding]; other site 499177002995 nucleotide binding site [chemical binding]; other site 499177002996 nucleotide binding site [chemical binding]; other site 499177002997 homodimer interface [polypeptide binding]; other site 499177002998 Predicted transcriptional regulators [Transcription]; Region: COG1378 499177002999 Helix-turn-helix domains; Region: HTH; cl00088 499177003000 Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; Region: PLDc_like_TrmB_middle; cd09124 499177003001 C-terminal domain interface [polypeptide binding]; other site 499177003002 sugar binding site [chemical binding]; other site 499177003003 Protein of unknown function (DUF1021); Region: DUF1021; cl01852 499177003004 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00128 499177003005 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 499177003006 Transcriptional regulators [Transcription]; Region: GntR; COG1802 499177003007 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 499177003008 DNA-binding site [nucleotide binding]; DNA binding site 499177003009 FCD domain; Region: FCD; cl11656 499177003010 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 499177003011 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177003012 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177003013 Domain of unknown function (DUF1934); Region: DUF1934; cl01870 499177003014 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 499177003015 Ligand Binding Site [chemical binding]; other site 499177003016 B3/4 domain; Region: B3_4; cl11458 499177003017 FtsH Extracellular; Region: FtsH_ext; pfam06480 499177003018 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 499177003019 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 499177003020 Walker A motif; other site 499177003021 ATP binding site [chemical binding]; other site 499177003022 Walker B motif; other site 499177003023 arginine finger; other site 499177003024 Peptidase family M41; Region: Peptidase_M41; pfam01434 499177003025 Methylmalonyl-CoA mutase, N-terminal domain/subunit [Lipid metabolism]; Region: Sbm; COG1884 499177003026 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM...; Region: MM_CoA_mutase_ICM_like; cd03680 499177003027 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 499177003028 B12 binding site [chemical binding]; other site 499177003029 cobalt ligand [ion binding]; other site 499177003030 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 499177003031 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 499177003032 Walker A; other site 499177003033 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 499177003034 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 499177003035 dimer interface [polypeptide binding]; other site 499177003036 substrate binding site [chemical binding]; other site 499177003037 metal binding site [ion binding]; metal-binding site 499177003038 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 499177003039 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 499177003040 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 499177003041 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; cl01458 499177003042 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06549 499177003043 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 499177003044 carboxyltransferase (CT) interaction site; other site 499177003045 biotinylation site [posttranslational modification]; other site 499177003046 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 499177003047 Helix-turn-helix domains; Region: HTH; cl00088 499177003048 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 499177003049 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 499177003050 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 499177003051 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 499177003052 putative active site pocket [active] 499177003053 cleavage site 499177003054 Predicted membrane protein [Function unknown]; Region: COG4684 499177003055 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 499177003056 Type III pantothenate kinase; Region: Pan_kinase; cl09130 499177003057 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 499177003058 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 499177003059 FMN binding site [chemical binding]; other site 499177003060 active site 499177003061 catalytic residues [active] 499177003062 substrate binding site [chemical binding]; other site 499177003063 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 499177003064 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 499177003065 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 499177003066 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 499177003067 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 499177003068 dimer interface [polypeptide binding]; other site 499177003069 putative anticodon binding site; other site 499177003070 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 499177003071 motif 1; other site 499177003072 active site 499177003073 motif 2; other site 499177003074 motif 3; other site 499177003075 aspartate aminotransferase; Provisional; Region: PRK05764 499177003076 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 499177003077 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177003078 homodimer interface [polypeptide binding]; other site 499177003079 catalytic residue [active] 499177003080 cobyric acid synthase; Provisional; Region: PRK00784 499177003081 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003082 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 499177003083 catalytic triad [active] 499177003084 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK07111 499177003085 ATP cone domain; Region: ATP-cone; pfam03477 499177003086 Class III ribonucleotide reductase; Region: RNR_III; cd01675 499177003087 effector binding site; other site 499177003088 active site 499177003089 Zn binding site [ion binding]; other site 499177003090 glycine loop; other site 499177003091 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 499177003092 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 499177003093 FeS/SAM binding site; other site 499177003094 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 499177003095 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 499177003096 dimerization interface [polypeptide binding]; other site 499177003097 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177003098 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177003099 dimer interface [polypeptide binding]; other site 499177003100 putative CheW interface [polypeptide binding]; other site 499177003101 Uncharacterized conserved protein [Function unknown]; Region: COG2006 499177003102 Domain of unknown function (DUF362); Region: DUF362; pfam04015 499177003103 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 499177003104 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 499177003105 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 499177003106 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 499177003107 ligand binding site [chemical binding]; other site 499177003108 flexible hinge region; other site 499177003109 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 499177003110 putative switch regulator; other site 499177003111 non-specific DNA interactions [nucleotide binding]; other site 499177003112 DNA binding site [nucleotide binding] 499177003113 sequence specific DNA binding site [nucleotide binding]; other site 499177003114 putative cAMP binding site [chemical binding]; other site 499177003115 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 499177003116 peptidase T; Region: peptidase-T; TIGR01882 499177003117 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 499177003118 metal binding site [ion binding]; metal-binding site 499177003119 dimer interface [polypeptide binding]; other site 499177003120 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK05293 499177003121 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 499177003122 ligand binding site; other site 499177003123 oligomer interface; other site 499177003124 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 499177003125 dimer interface [polypeptide binding]; other site 499177003126 N-terminal domain interface [polypeptide binding]; other site 499177003127 sulfate 1 binding site; other site 499177003128 glucose-1-phosphate adenylyltransferase, GlgD subunit; Region: glgD; TIGR02092 499177003129 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 499177003130 ligand binding site; other site 499177003131 oligomer interface; other site 499177003132 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 499177003133 dimer interface [polypeptide binding]; other site 499177003134 N-terminal domain interface [polypeptide binding]; other site 499177003135 sulfate 1 binding site; other site 499177003136 glycogen synthase; Provisional; Region: glgA; PRK00654 499177003137 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 499177003138 ADP-binding pocket [chemical binding]; other site 499177003139 homodimer interface [polypeptide binding]; other site 499177003140 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 499177003141 homodimer interface [polypeptide binding]; other site 499177003142 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 499177003143 active site pocket [active] 499177003144 Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins; Region: AmyAc_CMD; cd11338 499177003145 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 499177003146 active site 499177003147 homodimer interface [polypeptide binding]; other site 499177003148 catalytic site [active] 499177003149 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 499177003150 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 499177003151 ATP binding site [chemical binding]; other site 499177003152 Mg++ binding site [ion binding]; other site 499177003153 motif III; other site 499177003154 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 499177003155 nucleotide binding region [chemical binding]; other site 499177003156 ATP-binding site [chemical binding]; other site 499177003157 PilZ domain; Region: PilZ; cl01260 499177003158 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 499177003159 anthranilate synthase, alpha proteobacterial clade; Region: TrpE-clade3; TIGR01815 499177003160 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 499177003161 homodimer interface [polypeptide binding]; other site 499177003162 Walker A motif; other site 499177003163 ATP binding site [chemical binding]; other site 499177003164 hydroxycobalamin binding site [chemical binding]; other site 499177003165 Walker B motif; other site 499177003166 Helix-turn-helix domains; Region: HTH; cl00088 499177003167 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 499177003168 catalytic residues [active] 499177003169 dimer interface [polypeptide binding]; other site 499177003170 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 499177003171 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 499177003172 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 499177003173 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003174 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 499177003175 catalytic triad [active] 499177003176 CobD/Cbib protein; Region: CobD_Cbib; cl00561 499177003177 threonine-phosphate decarboxylase; Provisional; Region: PRK06358 499177003178 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 499177003179 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177003180 homodimer interface [polypeptide binding]; other site 499177003181 catalytic residue [active] 499177003182 Protein involved in propanediol utilization, and related proteins (includes coumermycin biosynthetic protein), possible kinase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PduX; COG4542 499177003183 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 499177003184 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 499177003185 Precorrin isomerase [Coenzyme metabolism]; Region: CobH; cl00913 499177003186 Precorrin-8X methylmutase; Region: CbiC; pfam02570 499177003187 CbiD; Region: CbiD; cl00828 499177003188 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 499177003189 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 499177003190 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; cl15754 499177003191 cobalt-precorrin-6Y C(15)-methyltransferase; Validated; Region: PRK08287 499177003192 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 499177003193 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 499177003194 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 499177003195 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 499177003196 cobalamin biosynthesis protein CbiG; Validated; Region: PRK05788 499177003197 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 499177003198 Cobalamin synthesis G C-terminus; Region: CbiG_C; cl12133 499177003199 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 499177003200 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 499177003201 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 499177003202 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; cl00922 499177003203 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 499177003204 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 499177003205 tRNA; other site 499177003206 putative tRNA binding site [nucleotide binding]; other site 499177003207 putative NADP binding site [chemical binding]; other site 499177003208 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 499177003209 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177003210 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 499177003211 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 499177003212 domain interfaces; other site 499177003213 active site 499177003214 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 499177003215 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 499177003216 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 499177003217 active site 499177003218 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 499177003219 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; cd00384 499177003220 dimer interface [polypeptide binding]; other site 499177003221 active site 499177003222 Schiff base residues; other site 499177003223 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 499177003224 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 499177003225 inhibitor-cofactor binding pocket; inhibition site 499177003226 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177003227 catalytic residue [active] 499177003228 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177003229 Coenzyme A binding pocket [chemical binding]; other site 499177003230 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 499177003231 TM-ABC transporter signature motif; other site 499177003232 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 499177003233 TM-ABC transporter signature motif; other site 499177003234 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 499177003235 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003236 Walker A/P-loop; other site 499177003237 ATP binding site [chemical binding]; other site 499177003238 Q-loop/lid; other site 499177003239 ABC transporter signature motif; other site 499177003240 Walker B; other site 499177003241 D-loop; other site 499177003242 H-loop/switch region; other site 499177003243 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 499177003244 Protein of unknown function (DUF3798); Region: DUF3798; pfam12683 499177003245 Adenine deaminase [Nucleotide transport and metabolism]; Region: AdeC; COG1001 499177003246 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 499177003247 Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen source...; Region: AdeC; cd01295 499177003248 active site 499177003249 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 499177003250 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 499177003251 Ligand Binding Site [chemical binding]; other site 499177003252 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 499177003253 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 499177003254 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 499177003255 Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the...; Region: P_permease; cd01116 499177003256 transmembrane helices; other site 499177003257 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 499177003258 EamA-like transporter family; Region: EamA; cl01037 499177003259 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 499177003260 Ligand Binding Site [chemical binding]; other site 499177003261 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 499177003262 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177003263 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 499177003264 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 499177003265 active site 499177003266 phosphorylation site [posttranslational modification] 499177003267 intermolecular recognition site; other site 499177003268 dimerization interface [polypeptide binding]; other site 499177003269 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 499177003270 DNA binding site [nucleotide binding] 499177003271 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; cl00080 499177003272 dimer interface [polypeptide binding]; other site 499177003273 phosphorylation site [posttranslational modification] 499177003274 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 499177003275 ATP binding site [chemical binding]; other site 499177003276 Mg2+ binding site [ion binding]; other site 499177003277 G-X-G motif; other site 499177003278 NAD-dependent deacetylase; Provisional; Region: PRK00481 499177003279 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 499177003280 B3/4 domain; Region: B3_4; cl11458 499177003281 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the...; Region: MTH1; cd03427 499177003282 putative active site [active] 499177003283 nucleotide binding site [chemical binding]; other site 499177003284 nudix motif; other site 499177003285 putative metal binding site [ion binding]; other site 499177003286 Uncharacterized Fe-S center protein [General function prediction only]; Region: COG2768 499177003287 4Fe-4S binding domain; Region: Fer4; cl02805 499177003288 4Fe-4S binding domain; Region: Fer4; cl02805 499177003289 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 499177003290 active site 499177003291 Predicted membrane protein [Function unknown]; Region: COG2364 499177003292 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 499177003293 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]; Region: GlgB; COG0296 499177003294 N-terminal Early set domain associated with the catalytic domain of eukaryotic glycogen branching enzyme (also called 1,4 alpha glucan branching enzyme); Region: E_set_GBE_euk_N; cd02854 499177003295 Alpha amylase catalytic domain found in bacterial and eukaryotic branching enzymes; Region: AmyAc_bac_euk_BE; cd11321 499177003296 active site 499177003297 catalytic site [active] 499177003298 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 499177003299 Mitochondrial biogenesis AIM24; Region: AIM24; cl00884 499177003300 Fic/DOC family; Region: Fic; cl00960 499177003301 Putative inner membrane protein (DUF1819); Region: DUF1819; pfam08849 499177003302 Domain of unknown function (DUF1788); Region: DUF1788; pfam08747 499177003303 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177003304 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177003305 Uncharacterized conserved protein [Function unknown]; Region: COG4938 499177003306 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003307 AAA domain; Region: AAA_21; pfam13304 499177003308 Walker A/P-loop; other site 499177003309 ATP binding site [chemical binding]; other site 499177003310 ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The...; Region: ABC_ATPase; cd00267 499177003311 Q-loop/lid; other site 499177003312 Walker B; other site 499177003313 D-loop; other site 499177003314 H-loop/switch region; other site 499177003315 TIGR02687 family protein; Region: TIGR02687 499177003316 PglZ domain; Region: PglZ; pfam08665 499177003317 conserved hypothetical protein; Region: Lon_rel_chp; TIGR02653 499177003318 Putative ATP-dependent Lon protease; Region: Lon_2; cl11979 499177003319 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 499177003320 Divergent AAA domain; Region: AAA_4; pfam04326 499177003321 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 499177003322 Uncharacterized conserved protein [Function unknown]; Region: COG1915 499177003323 histidyl-tRNA synthetase; Region: hisS; TIGR00442 499177003324 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 499177003325 dimer interface [polypeptide binding]; other site 499177003326 motif 1; other site 499177003327 active site 499177003328 motif 2; other site 499177003329 motif 3; other site 499177003330 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177003331 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 499177003332 non-specific DNA binding site [nucleotide binding]; other site 499177003333 salt bridge; other site 499177003334 sequence-specific DNA binding site [nucleotide binding]; other site 499177003335 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177003336 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_b1; cd09203 499177003337 PLD-like domain; Region: PLDc_2; pfam13091 499177003338 putative homodimer interface [polypeptide binding]; other site 499177003339 putative active site [active] 499177003340 catalytic site [active] 499177003341 DEAD-like helicases superfamily; Region: DEXDc; smart00487 499177003342 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 499177003343 ATP binding site [chemical binding]; other site 499177003344 putative Mg++ binding site [ion binding]; other site 499177003345 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 499177003346 nucleotide binding region [chemical binding]; other site 499177003347 ATP-binding site [chemical binding]; other site 499177003348 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 499177003349 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 499177003350 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 499177003351 substrate binding pocket [chemical binding]; other site 499177003352 membrane-bound complex binding site; other site 499177003353 hinge residues; other site 499177003354 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 499177003355 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 499177003356 dimer interface [polypeptide binding]; other site 499177003357 phosphorylation site [posttranslational modification] 499177003358 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 499177003359 ATP binding site [chemical binding]; other site 499177003360 Mg2+ binding site [ion binding]; other site 499177003361 G-X-G motif; other site 499177003362 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 499177003363 active site 499177003364 phosphorylation site [posttranslational modification] 499177003365 intermolecular recognition site; other site 499177003366 dimerization interface [polypeptide binding]; other site 499177003367 Response regulator receiver domain; Region: Response_reg; pfam00072 499177003368 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 499177003369 active site 499177003370 phosphorylation site [posttranslational modification] 499177003371 intermolecular recognition site; other site 499177003372 dimerization interface [polypeptide binding]; other site 499177003373 PAS domain S-box; Region: sensory_box; TIGR00229 499177003374 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 499177003375 putative active site [active] 499177003376 heme pocket [chemical binding]; other site 499177003377 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 499177003378 PAS fold; Region: PAS_3; pfam08447 499177003379 putative active site [active] 499177003380 heme pocket [chemical binding]; other site 499177003381 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 499177003382 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 499177003383 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 499177003384 dimerization interface [polypeptide binding]; other site 499177003385 putative DNA binding site [nucleotide binding]; other site 499177003386 putative Zn2+ binding site [ion binding]; other site 499177003387 H+ Antiporter protein; Region: 2A0121; TIGR00900 499177003388 Ferroportin1 (FPN1); Region: FPN1; pfam06963 499177003389 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177003390 Zn2+ binding site [ion binding]; other site 499177003391 Mg2+ binding site [ion binding]; other site 499177003392 Macro domain, Appr-1'-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Appr_pase_like; cd02908 499177003393 putative ADP-ribose binding site [chemical binding]; other site 499177003394 putative active site [active] 499177003395 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 499177003396 Uncharacterized conserved protein [Function unknown]; Region: COG3760 499177003397 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 499177003398 putative deacylase active site [active] 499177003399 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 499177003400 Helix-turn-helix domains; Region: HTH; cl00088 499177003401 Glycine/sarcosine/betaine reductase component B subunits; Region: Gly_reductase; pfam09338 499177003402 Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); Region: GRDB; cl06409 499177003403 selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family; Region: various_sel_PB; TIGR01918 499177003404 BCCT family transporter; Region: BCCT; cl00569 499177003405 FeoA domain; Region: FeoA; cl00838 499177003406 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 499177003407 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 499177003408 G1 box; other site 499177003409 GTP/Mg2+ binding site [chemical binding]; other site 499177003410 Switch I region; other site 499177003411 G2 box; other site 499177003412 G3 box; other site 499177003413 Switch II region; other site 499177003414 G4 box; other site 499177003415 G5 box; other site 499177003416 Nucleoside recognition; Region: Gate; cl00486 499177003417 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 499177003418 Nucleoside recognition; Region: Gate; cl00486 499177003419 Cytochrome b5-like Heme/Steroid binding domain; Region: Cyt-b5; cl02041 499177003420 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 499177003421 Fumarase C-terminus; Region: Fumerase_C; cl00795 499177003422 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 499177003423 probable dihydroxyacetone kinase regulator; Region: DHAK_reg; TIGR02366 499177003424 Helix-turn-helix domains; Region: HTH; cl00088 499177003425 Transcriptional regulator C-terminal region; Region: TetR_C_8; pfam14278 499177003426 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 499177003427 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; Region: COG1924 499177003428 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 499177003429 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3580 499177003430 CoA enzyme activase uncharacterized domain (DUF2229); Region: DUF2229; pfam09989 499177003431 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 499177003432 CoA enzyme activase uncharacterized domain (DUF2229); Region: DUF2229; pfam09989 499177003433 Peptidase C26; Region: Peptidase_C26; pfam07722 499177003434 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 499177003435 catalytic triad [active] 499177003436 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 499177003437 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 499177003438 active site 499177003439 phosphorylation site [posttranslational modification] 499177003440 intermolecular recognition site; other site 499177003441 dimerization interface [polypeptide binding]; other site 499177003442 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 499177003443 DNA binding site [nucleotide binding] 499177003444 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 499177003445 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 499177003446 dimer interface [polypeptide binding]; other site 499177003447 phosphorylation site [posttranslational modification] 499177003448 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 499177003449 ATP binding site [chemical binding]; other site 499177003450 Mg2+ binding site [ion binding]; other site 499177003451 G-X-G motif; other site 499177003452 Carbon starvation protein CstA; Region: CstA; pfam02554 499177003453 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 499177003454 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 499177003455 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 499177003456 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 499177003457 active site 499177003458 phosphorylation site [posttranslational modification] 499177003459 intermolecular recognition site; other site 499177003460 dimerization interface [polypeptide binding]; other site 499177003461 LytTr DNA-binding domain; Region: LytTR; cl04498 499177003462 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 499177003463 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 499177003464 Histidine kinase; Region: His_kinase; pfam06580 499177003465 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 499177003466 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 499177003467 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 499177003468 active site 499177003469 HIGH motif; other site 499177003470 nucleotide binding site [chemical binding]; other site 499177003471 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 499177003472 active site 499177003473 KMSKS motif; other site 499177003474 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 499177003475 Predicted membrane protein [Function unknown]; Region: COG2364 499177003476 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 499177003477 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 499177003478 Walker A motif; other site 499177003479 ATP binding site [chemical binding]; other site 499177003480 Walker B motif; other site 499177003481 arginine finger; other site 499177003482 Helix-turn-helix domains; Region: HTH; cl00088 499177003483 tRNA pseudouridine synthase A; Reviewed; Region: PRK12434 499177003484 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 499177003485 dimerization interface 3.5A [polypeptide binding]; other site 499177003486 active site 499177003487 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 499177003488 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 499177003489 ligand binding site [chemical binding]; other site 499177003490 active site 499177003491 UGI interface [polypeptide binding]; other site 499177003492 catalytic site [active] 499177003493 Domain of unknown function (DUF3783); Region: DUF3783; pfam12646 499177003494 Protease prsW family; Region: PrsW-protease; cl15823 499177003495 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 499177003496 active site 499177003497 dimerization interface [polypeptide binding]; other site 499177003498 Uncharacterized conserved protein [Function unknown]; Region: COG3461 499177003499 Uncharacterized protein, linocin/CFP29 homolog [Function unknown]; Region: COG1659 499177003500 Encapsulating protein for peroxidase; Region: Linocin_M18; cl12047 499177003501 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 499177003502 putative active site [active] 499177003503 metal binding site [ion binding]; metal-binding site 499177003504 proteins similar to Escherichia coli yceG; Region: yceG_like; cl00675 499177003505 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 499177003506 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177003507 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 499177003508 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 499177003509 Catalytic site [active] 499177003510 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 499177003511 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 499177003512 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 499177003513 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 499177003514 active site 499177003515 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 499177003516 dimerization interface [polypeptide binding]; other site 499177003517 putative DNA binding site [nucleotide binding]; other site 499177003518 putative Zn2+ binding site [ion binding]; other site 499177003519 Endodeoxyribonuclease RusA; Region: RusA; cl01885 499177003520 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 499177003521 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 499177003522 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 499177003523 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 499177003524 minor groove reading motif; other site 499177003525 helix-hairpin-helix signature motif; other site 499177003526 substrate binding pocket [chemical binding]; other site 499177003527 active site 499177003528 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 499177003529 Putative peptidoglycan binding domain; Region: PG_binding_4; pfam12229 499177003530 VanW like protein; Region: VanW; pfam04294 499177003531 G5 domain; Region: G5; pfam07501 499177003532 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 499177003533 homotrimer interface [polypeptide binding]; other site 499177003534 Walker A motif; other site 499177003535 GTP binding site [chemical binding]; other site 499177003536 Walker B motif; other site 499177003537 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 499177003538 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 499177003539 catalytic core [active] 499177003540 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 499177003541 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 499177003542 active site 499177003543 motif I; other site 499177003544 motif II; other site 499177003545 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 499177003546 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 499177003547 Uncharacterized protein, DegV family COG1307; Region: DegV; cl00577 499177003548 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 499177003549 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177003550 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177003551 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 499177003552 catalytic residues [active] 499177003553 Glycine/sarcosine/betaine reductase component B subunits; Region: Gly_reductase; pfam09338 499177003554 Glycine reductase complex selenoprotein A; Region: GRDA; cl04705 499177003555 Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); Region: GRDB; cl06409 499177003556 selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family; Region: various_sel_PB; TIGR01918 499177003557 'initiating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the...; Region: init_cond_enzymes; cd00827 499177003558 dimer interface [polypeptide binding]; other site 499177003559 active site 499177003560 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 499177003561 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 499177003562 ligand binding site [chemical binding]; other site 499177003563 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 499177003564 Walker A/P-loop; other site 499177003565 ATP binding site [chemical binding]; other site 499177003566 ABC transporter; Region: ABC_tran; pfam00005 499177003567 Q-loop/lid; other site 499177003568 ABC transporter signature motif; other site 499177003569 Walker B; other site 499177003570 D-loop; other site 499177003571 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 499177003572 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 499177003573 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 499177003574 TM-ABC transporter signature motif; other site 499177003575 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 499177003576 TM-ABC transporter signature motif; other site 499177003577 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 499177003578 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 499177003579 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 499177003580 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 499177003581 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 499177003582 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 499177003583 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 499177003584 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 499177003585 active site 499177003586 dimer interface [polypeptide binding]; other site 499177003587 motif 1; other site 499177003588 motif 2; other site 499177003589 motif 3; other site 499177003590 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 499177003591 anticodon binding site; other site 499177003592 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177003593 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 499177003594 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 499177003595 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 499177003596 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 499177003597 ribosomal protein L20; Region: rpl20; CHL00068 499177003598 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 499177003599 23S rRNA binding site [nucleotide binding]; other site 499177003600 L21 binding site [polypeptide binding]; other site 499177003601 L13 binding site [polypeptide binding]; other site 499177003602 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 499177003603 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 499177003604 substrate binding site [chemical binding]; other site 499177003605 oxyanion hole (OAH) forming residues; other site 499177003606 trimer interface [polypeptide binding]; other site 499177003607 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 499177003608 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177003609 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 499177003610 putative acyltransferase; Provisional; Region: PRK05790 499177003611 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 499177003612 dimer interface [polypeptide binding]; other site 499177003613 active site 499177003614 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 499177003615 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 499177003616 FAD binding site [chemical binding]; other site 499177003617 homotetramer interface [polypeptide binding]; other site 499177003618 substrate binding pocket [chemical binding]; other site 499177003619 catalytic base [active] 499177003620 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 499177003621 Ligand binding site [chemical binding]; other site 499177003622 Electron transfer flavoprotein domain; Region: ETF; pfam01012 499177003623 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 499177003624 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 499177003625 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 499177003626 Cache domain; Region: Cache_1; pfam02743 499177003627 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 499177003628 dimerization interface [polypeptide binding]; other site 499177003629 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177003630 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177003631 dimer interface [polypeptide binding]; other site 499177003632 putative CheW interface [polypeptide binding]; other site 499177003633 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 499177003634 Cation transport protein; Region: TrkH; cl10514 499177003635 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 499177003636 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177003637 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 499177003638 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 499177003639 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 499177003640 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 499177003641 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 499177003642 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 499177003643 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 499177003644 dimer interface [polypeptide binding]; other site 499177003645 motif 1; other site 499177003646 active site 499177003647 motif 2; other site 499177003648 motif 3; other site 499177003649 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 499177003650 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 499177003651 putative tRNA-binding site [nucleotide binding]; other site 499177003652 B3/4 domain; Region: B3_4; cl11458 499177003653 tRNA synthetase B5 domain; Region: B5; cl08394 499177003654 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 499177003655 dimer interface [polypeptide binding]; other site 499177003656 motif 1; other site 499177003657 motif 3; other site 499177003658 motif 2; other site 499177003659 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 499177003660 Cell division protein ZapA; Region: ZapA; cl01146 499177003661 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 499177003662 Peptidase family U32; Region: Peptidase_U32; cl03113 499177003663 Collagenase; Region: DUF3656; pfam12392 499177003664 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 499177003665 MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also...; Region: ABC_MutS2; cd03280 499177003666 Walker A/P-loop; other site 499177003667 ATP binding site [chemical binding]; other site 499177003668 Q-loop/lid; other site 499177003669 ABC transporter signature motif; other site 499177003670 Walker B; other site 499177003671 D-loop; other site 499177003672 H-loop/switch region; other site 499177003673 Plant ATP synthase F0; Region: YMF19; cl07975 499177003674 Smr domain; Region: Smr; cl02619 499177003675 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 499177003676 active site 499177003677 substrate binding site [chemical binding]; other site 499177003678 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 499177003679 FMN binding site [chemical binding]; other site 499177003680 putative catalytic residues [active] 499177003681 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 499177003682 metal binding site 2 [ion binding]; metal-binding site 499177003683 putative DNA binding helix; other site 499177003684 metal binding site 1 [ion binding]; metal-binding site 499177003685 dimer interface [polypeptide binding]; other site 499177003686 structural Zn2+ binding site [ion binding]; other site 499177003687 arginyl-tRNA synthetase; Reviewed; Region: PRK12451 499177003688 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 499177003689 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 499177003690 active site 499177003691 HIGH motif; other site 499177003692 KMSK motif region; other site 499177003693 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 499177003694 tRNA binding surface [nucleotide binding]; other site 499177003695 anticodon binding site; other site 499177003696 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; cl03005 499177003697 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 499177003698 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177003699 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 499177003700 FeS/SAM binding site; other site 499177003701 Protein of unknown function (DUF4080); Region: DUF4080; pfam13311 499177003702 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 499177003703 binding surface 499177003704 TPR repeat; Region: TPR_11; pfam13414 499177003705 TPR motif; other site 499177003706 TPR repeat; Region: TPR_11; pfam13414 499177003707 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 499177003708 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 499177003709 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 499177003710 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 499177003711 2-ketoisovalerate ferredoxin reductase; Validated; Region: PRK07119 499177003712 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 499177003713 dimer interface [polypeptide binding]; other site 499177003714 PYR/PP interface [polypeptide binding]; other site 499177003715 TPP binding site [chemical binding]; other site 499177003716 substrate binding site [chemical binding]; other site 499177003717 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 499177003718 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 499177003719 TPP-binding site [chemical binding]; other site 499177003720 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 499177003721 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 499177003722 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 499177003723 Prismane/CO dehydrogenase family; Region: Prismane; pfam03063 499177003724 ACS interaction site; other site 499177003725 CODH interaction site; other site 499177003726 metal cluster binding site [ion binding]; other site 499177003727 The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible...; Region: CooC; cd02034 499177003728 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003729 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 499177003730 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 499177003731 Potassium binding sites [ion binding]; other site 499177003732 Cesium cation binding sites [ion binding]; other site 499177003733 Formiminotransferase-cyclodeaminase; Region: FTCD_C; cl01350 499177003734 Methylene-tetrahydrofolate reductase C terminal; Region: MTHFR_C; pfam12225 499177003735 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 499177003736 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 499177003737 FAD binding site [chemical binding]; other site 499177003738 dihydrolipoamide dehydrogenase; Region: lipoamide_DH; TIGR01350 499177003739 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177003740 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 499177003741 CO dehydrogenase maturation factor [Cell division and chromosome partitioning]; Region: CooC; COG3640 499177003742 The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible...; Region: CooC; cd02034 499177003743 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003744 acetyl-CoA decarbonylase/synthase complex subunit delta; Provisional; Region: PRK04452 499177003745 acetyl-CoA decarbonylase/synthase complex subunit gamma; Provisional; Region: PRK04165 499177003746 Putative Fe-S cluster; Region: FeS; pfam04060 499177003747 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 499177003748 substrate binding pocket [chemical binding]; other site 499177003749 dimer interface [polypeptide binding]; other site 499177003750 inhibitor binding site; inhibition site 499177003751 bifunctional acetyl-CoA decarbonylase/synthase complex subunit alpha/beta; Reviewed; Region: PRK09529 499177003752 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 499177003753 metal cluster binding site [ion binding]; other site 499177003754 CO dehydrogenase/acetyl-CoA synthase complex beta subunit; Region: CdhC; cl11685 499177003755 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 499177003756 lipoyl attachment site [posttranslational modification]; other site 499177003757 Uncharacterized metal-binding protein [General function prediction only]; Region: COG3894 499177003758 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 499177003759 catalytic loop [active] 499177003760 iron binding site [ion binding]; other site 499177003761 Predicted RNA-binding protein; Region: RNA_bind_2; cl00662 499177003762 Domain of unknown function (DUF3842); Region: DUF3842; pfam12953 499177003763 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 499177003764 active site 499177003765 catalytic site [active] 499177003766 substrate binding site [chemical binding]; other site 499177003767 RecB family nuclease, putative, TM0106 family; Region: TIGR03491 499177003768 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 499177003769 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003770 Family description; Region: UvrD_C_2; cl15862 499177003771 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 499177003772 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 499177003773 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 499177003774 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 499177003775 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 499177003776 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 499177003777 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 499177003778 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 499177003779 S-adenosylmethionine binding site [chemical binding]; other site 499177003780 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 499177003781 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 499177003782 hypothetical protein; Provisional; Region: PRK08185 499177003783 intersubunit interface [polypeptide binding]; other site 499177003784 active site 499177003785 zinc binding site [ion binding]; other site 499177003786 Na+ binding site [ion binding]; other site 499177003787 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 499177003788 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; cl15754 499177003789 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; cl01283 499177003790 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 499177003791 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 499177003792 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 499177003793 active site 499177003794 uracil binding [chemical binding]; other site 499177003795 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 499177003796 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; cl15754 499177003797 Uncharacterized conserved protein [Function unknown]; Region: COG3586 499177003798 Protein of unknown function (DUF3788); Region: DUF3788; pfam12663 499177003799 Protein of unknown function (DUF1002); Region: DUF1002; pfam06207 499177003800 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 499177003801 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 499177003802 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 499177003803 DNA-binding site [nucleotide binding]; DNA binding site 499177003804 UTRA domain; Region: UTRA; cl01230 499177003805 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 499177003806 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003807 Walker A/P-loop; other site 499177003808 ATP binding site [chemical binding]; other site 499177003809 Q-loop/lid; other site 499177003810 ABC transporter signature motif; other site 499177003811 Walker B; other site 499177003812 D-loop; other site 499177003813 H-loop/switch region; other site 499177003814 TOBE domain; Region: TOBE_2; cl01440 499177003815 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 499177003816 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 499177003817 dimer interface [polypeptide binding]; other site 499177003818 conserved gate region; other site 499177003819 putative PBP binding loops; other site 499177003820 ABC-ATPase subunit interface; other site 499177003821 sulfate transport protein; Provisional; Region: cysT; CHL00187 499177003822 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 499177003823 dimer interface [polypeptide binding]; other site 499177003824 conserved gate region; other site 499177003825 putative PBP binding loops; other site 499177003826 ABC-ATPase subunit interface; other site 499177003827 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 499177003828 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 499177003829 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 499177003830 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS_1; cd05710 499177003831 putative active site [active] 499177003832 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 499177003833 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 499177003834 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 499177003835 substrate binding site [chemical binding]; other site 499177003836 ATP binding site [chemical binding]; other site 499177003837 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 499177003838 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 499177003839 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 499177003840 putative substrate translocation pore; other site 499177003841 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 499177003842 carbohydrate ABC transporter substrate-binding protein, CPR_0540 family; Region: bind_CPR_0540; TIGR03850 499177003843 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 499177003844 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 499177003845 dimer interface [polypeptide binding]; other site 499177003846 conserved gate region; other site 499177003847 putative PBP binding loops; other site 499177003848 ABC-ATPase subunit interface; other site 499177003849 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 499177003850 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 499177003851 dimer interface [polypeptide binding]; other site 499177003852 conserved gate region; other site 499177003853 putative PBP binding loops; other site 499177003854 ABC-ATPase subunit interface; other site 499177003855 Transcriptional regulators [Transcription]; Region: PurR; COG1609 499177003856 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 499177003857 DNA binding site [nucleotide binding] 499177003858 domain linker motif; other site 499177003859 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 499177003860 dimerization interface [polypeptide binding]; other site 499177003861 ligand binding site [chemical binding]; other site 499177003862 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 499177003863 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 499177003864 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 499177003865 Walker A/P-loop; other site 499177003866 ATP binding site [chemical binding]; other site 499177003867 Q-loop/lid; other site 499177003868 ABC transporter signature motif; other site 499177003869 Walker B; other site 499177003870 D-loop; other site 499177003871 H-loop/switch region; other site 499177003872 TOBE domain; Region: TOBE_2; cl01440 499177003873 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 499177003874 homodimer interface [polypeptide binding]; other site 499177003875 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 499177003876 active site pocket [active] 499177003877 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 499177003878 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 499177003879 amino acid transporter; Region: 2A0306; TIGR00909 499177003880 Spore germination protein; Region: Spore_permease; cl15802 499177003881 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 499177003882 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 499177003883 PHP-associated; Region: PHP_C; pfam13263 499177003884 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 499177003885 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 499177003886 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177003887 homodimer interface [polypeptide binding]; other site 499177003888 catalytic residue [active] 499177003889 photolyase PhrII; Region: phr2; TIGR00591 499177003890 DNA photolyase; Region: DNA_photolyase; pfam00875 499177003891 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 499177003892 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177003893 Coenzyme A binding pocket [chemical binding]; other site 499177003894 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 499177003895 Ligand Binding Site [chemical binding]; other site 499177003896 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14328 499177003897 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 499177003898 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 499177003899 FeS/SAM binding site; other site 499177003900 TRAM domain; Region: TRAM; cl01282 499177003901 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 499177003902 MutS domain I; Region: MutS_I; pfam01624 499177003903 MutS family domain IV; Region: MutS_IV; pfam05190 499177003904 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 499177003905 Walker A/P-loop; other site 499177003906 ATP binding site [chemical binding]; other site 499177003907 Q-loop/lid; other site 499177003908 ABC transporter signature motif; other site 499177003909 Walker B; other site 499177003910 D-loop; other site 499177003911 H-loop/switch region; other site 499177003912 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 499177003913 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 499177003914 ATP binding site [chemical binding]; other site 499177003915 Mg2+ binding site [ion binding]; other site 499177003916 G-X-G motif; other site 499177003917 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 499177003918 ATP binding site [chemical binding]; other site 499177003919 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 499177003920 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003921 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 499177003922 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 499177003923 Sm1 motif; other site 499177003924 D1 - D2 interaction site; other site 499177003925 D3 - B interaction site; other site 499177003926 Hfq - Hfq interaction site; other site 499177003927 RNA binding pocket [nucleotide binding]; other site 499177003928 Sm2 motif; other site 499177003929 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 499177003930 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 499177003931 active site 499177003932 DNA binding site [nucleotide binding] 499177003933 Int/Topo IB signature motif; other site 499177003934 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]; Region: COG4100 499177003935 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 499177003936 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177003937 catalytic residue [active] 499177003938 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 499177003939 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 499177003940 Helix-turn-helix domains; Region: HTH; cl00088 499177003941 LexA repressor; Validated; Region: PRK00215 499177003942 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 499177003943 Catalytic site [active] 499177003944 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 499177003945 putative peptidoglycan binding site; other site 499177003946 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 499177003947 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 499177003948 active site 499177003949 DNA binding site [nucleotide binding] 499177003950 Int/Topo IB signature motif; other site 499177003951 Adenylosuccinate lyase [Nucleotide transport and metabolism]; Region: PurB; COG0015 499177003952 Adenylsuccinate lyase (ASL)_subgroup 2; Region: Adenylsuccinate_lyase_2; cd03302 499177003953 tetramer interface [polypeptide binding]; other site 499177003954 active site 499177003955 aspartate aminotransferase; Provisional; Region: PRK05764 499177003956 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 499177003957 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177003958 homodimer interface [polypeptide binding]; other site 499177003959 catalytic residue [active] 499177003960 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 499177003961 metal ion-dependent adhesion site (MIDAS); other site 499177003962 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177003963 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 499177003964 isocitrate dehydrogenase; Validated; Region: PRK06451 499177003965 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate...; Region: citrate_synt_like_1_2; cd06113 499177003966 dimer interface [polypeptide binding]; other site 499177003967 Citrate synthase; Region: Citrate_synt; pfam00285 499177003968 active site 499177003969 citrylCoA binding site [chemical binding]; other site 499177003970 oxalacetate/citrate binding site [chemical binding]; other site 499177003971 coenzyme A binding site [chemical binding]; other site 499177003972 catalytic triad [active] 499177003973 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 499177003974 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 499177003975 active site 499177003976 DNA binding site [nucleotide binding] 499177003977 Int/Topo IB signature motif; other site 499177003978 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 499177003979 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 499177003980 active site 499177003981 catalytic residues [active] 499177003982 DNA binding site [nucleotide binding] 499177003983 Int/Topo IB signature motif; other site 499177003984 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 499177003985 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 499177003986 active site 499177003987 catalytic residues [active] 499177003988 DNA binding site [nucleotide binding] 499177003989 Int/Topo IB signature motif; other site 499177003990 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177003991 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 499177003992 putative active site [active] 499177003993 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 499177003994 ATP binding site [chemical binding]; other site 499177003995 putative Mg++ binding site [ion binding]; other site 499177003996 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 499177003997 nucleotide binding region [chemical binding]; other site 499177003998 ATP-binding site [chemical binding]; other site 499177003999 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 499177004000 Tubulin/FtsZ family, GTPase domain; Region: Tubulin; pfam00091 499177004001 Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved...; Region: Tubulin_FtsZ; cl10017 499177004002 nucleotide binding site [chemical binding]; other site 499177004003 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 499177004004 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 499177004005 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 499177004006 ATP binding site [chemical binding]; other site 499177004007 putative Mg++ binding site [ion binding]; other site 499177004008 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 499177004009 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 499177004010 HsdM N-terminal domain; Region: HsdM_N; pfam12161 499177004011 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 499177004012 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004013 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 499177004014 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177004015 Family description; Region: UvrD_C_2; cl15862 499177004016 Protein of unknown function (DUF3232); Region: DUF3232; pfam11554 499177004017 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 499177004018 4Fe-4S single cluster domain; Region: Fer4_15; pfam13459 499177004019 Predicted transcriptional regulator [Transcription]; Region: COG2378 499177004020 WYL domain; Region: WYL; cl14852 499177004021 glutamate formiminotransferase; Region: FtcD; TIGR02024 499177004022 Formiminotransferase domain, N-terminal subdomain; Region: FTCD_N; pfam07837 499177004023 Formiminotransferase domain; Region: FTCD; pfam02971 499177004024 Formiminotransferase-cyclodeaminase; Region: FTCD_C; cl01350 499177004025 imidazolonepropionase; Validated; Region: PRK09356 499177004026 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 499177004027 active site 499177004028 Membrane protein of unknown function (DUF340); Region: DUF340; cl01028 499177004029 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; Region: PLPDE_III_AR_like_1; cd06815 499177004030 Predicted amino acid racemase [Amino acid transport and metabolism]; Region: COG3457 499177004031 dimer interface [polypeptide binding]; other site 499177004032 active site 499177004033 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 499177004034 substrate binding site [chemical binding]; other site 499177004035 catalytic residue [active] 499177004036 MutL protein; Region: MutL; pfam13941 499177004037 D-Lysine 5,6-aminomutase alpha subunit; Region: Lys-AminoMut_A; pfam09043 499177004038 B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase...; Region: B12-binding; cd02067 499177004039 B12 binding site [chemical binding]; other site 499177004040 cobalt ligand [ion binding]; other site 499177004041 D-Lysine 5,6-aminomutase alpha subunit; Region: Lys-AminoMut_A; pfam09043 499177004042 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 499177004043 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; cd00640 499177004044 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177004045 catalytic residue [active] 499177004046 Uncharacterized conserved protein related to dihydrodipicolinate reductase [Function unknown]; Region: COG3804 499177004047 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 499177004048 sensory histidine kinase AtoS; Provisional; Region: PRK11360 499177004049 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 499177004050 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 499177004051 Walker A motif; other site 499177004052 ATP binding site [chemical binding]; other site 499177004053 Walker B motif; other site 499177004054 arginine finger; other site 499177004055 Helix-turn-helix domains; Region: HTH; cl00088 499177004056 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 499177004057 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 499177004058 dimer interface [polypeptide binding]; other site 499177004059 active site 499177004060 glycine-pyridoxal phosphate binding site [chemical binding]; other site 499177004061 folate binding site [chemical binding]; other site 499177004062 Uncharacterized conserved protein [Function unknown]; Region: COG2966 499177004063 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 499177004064 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 499177004065 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 499177004066 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 499177004067 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 499177004068 dimer interface [polypeptide binding]; other site 499177004069 anticodon binding site; other site 499177004070 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 499177004071 homodimer interface [polypeptide binding]; other site 499177004072 motif 1; other site 499177004073 active site 499177004074 motif 2; other site 499177004075 GAD domain; Region: GAD; pfam02938 499177004076 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 499177004077 motif 3; other site 499177004078 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 499177004079 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 499177004080 dimer interface [polypeptide binding]; other site 499177004081 motif 1; other site 499177004082 active site 499177004083 motif 2; other site 499177004084 motif 3; other site 499177004085 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 499177004086 anticodon binding site; other site 499177004087 coproporphyrinogen III oxidase; Provisional; Region: PRK08207 499177004088 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 499177004089 FeS/SAM binding site; other site 499177004090 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177004091 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 499177004092 putative active site [active] 499177004093 dimerization interface [polypeptide binding]; other site 499177004094 putative tRNAtyr binding site [nucleotide binding]; other site 499177004095 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 499177004096 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177004097 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 499177004098 synthetase active site [active] 499177004099 NTP binding site [chemical binding]; other site 499177004100 metal binding site [ion binding]; metal-binding site 499177004101 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 499177004102 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 499177004103 Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]; Region: Apt; COG0503 499177004104 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177004105 active site 499177004106 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 499177004107 DHH family; Region: DHH; pfam01368 499177004108 DHHA1 domain; Region: DHHA1; pfam02272 499177004109 Single-strand DNA-specific exonuclease, C terminal domain; Region: ssDNA-exonuc_C; cl11538 499177004110 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 499177004111 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 499177004112 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 499177004113 Protein export membrane protein; Region: SecD_SecF; cl14618 499177004114 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 499177004115 Protein export membrane protein; Region: SecD_SecF; cl14618 499177004116 Preprotein translocase subunit; Region: YajC; cl00806 499177004117 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 499177004118 tRNA-guanine transglycosylases, various specificities; Region: tgt_general; TIGR00449 499177004119 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 499177004120 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 499177004121 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 499177004122 Stage II sporulation protein; Region: SpoIID; pfam08486 499177004123 Stage II sporulation protein; Region: SpoIID; pfam08486 499177004124 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 499177004125 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 499177004126 Walker A motif; other site 499177004127 ATP binding site [chemical binding]; other site 499177004128 Walker B motif; other site 499177004129 arginine finger; other site 499177004130 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 499177004131 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 499177004132 RuvA N terminal domain; Region: RuvA_N; pfam01330 499177004133 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 499177004134 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 499177004135 active site 499177004136 putative DNA-binding cleft [nucleotide binding]; other site 499177004137 dimer interface [polypeptide binding]; other site 499177004138 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 499177004139 MatE; Region: MatE; cl10513 499177004140 MatE; Region: MatE; cl10513 499177004141 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 499177004142 Helix-turn-helix domains; Region: HTH; cl00088 499177004143 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 499177004144 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 499177004145 Transcriptional regulator; Region: Transcrip_reg; cl00361 499177004146 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 499177004147 homodimer interface [polypeptide binding]; other site 499177004148 NAD synthase; Region: NAD_synthase; pfam02540 499177004149 NAD binding pocket [chemical binding]; other site 499177004150 ATP binding pocket [chemical binding]; other site 499177004151 Mg binding site [ion binding]; other site 499177004152 active-site loop [active] 499177004153 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004154 Uncharacterized conserved protein [Function unknown]; Region: COG1739 499177004155 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 499177004156 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 499177004157 HEAT repeats; Region: HEAT_2; pfam13646 499177004158 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 499177004159 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 499177004160 HflX GTPase family; Region: HflX; cd01878 499177004161 G1 box; other site 499177004162 GTP/Mg2+ binding site [chemical binding]; other site 499177004163 Switch I region; other site 499177004164 G2 box; other site 499177004165 G3 box; other site 499177004166 Switch II region; other site 499177004167 G4 box; other site 499177004168 G5 box; other site 499177004169 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 499177004170 Transglycosylase; Region: Transgly; cl07896 499177004171 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 499177004172 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 499177004173 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 499177004174 Peptidase family U32; Region: Peptidase_U32; cl03113 499177004175 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 499177004176 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 499177004177 S-adenosylmethionine binding site [chemical binding]; other site 499177004178 YceG-like family; Region: YceG; pfam02618 499177004179 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 499177004180 dimerization interface [polypeptide binding]; other site 499177004181 pyrimidine-nucleoside phosphorylase; Region: Y_phosphoryl; TIGR02644 499177004182 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 499177004183 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 499177004184 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; cl06734 499177004185 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 499177004186 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 499177004187 active site 499177004188 Int/Topo IB signature motif; other site 499177004189 DNA binding site [nucleotide binding] 499177004190 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 499177004191 dimer interface [polypeptide binding]; other site 499177004192 ADP-ribose binding site [chemical binding]; other site 499177004193 active site 499177004194 nudix motif; other site 499177004195 metal binding site [ion binding]; metal-binding site 499177004196 Protein of unknown function (DUF3866); Region: DUF3866; pfam12982 499177004197 Glycosyltransferase 4 (GT4) includes both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases. They catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound...; Region: GT_MraY-like; cl10571 499177004198 Mg++ binding site [ion binding]; other site 499177004199 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 499177004200 Ligand binding site; other site 499177004201 Putative Catalytic site; other site 499177004202 DXD motif; other site 499177004203 Protein of unknown function (DUF3186); Region: DUF3186; pfam11382 499177004204 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4825 499177004205 Thiamine pyrophosphokinase; Region: TPK; cl08415 499177004206 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 499177004207 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 499177004208 Walker A/P-loop; other site 499177004209 ATP binding site [chemical binding]; other site 499177004210 Q-loop/lid; other site 499177004211 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 499177004212 ABC transporter signature motif; other site 499177004213 Walker B; other site 499177004214 D-loop; other site 499177004215 H-loop/switch region; other site 499177004216 arginine repressor; Provisional; Region: argR; PRK00441 499177004217 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 499177004218 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 499177004219 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 499177004220 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 499177004221 RNA binding surface [nucleotide binding]; other site 499177004222 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; cl15754 499177004223 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 499177004224 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 499177004225 TPP-binding site; other site 499177004226 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 499177004227 PYR/PP interface [polypeptide binding]; other site 499177004228 dimer interface [polypeptide binding]; other site 499177004229 TPP binding site [chemical binding]; other site 499177004230 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 499177004231 Divergent PAP2 family; Region: DUF212; cl00855 499177004232 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 499177004233 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 499177004234 substrate binding pocket [chemical binding]; other site 499177004235 chain length determination region; other site 499177004236 substrate-Mg2+ binding site; other site 499177004237 catalytic residues [active] 499177004238 aspartate-rich region 1; other site 499177004239 active site lid residues [active] 499177004240 aspartate-rich region 2; other site 499177004241 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 499177004242 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 499177004243 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 499177004244 generic binding surface II; other site 499177004245 generic binding surface I; other site 499177004246 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: QRI7; COG0533 499177004247 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 499177004248 putative RNA binding site [nucleotide binding]; other site 499177004249 Asp23 family; Region: Asp23; cl00574 499177004250 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 499177004251 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 499177004252 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 499177004253 Acetokinase family; Region: Acetate_kinase; cl01029 499177004254 propionate/acetate kinase; Provisional; Region: PRK12379 499177004255 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 499177004256 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 499177004257 dimer interface [polypeptide binding]; other site 499177004258 phosphorylation site [posttranslational modification] 499177004259 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 499177004260 ATP binding site [chemical binding]; other site 499177004261 Mg2+ binding site [ion binding]; other site 499177004262 G-X-G motif; other site 499177004263 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 499177004264 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 499177004265 active site 499177004266 phosphorylation site [posttranslational modification] 499177004267 intermolecular recognition site; other site 499177004268 dimerization interface [polypeptide binding]; other site 499177004269 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 499177004270 DNA binding site [nucleotide binding] 499177004271 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 499177004272 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 499177004273 G1 box; other site 499177004274 putative GEF interaction site [polypeptide binding]; other site 499177004275 GTP/Mg2+ binding site [chemical binding]; other site 499177004276 Switch I region; other site 499177004277 G2 box; other site 499177004278 G3 box; other site 499177004279 Switch II region; other site 499177004280 G4 box; other site 499177004281 G5 box; other site 499177004282 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 499177004283 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 499177004284 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 499177004285 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 499177004286 selenocysteine synthase; Provisional; Region: PRK04311 499177004287 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 499177004288 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 499177004289 selenophosphate synthetase; Provisional; Region: PRK00943 499177004290 dimerization interface [polypeptide binding]; other site 499177004291 putative ATP binding site [chemical binding]; other site 499177004292 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 499177004293 dimer interface [polypeptide binding]; other site 499177004294 catalytic triad [active] 499177004295 peroxidatic and resolving cysteines [active] 499177004296 SLBB domain; Region: SLBB; pfam10531 499177004297 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 499177004298 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 499177004299 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 499177004300 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 499177004301 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 499177004302 L-serine deaminase [Amino acid transport and metabolism]; Region: SdaA; COG1760 499177004303 L-serine dehydratase, iron-sulfur-dependent, beta subunit; Region: sda_beta; TIGR00719 499177004304 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 499177004305 ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-like; cd04879 499177004306 L-serine binding site [chemical binding]; other site 499177004307 Oligomerisation domain; Region: Oligomerisation; cl00519 499177004308 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; cl00581 499177004309 LytR cell envelope-related transcriptional attenuator; Region: LytR_C; pfam13399 499177004310 Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]; Region: COG1713 499177004311 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177004312 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 499177004313 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 499177004314 active site 499177004315 (T/H)XGH motif; other site 499177004316 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 499177004317 GTPase CgtA; Reviewed; Region: obgE; PRK12297 499177004318 GTP1/OBG; Region: GTP1_OBG; pfam01018 499177004319 Obg GTPase; Region: Obg; cd01898 499177004320 G1 box; other site 499177004321 GTP/Mg2+ binding site [chemical binding]; other site 499177004322 Switch I region; other site 499177004323 G2 box; other site 499177004324 G3 box; other site 499177004325 Switch II region; other site 499177004326 G4 box; other site 499177004327 G5 box; other site 499177004328 Domain of unknown function (DUF1967); Region: DUF1967; cl07779 499177004329 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 499177004330 Protein of unknown function (DUF464); Region: DUF464; cl01080 499177004331 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 499177004332 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 499177004333 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 499177004334 RNA binding site [nucleotide binding]; other site 499177004335 radical SAM-linked protein; Region: sam_1_link_chp; TIGR03936 499177004336 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; cl02090 499177004337 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 499177004338 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 499177004339 FeS/SAM binding site; other site 499177004340 Predicted cobalamin binding protein [General function prediction only]; Region: COG5012 499177004341 B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase...; Region: B12-binding; cd02067 499177004342 B12 binding site [chemical binding]; other site 499177004343 cobalt ligand [ion binding]; other site 499177004344 D-Lysine 5,6-aminomutase alpha subunit; Region: Lys-AminoMut_A; pfam09043 499177004345 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]; Region: COG1193 499177004346 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177004347 Walker A/P-loop; other site 499177004348 ATP binding site [chemical binding]; other site 499177004349 Q-loop/lid; other site 499177004350 ABC transporter signature motif; other site 499177004351 Walker B; other site 499177004352 D-loop; other site 499177004353 H-loop/switch region; other site 499177004354 lysine-2,3-aminomutase; Region: lys_2_3_AblA; TIGR03820 499177004355 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 499177004356 FeS/SAM binding site; other site 499177004357 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 499177004358 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004359 NAD(P) binding site [chemical binding]; other site 499177004360 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004361 NAD(P) binding site [chemical binding]; other site 499177004362 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl15827 499177004363 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 499177004364 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 499177004365 active site 499177004366 dimer interfaces [polypeptide binding]; other site 499177004367 catalytic residues [active] 499177004368 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 499177004369 Septum formation topological specificity factor MinE; Region: MinE; cl00538 499177004370 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 499177004371 Switch II; other site 499177004372 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177004373 septum formation inhibitor; Reviewed; Region: minC; PRK00513 499177004374 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 499177004375 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 499177004376 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 499177004377 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 499177004378 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 499177004379 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 499177004380 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 499177004381 rod shape-determining protein MreC; Provisional; Region: PRK14872 499177004382 rod shape-determining protein MreC; Region: MreC; pfam04085 499177004383 hypothetical protein; Reviewed; Region: PRK00024 499177004384 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 499177004385 MPN+ (JAMM) motif; other site 499177004386 Zinc-binding site [ion binding]; other site 499177004387 Maf-like protein; Region: Maf; pfam02545 499177004388 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 499177004389 active site 499177004390 dimer interface [polypeptide binding]; other site 499177004391 ferredoxin; Validated; Region: PRK07118 499177004392 4Fe-4S binding domain; Region: Fer4; cl02805 499177004393 4Fe-4S binding domain; Region: Fer4; cl02805 499177004394 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 499177004395 4Fe-4S binding domain; Region: Fer4; cl02805 499177004396 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 499177004397 4Fe-4S binding domain; Region: Fer4; cl02805 499177004398 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 499177004399 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 499177004400 FMN-binding domain; Region: FMN_bind; cl01081 499177004401 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 499177004402 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 499177004403 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 499177004404 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 499177004405 SLBB domain; Region: SLBB; pfam10531 499177004406 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 499177004407 Bacterial SH3 domain; Region: SH3_3; cl02551 499177004408 Bacterial SH3 domain; Region: SH3_3; cl02551 499177004409 NlpC/P60 family; Region: NLPC_P60; cl11438 499177004410 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 499177004411 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 499177004412 N-acetyl-D-glucosamine binding site [chemical binding]; other site 499177004413 catalytic residue [active] 499177004414 dephospho-CoA kinase; Region: TIGR00152 499177004415 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 499177004416 CoA-binding site [chemical binding]; other site 499177004417 DNA polymerase I; Provisional; Region: PRK05755 499177004418 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 499177004419 active site 499177004420 metal binding site 1 [ion binding]; metal-binding site 499177004421 putative 5' ssDNA interaction site; other site 499177004422 metal binding site 3; metal-binding site 499177004423 metal binding site 2 [ion binding]; metal-binding site 499177004424 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 499177004425 putative DNA binding site [nucleotide binding]; other site 499177004426 putative metal binding site [ion binding]; other site 499177004427 inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Region: DNA_polA_I_Bacillus_like_exo; cd06140 499177004428 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 499177004429 active site 499177004430 DNA binding site [nucleotide binding] 499177004431 catalytic site [active] 499177004432 aspartate kinase; Reviewed; Region: PRK09034 499177004433 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 499177004434 nucleotide binding site [chemical binding]; other site 499177004435 substrate binding site [chemical binding]; other site 499177004436 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-YclM-BS_1; cd04911 499177004437 allosteric regulatory residue; other site 499177004438 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 499177004439 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177004440 ApbE family; Region: ApbE; cl00643 499177004441 UbiA prenyltransferase family; Region: UbiA; cl00337 499177004442 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 499177004443 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 499177004444 substrate binding pocket [chemical binding]; other site 499177004445 chain length determination region; other site 499177004446 substrate-Mg2+ binding site; other site 499177004447 catalytic residues [active] 499177004448 aspartate-rich region 1; other site 499177004449 active site lid residues [active] 499177004450 aspartate-rich region 2; other site 499177004451 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 499177004452 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177004453 ketol-acid reductoisomerase; Provisional; Region: PRK05479 499177004454 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004455 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 499177004456 Dehydratase family; Region: ILVD_EDD; cl00340 499177004457 6-phosphogluconate dehydratase; Region: edd; TIGR01196 499177004458 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 499177004459 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 499177004460 PYR/PP interface [polypeptide binding]; other site 499177004461 dimer interface [polypeptide binding]; other site 499177004462 TPP binding site [chemical binding]; other site 499177004463 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 499177004464 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; cl01629 499177004465 TPP-binding site [chemical binding]; other site 499177004466 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 499177004467 Cation efflux family; Region: Cation_efflux; cl00316 499177004468 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 499177004469 active site residue [active] 499177004470 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 499177004471 active site residue [active] 499177004472 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 499177004473 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 499177004474 Walker A/P-loop; other site 499177004475 ATP binding site [chemical binding]; other site 499177004476 Q-loop/lid; other site 499177004477 ABC transporter signature motif; other site 499177004478 Walker B; other site 499177004479 D-loop; other site 499177004480 H-loop/switch region; other site 499177004481 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 499177004482 dimer interface [polypeptide binding]; other site 499177004483 conserved gate region; other site 499177004484 putative PBP binding loops; other site 499177004485 ABC-ATPase subunit interface; other site 499177004486 NMT1-like family; Region: NMT1_2; cl15260 499177004487 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 499177004488 argininosuccinate lyase; Provisional; Region: PRK02186 499177004489 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177004490 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 499177004491 Ligand binding site; other site 499177004492 Putative Catalytic site; other site 499177004493 DXD motif; other site 499177004494 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 499177004495 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 499177004496 inhibitor-cofactor binding pocket; inhibition site 499177004497 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177004498 catalytic residue [active] 499177004499 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 499177004500 CPxP motif; other site 499177004501 Transcriptional regulator [Transcription]; Region: LysR; COG0583 499177004502 Helix-turn-helix domains; Region: HTH; cl00088 499177004503 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 499177004504 dimerization interface [polypeptide binding]; other site 499177004505 putative inner membrane protein; Provisional; Region: PRK11099 499177004506 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 499177004507 CPxP motif; other site 499177004508 putative inner membrane protein; Provisional; Region: PRK11099 499177004509 Sulphur transport; Region: Sulf_transp; cl01018 499177004510 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 499177004511 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177004512 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 499177004513 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 499177004514 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 499177004515 molybdopterin cofactor binding site; other site 499177004516 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 499177004517 molybdopterin cofactor binding site; other site 499177004518 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 499177004519 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 499177004520 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 499177004521 metal binding site [ion binding]; metal-binding site 499177004522 dimer interface [polypeptide binding]; other site 499177004523 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 499177004524 THUMP domain; Region: THUMP; cl12076 499177004525 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 499177004526 Ligand Binding Site [chemical binding]; other site 499177004527 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 499177004528 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 499177004529 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177004530 catalytic residue [active] 499177004531 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 499177004532 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 499177004533 active site 499177004534 homotetramer interface [polypeptide binding]; other site 499177004535 homodimer interface [polypeptide binding]; other site 499177004536 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 499177004537 Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]; Region: HgdB; COG1775 499177004538 benzoyl-CoA reductase, bzd-type, N subunit; Region: benz_CoA_bzdN; cl11464 499177004539 flavoprotein, HI0933 family; Region: TIGR00275 499177004540 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004541 Chorismate mutase type II; Region: CM_2; cl00693 499177004542 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 499177004543 Cell division protein FtsA; Region: FtsA; cl11496 499177004544 Cell division protein FtsA; Region: FtsA; cl11496 499177004545 Transcriptional regulator [Transcription]; Region: LysR; COG0583 499177004546 Helix-turn-helix domains; Region: HTH; cl00088 499177004547 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 499177004548 putative dimerization interface [polypeptide binding]; other site 499177004549 M18 Peptidase Aminopeptidase I; Region: M18_API; cd05659 499177004550 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 499177004551 oligomer interface [polypeptide binding]; other site 499177004552 putative active site [active] 499177004553 metal binding site [ion binding]; metal-binding site 499177004554 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177004555 Zn2+ binding site [ion binding]; other site 499177004556 Mg2+ binding site [ion binding]; other site 499177004557 Bacterial SH3 domain; Region: SH3_3; cl02551 499177004558 NlpC/P60 family; Region: NLPC_P60; cl11438 499177004559 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 499177004560 ligand binding site [chemical binding]; other site 499177004561 flexible hinge region; other site 499177004562 Helix-turn-helix domains; Region: HTH; cl00088 499177004563 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 499177004564 active site residue [active] 499177004565 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 499177004566 active site residue [active] 499177004567 poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Region: deacetyl_PgaB; TIGR03938 499177004568 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u3_5s; cd10972 499177004569 putative active site [active] 499177004570 putative metal binding site [ion binding]; other site 499177004571 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 499177004572 Rubredoxin; Region: Rubredoxin; pfam00301 499177004573 iron binding site [ion binding]; other site 499177004574 Stage V sporulation protein S (SpoVS); Region: SpoVS; cl01005 499177004575 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 499177004576 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 499177004577 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004578 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 499177004579 RNA binding site [nucleotide binding]; other site 499177004580 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 499177004581 RNA binding site [nucleotide binding]; other site 499177004582 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 499177004583 RNA binding site [nucleotide binding]; other site 499177004584 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 499177004585 RNA binding site [nucleotide binding]; other site 499177004586 LytB protein; Region: LYTB; cl00507 499177004587 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 499177004588 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 499177004589 putative acyl-acceptor binding pocket; other site 499177004590 cytidylate kinase; Provisional; Region: cmk; PRK00023 499177004591 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 499177004592 CMP-binding site; other site 499177004593 The sites determining sugar specificity; other site 499177004594 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 499177004595 catalytic core [active] 499177004596 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 499177004597 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 499177004598 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 499177004599 putative active site [active] 499177004600 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 499177004601 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated; Region: PRK05778 499177004602 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 499177004603 TPP-binding site [chemical binding]; other site 499177004604 2-oxoglutarate ferredoxin oxidoreductase subunit alpha; Validated; Region: PRK08659 499177004605 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 499177004606 dimer interface [polypeptide binding]; other site 499177004607 PYR/PP interface [polypeptide binding]; other site 499177004608 TPP binding site [chemical binding]; other site 499177004609 substrate binding site [chemical binding]; other site 499177004610 Ferredoxin [Energy production and conversion]; Region: COG1146 499177004611 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 499177004612 oxaloacetate decarboxylase; Provisional; Region: PRK12331 499177004613 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 499177004614 active site 499177004615 catalytic residues [active] 499177004616 metal binding site [ion binding]; metal-binding site 499177004617 homodimer binding site [polypeptide binding]; other site 499177004618 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177004619 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 499177004620 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 499177004621 RNA binding surface [nucleotide binding]; other site 499177004622 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this...; Region: PseudoU_synth_RsuA_like; cd02870 499177004623 active site 499177004624 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 499177004625 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 499177004626 non-specific DNA binding site [nucleotide binding]; other site 499177004627 salt bridge; other site 499177004628 sequence-specific DNA binding site [nucleotide binding]; other site 499177004629 Cupin domain; Region: Cupin_2; cl09118 499177004630 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 499177004631 ScpA/B protein; Region: ScpA_ScpB; cl00598 499177004632 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 499177004633 active site 499177004634 putative substrate binding region [chemical binding]; other site 499177004635 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 499177004636 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177004637 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 499177004638 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 499177004639 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 499177004640 metal binding site 2 [ion binding]; metal-binding site 499177004641 putative DNA binding helix; other site 499177004642 metal binding site 1 [ion binding]; metal-binding site 499177004643 dimer interface [polypeptide binding]; other site 499177004644 structural Zn2+ binding site [ion binding]; other site 499177004645 Protein of unknown function (DUF1292); Region: DUF1292; cl01608 499177004646 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 499177004647 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 499177004648 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 499177004649 active site 499177004650 catalytic tetrad [active] 499177004651 4Fe-4S binding domain; Region: Fer4; cl02805 499177004652 ferredoxin; Validated; Region: PRK07118 499177004653 Bacterial protein of unknown function (DUF965); Region: DUF965; cl01857 499177004654 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 499177004655 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 499177004656 motif 1; other site 499177004657 active site 499177004658 motif 2; other site 499177004659 motif 3; other site 499177004660 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 499177004661 DHHA1 domain; Region: DHHA1; pfam02272 499177004662 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 499177004663 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 499177004664 trimerization site [polypeptide binding]; other site 499177004665 active site 499177004666 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 499177004667 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 499177004668 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177004669 catalytic residue [active] 499177004670 Helix-turn-helix domains; Region: HTH; cl00088 499177004671 Rrf2 family protein; Region: rrf2_super; TIGR00738 499177004672 recombination factor protein RarA; Reviewed; Region: PRK13342 499177004673 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 499177004674 Walker A motif; other site 499177004675 ATP binding site [chemical binding]; other site 499177004676 Walker B motif; other site 499177004677 arginine finger; other site 499177004678 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 499177004679 transcriptional repressor CodY; Validated; Region: PRK04158 499177004680 CodY GAF-like domain; Region: CodY; pfam06018 499177004681 Helix-turn-helix domains; Region: HTH; cl00088 499177004682 DNA topoisomerase I; Validated; Region: PRK05582 499177004683 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 499177004684 active site 499177004685 interdomain interaction site; other site 499177004686 putative metal-binding site [ion binding]; other site 499177004687 nucleotide binding site [chemical binding]; other site 499177004688 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 499177004689 domain I; other site 499177004690 DNA binding groove [nucleotide binding] 499177004691 phosphate binding site [ion binding]; other site 499177004692 domain II; other site 499177004693 domain III; other site 499177004694 nucleotide binding site [chemical binding]; other site 499177004695 catalytic site [active] 499177004696 domain IV; other site 499177004697 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 499177004698 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 499177004699 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 499177004700 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 499177004701 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 499177004702 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177004703 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 499177004704 NlpC/P60 family; Region: NLPC_P60; cl11438 499177004705 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; cl01542 499177004706 Baseplate J-like protein; Region: Baseplate_J; cl01294 499177004707 Protein of unknown function (DUF1371); Region: DUF1371; pfam07115 499177004708 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 499177004709 Predicted glycosyl hydrolase [General function prediction only]; Region: COG3858 499177004710 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 499177004711 putative peptidoglycan binding site; other site 499177004712 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 499177004713 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 499177004714 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 499177004715 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 499177004716 Phage capsid family; Region: Phage_capsid; pfam05065 499177004717 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 499177004718 Phage terminase large subunit; Region: Terminase_3; cl12054 499177004719 Terminase-like family; Region: Terminase_6; pfam03237 499177004720 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 499177004721 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177004722 Terminase small subunit; Region: Terminase_2; cl01513 499177004723 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177004724 DNA binding residues [nucleotide binding] 499177004725 Mu-like prophage protein Com; Region: Mu-like_Com; cl11540 499177004726 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 499177004727 Protein of unknown function (DUF1064); Region: DUF1064; pfam06356 499177004728 Dimeric dUTPase [Carbohydrate transport and metabolism]; Region: COG4508 499177004729 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 499177004730 dimer interface [polypeptide binding]; other site 499177004731 ssDNA binding site [nucleotide binding]; other site 499177004732 tetramer (dimer of dimers) interface [polypeptide binding]; other site 499177004733 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; cl15754 499177004734 cofactor binding site; other site 499177004735 DNA binding site [nucleotide binding] 499177004736 substrate interaction site [chemical binding]; other site 499177004737 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; cl15754 499177004738 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 499177004739 active site 499177004740 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004741 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 499177004742 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177004743 RecT family; Region: RecT; cl04285 499177004744 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177004745 AAA domain; Region: AAA_23; pfam13476 499177004746 Walker A/P-loop; other site 499177004747 ATP binding site [chemical binding]; other site 499177004748 endonuclease subunit; Provisional; Region: 46; PHA02562 499177004749 C-terminal peptidase (prc); Region: prc; TIGR00225 499177004750 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177004751 AntA/AntB antirepressor; Region: AntA; cl01430 499177004752 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 499177004753 non-specific DNA binding site [nucleotide binding]; other site 499177004754 salt bridge; other site 499177004755 sequence-specific DNA binding site [nucleotide binding]; other site 499177004756 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 499177004757 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 499177004758 non-specific DNA binding site [nucleotide binding]; other site 499177004759 salt bridge; other site 499177004760 sequence-specific DNA binding site [nucleotide binding]; other site 499177004761 Domain of unknown function (DUF955); Region: DUF955; cl01076 499177004762 Uncharacterized conserved protein [Function unknown]; Region: COG4748 499177004763 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 499177004764 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 499177004765 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 499177004766 catalytic residues [active] 499177004767 catalytic nucleophile [active] 499177004768 Recombinase; Region: Recombinase; pfam07508 499177004769 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 499177004770 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 499177004771 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177004772 Restriction endonuclease; Region: Mrr_cat; cl00516 499177004773 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 499177004774 Archaeal/vacuolar-type H+-ATPase subunit B [Energy production and conversion]; Region: NtpB; COG1156 499177004775 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 499177004776 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 499177004777 RNA/DNA hybrid binding site [nucleotide binding]; other site 499177004778 active site 499177004779 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 499177004780 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 499177004781 GTP/Mg2+ binding site [chemical binding]; other site 499177004782 G4 box; other site 499177004783 G5 box; other site 499177004784 G1 box; other site 499177004785 Switch I region; other site 499177004786 G2 box; other site 499177004787 G3 box; other site 499177004788 Switch II region; other site 499177004789 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 499177004790 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 499177004791 RimM N-terminal domain; Region: RimM; pfam01782 499177004792 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 499177004793 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 499177004794 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 499177004795 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 499177004796 signal recognition particle protein; Provisional; Region: PRK10867 499177004797 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 499177004798 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 499177004799 P loop; other site 499177004800 GTP binding site [chemical binding]; other site 499177004801 Signal peptide binding domain; Region: SRP_SPB; pfam02978 499177004802 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177004803 Putative helix-turn-helix protein, YlxM / p13 like; Region: UPF0122; pfam04297 499177004804 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 499177004805 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 499177004806 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 499177004807 P loop; other site 499177004808 GTP binding site [chemical binding]; other site 499177004809 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 499177004810 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 499177004811 Walker A/P-loop; other site 499177004812 ATP binding site [chemical binding]; other site 499177004813 Q-loop/lid; other site 499177004814 ABC transporter signature motif; other site 499177004815 D-loop; other site 499177004816 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 499177004817 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 499177004818 ABC transporter signature motif; other site 499177004819 Walker B; other site 499177004820 D-loop; other site 499177004821 H-loop/switch region; other site 499177004822 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177004823 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 499177004824 FeS/SAM binding site; other site 499177004825 ribonuclease III; Reviewed; Region: rnc; PRK00102 499177004826 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 499177004827 dimerization interface [polypeptide binding]; other site 499177004828 active site 499177004829 metal binding site [ion binding]; metal-binding site 499177004830 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 499177004831 elongation factor P; Validated; Region: PRK00529 499177004832 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 499177004833 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 499177004834 RNA binding site [nucleotide binding]; other site 499177004835 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 499177004836 RNA binding site [nucleotide binding]; other site 499177004837 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 499177004838 Response regulator receiver domain; Region: Response_reg; pfam00072 499177004839 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 499177004840 active site 499177004841 phosphorylation site [posttranslational modification] 499177004842 intermolecular recognition site; other site 499177004843 dimerization interface [polypeptide binding]; other site 499177004844 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 499177004845 trimer interface [polypeptide binding]; other site 499177004846 active site 499177004847 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 499177004848 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 499177004849 aspartate racemase; Region: asp_race; TIGR00035 499177004850 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 499177004851 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 499177004852 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 499177004853 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 499177004854 Predicted ATP-grasp enzyme [General function prediction only]; Region: COG3919 499177004855 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177004856 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 499177004857 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 499177004858 ADP binding site [chemical binding]; other site 499177004859 magnesium binding site [ion binding]; other site 499177004860 putative shikimate binding site; other site 499177004861 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase); Region: DHQase_I; cd00502 499177004862 3-dehydroquinate dehydratase, type I; Region: aroD; TIGR01093 499177004863 active site 499177004864 catalytic residue [active] 499177004865 dimer interface [polypeptide binding]; other site 499177004866 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 499177004867 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 499177004868 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 499177004869 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 499177004870 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 499177004871 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 499177004872 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 499177004873 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 499177004874 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 499177004875 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 499177004876 Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Region: PLDc_SMU_988_like_1; cd09154 499177004877 putative active site [active] 499177004878 catalytic site [active] 499177004879 Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Region: PLDc_SMU_988_like_2; cd09160 499177004880 putative active site [active] 499177004881 catalytic site [active] 499177004882 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 499177004883 Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) proteins VTC-2, -3 and- 4, and similar proteins; Region: PolyPPase_VTC_like; cd07750 499177004884 putative metal binding residues [ion binding]; other site 499177004885 signature motif; other site 499177004886 dimer interface [polypeptide binding]; other site 499177004887 active site 499177004888 polyP binding site; other site 499177004889 substrate binding site [chemical binding]; other site 499177004890 acceptor-phosphate pocket; other site 499177004891 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 499177004892 dimer interface [polypeptide binding]; other site 499177004893 phosphorylation site [posttranslational modification] 499177004894 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 499177004895 ATP binding site [chemical binding]; other site 499177004896 Mg2+ binding site [ion binding]; other site 499177004897 G-X-G motif; other site 499177004898 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 499177004899 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 499177004900 active site 499177004901 phosphorylation site [posttranslational modification] 499177004902 intermolecular recognition site; other site 499177004903 dimerization interface [polypeptide binding]; other site 499177004904 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 499177004905 DNA binding site [nucleotide binding] 499177004906 ornithine cyclodeaminase; Validated; Region: PRK08618 499177004907 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177004908 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 499177004909 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 499177004910 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 499177004911 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 499177004912 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 499177004913 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 499177004914 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 499177004915 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 499177004916 Walker A/P-loop; other site 499177004917 ATP binding site [chemical binding]; other site 499177004918 Q-loop/lid; other site 499177004919 ABC transporter signature motif; other site 499177004920 Walker B; other site 499177004921 D-loop; other site 499177004922 H-loop/switch region; other site 499177004923 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 499177004924 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 499177004925 dimer interface [polypeptide binding]; other site 499177004926 conserved gate region; other site 499177004927 putative PBP binding loops; other site 499177004928 ABC-ATPase subunit interface; other site 499177004929 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 499177004930 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 499177004931 substrate binding pocket [chemical binding]; other site 499177004932 membrane-bound complex binding site; other site 499177004933 hinge residues; other site 499177004934 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 499177004935 Sugar specificity; other site 499177004936 Pyrimidine base specificity; other site 499177004937 ATP-binding site [chemical binding]; other site 499177004938 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 499177004939 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 499177004940 Walker A/P-loop; other site 499177004941 ATP binding site [chemical binding]; other site 499177004942 Q-loop/lid; other site 499177004943 ABC transporter signature motif; other site 499177004944 Walker B; other site 499177004945 D-loop; other site 499177004946 H-loop/switch region; other site 499177004947 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 499177004948 DNA-binding site [nucleotide binding]; DNA binding site 499177004949 Nucleoside recognition; Region: Gate; cl00486 499177004950 Nucleoside recognition; Region: Gate; cl00486 499177004951 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 499177004952 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 499177004953 FeS/SAM binding site; other site 499177004954 Domain of unknown function (DUF4130; Region: DUF4130; cl14836 499177004955 EamA-like transporter family; Region: EamA; cl01037 499177004956 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 499177004957 EamA-like transporter family; Region: EamA; cl01037 499177004958 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 499177004959 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177004960 active site 499177004961 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177004962 active site 499177004963 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 499177004964 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 499177004965 substrate-cofactor binding pocket; other site 499177004966 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177004967 catalytic residue [active] 499177004968 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 499177004969 L-threonine dehydrogenase, extended (e) SDRs; Region: TDH_SDR_e; cd05272 499177004970 NAD binding site [chemical binding]; other site 499177004971 homodimer interface [polypeptide binding]; other site 499177004972 active site 499177004973 putative substrate binding site [chemical binding]; other site 499177004974 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 499177004975 Chemotaxis phosphatase CheX; Region: CheX; cl15816 499177004976 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 499177004977 Response regulator receiver domain; Region: Response_reg; pfam00072 499177004978 active site 499177004979 phosphorylation site [posttranslational modification] 499177004980 intermolecular recognition site; other site 499177004981 dimerization interface [polypeptide binding]; other site 499177004982 Chemotaxis phosphatase CheX; Region: CheX; cl15816 499177004983 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 499177004984 Helix-turn-helix domains; Region: HTH; cl00088 499177004985 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 499177004986 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_3; cd07241 499177004987 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 499177004988 putative metal binding site [ion binding]; other site 499177004989 EcsC protein family; Region: EcsC; pfam12787 499177004990 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 499177004991 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 499177004992 active site 499177004993 metal binding site [ion binding]; metal-binding site 499177004994 Flavin Reductases; Region: FlaRed; cl00801 499177004995 ABC-2 type transporter; Region: ABC2_membrane; cl11417 499177004996 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177004997 daunorubicin resistance ABC transporter ATP-binding subunit; Region: drrA; TIGR01188 499177004998 Walker A/P-loop; other site 499177004999 ATP binding site [chemical binding]; other site 499177005000 Q-loop/lid; other site 499177005001 ABC transporter signature motif; other site 499177005002 Walker B; other site 499177005003 D-loop; other site 499177005004 H-loop/switch region; other site 499177005005 Rifampin ADP-ribosyl transferase; Region: Arr-ms; pfam12120 499177005006 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 499177005007 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 499177005008 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 499177005009 putative active site [active] 499177005010 catalytic site [active] 499177005011 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 499177005012 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 499177005013 ATP binding site [chemical binding]; other site 499177005014 putative Mg++ binding site [ion binding]; other site 499177005015 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177005016 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 499177005017 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 499177005018 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 499177005019 DNA binding residues [nucleotide binding] 499177005020 TRAM domain; Region: TRAM; cl01282 499177005021 23S rRNA (uracil-5-)-methyltransferase RumA; Region: rumA; TIGR00479 499177005022 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; cl15754 499177005023 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 499177005024 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 499177005025 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]; Region: COG1453 499177005026 active site 499177005027 catalytic tetrad [active] 499177005028 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 499177005029 pyruvate kinase; Provisional; Region: PRK06354 499177005030 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cd00288 499177005031 domain interfaces; other site 499177005032 active site 499177005033 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 499177005034 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 499177005035 active site 499177005036 ADP/pyrophosphate binding site [chemical binding]; other site 499177005037 dimerization interface [polypeptide binding]; other site 499177005038 allosteric effector site; other site 499177005039 fructose-1,6-bisphosphate binding site; other site 499177005040 DNA polymerase III DnaE; Reviewed; Region: dnaE; PRK06826 499177005041 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 499177005042 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 499177005043 generic binding surface II; other site 499177005044 generic binding surface I; other site 499177005045 NMT1-like family; Region: NMT1_2; cl15260 499177005046 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 499177005047 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 499177005048 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 499177005049 Walker A/P-loop; other site 499177005050 ATP binding site [chemical binding]; other site 499177005051 Q-loop/lid; other site 499177005052 ABC transporter signature motif; other site 499177005053 Walker B; other site 499177005054 D-loop; other site 499177005055 H-loop/switch region; other site 499177005056 NIL domain; Region: NIL; cl09633 499177005057 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 499177005058 dimerization domain swap beta strand [polypeptide binding]; other site 499177005059 regulatory protein interface [polypeptide binding]; other site 499177005060 active site 499177005061 regulatory phosphorylation site [posttranslational modification]; other site 499177005062 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1481 499177005063 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 499177005064 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 499177005065 active site 499177005066 Ap6A binding site [chemical binding]; other site 499177005067 nudix motif; other site 499177005068 metal binding site [ion binding]; metal-binding site 499177005069 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 499177005070 putative substrate binding pocket [chemical binding]; other site 499177005071 dimer interface [polypeptide binding]; other site 499177005072 phosphate binding site [ion binding]; other site 499177005073 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 499177005074 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 499177005075 putative hydrolase; Validated; Region: PRK09248 499177005076 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 499177005077 FAD binding domain; Region: FAD_binding_4; pfam01565 499177005078 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 499177005079 MOSC domain; Region: MOSC; pfam03473 499177005080 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 499177005081 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 499177005082 FeS/SAM binding site; other site 499177005083 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 499177005084 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 499177005085 MPT binding site; other site 499177005086 trimer interface [polypeptide binding]; other site 499177005087 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 499177005088 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 499177005089 putative dimer interface [polypeptide binding]; other site 499177005090 [2Fe-2S] cluster binding site [ion binding]; other site 499177005091 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 499177005092 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 499177005093 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 499177005094 active site 499177005095 substrate binding site [chemical binding]; other site 499177005096 metal binding site [ion binding]; metal-binding site 499177005097 Protein of unknown function (DUF3954); Region: DUF3954; pfam13128 499177005098 Cobalt transport protein component CbiN; Region: CbiN; cl00842 499177005099 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 499177005100 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 499177005101 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 499177005102 intersubunit interface [polypeptide binding]; other site 499177005103 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 499177005104 hypothetical protein; Provisional; Region: PRK04164 499177005105 Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation,' the process of...; Region: Lipase_3; cd00519 499177005106 active site flap/lid [active] 499177005107 nucleophilic elbow; other site 499177005108 catalytic triad [active] 499177005109 Staphylococcal nuclease homologues; Region: SNc; smart00318 499177005110 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 499177005111 Catalytic site; other site 499177005112 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 499177005113 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 499177005114 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177005115 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 499177005116 phosphodiesterase; Provisional; Region: PRK12704 499177005117 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177005118 Zn2+ binding site [ion binding]; other site 499177005119 Mg2+ binding site [ion binding]; other site 499177005120 recombinase A; Provisional; Region: recA; PRK09354 499177005121 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 499177005122 hexamer interface [polypeptide binding]; other site 499177005123 Walker A motif; other site 499177005124 ATP binding site [chemical binding]; other site 499177005125 Walker B motif; other site 499177005126 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 499177005127 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 499177005128 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 499177005129 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 499177005130 FeS/SAM binding site; other site 499177005131 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 499177005132 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 499177005133 active site residue [active] 499177005134 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 499177005135 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177005136 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 499177005137 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 499177005138 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 499177005139 RNase E interface [polypeptide binding]; other site 499177005140 trimer interface [polypeptide binding]; other site 499177005141 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 499177005142 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 499177005143 RNase E interface [polypeptide binding]; other site 499177005144 trimer interface [polypeptide binding]; other site 499177005145 active site 499177005146 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 499177005147 putative nucleic acid binding region [nucleotide binding]; other site 499177005148 G-X-X-G motif; other site 499177005149 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 499177005150 RNA binding site [nucleotide binding]; other site 499177005151 domain interface; other site 499177005152 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 499177005153 16S/18S rRNA binding site [nucleotide binding]; other site 499177005154 S13e-L30e interaction site [polypeptide binding]; other site 499177005155 25S rRNA binding site [nucleotide binding]; other site 499177005156 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 499177005157 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 499177005158 active site 499177005159 Riboflavin kinase; Region: Flavokinase; cl03312 499177005160 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 499177005161 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 499177005162 RNA binding site [nucleotide binding]; other site 499177005163 active site 499177005164 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 499177005165 DHH family; Region: DHH; pfam01368 499177005166 DHHA1 domain; Region: DHHA1; pfam02272 499177005167 Ribosome-binding factor A; Region: RBFA; cl00542 499177005168 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 499177005169 translation initiation factor IF-2; Region: IF-2; TIGR00487 499177005170 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 499177005171 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 499177005172 G1 box; other site 499177005173 putative GEF interaction site [polypeptide binding]; other site 499177005174 GTP/Mg2+ binding site [chemical binding]; other site 499177005175 Switch I region; other site 499177005176 G2 box; other site 499177005177 G3 box; other site 499177005178 Switch II region; other site 499177005179 G4 box; other site 499177005180 G5 box; other site 499177005181 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 499177005182 Translation-initiation factor 2; Region: IF-2; pfam11987 499177005183 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 499177005184 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 499177005185 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 499177005186 putative RNA binding cleft [nucleotide binding]; other site 499177005187 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 499177005188 NusA N-terminal domain; Region: NusA_N; pfam08529 499177005189 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 499177005190 RNA binding site [nucleotide binding]; other site 499177005191 homodimer interface [polypeptide binding]; other site 499177005192 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 499177005193 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 499177005194 G-X-X-G motif; other site 499177005195 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 499177005196 ribosome maturation protein RimP; Reviewed; Region: PRK00092 499177005197 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 499177005198 Sm1 motif; other site 499177005199 predicted subunit interaction site [polypeptide binding]; other site 499177005200 RNA binding pocket [nucleotide binding]; other site 499177005201 Sm2 motif; other site 499177005202 DNA polymerase III PolC; Validated; Region: polC; PRK00448 499177005203 DNA polymerase III polC-type N-terminus; Region: DNA_pol3_alph_N; pfam11490 499177005204 polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two...; Region: polC_OBF; cd04484 499177005205 generic binding surface II; other site 499177005206 generic binding surface I; other site 499177005207 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 499177005208 active site 499177005209 catalytic site [active] 499177005210 substrate binding site [chemical binding]; other site 499177005211 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 499177005212 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 499177005213 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 499177005214 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 499177005215 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 499177005216 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 499177005217 active site 499177005218 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 499177005219 protein binding site [polypeptide binding]; other site 499177005220 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 499177005221 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 499177005222 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 499177005223 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 499177005224 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 499177005225 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 499177005226 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 499177005227 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 499177005228 catalytic residue [active] 499177005229 putative FPP diphosphate binding site; other site 499177005230 putative FPP binding hydrophobic cleft; other site 499177005231 dimer interface [polypeptide binding]; other site 499177005232 putative IPP diphosphate binding site; other site 499177005233 ribosome recycling factor; Reviewed; Region: frr; PRK00083 499177005234 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 499177005235 hinge region; other site 499177005236 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 499177005237 putative nucleotide binding site [chemical binding]; other site 499177005238 uridine monophosphate binding site [chemical binding]; other site 499177005239 homohexameric interface [polypeptide binding]; other site 499177005240 elongation factor Ts; Provisional; Region: tsf; PRK09377 499177005241 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 499177005242 Elongation factor TS; Region: EF_TS; pfam00889 499177005243 Elongation factor TS; Region: EF_TS; pfam00889 499177005244 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 499177005245 rRNA interaction site [nucleotide binding]; other site 499177005246 S8 interaction site; other site 499177005247 putative laminin-1 binding site; other site 499177005248 Protein of unknown function (DUF342); Region: DUF342; pfam03961 499177005249 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 499177005250 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 499177005251 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 499177005252 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 499177005253 DNA binding residues [nucleotide binding] 499177005254 CheD chemotactic sensory transduction; Region: CheD; cl00810 499177005255 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 499177005256 Chemotaxis phosphatase CheX; Region: CheX; cl15816 499177005257 Chemotaxis phosphatase CheX; Region: CheX; cl15816 499177005258 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 499177005259 putative CheA interaction surface; other site 499177005260 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 499177005261 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 499177005262 putative binding surface; other site 499177005263 active site 499177005264 P2 response regulator binding domain; Region: P2; pfam07194 499177005265 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 499177005266 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 499177005267 ATP binding site [chemical binding]; other site 499177005268 Mg2+ binding site [ion binding]; other site 499177005269 G-X-G motif; other site 499177005270 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 499177005271 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 499177005272 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 499177005273 active site 499177005274 phosphorylation site [posttranslational modification] 499177005275 intermolecular recognition site; other site 499177005276 dimerization interface [polypeptide binding]; other site 499177005277 CheB methylesterase; Region: CheB_methylest; pfam01339 499177005278 Flagellar protein YcgR; Region: YcgR_2; pfam12945 499177005279 PilZ domain; Region: PilZ; cl01260 499177005280 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 499177005281 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 499177005282 P-loop; other site 499177005283 ADP binding residues [chemical binding]; other site 499177005284 Switch I; other site 499177005285 Switch II; other site 499177005286 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 499177005287 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177005288 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 499177005289 FHIPEP family; Region: FHIPEP; pfam00771 499177005290 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 499177005291 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 499177005292 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 499177005293 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 499177005294 FliP family; Region: FliP; cl00593 499177005295 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 499177005296 Response regulator receiver domain; Region: Response_reg; pfam00072 499177005297 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 499177005298 active site 499177005299 phosphorylation site [posttranslational modification] 499177005300 intermolecular recognition site; other site 499177005301 dimerization interface [polypeptide binding]; other site 499177005302 flagellar motor switch protein; Validated; Region: PRK08119 499177005303 Chemotaxis phosphatase CheX; Region: CheX; cl15816 499177005304 Chemotaxis phosphatase CheX; Region: CheX; cl15816 499177005305 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 499177005306 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 499177005307 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 499177005308 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK07718 499177005309 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 499177005310 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 499177005311 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 499177005312 ligand binding site [chemical binding]; other site 499177005313 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 499177005314 flagellar motor protein MotA; Validated; Region: PRK08124 499177005315 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 499177005316 Flagellar protein (FlbD); Region: FlbD; cl00683 499177005317 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 499177005318 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 499177005319 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 499177005320 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 499177005321 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 499177005322 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 499177005323 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 499177005324 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 499177005325 flagellar protein export ATPase FliI; Region: FliI_clade2; TIGR03497 499177005326 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 499177005327 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 499177005328 Walker A motif/ATP binding site; other site 499177005329 Walker B motif; other site 499177005330 Flagellar biosynthesis/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliH; COG1317 499177005331 Plant ATP synthase F0; Region: YMF19; cl07975 499177005332 Flagellar assembly protein FliH; Region: FliH; pfam02108 499177005333 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 499177005334 FliG C-terminal domain; Region: FliG_C; pfam01706 499177005335 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 499177005336 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 499177005337 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 499177005338 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 499177005339 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 499177005340 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 499177005341 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 499177005342 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 499177005343 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 499177005344 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 499177005345 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 499177005346 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 499177005347 dimer interface [polypeptide binding]; other site 499177005348 conserved gate region; other site 499177005349 putative PBP binding loops; other site 499177005350 ABC-ATPase subunit interface; other site 499177005351 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 499177005352 dimer interface [polypeptide binding]; other site 499177005353 conserved gate region; other site 499177005354 putative PBP binding loops; other site 499177005355 ABC-ATPase subunit interface; other site 499177005356 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 499177005357 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required...; Region: ABC_PotA_N; cd03300 499177005358 Walker A/P-loop; other site 499177005359 ATP binding site [chemical binding]; other site 499177005360 Q-loop/lid; other site 499177005361 ABC transporter signature motif; other site 499177005362 Walker B; other site 499177005363 D-loop; other site 499177005364 H-loop/switch region; other site 499177005365 TOBE domain; Region: TOBE_2; cl01440 499177005366 teichoic acids export protein ATP-binding subunit; Provisional; Region: tagH; PRK13545 499177005367 Bacterial SH3 domain; Region: SH3_3; cl02551 499177005368 Uncharacterized BCR, COG1649; Region: DUF187; cl15398 499177005369 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 499177005370 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177005371 RNAse HI family that includes Archaeal RNase HI; Region: RNase_HI_archaeal_like; cd09279 499177005372 RNA/DNA hybrid binding site [nucleotide binding]; other site 499177005373 active site 499177005374 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]; Region: COG1606 499177005375 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily. Adenine 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_I; cd01990 499177005376 Ligand Binding Site [chemical binding]; other site 499177005377 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 499177005378 Putative zinc ribbon domain; Region: DUF164; pfam02591 499177005379 Uncharacterized conserved protein [Function unknown]; Region: COG0327 499177005380 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 499177005381 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177005382 RNA polymerase sigma factor RpoD; Validated; Region: PRK09210 499177005383 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 499177005384 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 499177005385 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 499177005386 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 499177005387 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 499177005388 DNA binding residues [nucleotide binding] 499177005389 DNA primase; Validated; Region: dnaG; PRK05667 499177005390 CHC2 zinc finger; Region: zf-CHC2; cl15369 499177005391 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 499177005392 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 499177005393 active site 499177005394 metal binding site [ion binding]; metal-binding site 499177005395 interdomain interaction site; other site 499177005396 NeuB family; Region: NeuB; cl00496 499177005397 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 499177005398 catalytic center binding site [active] 499177005399 ATP binding site [chemical binding]; other site 499177005400 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 499177005401 homooctamer interface [polypeptide binding]; other site 499177005402 active site 499177005403 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 499177005404 dihydropteroate synthase; Region: DHPS; TIGR01496 499177005405 substrate binding pocket [chemical binding]; other site 499177005406 dimer interface [polypeptide binding]; other site 499177005407 inhibitor binding site; inhibition site 499177005408 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 499177005409 homodecamer interface [polypeptide binding]; other site 499177005410 GTP cyclohydrolase I; Provisional; Region: PLN03044 499177005411 active site 499177005412 putative catalytic site residues [active] 499177005413 zinc binding site [ion binding]; other site 499177005414 GTP-CH-I/GFRP interaction surface; other site 499177005415 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cd00449 499177005416 homodimer interface [polypeptide binding]; other site 499177005417 substrate-cofactor binding pocket; other site 499177005418 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177005419 catalytic residue [active] 499177005420 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 499177005421 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 499177005422 chorismate binding enzyme; Region: Chorismate_bind; cl10555 499177005423 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 499177005424 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 499177005425 glutamine binding [chemical binding]; other site 499177005426 catalytic triad [active] 499177005427 hypothetical protein; Provisional; Region: PRK04435 499177005428 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 499177005429 DNA-binding interface [nucleotide binding]; DNA binding site 499177005430 C-terminal ACT domain of a small (; 147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains; Region: ACT_PheB-BS; cd04888 499177005431 transketolase; Reviewed; Region: PRK05899 499177005432 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 499177005433 TPP-binding site [chemical binding]; other site 499177005434 dimer interface [polypeptide binding]; other site 499177005435 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 499177005436 PYR/PP interface [polypeptide binding]; other site 499177005437 dimer interface [polypeptide binding]; other site 499177005438 TPP binding site [chemical binding]; other site 499177005439 pyruvate phosphate dikinase; Provisional; Region: PRK09279 499177005440 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 499177005441 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 499177005442 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 499177005443 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 499177005444 Helix-turn-helix domains; Region: HTH; cl00088 499177005445 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 499177005446 FOG: CBS domain [General function prediction only]; Region: COG0517 499177005447 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 499177005448 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 499177005449 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 499177005450 dimer interface [polypeptide binding]; other site 499177005451 motif 1; other site 499177005452 active site 499177005453 motif 2; other site 499177005454 motif 3; other site 499177005455 nascent polypeptide-associated complex protein; Reviewed; Region: nac; PRK06369 499177005456 Domain of unknown function (DUF4342); Region: DUF4342; pfam14242 499177005457 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 499177005458 Recombination protein O N terminal; Region: RecO_N; cl15812 499177005459 Recombination protein O C terminal; Region: RecO_C; pfam02565 499177005460 GTPase Era; Reviewed; Region: era; PRK00089 499177005461 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 499177005462 G1 box; other site 499177005463 GTP/Mg2+ binding site [chemical binding]; other site 499177005464 Switch I region; other site 499177005465 G2 box; other site 499177005466 Switch II region; other site 499177005467 G3 box; other site 499177005468 G4 box; other site 499177005469 G5 box; other site 499177005470 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 499177005471 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 499177005472 active site 499177005473 catalytic motif [active] 499177005474 Zn binding site [ion binding]; other site 499177005475 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 499177005476 PAP2_like proteins, diacylglycerol_kinase like sub-family. In some prokaryotes, PAP2_like phosphatase domains appear fused to E. coli DAGK-like trans-membrane diacylglycerol kinase domains. The cellular function of these architectures remains to be...; Region: PAP2_diacylglycerolkinase; cd03383 499177005477 active site 499177005478 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 499177005479 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 499177005480 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 499177005481 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177005482 Superoxide reductase-like (SORL) domain, class II; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals...; Region: SORL_classII; cd03172 499177005483 non-heme iron binding site [ion binding]; other site 499177005484 tetramer interface [polypeptide binding]; other site 499177005485 general stress protein 13; Validated; Region: PRK08059 499177005486 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_hs4; cd05692 499177005487 RNA binding site [nucleotide binding]; other site 499177005488 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177005489 SigmaW regulon antibacterial; Region: YdfA_immunity; cl12057 499177005490 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 499177005491 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_like; cd07021 499177005492 dimer interface [polypeptide binding]; other site 499177005493 active site residues [active] 499177005494 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 499177005495 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 499177005496 Major Facilitator Superfamily; Region: MFS_1; pfam07690 499177005497 putative substrate translocation pore; other site 499177005498 GatB domain; Region: GatB_Yqey; cl11497 499177005499 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 499177005500 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 499177005501 nucleotide binding site/active site [active] 499177005502 HIT family signature motif; other site 499177005503 catalytic residue [active] 499177005504 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 499177005505 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 499177005506 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 499177005507 FeS/SAM binding site; other site 499177005508 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 499177005509 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 499177005510 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 499177005511 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 499177005512 S-adenosylmethionine binding site [chemical binding]; other site 499177005513 chaperone protein DnaJ; Provisional; Region: PRK10767 499177005514 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 499177005515 HSP70 interaction site [polypeptide binding]; other site 499177005516 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 499177005517 Zn binding sites [ion binding]; other site 499177005518 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 499177005519 dimer interface [polypeptide binding]; other site 499177005520 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 499177005521 heat shock protein GrpE; Provisional; Region: PRK14140 499177005522 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 499177005523 dimer interface [polypeptide binding]; other site 499177005524 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 499177005525 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 499177005526 Helix-turn-helix domains; Region: HTH; cl00088 499177005527 HrcA protein C terminal domain; Region: HrcA; pfam01628 499177005528 coproporphyrinogen III oxidase; Provisional; Region: PRK05799 499177005529 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 499177005530 FeS/SAM binding site; other site 499177005531 HemN C-terminal domain; Region: HemN_C; pfam06969 499177005532 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 499177005533 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 499177005534 catalytic residues [active] 499177005535 nicotinate-nucleotide pyrophosphorylase; Region: nadC; TIGR00078 499177005536 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 499177005537 dimerization interface [polypeptide binding]; other site 499177005538 active site 499177005539 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177005540 FAD binding domain; Region: FAD_binding_2; pfam00890 499177005541 Quinolinate synthetase A protein; Region: NadA; cl00420 499177005542 GTP-binding protein LepA; Provisional; Region: PRK05433 499177005543 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 499177005544 G1 box; other site 499177005545 putative GEF interaction site [polypeptide binding]; other site 499177005546 GTP/Mg2+ binding site [chemical binding]; other site 499177005547 Switch I region; other site 499177005548 G2 box; other site 499177005549 G3 box; other site 499177005550 Switch II region; other site 499177005551 G4 box; other site 499177005552 G5 box; other site 499177005553 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 499177005554 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 499177005555 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 499177005556 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 499177005557 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 499177005558 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 499177005559 Competence protein; Region: Competence; cl00471 499177005560 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 499177005561 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177005562 Predicted acetyltransferase involved in intracellular survival and related acetyltransferases [General function prediction only]; Region: Eis; COG4552 499177005563 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 499177005564 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177005565 Protein of unknown function (DUF3006); Region: DUF3006; pfam11213 499177005566 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 499177005567 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 499177005568 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177005569 catalytic residue [active] 499177005570 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 499177005571 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177005572 competence damage-inducible protein A; Provisional; Region: PRK00549 499177005573 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 499177005574 putative MPT binding site; other site 499177005575 Competence-damaged protein; Region: CinA; cl00666 499177005576 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 499177005577 FMN binding site [chemical binding]; other site 499177005578 substrate binding site [chemical binding]; other site 499177005579 putative catalytic residue [active] 499177005580 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 499177005581 aromatic arch; other site 499177005582 DCoH dimer interaction site [polypeptide binding]; other site 499177005583 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 499177005584 DCoH tetramer interaction site [polypeptide binding]; other site 499177005585 substrate binding site [chemical binding]; other site 499177005586 Predicted membrane protein [Function unknown]; Region: COG4129 499177005587 HutD; Region: HutD; cl01532 499177005588 Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it, thus inhibiting its potentially lethal RNase activity inside the...; Region: Barstar_like; cl01048 499177005589 RNAase interaction site [polypeptide binding]; other site 499177005590 microbial_RNases. Ribonucleases (RNAses) cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. The alignment contains fungal RNases (U2, T1, F1, Th, Pb, N1, and Ms) and...; Region: microbial_RNases; cl00212 499177005591 active site 499177005592 Glutaminase; Region: Glutaminase; cl00907 499177005593 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 499177005594 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 499177005595 PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluF; cd02554 499177005596 probable active site [active] 499177005597 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 499177005598 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 499177005599 Walker A/P-loop; other site 499177005600 ATP binding site [chemical binding]; other site 499177005601 Q-loop/lid; other site 499177005602 ABC transporter signature motif; other site 499177005603 Walker B; other site 499177005604 D-loop; other site 499177005605 H-loop/switch region; other site 499177005606 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 499177005607 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 499177005608 ABC-ATPase subunit interface; other site 499177005609 dimer interface [polypeptide binding]; other site 499177005610 putative PBP binding regions; other site 499177005611 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 499177005612 Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct...; Region: YvrC; cd01143 499177005613 putative binding site residues; other site 499177005614 Tetrahydrodipicolinate succinyltransferase N-terminal; Region: DapH_N; pfam08503 499177005615 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Region: DapD_Ac; TIGR03532 499177005616 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 499177005617 active site 499177005618 trimer interface [polypeptide binding]; other site 499177005619 substrate binding site [chemical binding]; other site 499177005620 CoA binding site [chemical binding]; other site 499177005621 dihydrodipicolinate reductase; Provisional; Region: PRK00048 499177005622 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177005623 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 499177005624 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 499177005625 dihydrodipicolinate synthase; Region: dapA; TIGR00674 499177005626 dimer interface [polypeptide binding]; other site 499177005627 active site 499177005628 catalytic residue [active] 499177005629 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 499177005630 putative deacylase active site [active] 499177005631 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 499177005632 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 499177005633 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177005634 metal binding site [ion binding]; metal-binding site 499177005635 active site 499177005636 I-site; other site 499177005637 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 499177005638 GAF domain; Region: GAF; cl15785 499177005639 Protein of unknown function (DUF342); Region: DUF342; pfam03961 499177005640 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 499177005641 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 499177005642 putative ATP binding site [chemical binding]; other site 499177005643 putative substrate interface [chemical binding]; other site 499177005644 flagellar capping protein; Validated; Region: fliD; PRK07737 499177005645 hypothetical protein; Provisional; Region: PRK13670 499177005646 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 499177005647 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 499177005648 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 499177005649 active site 499177005650 (T/H)XGH motif; other site 499177005651 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 499177005652 S-adenosylmethionine binding site [chemical binding]; other site 499177005653 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 499177005654 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 499177005655 generic binding surface II; other site 499177005656 ssDNA binding site; other site 499177005657 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 499177005658 ATP binding site [chemical binding]; other site 499177005659 putative Mg++ binding site [ion binding]; other site 499177005660 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 499177005661 nucleotide binding region [chemical binding]; other site 499177005662 ATP-binding site [chemical binding]; other site 499177005663 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 499177005664 DAK2 domain; Region: Dak2; cl03685 499177005665 Uncharacterized protein, DegV family COG1307; Region: DegV; cl00577 499177005666 Asp23 family; Region: Asp23; cl00574 499177005667 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 499177005668 Thiamine pyrophosphokinase; Region: TPK; cd07995 499177005669 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 499177005670 active site 499177005671 dimerization interface [polypeptide binding]; other site 499177005672 thiamine binding site [chemical binding]; other site 499177005673 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 499177005674 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 499177005675 substrate binding site [chemical binding]; other site 499177005676 hexamer interface [polypeptide binding]; other site 499177005677 metal binding site [ion binding]; metal-binding site 499177005678 GTPase RsgA; Reviewed; Region: PRK00098 499177005679 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 499177005680 RNA binding site [nucleotide binding]; other site 499177005681 homodimer interface [polypeptide binding]; other site 499177005682 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 499177005683 GTPase/Zn-binding domain interface [polypeptide binding]; other site 499177005684 GTP/Mg2+ binding site [chemical binding]; other site 499177005685 G4 box; other site 499177005686 G5 box; other site 499177005687 G1 box; other site 499177005688 Switch I region; other site 499177005689 G2 box; other site 499177005690 G3 box; other site 499177005691 Switch II region; other site 499177005692 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 499177005693 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 499177005694 active site 499177005695 ATP binding site [chemical binding]; other site 499177005696 substrate binding site [chemical binding]; other site 499177005697 activation loop (A-loop); other site 499177005698 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 499177005699 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 499177005700 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 499177005701 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 499177005702 active site 499177005703 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14454 499177005704 16S rRNA methyltransferase B; Provisional; Region: PRK14902 499177005705 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 499177005706 putative RNA binding site [nucleotide binding]; other site 499177005707 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 499177005708 S-adenosylmethionine binding site [chemical binding]; other site 499177005709 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; cl01049 499177005710 Protein of unknown function DUF116; Region: DUF116; cl00800 499177005711 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 499177005712 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 499177005713 putative active site [active] 499177005714 substrate binding site [chemical binding]; other site 499177005715 putative cosubstrate binding site; other site 499177005716 catalytic site [active] 499177005717 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 499177005718 substrate binding site [chemical binding]; other site 499177005719 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 499177005720 active site 499177005721 catalytic residues [active] 499177005722 metal binding site [ion binding]; metal-binding site 499177005723 primosome assembly protein PriA; Validated; Region: PRK05580 499177005724 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 499177005725 ATP binding site [chemical binding]; other site 499177005726 putative Mg++ binding site [ion binding]; other site 499177005727 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177005728 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 499177005729 Flavoprotein; Region: Flavoprotein; cl08021 499177005730 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 499177005731 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 499177005732 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 499177005733 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 499177005734 catalytic site [active] 499177005735 G-X2-G-X-G-K; other site 499177005736 Domain of unknown function (DUF370); Region: DUF370; cl00898 499177005737 hypothetical protein; Provisional; Region: PRK11820 499177005738 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 499177005739 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 499177005740 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 499177005741 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 499177005742 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 499177005743 Fibronectin-binding protein A N-terminus (FbpA); Region: FbpA; pfam05833 499177005744 Domain of unknown function (DUF814); Region: DUF814; pfam05670 499177005745 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 499177005746 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 499177005747 Transcriptional regulator [Transcription]; Region: LysR; COG0583 499177005748 Helix-turn-helix domains; Region: HTH; cl00088 499177005749 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 499177005750 dimerization interface [polypeptide binding]; other site 499177005751 Permease family; Region: Xan_ur_permease; pfam00860 499177005752 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 499177005753 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177005754 active site 499177005755 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 499177005756 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 499177005757 RNA binding surface [nucleotide binding]; other site 499177005758 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 499177005759 active site 499177005760 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 499177005761 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 499177005762 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 499177005763 active site 499177005764 HIGH motif; other site 499177005765 dimer interface [polypeptide binding]; other site 499177005766 KMSKS motif; other site 499177005767 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 499177005768 Low molecular weight phosphatase family; Region: LMWPc; cd00115 499177005769 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 499177005770 active site 499177005771 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 499177005772 MatE; Region: MatE; cl10513 499177005773 MatE; Region: MatE; cl10513 499177005774 Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: IleS; COG0060 499177005775 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 499177005776 HIGH motif; other site 499177005777 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 499177005778 active site 499177005779 KMSKS motif; other site 499177005780 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 499177005781 tRNA binding surface [nucleotide binding]; other site 499177005782 anticodon binding site; other site 499177005783 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 499177005784 DivIVA protein; Region: DivIVA; pfam05103 499177005785 DivIVA domain; Region: DivI1A_domain; TIGR03544 499177005786 Uncharacterized conserved protein, contains S4-like domain [Function unknown]; Region: COG2302 499177005787 YGGT family; Region: YGGT; cl00508 499177005788 Protein of unknown function (DUF552); Region: DUF552; cl00775 499177005789 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 499177005790 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 499177005791 catalytic residue [active] 499177005792 HlyD family secretion protein; Region: HlyD_2; pfam12700 499177005793 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 499177005794 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 499177005795 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177005796 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 499177005797 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 499177005798 GTP-binding protein Der; Reviewed; Region: PRK00093 499177005799 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 499177005800 G1 box; other site 499177005801 GTP/Mg2+ binding site [chemical binding]; other site 499177005802 Switch I region; other site 499177005803 G2 box; other site 499177005804 Switch II region; other site 499177005805 G3 box; other site 499177005806 G4 box; other site 499177005807 G5 box; other site 499177005808 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 499177005809 G1 box; other site 499177005810 GTP/Mg2+ binding site [chemical binding]; other site 499177005811 Switch I region; other site 499177005812 G2 box; other site 499177005813 G3 box; other site 499177005814 Switch II region; other site 499177005815 G4 box; other site 499177005816 G5 box; other site 499177005817 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 499177005818 putative FeS-containing Cyanobacterial-specific oxidoreductase; Region: cyano_FeS_chp; TIGR03279 499177005819 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 499177005820 Protein of unknown function (DUF512); Region: DUF512; pfam04459 499177005821 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 499177005822 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 499177005823 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 499177005824 dimer interface [polypeptide binding]; other site 499177005825 phosphorylation site [posttranslational modification] 499177005826 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 499177005827 ATP binding site [chemical binding]; other site 499177005828 Mg2+ binding site [ion binding]; other site 499177005829 G-X-G motif; other site 499177005830 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 499177005831 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 499177005832 active site 499177005833 phosphorylation site [posttranslational modification] 499177005834 intermolecular recognition site; other site 499177005835 dimerization interface [polypeptide binding]; other site 499177005836 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 499177005837 DNA binding site [nucleotide binding] 499177005838 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 499177005839 ATP cone domain; Region: ATP-cone; pfam03477 499177005840 cell division protein FtsZ; Region: ftsZ; TIGR00065 499177005841 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 499177005842 nucleotide binding site [chemical binding]; other site 499177005843 SulA interaction site; other site 499177005844 Protein of unknown function (DUF1290); Region: DUF1290; cl01587 499177005845 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 499177005846 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 499177005847 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 499177005848 Cell division protein FtsQ; Region: FtsQ; pfam03799 499177005849 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 499177005850 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 499177005851 active site 499177005852 homodimer interface [polypeptide binding]; other site 499177005853 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 499177005854 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK14106 499177005855 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 499177005856 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 499177005857 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 499177005858 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 499177005859 Mg++ binding site [ion binding]; other site 499177005860 putative catalytic motif [active] 499177005861 putative substrate binding site [chemical binding]; other site 499177005862 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 499177005863 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 499177005864 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 499177005865 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 499177005866 stage V sporulation protein D; Region: spoVD_pbp; TIGR02214 499177005867 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 499177005868 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 499177005869 PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and...; Region: PASTA; cl02768 499177005870 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 499177005871 Septum formation initiator; Region: DivIC; cl11433 499177005872 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 499177005873 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177005874 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 499177005875 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 499177005876 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 499177005877 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 499177005878 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 499177005879 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 499177005880 GTP-binding protein YchF; Reviewed; Region: PRK09601 499177005881 YchF GTPase; Region: YchF; cd01900 499177005882 G1 box; other site 499177005883 GTP/Mg2+ binding site [chemical binding]; other site 499177005884 Switch I region; other site 499177005885 G2 box; other site 499177005886 Switch II region; other site 499177005887 G3 box; other site 499177005888 G4 box; other site 499177005889 G5 box; other site 499177005890 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 499177005891 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 499177005892 non-specific DNA binding site [nucleotide binding]; other site 499177005893 salt bridge; other site 499177005894 sequence-specific DNA binding site [nucleotide binding]; other site 499177005895 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 499177005896 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177005897 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 499177005898 active site 499177005899 catalytic site [active] 499177005900 substrate binding site [chemical binding]; other site 499177005901 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 499177005902 Family description; Region: UvrD_C_2; cl15862 499177005903 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177005904 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 499177005905 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 499177005906 metal binding site [ion binding]; metal-binding site 499177005907 dimer interface [polypeptide binding]; other site 499177005908 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 499177005909 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 499177005910 dimer interface [polypeptide binding]; other site 499177005911 PYR/PP interface [polypeptide binding]; other site 499177005912 TPP binding site [chemical binding]; other site 499177005913 substrate binding site [chemical binding]; other site 499177005914 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 499177005915 Domain of unknown function; Region: EKR; cl11037 499177005916 4Fe-4S binding domain; Region: Fer4; cl02805 499177005917 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 499177005918 TPP-binding site [chemical binding]; other site 499177005919 dimer interface [polypeptide binding]; other site 499177005920 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 499177005921 intersubunit interface [polypeptide binding]; other site 499177005922 active site 499177005923 catalytic residue [active] 499177005924 Propanediol utilisation protein PduL; Region: PduL; pfam06130 499177005925 Propanediol utilisation protein PduL; Region: PduL; pfam06130 499177005926 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177005927 GAF domain; Region: GAF; cl15785 499177005928 GAF domain; Region: GAF_2; pfam13185 499177005929 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 499177005930 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 499177005931 Protein of unknown function (DUF1461); Region: DUF1461; cl01862 499177005932 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177005933 active site 499177005934 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 499177005935 threonine-phosphate decarboxylase; Provisional; Region: PRK06358 499177005936 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 499177005937 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177005938 homodimer interface [polypeptide binding]; other site 499177005939 catalytic residue [active] 499177005940 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 499177005941 putative active site [active] 499177005942 putative CoA binding site [chemical binding]; other site 499177005943 nudix motif; other site 499177005944 metal binding site [ion binding]; metal-binding site 499177005945 EamA-like transporter family; Region: EamA; cl01037 499177005946 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 499177005947 EamA-like transporter family; Region: EamA; cl01037 499177005948 Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is...; Region: Sortase; cl09098 499177005949 active site 499177005950 catalytic site [active] 499177005951 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 499177005952 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 499177005953 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 499177005954 dimer interface [polypeptide binding]; other site 499177005955 PYR/PP interface [polypeptide binding]; other site 499177005956 TPP binding site [chemical binding]; other site 499177005957 substrate binding site [chemical binding]; other site 499177005958 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 499177005959 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 499177005960 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 499177005961 TPP-binding site; other site 499177005962 4Fe-4S binding domain; Region: Fer4; cl02805 499177005963 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 499177005964 diiron binding motif [ion binding]; other site 499177005965 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 499177005966 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 499177005967 active site 499177005968 phosphorylation site [posttranslational modification] 499177005969 intermolecular recognition site; other site 499177005970 dimerization interface [polypeptide binding]; other site 499177005971 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 499177005972 DNA binding residues [nucleotide binding] 499177005973 dimerization interface [polypeptide binding]; other site 499177005974 Sensor protein DegS; Region: DegS; pfam05384 499177005975 Histidine kinase; Region: HisKA_3; pfam07730 499177005976 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 499177005977 ATP binding site [chemical binding]; other site 499177005978 Mg2+ binding site [ion binding]; other site 499177005979 G-X-G motif; other site 499177005980 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 499177005981 putative CheA interaction surface; other site 499177005982 Bacterial protein of unknown function (DUF896); Region: DUF896; cl01722 499177005983 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 499177005984 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 499177005985 DNA-binding site [nucleotide binding]; DNA binding site 499177005986 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 499177005987 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177005988 homodimer interface [polypeptide binding]; other site 499177005989 catalytic residue [active] 499177005990 Transcriptional regulators [Transcription]; Region: PurR; COG1609 499177005991 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 499177005992 DNA binding site [nucleotide binding] 499177005993 domain linker motif; other site 499177005994 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 499177005995 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 499177005996 S-adenosylmethionine binding site [chemical binding]; other site 499177005997 Phosphopantetheine attachment site; Region: PP-binding; cl09936 499177005998 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 499177005999 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 499177006000 active site 499177006001 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 499177006002 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 499177006003 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 499177006004 active site 499177006005 metal binding site [ion binding]; metal-binding site 499177006006 homotetramer interface [polypeptide binding]; other site 499177006007 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177006008 metal binding site [ion binding]; metal-binding site 499177006009 active site 499177006010 I-site; other site 499177006011 Domain of unknown function DUF21; Region: DUF21; pfam01595 499177006012 gliding motility-associated protein GldE; Region: GldE; TIGR03520 499177006013 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 499177006014 Transporter associated domain; Region: CorC_HlyC; cl08393 499177006015 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 499177006016 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 499177006017 active site 499177006018 nucleotide binding site [chemical binding]; other site 499177006019 HIGH motif; other site 499177006020 KMSKS motif; other site 499177006021 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177006022 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177006023 PspC domain; Region: PspC; cl00864 499177006024 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 499177006025 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 499177006026 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 499177006027 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 499177006028 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 499177006029 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177006030 Predicted dehydrogenase [General function prediction only]; Region: COG0579 499177006031 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177006032 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 499177006033 glycerol kinase; Provisional; Region: glpK; PRK00047 499177006034 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 499177006035 N- and C-terminal domain interface [polypeptide binding]; other site 499177006036 active site 499177006037 MgATP binding site [chemical binding]; other site 499177006038 catalytic site [active] 499177006039 metal binding site [ion binding]; metal-binding site 499177006040 glycerol binding site [chemical binding]; other site 499177006041 homotetramer interface [polypeptide binding]; other site 499177006042 homodimer interface [polypeptide binding]; other site 499177006043 FBP binding site [chemical binding]; other site 499177006044 protein IIAGlc interface [polypeptide binding]; other site 499177006045 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cl00200 499177006046 amphipathic channel; other site 499177006047 Asn-Pro-Ala signature motifs; other site 499177006048 Glycerol-3-phosphate responsive antiterminator; Region: G3P_antiterm; cl00852 499177006049 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 499177006050 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 499177006051 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 499177006052 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 499177006053 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 499177006054 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 499177006055 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 499177006056 Active site serine [active] 499177006057 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177006058 active site 499177006059 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 499177006060 Zeta-crystallin with NADP-dependent quinone reductase activity (QOR); Region: zeta_crystallin; cd08253 499177006061 NAD(P) binding site [chemical binding]; other site 499177006062 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 499177006063 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 499177006064 Helix-turn-helix domains; Region: HTH; cl00088 499177006065 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 499177006066 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 499177006067 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 499177006068 ATP binding site [chemical binding]; other site 499177006069 putative Mg++ binding site [ion binding]; other site 499177006070 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 499177006071 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 499177006072 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 499177006073 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 499177006074 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 499177006075 HsdM N-terminal domain; Region: HsdM_N; pfam12161 499177006076 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177006077 Domain of unknown function DUF302; Region: DUF302; cl01364 499177006078 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177006079 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 499177006080 Tetratricopeptide repeat; Region: TPR_12; pfam13424 499177006081 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 499177006082 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177006083 Coenzyme A binding pocket [chemical binding]; other site 499177006084 OPT oligopeptide transporter protein; Region: OPT; cl14607 499177006085 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 499177006086 Putative cyclase; Region: Cyclase; cl00814 499177006087 D-cysteine desulfhydrase; Validated; Region: PRK03910 499177006088 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 499177006089 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177006090 catalytic residue [active] 499177006091 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 499177006092 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 499177006093 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177006094 catalytic residue [active] 499177006095 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 499177006096 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 499177006097 DNA binding site [nucleotide binding] 499177006098 active site 499177006099 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 499177006100 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 499177006101 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 499177006102 Clp amino terminal domain; Region: Clp_N; pfam02861 499177006103 Clp amino terminal domain; Region: Clp_N; pfam02861 499177006104 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 499177006105 Walker A motif; other site 499177006106 ATP binding site [chemical binding]; other site 499177006107 Walker B motif; other site 499177006108 arginine finger; other site 499177006109 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 499177006110 Walker A motif; other site 499177006111 ATP binding site [chemical binding]; other site 499177006112 Walker B motif; other site 499177006113 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 499177006114 Indigoidine synthase A like protein; Region: Indigoidine_A; cl00983 499177006115 putative kinase; Provisional; Region: PRK09954 499177006116 Helix-turn-helix domains; Region: HTH; cl00088 499177006117 YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; Region: YeiC_kinase_like; cd01941 499177006118 substrate binding site [chemical binding]; other site 499177006119 ATP binding site [chemical binding]; other site 499177006120 MgtC family; Region: MgtC; pfam02308 499177006121 TraX protein; Region: TraX; cl05434 499177006122 conjugal transfer protein TrbP; Provisional; Region: PRK13882 499177006123 heat shock protein 90; Provisional; Region: PRK05218 499177006124 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 499177006125 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 499177006126 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 499177006127 substrate binding site [chemical binding]; other site 499177006128 active site 499177006129 catalytic residues [active] 499177006130 heterodimer interface [polypeptide binding]; other site 499177006131 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 499177006132 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 499177006133 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177006134 catalytic residue [active] 499177006135 NeuB family; Region: NeuB; cl00496 499177006136 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 499177006137 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric; Region: PRAI; cd00405 499177006138 active site 499177006139 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 499177006140 active site 499177006141 ribulose/triose binding site [chemical binding]; other site 499177006142 phosphate binding site [ion binding]; other site 499177006143 substrate (anthranilate) binding pocket [chemical binding]; other site 499177006144 product (indole) binding pocket [chemical binding]; other site 499177006145 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 499177006146 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 499177006147 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 499177006148 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 499177006149 Glutamine amidotransferase class-I; Region: GATase; pfam00117 499177006150 glutamine binding [chemical binding]; other site 499177006151 catalytic triad [active] 499177006152 anthranilate synthase component I, non-proteobacterial lineages; Region: trpE_most; TIGR00564 499177006153 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 499177006154 chorismate binding enzyme; Region: Chorismate_bind; cl10555 499177006155 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 499177006156 4Fe-4S binding domain; Region: Fer4; cl02805 499177006157 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 499177006158 ZIP Zinc transporter; Region: Zip; pfam02535 499177006159 Protein of unknown function (DUF523); Region: DUF523; cl00733 499177006160 Rrf2 family protein; Region: rrf2_super; TIGR00738 499177006161 Helix-turn-helix domains; Region: HTH; cl00088 499177006162 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 499177006163 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 499177006164 Phosphotransferase system, EIIC; Region: PTS_EIIC_2; pfam13303 499177006165 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 499177006166 Helix-turn-helix domains; Region: HTH; cl00088 499177006167 3H domain; Region: 3H; pfam02829 499177006168 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177006169 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 499177006170 Bleomycin binding protein (BLMA) and similar proteins; BLMA confers bleomycin (Bm) resistance by directly binding to Bm; Region: BLMA_like; cd08349 499177006171 dimer interface [polypeptide binding]; other site 499177006172 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 499177006173 ligand binding site [chemical binding]; other site 499177006174 ThiC family; Region: ThiC; cl08031 499177006175 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 499177006176 thiamine phosphate binding site [chemical binding]; other site 499177006177 active site 499177006178 pyrophosphate binding site [ion binding]; other site 499177006179 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 499177006180 substrate binding site [chemical binding]; other site 499177006181 multimerization interface [polypeptide binding]; other site 499177006182 ATP binding site [chemical binding]; other site 499177006183 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 499177006184 dimer interface [polypeptide binding]; other site 499177006185 substrate binding site [chemical binding]; other site 499177006186 ATP binding site [chemical binding]; other site 499177006187 Thiamine-precursor transporter protein (ThiW); Region: ThiW; cl01952 499177006188 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 499177006189 M42 Peptidase, Endoglucanase-like subfamily; Region: M42_glucanase_like; cd05657 499177006190 putative oligomer interface [polypeptide binding]; other site 499177006191 putative active site [active] 499177006192 metal binding site [ion binding]; metal-binding site 499177006193 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 499177006194 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 499177006195 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177006196 catalytic residue [active] 499177006197 Sulphur transport; Region: Sulf_transp; cl01018 499177006198 SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response...; Region: SirA_like_N; cd03421 499177006199 CPxP motif; other site 499177006200 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 499177006201 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 499177006202 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 499177006203 S-adenosylmethionine binding site [chemical binding]; other site 499177006204 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 499177006205 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 499177006206 trimer interface [polypeptide binding]; other site 499177006207 putative metal binding site [ion binding]; other site 499177006208 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 499177006209 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 499177006210 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 499177006211 phosphate binding site [ion binding]; other site 499177006212 This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion; Region: Fer4_NifH_child; cd03110 499177006213 P loop nucleotide binding; other site 499177006214 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 499177006215 switch II; other site 499177006216 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 499177006217 This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion; Region: Fer4_NifH_child; cd03110 499177006218 P loop nucleotide binding; other site 499177006219 switch II; other site 499177006220 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 499177006221 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1655 499177006222 Uncharacterized protein conserved in bacteria (DUF2225); Region: DUF2225; pfam09986 499177006223 alanyl-tRNA synthetase; Provisional; Region: alaS; PRK13902 499177006224 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 499177006225 DHHA1 domain; Region: DHHA1; pfam02272 499177006226 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 499177006227 active site 499177006228 putative catalytic site [active] 499177006229 DNA binding site [nucleotide binding] 499177006230 putative phosphate binding site [ion binding]; other site 499177006231 metal binding site A [ion binding]; metal-binding site 499177006232 AP binding site [nucleotide binding]; other site 499177006233 metal binding site B [ion binding]; metal-binding site 499177006234 sulfite reductase, subunit C; Region: sulfite_red_C; TIGR02912 499177006235 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 499177006236 4Fe-4S binding domain; Region: Fer4; cl02805 499177006237 anaerobic sulfite reductase subunit B; Provisional; Region: PRK08221 499177006238 Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is...; Region: sulfite_reductase_like; cd06221 499177006239 FAD binding pocket [chemical binding]; other site 499177006240 FAD binding motif [chemical binding]; other site 499177006241 phosphate binding motif [ion binding]; other site 499177006242 beta-alpha-beta structure motif; other site 499177006243 NAD binding pocket [chemical binding]; other site 499177006244 Iron coordination center [ion binding]; other site 499177006245 anaerobic sulfite reductase subunit A; Provisional; Region: PRK15055 499177006246 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 499177006247 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 499177006248 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 499177006249 dimer interface [polypeptide binding]; other site 499177006250 decamer (pentamer of dimers) interface [polypeptide binding]; other site 499177006251 catalytic triad [active] 499177006252 peroxidatic and resolving cysteines [active] 499177006253 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 499177006254 ligand binding site [chemical binding]; other site 499177006255 flexible hinge region; other site 499177006256 Helix-turn-helix domains; Region: HTH; cl00088 499177006257 HAD superfamily (subfamily IA) hydrolase, TIGR02254; Region: YjjG/YfnB 499177006258 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 499177006259 active site 499177006260 motif I; other site 499177006261 motif II; other site 499177006262 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 499177006263 octamerization interface [polypeptide binding]; other site 499177006264 diferric-oxygen binding site [ion binding]; other site 499177006265 Arginase family; Region: Arginase; cl00306 499177006266 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 499177006267 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177006268 Coenzyme A binding pocket [chemical binding]; other site 499177006269 Uncharacterized vancomycin resistance protein [Defense mechanisms]; Region: COG2720 499177006270 VanW like protein; Region: VanW; pfam04294 499177006271 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 499177006272 Helix-turn-helix domains; Region: HTH; cl00088 499177006273 Integrase core domain; Region: rve; cl01316 499177006274 methionine gamma-lyase; Provisional; Region: PRK06234 499177006275 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 499177006276 homodimer interface [polypeptide binding]; other site 499177006277 substrate-cofactor binding pocket; other site 499177006278 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177006279 catalytic residue [active] 499177006280 Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]; Region: TyrR; COG3283 499177006281 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 499177006282 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 499177006283 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 499177006284 Walker A motif; other site 499177006285 ATP binding site [chemical binding]; other site 499177006286 Walker B motif; other site 499177006287 arginine finger; other site 499177006288 Helix-turn-helix domains; Region: HTH; cl00088 499177006289 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 499177006290 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 499177006291 HIGH motif; other site 499177006292 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 499177006293 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 499177006294 active site 499177006295 KMSKS motif; other site 499177006296 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 499177006297 tRNA binding surface [nucleotide binding]; other site 499177006298 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 499177006299 Helix-turn-helix domains; Region: HTH; cl00088 499177006300 Haemolysin-III related; Region: HlyIII; cl03831 499177006301 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 499177006302 non-specific DNA binding site [nucleotide binding]; other site 499177006303 salt bridge; other site 499177006304 sequence-specific DNA binding site [nucleotide binding]; other site 499177006305 Bacillus subtilis copper-sensitive operon repressor (BsCsoR), and related domains; this family was previously known as part of DUF156; Region: BsCsoR-like_DUF156; cd10157 499177006306 putative homodimer interface [polypeptide binding]; other site 499177006307 putative homotetramer interface [polypeptide binding]; other site 499177006308 allosteric switch controlling residues; other site 499177006309 putative metal binding site [ion binding]; other site 499177006310 putative homodimer-homodimer interface [polypeptide binding]; other site 499177006311 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 499177006312 metal-binding site [ion binding] 499177006313 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 499177006314 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 499177006315 metal-binding site [ion binding] 499177006316 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 499177006317 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 499177006318 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 499177006319 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 499177006320 active site 499177006321 phosphorylation site [posttranslational modification] 499177006322 intermolecular recognition site; other site 499177006323 dimerization interface [polypeptide binding]; other site 499177006324 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177006325 Zn2+ binding site [ion binding]; other site 499177006326 Mg2+ binding site [ion binding]; other site 499177006327 Tetratricopeptide repeat; Region: TPR_12; pfam13424 499177006328 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 499177006329 TPR motif; other site 499177006330 binding surface 499177006331 TPR repeat; Region: TPR_11; pfam13414 499177006332 Tetratricopeptide repeat; Region: TPR_12; pfam13424 499177006333 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177006334 metal binding site [ion binding]; metal-binding site 499177006335 active site 499177006336 I-site; other site 499177006337 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 499177006338 Sulfate transporter family; Region: Sulfate_transp; cl15842 499177006339 Sulfate transporter family; Region: Sulfate_transp; cl15842 499177006340 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 499177006341 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 499177006342 translation initiation factor IF-2 subunit beta; Provisional; Region: PRK12336 499177006343 potential frameshift: common BLAST hit: gi|150391759|ref|YP_001321808.1| PAS/PAC sensor protein 499177006344 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 499177006345 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 499177006346 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 499177006347 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 499177006348 Putative Fe-S cluster; Region: FeS; pfam04060 499177006349 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 499177006350 PAS domain; Region: PAS_9; pfam13426 499177006351 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 499177006352 synthetase active site [active] 499177006353 NTP binding site [chemical binding]; other site 499177006354 metal binding site [ion binding]; metal-binding site 499177006355 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177006356 Zn2+ binding site [ion binding]; other site 499177006357 Mg2+ binding site [ion binding]; other site 499177006358 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177006359 Zn2+ binding site [ion binding]; other site 499177006360 Mg2+ binding site [ion binding]; other site 499177006361 FOG: CBS domain [General function prediction only]; Region: COG0517 499177006362 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 499177006363 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 499177006364 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 499177006365 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 499177006366 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 499177006367 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 499177006368 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177006369 metal binding site [ion binding]; metal-binding site 499177006370 active site 499177006371 I-site; other site 499177006372 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 499177006373 N-Utilization Substance G (NusG) N terminal (NGN) insert and Lin0431 are part of DUF1312; Region: DUF1312; cd09846 499177006374 Uncharacterized conserved protein [Function unknown]; Region: COG1284 499177006375 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 499177006376 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 499177006377 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 499177006378 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; cd02205 499177006379 FOG: CBS domain [General function prediction only]; Region: COG0517 499177006380 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cd02116 499177006381 YheO-like PAS domain; Region: PAS_6; pfam08348 499177006382 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 499177006383 Helix-turn-helix domains; Region: HTH; cl00088 499177006384 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 499177006385 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177006386 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177006387 Coenzyme A binding pocket [chemical binding]; other site 499177006388 lipoyltransferase and lipoate-protein ligase; Region: lipoyltrans; TIGR00545 499177006389 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 499177006390 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 499177006391 Domain of unknown function DUF20; Region: UPF0118; pfam01594 499177006392 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 499177006393 Survival protein SurE; Region: SurE; cl00448 499177006394 Domain of unknown function (DUF3841); Region: DUF3841; pfam12952 499177006395 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177006396 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 499177006397 MatE; Region: MatE; cl10513 499177006398 MatE; Region: MatE; cl10513 499177006399 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 499177006400 MatE; Region: MatE; cl10513 499177006401 MatE; Region: MatE; cl10513 499177006402 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 499177006403 Ferritin-like domain; Region: Ferritin; pfam00210 499177006404 ferroxidase diiron center [ion binding]; other site 499177006405 Protein of unknown function (DUF2680); Region: DUF2680; pfam10925 499177006406 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 499177006407 C-terminal peptidase (prc); Region: prc; TIGR00225 499177006408 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 499177006409 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 499177006410 Catalytic dyad [active] 499177006411 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3883 499177006412 Peptidase family M23; Region: Peptidase_M23; pfam01551 499177006413 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 499177006414 FtsX-like permease family; Region: FtsX; cl15850 499177006415 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177006416 H-loop/switch region; other site 499177006417 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177006418 Walker A/P-loop; other site 499177006419 ATP binding site [chemical binding]; other site 499177006420 Q-loop/lid; other site 499177006421 ABC transporter signature motif; other site 499177006422 lipoyltransferase and lipoate-protein ligase; Region: lipoyltrans; TIGR00545 499177006423 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 499177006424 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 499177006425 lipoyl synthase; Provisional; Region: PRK05481 499177006426 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 499177006427 FeS/SAM binding site; other site 499177006428 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 499177006429 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 499177006430 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177006431 Cobalt transport protein; Region: CbiQ; cl00463 499177006432 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 499177006433 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 499177006434 Walker A/P-loop; other site 499177006435 ATP binding site [chemical binding]; other site 499177006436 Q-loop/lid; other site 499177006437 ABC transporter signature motif; other site 499177006438 Walker B; other site 499177006439 D-loop; other site 499177006440 H-loop/switch region; other site 499177006441 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 499177006442 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 499177006443 Walker A/P-loop; other site 499177006444 ATP binding site [chemical binding]; other site 499177006445 Q-loop/lid; other site 499177006446 ABC transporter signature motif; other site 499177006447 Walker B; other site 499177006448 D-loop; other site 499177006449 H-loop/switch region; other site 499177006450 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 499177006451 Moco binding site; other site 499177006452 metal coordination site [ion binding]; other site 499177006453 PglZ domain; Region: PglZ; pfam08665 499177006454 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 499177006455 4Fe-4S binding domain; Region: Fer4_5; pfam12801 499177006456 4Fe-4S binding domain; Region: Fer4_5; pfam12801 499177006457 FMN-binding domain; Region: FMN_bind; cl01081 499177006458 FMN-binding domain; Region: FMN_bind; cl01081 499177006459 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 499177006460 Moco binding site; other site 499177006461 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 499177006462 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 499177006463 metal coordination site [ion binding]; other site 499177006464 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 499177006465 Moco binding site; other site 499177006466 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 499177006467 Two component regulator propeller; Region: Reg_prop; pfam07494 499177006468 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 499177006469 S-layer homology domain; Region: SLH; pfam00395 499177006470 S-layer homology domain; Region: SLH; pfam00395 499177006471 S-layer homology domain; Region: SLH; pfam00395 499177006472 AAA domain; Region: AAA_32; pfam13654 499177006473 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 499177006474 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 499177006475 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 499177006476 Sulfatase; Region: Sulfatase; cl10460 499177006477 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 499177006478 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases; Region: PI-PLCc_GDPD_SF_unchar1; cd08583 499177006479 putative active site [active] 499177006480 catalytic site [active] 499177006481 PemK-like protein; Region: PemK; cl00995 499177006482 alanine racemase; Reviewed; Region: alr; PRK00053 499177006483 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 499177006484 active site 499177006485 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 499177006486 dimer interface [polypeptide binding]; other site 499177006487 substrate binding site [chemical binding]; other site 499177006488 catalytic residues [active] 499177006489 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 499177006490 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 499177006491 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 499177006492 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 499177006493 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 499177006494 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 499177006495 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 499177006496 alpha subunit interaction interface [polypeptide binding]; other site 499177006497 Walker A motif; other site 499177006498 ATP binding site [chemical binding]; other site 499177006499 Walker B motif; other site 499177006500 inhibitor binding site; inhibition site 499177006501 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 499177006502 ATP synthase; Region: ATP-synt; cl00365 499177006503 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 499177006504 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 499177006505 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 499177006506 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 499177006507 beta subunit interaction interface [polypeptide binding]; other site 499177006508 Walker A motif; other site 499177006509 ATP binding site [chemical binding]; other site 499177006510 Walker B motif; other site 499177006511 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 499177006512 Plant ATP synthase F0; Region: YMF19; cl07975 499177006513 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 499177006514 Plant ATP synthase F0; Region: YMF19; cl07975 499177006515 ATP synthase subunit C; Region: ATP-synt_C; cl00466 499177006516 ATP synthase A chain; Region: ATP-synt_A; cl00413 499177006517 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 499177006518 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 499177006519 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 499177006520 active site 499177006521 homodimer interface [polypeptide binding]; other site 499177006522 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 499177006523 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 499177006524 Mg++ binding site [ion binding]; other site 499177006525 putative catalytic motif [active] 499177006526 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 499177006527 active site 499177006528 Zn binding site [ion binding]; other site 499177006529 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177006530 active site 499177006531 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 499177006532 Low molecular weight phosphatase family; Region: LMWPc; cd00115 499177006533 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 499177006534 active site 499177006535 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 499177006536 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 499177006537 peptide chain release factor 1; Validated; Region: prfA; PRK00591 499177006538 RF-1 domain; Region: RF-1; cl02875 499177006539 RF-1 domain; Region: RF-1; cl02875 499177006540 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 499177006541 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 499177006542 S-adenosylmethionine binding site [chemical binding]; other site 499177006543 Protein of unknown function (DUF1385); Region: DUF1385; cl01595 499177006544 thymidine kinase; Provisional; Region: PRK04296 499177006545 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 499177006546 transcription termination factor Rho; Provisional; Region: rho; PRK09376 499177006547 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 499177006548 RNA binding site [nucleotide binding]; other site 499177006549 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 499177006550 multimer interface [polypeptide binding]; other site 499177006551 Walker A motif; other site 499177006552 ATP binding site [chemical binding]; other site 499177006553 Walker B motif; other site 499177006554 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 499177006555 putative active site [active] 499177006556 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 499177006557 putative active site [active] 499177006558 tRNA adenylyltransferase; Region: tRNA_CCA_actino; TIGR02692 499177006559 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 499177006560 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 499177006561 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 499177006562 Predicted methyltransferases [General function prediction only]; Region: COG0313 499177006563 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 499177006564 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 499177006565 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 499177006566 S-adenosylmethionine binding site [chemical binding]; other site 499177006567 Sep15/SelM redox domain; Region: Sep15_SelM; pfam08806 499177006568 PSP1 C-terminal conserved region; Region: PSP1; cl00770 499177006569 DNA polymerase III subunit delta'; Validated; Region: PRK05564 499177006570 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177006571 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 499177006572 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 499177006573 TMP-binding site; other site 499177006574 ATP-binding site [chemical binding]; other site 499177006575 Homoserine O-succinyltransferase; Region: HTS; pfam04204 499177006576 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 499177006577 proposed active site lysine [active] 499177006578 conserved cys residue [active] 499177006579 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 499177006580 nucleotide binding site [chemical binding]; other site 499177006581 substrate binding site [chemical binding]; other site 499177006582 OAH/OAS sulfhydrylase; Region: OAH_OAS_sulfhy; TIGR01326 499177006583 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 499177006584 homodimer interface [polypeptide binding]; other site 499177006585 substrate-cofactor binding pocket; other site 499177006586 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177006587 catalytic residue [active] 499177006588 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 499177006589 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 499177006590 Cl- selectivity filter; other site 499177006591 Cl- binding residues [ion binding]; other site 499177006592 pore gating glutamate residue; other site 499177006593 dimer interface [polypeptide binding]; other site 499177006594 H+/Cl- coupling transport residue; other site 499177006595 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 499177006596 Cache domain; Region: Cache_2; cl07034 499177006597 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177006598 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177006599 dimer interface [polypeptide binding]; other site 499177006600 putative CheW interface [polypeptide binding]; other site 499177006601 Domain of unknown function (DUF3841); Region: DUF3841; pfam12952 499177006602 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 499177006603 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4877 499177006604 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_2; cd03402 499177006605 Protein of unknown function (DUF523); Region: DUF523; cl00733 499177006606 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 499177006607 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 499177006608 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 499177006609 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 499177006610 23S rRNA interface [nucleotide binding]; other site 499177006611 L3 interface [polypeptide binding]; other site 499177006612 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 499177006613 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 499177006614 dimerization interface 3.5A [polypeptide binding]; other site 499177006615 active site 499177006616 Cobalt transport protein; Region: CbiQ; cl00463 499177006617 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13637 499177006618 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 499177006619 Walker A/P-loop; other site 499177006620 ATP binding site [chemical binding]; other site 499177006621 Q-loop/lid; other site 499177006622 ABC transporter signature motif; other site 499177006623 Walker B; other site 499177006624 D-loop; other site 499177006625 H-loop/switch region; other site 499177006626 cobalt transporter ATP-binding subunit; Provisional; Region: PRK13633 499177006627 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 499177006628 Walker A/P-loop; other site 499177006629 ATP binding site [chemical binding]; other site 499177006630 Q-loop/lid; other site 499177006631 ABC transporter signature motif; other site 499177006632 Walker B; other site 499177006633 D-loop; other site 499177006634 H-loop/switch region; other site 499177006635 YARHG domain; Region: YARHG; pfam13308 499177006636 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 499177006637 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 499177006638 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 499177006639 alphaNTD homodimer interface [polypeptide binding]; other site 499177006640 alphaNTD - beta interaction site [polypeptide binding]; other site 499177006641 alphaNTD - beta' interaction site [polypeptide binding]; other site 499177006642 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 499177006643 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 499177006644 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 499177006645 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 499177006646 RNA binding surface [nucleotide binding]; other site 499177006647 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 499177006648 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 499177006649 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 499177006650 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 499177006651 rRNA binding site [nucleotide binding]; other site 499177006652 predicted 30S ribosome binding site; other site 499177006653 Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]; Region: RPL14A; COG2163 499177006654 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 499177006655 active site 499177006656 adenylate kinase; Reviewed; Region: adk; PRK00279 499177006657 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 499177006658 AMP-binding site [chemical binding]; other site 499177006659 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 499177006660 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 499177006661 SecY translocase; Region: SecY; pfam00344 499177006662 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 499177006663 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 499177006664 23S rRNA binding site [nucleotide binding]; other site 499177006665 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 499177006666 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 499177006667 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 499177006668 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 499177006669 5S rRNA interface [nucleotide binding]; other site 499177006670 L27 interface [polypeptide binding]; other site 499177006671 23S rRNA interface [nucleotide binding]; other site 499177006672 L5 interface [polypeptide binding]; other site 499177006673 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 499177006674 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 499177006675 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 499177006676 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 499177006677 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 499177006678 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 499177006679 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 499177006680 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 499177006681 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 499177006682 KOW motif; Region: KOW; cl00354 499177006683 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 499177006684 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 499177006685 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 499177006686 23S rRNA interface [nucleotide binding]; other site 499177006687 putative translocon interaction site; other site 499177006688 signal recognition particle (SRP54) interaction site; other site 499177006689 L23 interface [polypeptide binding]; other site 499177006690 trigger factor interaction site; other site 499177006691 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 499177006692 23S rRNA interface [nucleotide binding]; other site 499177006693 5S rRNA interface [nucleotide binding]; other site 499177006694 putative antibiotic binding site [chemical binding]; other site 499177006695 L25 interface [polypeptide binding]; other site 499177006696 L27 interface [polypeptide binding]; other site 499177006697 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 499177006698 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 499177006699 G-X-X-G motif; other site 499177006700 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 499177006701 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 499177006702 putative translocon binding site; other site 499177006703 protein-rRNA interface [nucleotide binding]; other site 499177006704 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 499177006705 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 499177006706 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 499177006707 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 499177006708 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 499177006709 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 499177006710 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 499177006711 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 499177006712 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 499177006713 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 499177006714 Walker A/P-loop; other site 499177006715 ATP binding site [chemical binding]; other site 499177006716 Q-loop/lid; other site 499177006717 ABC transporter signature motif; other site 499177006718 Walker B; other site 499177006719 D-loop; other site 499177006720 H-loop/switch region; other site 499177006721 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 499177006722 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 499177006723 Walker A/P-loop; other site 499177006724 ATP binding site [chemical binding]; other site 499177006725 Q-loop/lid; other site 499177006726 ABC transporter signature motif; other site 499177006727 Walker B; other site 499177006728 D-loop; other site 499177006729 H-loop/switch region; other site 499177006730 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 499177006731 TM-ABC transporter signature motif; other site 499177006732 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 499177006733 TM-ABC transporter signature motif; other site 499177006734 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 499177006735 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_12; cd06347 499177006736 putative ligand binding site [chemical binding]; other site 499177006737 elongation factor Tu; Reviewed; Region: PRK00049 499177006738 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 499177006739 G1 box; other site 499177006740 GEF interaction site [polypeptide binding]; other site 499177006741 GTP/Mg2+ binding site [chemical binding]; other site 499177006742 Switch I region; other site 499177006743 G2 box; other site 499177006744 G3 box; other site 499177006745 Switch II region; other site 499177006746 G4 box; other site 499177006747 G5 box; other site 499177006748 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 499177006749 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 499177006750 Antibiotic Binding Site [chemical binding]; other site 499177006751 elongation factor G; Reviewed; Region: PRK00007 499177006752 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 499177006753 G1 box; other site 499177006754 putative GEF interaction site [polypeptide binding]; other site 499177006755 GTP/Mg2+ binding site [chemical binding]; other site 499177006756 Switch I region; other site 499177006757 G2 box; other site 499177006758 G3 box; other site 499177006759 Switch II region; other site 499177006760 G4 box; other site 499177006761 G5 box; other site 499177006762 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 499177006763 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 499177006764 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 499177006765 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 499177006766 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 499177006767 S17 interaction site [polypeptide binding]; other site 499177006768 S8 interaction site; other site 499177006769 16S rRNA interaction site [nucleotide binding]; other site 499177006770 streptomycin interaction site [chemical binding]; other site 499177006771 23S rRNA interaction site [nucleotide binding]; other site 499177006772 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 499177006773 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 499177006774 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 499177006775 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 499177006776 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 499177006777 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 499177006778 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 499177006779 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 499177006780 G-loop; other site 499177006781 Apocytochrome F, C-terminal; Region: Apocytochr_F_C; cl03168 499177006782 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 499177006783 DNA binding site [nucleotide binding] 499177006784 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 499177006785 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 499177006786 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 499177006787 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 499177006788 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 499177006789 RPB1 interaction site [polypeptide binding]; other site 499177006790 RPB10 interaction site [polypeptide binding]; other site 499177006791 RPB11 interaction site [polypeptide binding]; other site 499177006792 RPB3 interaction site [polypeptide binding]; other site 499177006793 RPB12 interaction site [polypeptide binding]; other site 499177006794 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 499177006795 core dimer interface [polypeptide binding]; other site 499177006796 peripheral dimer interface [polypeptide binding]; other site 499177006797 L10 interface [polypeptide binding]; other site 499177006798 L11 interface [polypeptide binding]; other site 499177006799 putative EF-Tu interaction site [polypeptide binding]; other site 499177006800 putative EF-G interaction site [polypeptide binding]; other site 499177006801 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 499177006802 23S rRNA interface [nucleotide binding]; other site 499177006803 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 499177006804 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 499177006805 mRNA/rRNA interface [nucleotide binding]; other site 499177006806 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 499177006807 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 499177006808 23S rRNA interface [nucleotide binding]; other site 499177006809 L7/L12 interface [polypeptide binding]; other site 499177006810 putative thiostrepton binding site; other site 499177006811 L25 interface [polypeptide binding]; other site 499177006812 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 499177006813 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 499177006814 putative homodimer interface [polypeptide binding]; other site 499177006815 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 499177006816 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 499177006817 elongation factor Tu; Reviewed; Region: PRK00049 499177006818 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 499177006819 G1 box; other site 499177006820 GEF interaction site [polypeptide binding]; other site 499177006821 GTP/Mg2+ binding site [chemical binding]; other site 499177006822 Switch I region; other site 499177006823 G2 box; other site 499177006824 G3 box; other site 499177006825 Switch II region; other site 499177006826 G4 box; other site 499177006827 G5 box; other site 499177006828 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 499177006829 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 499177006830 Antibiotic Binding Site [chemical binding]; other site 499177006831 RNA polymerase factor sigma-70; Validated; Region: PRK08295 499177006832 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 499177006833 Helix-turn-helix domains; Region: HTH; cl00088 499177006834 YacP-like NYN domain; Region: NYN_YacP; cl01491 499177006835 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 499177006836 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 499177006837 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 499177006838 Thymidylate synthase complementing protein; Region: Thy1; cl03630 499177006839 EamA-like transporter family; Region: EamA; cl01037 499177006840 EamA-like transporter family; Region: EamA; cl01037 499177006841 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 499177006842 dimerization interface [polypeptide binding]; other site 499177006843 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177006844 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177006845 dimer interface [polypeptide binding]; other site 499177006846 putative CheW interface [polypeptide binding]; other site 499177006847 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 499177006848 proline racemase; Provisional; Region: PRK13969 499177006849 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 499177006850 Glycine/sarcosine/betaine reductase component B subunits; Region: Gly_reductase; pfam09338 499177006851 Glycine/sarcosine/betaine reductase component B subunits; Region: Gly_reductase; pfam09338 499177006852 Glycine/sarcosine/betaine reductase selenoprotein B (GRDB); Region: GRDB; cl06409 499177006853 Glycine/sarcosine/betaine reductase component B subunits; Region: Gly_reductase; pfam09338 499177006854 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 499177006855 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 499177006856 FOG: CBS domain [General function prediction only]; Region: COG0517 499177006857 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_13; cd04626 499177006858 PAS domain S-box; Region: sensory_box; TIGR00229 499177006859 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 499177006860 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 499177006861 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 499177006862 Walker A motif; other site 499177006863 ATP binding site [chemical binding]; other site 499177006864 Walker B motif; other site 499177006865 arginine finger; other site 499177006866 Helix-turn-helix domains; Region: HTH; cl00088 499177006867 Uncharacterized conserved protein [Function unknown]; Region: COG3760 499177006868 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 499177006869 putative deacylase active site [active] 499177006870 prolyl-tRNA synthetase; Provisional; Region: PRK08661 499177006871 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_arch_euk; cd00778 499177006872 dimer interface [polypeptide binding]; other site 499177006873 motif 1; other site 499177006874 active site 499177006875 motif 2; other site 499177006876 motif 3; other site 499177006877 ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in...; Region: ProRS_anticodon_zinc; cd00862 499177006878 anticodon binding site; other site 499177006879 zinc-binding site [ion binding]; other site 499177006880 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; cl00258 499177006881 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 499177006882 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 499177006883 active site 499177006884 HIGH motif; other site 499177006885 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 499177006886 KMSKS motif; other site 499177006887 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 499177006888 tRNA binding surface [nucleotide binding]; other site 499177006889 anticodon binding site; other site 499177006890 serine O-acetyltransferase; Region: cysE; TIGR01172 499177006891 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 499177006892 trimer interface [polypeptide binding]; other site 499177006893 active site 499177006894 substrate binding site [chemical binding]; other site 499177006895 CoA binding site [chemical binding]; other site 499177006896 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 499177006897 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 499177006898 dimer interface [polypeptide binding]; other site 499177006899 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177006900 catalytic residue [active] 499177006901 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 499177006902 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 499177006903 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 499177006904 active site 499177006905 HIGH motif; other site 499177006906 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 499177006907 active site 499177006908 KMSKS motif; other site 499177006909 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 499177006910 homotrimer interaction site [polypeptide binding]; other site 499177006911 zinc binding site [ion binding]; other site 499177006912 CDP-binding sites; other site 499177006913 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 499177006914 substrate binding site; other site 499177006915 dimer interface; other site 499177006916 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 499177006917 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177006918 Walker A/P-loop; other site 499177006919 ATP binding site [chemical binding]; other site 499177006920 Q-loop/lid; other site 499177006921 ABC transporter signature motif; other site 499177006922 Walker B; other site 499177006923 D-loop; other site 499177006924 H-loop/switch region; other site 499177006925 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 499177006926 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 499177006927 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177006928 Walker A/P-loop; other site 499177006929 ATP binding site [chemical binding]; other site 499177006930 Q-loop/lid; other site 499177006931 ABC transporter signature motif; other site 499177006932 Walker B; other site 499177006933 D-loop; other site 499177006934 H-loop/switch region; other site 499177006935 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 499177006936 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 499177006937 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 499177006938 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 499177006939 dimer interface [polypeptide binding]; other site 499177006940 conserved gate region; other site 499177006941 putative PBP binding loops; other site 499177006942 ABC-ATPase subunit interface; other site 499177006943 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 499177006944 dimer interface [polypeptide binding]; other site 499177006945 conserved gate region; other site 499177006946 putative PBP binding loops; other site 499177006947 ABC-ATPase subunit interface; other site 499177006948 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 499177006949 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 499177006950 Protein of unknown function (DUF1292); Region: DUF1292; cl01608 499177006951 ATP cone domain; Region: ATP-cone; pfam03477 499177006952 ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent; Region: RTPR; TIGR02505 499177006953 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 499177006954 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 499177006955 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177006956 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 499177006957 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 499177006958 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 499177006959 dimerization interface [polypeptide binding]; other site 499177006960 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 499177006961 dimer interface [polypeptide binding]; other site 499177006962 phosphorylation site [posttranslational modification] 499177006963 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 499177006964 ATP binding site [chemical binding]; other site 499177006965 Mg2+ binding site [ion binding]; other site 499177006966 G-X-G motif; other site 499177006967 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 499177006968 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 499177006969 active site 499177006970 phosphorylation site [posttranslational modification] 499177006971 intermolecular recognition site; other site 499177006972 dimerization interface [polypeptide binding]; other site 499177006973 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 499177006974 DNA binding site [nucleotide binding] 499177006975 nascent polypeptide-associated complex protein; Reviewed; Region: nac; PRK06369 499177006976 Domain of unknown function (DUF4342); Region: DUF4342; pfam14242 499177006977 PAS fold; Region: PAS; pfam00989 499177006978 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 499177006979 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 499177006980 PAS domain; Region: PAS_9; pfam13426 499177006981 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177006982 metal binding site [ion binding]; metal-binding site 499177006983 active site 499177006984 I-site; other site 499177006985 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 499177006986 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177006987 Zn2+ binding site [ion binding]; other site 499177006988 Mg2+ binding site [ion binding]; other site 499177006989 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 499177006990 DEAD-like helicases superfamily; Region: DEXDc; smart00487 499177006991 ATP binding site [chemical binding]; other site 499177006992 Mg++ binding site [ion binding]; other site 499177006993 motif III; other site 499177006994 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 499177006995 nucleotide binding region [chemical binding]; other site 499177006996 ATP-binding site [chemical binding]; other site 499177006997 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 499177006998 DNA-binding site [nucleotide binding]; DNA binding site 499177006999 RNA-binding motif; other site 499177007000 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 499177007001 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177007002 Walker A/P-loop; other site 499177007003 ATP binding site [chemical binding]; other site 499177007004 Q-loop/lid; other site 499177007005 ABC transporter signature motif; other site 499177007006 Walker B; other site 499177007007 D-loop; other site 499177007008 H-loop/switch region; other site 499177007009 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 499177007010 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 499177007011 Walker A/P-loop; other site 499177007012 ATP binding site [chemical binding]; other site 499177007013 Q-loop/lid; other site 499177007014 ABC transporter signature motif; other site 499177007015 Walker B; other site 499177007016 D-loop; other site 499177007017 H-loop/switch region; other site 499177007018 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 499177007019 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 499177007020 dimer interface [polypeptide binding]; other site 499177007021 conserved gate region; other site 499177007022 putative PBP binding loops; other site 499177007023 ABC-ATPase subunit interface; other site 499177007024 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 499177007025 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 499177007026 dimer interface [polypeptide binding]; other site 499177007027 conserved gate region; other site 499177007028 putative PBP binding loops; other site 499177007029 ABC-ATPase subunit interface; other site 499177007030 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_21; cd08520 499177007031 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 499177007032 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 499177007033 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 499177007034 S-adenosylmethionine binding site [chemical binding]; other site 499177007035 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]; Region: COG2191 499177007036 FmdE, Molybdenum formylmethanofuran dehydrogenase operon; Region: FmdE; pfam02663 499177007037 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 499177007038 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 499177007039 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 499177007040 Walker A motif; other site 499177007041 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177007042 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 499177007043 metal binding site 2 [ion binding]; metal-binding site 499177007044 putative DNA binding helix; other site 499177007045 metal binding site 1 [ion binding]; metal-binding site 499177007046 dimer interface [polypeptide binding]; other site 499177007047 structural Zn2+ binding site [ion binding]; other site 499177007048 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 499177007049 putative hydratase; Provisional; Region: PRK11413 499177007050 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 499177007051 substrate binding site [chemical binding]; other site 499177007052 ligand binding site [chemical binding]; other site 499177007053 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 499177007054 substrate binding site [chemical binding]; other site 499177007055 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 499177007056 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177007057 Walker A/P-loop; other site 499177007058 ATP binding site [chemical binding]; other site 499177007059 Q-loop/lid; other site 499177007060 ABC transporter signature motif; other site 499177007061 Walker B; other site 499177007062 D-loop; other site 499177007063 H-loop/switch region; other site 499177007064 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 499177007065 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 499177007066 NMT1-like family; Region: NMT1_2; cl15260 499177007067 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 499177007068 PAS domain S-box; Region: sensory_box; TIGR00229 499177007069 PAS domain S-box; Region: sensory_box; TIGR00229 499177007070 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 499177007071 putative active site [active] 499177007072 heme pocket [chemical binding]; other site 499177007073 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177007074 metal binding site [ion binding]; metal-binding site 499177007075 active site 499177007076 I-site; other site 499177007077 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 499177007078 octamerization interface [polypeptide binding]; other site 499177007079 diferric-oxygen binding site [ion binding]; other site 499177007080 PAS domain S-box; Region: sensory_box; TIGR00229 499177007081 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 499177007082 putative active site [active] 499177007083 heme pocket [chemical binding]; other site 499177007084 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177007085 metal binding site [ion binding]; metal-binding site 499177007086 active site 499177007087 I-site; other site 499177007088 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 499177007089 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 499177007090 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 499177007091 DNA binding residues [nucleotide binding] 499177007092 dimerization interface [polypeptide binding]; other site 499177007093 S-layer homology domain; Region: SLH; pfam00395 499177007094 S-layer homology domain; Region: SLH; pfam00395 499177007095 S-layer homology domain; Region: SLH; pfam00395 499177007096 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 499177007097 Restriction endonuclease; Region: Mrr_cat; cl00516 499177007098 HRDC domain; Region: HRDC; cl02578 499177007099 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 499177007100 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007101 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007102 ABC transporter; Region: ABC_tran_2; pfam12848 499177007103 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007104 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_1; cd09606 499177007105 oligoendopeptidase, M3 family; Region: M3_not_pepF; TIGR02289 499177007106 active site 499177007107 Zn binding site [ion binding]; other site 499177007108 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 499177007109 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177007110 Walker A/P-loop; other site 499177007111 ATP binding site [chemical binding]; other site 499177007112 Q-loop/lid; other site 499177007113 ABC transporter signature motif; other site 499177007114 Walker B; other site 499177007115 D-loop; other site 499177007116 H-loop/switch region; other site 499177007117 ABC transporter; Region: ABC_tran_2; pfam12848 499177007118 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007119 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as...; Region: NfsA_FRP; cd02146 499177007120 dimer interface [polypeptide binding]; other site 499177007121 FMN binding site [chemical binding]; other site 499177007122 NADPH bind site [chemical binding]; other site 499177007123 4Fe-4S binding domain; Region: Fer4; cl02805 499177007124 glycine radical enzyme activase, YjjW family; Region: activase_YjjW; TIGR04041 499177007125 glutamate dehydrogenase; Provisional; Region: PRK09414 499177007126 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 499177007127 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 499177007128 NAD(P) binding site [chemical binding]; other site 499177007129 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 499177007130 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 499177007131 catalytic loop [active] 499177007132 iron binding site [ion binding]; other site 499177007133 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007134 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 499177007135 4Fe-4S binding domain; Region: Fer4; cl02805 499177007136 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 499177007137 4Fe-4S binding domain; Region: Fer4; cl02805 499177007138 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 499177007139 molybdopterin cofactor binding site; other site 499177007140 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 499177007141 dimer interface [polypeptide binding]; other site 499177007142 [2Fe-2S] cluster binding site [ion binding]; other site 499177007143 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 499177007144 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 499177007145 SLBB domain; Region: SLBB; pfam10531 499177007146 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 499177007147 4Fe-4S binding domain; Region: Fer4; cl02805 499177007148 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 499177007149 4Fe-4S binding domain; Region: Fer4; cl02805 499177007150 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 499177007151 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 499177007152 putative dimer interface [polypeptide binding]; other site 499177007153 [2Fe-2S] cluster binding site [ion binding]; other site 499177007154 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 499177007155 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 499177007156 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007157 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 499177007158 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007159 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007160 ABC transporter; Region: ABC_tran_2; pfam12848 499177007161 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007162 UGMP family protein; Validated; Region: PRK09604 499177007163 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 499177007164 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 499177007165 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177007166 Coenzyme A binding pocket [chemical binding]; other site 499177007167 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 499177007168 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 499177007169 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 499177007170 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 499177007171 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 499177007172 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 499177007173 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 499177007174 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 499177007175 RNA binding site [nucleotide binding]; other site 499177007176 Flagellar protein FliS; Region: FliS; cl00654 499177007177 flagellin; Provisional; Region: PRK12804 499177007178 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 499177007179 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 499177007180 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 499177007181 Protein of unknown function (DUF327); Region: DUF327; cl00753 499177007182 Uncharacterized protein, DegV family COG1307; Region: DegV; cl00577 499177007183 peptide chain release factor 2; Provisional; Region: PRK05589 499177007184 RF-1 domain; Region: RF-1; cl02875 499177007185 RF-1 domain; Region: RF-1; cl02875 499177007186 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 499177007187 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177007188 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 499177007189 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177007190 nucleotide binding region [chemical binding]; other site 499177007191 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 499177007192 30S subunit binding site; other site 499177007193 ATP synthase subunit D; Region: ATP-synt_D; cl00613 499177007194 V-type ATP synthase subunit B; Provisional; Region: PRK04196 499177007195 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 499177007196 V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_B; cd01135 499177007197 Walker A motif homologous position; other site 499177007198 Walker B motif; other site 499177007199 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 499177007200 V-type ATP synthase subunit A; Provisional; Region: PRK04192 499177007201 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 499177007202 V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_A; cd01134 499177007203 Walker A motif/ATP binding site; other site 499177007204 Walker B motif; other site 499177007205 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 499177007206 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; cl00632 499177007207 V-type ATP synthase subunit I; Validated; Region: PRK05771 499177007208 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 499177007209 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 499177007210 GAF domain; Region: GAF; cl15785 499177007211 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 499177007212 ATP binding site [chemical binding]; other site 499177007213 Mg2+ binding site [ion binding]; other site 499177007214 G-X-G motif; other site 499177007215 flagellar operon protein TIGR03826; Region: YvyF 499177007216 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 499177007217 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 499177007218 active site 499177007219 phosphorylation site [posttranslational modification] 499177007220 intermolecular recognition site; other site 499177007221 dimerization interface [polypeptide binding]; other site 499177007222 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 499177007223 DNA binding residues [nucleotide binding] 499177007224 dimerization interface [polypeptide binding]; other site 499177007225 Putative motility protein; Region: YjfB_motility; pfam14070 499177007226 Flagellar protein FliS; Region: FliS; cl00654 499177007227 flagellar capping protein; Validated; Region: fliD; PRK07737 499177007228 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 499177007229 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 499177007230 FlaG protein; Region: FlaG; cl00591 499177007231 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 499177007232 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 499177007233 inhibitor-cofactor binding pocket; inhibition site 499177007234 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177007235 catalytic residue [active] 499177007236 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 499177007237 putative trimer interface [polypeptide binding]; other site 499177007238 putative CoA binding site [chemical binding]; other site 499177007239 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 499177007240 putative trimer interface [polypeptide binding]; other site 499177007241 putative active site [active] 499177007242 putative substrate binding site [chemical binding]; other site 499177007243 putative CoA binding site [chemical binding]; other site 499177007244 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 499177007245 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007246 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 499177007247 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 499177007248 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 499177007249 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007250 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 499177007251 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 499177007252 trimer interface [polypeptide binding]; other site 499177007253 active site 499177007254 UDP-GlcNAc binding site [chemical binding]; other site 499177007255 lipid binding site [chemical binding]; lipid-binding site 499177007256 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 499177007257 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 499177007258 trimer interface [polypeptide binding]; other site 499177007259 active site 499177007260 substrate binding site [chemical binding]; other site 499177007261 CoA binding site [chemical binding]; other site 499177007262 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 499177007263 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 499177007264 inhibitor-cofactor binding pocket; inhibition site 499177007265 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177007266 catalytic residue [active] 499177007267 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007268 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 499177007269 NAD(P) binding site [chemical binding]; other site 499177007270 active site 499177007271 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 499177007272 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 499177007273 putative metal binding site; other site 499177007274 flagellin; Provisional; Region: PRK12804 499177007275 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 499177007276 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 499177007277 Global regulator protein family; Region: CsrA; cl00670 499177007278 FliW protein; Region: FliW; cl00740 499177007279 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK07701 499177007280 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 499177007281 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 499177007282 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07739 499177007283 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 499177007284 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 499177007285 FlgN protein; Region: FlgN; cl09176 499177007286 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 499177007287 flagellar operon protein TIGR03826; Region: YvyF 499177007288 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 499177007289 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 499177007290 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177007291 Family description; Region: UvrD_C_2; cl15862 499177007292 S-adenosylmethionine synthetase; Validated; Region: PRK05250 499177007293 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 499177007294 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 499177007295 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 499177007296 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 499177007297 Putative small multi-drug export protein; Region: Sm_multidrug_ex; cl01024 499177007298 Membrane transport protein; Region: Mem_trans; cl09117 499177007299 Rod binding protein; Region: Rod-binding; cl01626 499177007300 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 499177007301 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 499177007302 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 499177007303 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 499177007304 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 499177007305 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 499177007306 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 499177007307 rod shape-determining protein Mbl; Provisional; Region: PRK13928 499177007308 Cell division protein FtsA; Region: FtsA; cl11496 499177007309 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 499177007310 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 499177007311 hinge; other site 499177007312 active site 499177007313 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 499177007314 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 499177007315 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 499177007316 MgtE intracellular N domain; Region: MgtE_N; cl15244 499177007317 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 499177007318 Divalent cation transporter; Region: MgtE; cl00786 499177007319 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 499177007320 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 499177007321 putative dimer interface [polypeptide binding]; other site 499177007322 putative anticodon binding site; other site 499177007323 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 499177007324 homodimer interface [polypeptide binding]; other site 499177007325 motif 1; other site 499177007326 motif 2; other site 499177007327 active site 499177007328 motif 3; other site 499177007329 histidinol-phosphatase; Provisional; Region: PRK05588 499177007330 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 499177007331 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 499177007332 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 499177007333 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 499177007334 YheO-like PAS domain; Region: PAS_6; pfam08348 499177007335 Helix-turn-helix domains; Region: HTH; cl00088 499177007336 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 499177007337 RNA polymerase sigma-70 factor, TIGR02954 family; Region: Sig70_famx3 499177007338 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 499177007339 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 499177007340 DNA binding residues [nucleotide binding] 499177007341 PAS domain S-box; Region: sensory_box; TIGR00229 499177007342 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 499177007343 putative active site [active] 499177007344 heme pocket [chemical binding]; other site 499177007345 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177007346 metal binding site [ion binding]; metal-binding site 499177007347 active site 499177007348 I-site; other site 499177007349 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177007350 Zn2+ binding site [ion binding]; other site 499177007351 Mg2+ binding site [ion binding]; other site 499177007352 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 499177007353 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 499177007354 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 499177007355 shikimate binding site; other site 499177007356 NAD(P) binding site [chemical binding]; other site 499177007357 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 499177007358 Tetramer interface [polypeptide binding]; other site 499177007359 active site 499177007360 FMN-binding site [chemical binding]; other site 499177007361 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 499177007362 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 499177007363 hinge; other site 499177007364 active site 499177007365 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 499177007366 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 499177007367 active site 499177007368 dimer interface [polypeptide binding]; other site 499177007369 metal binding site [ion binding]; metal-binding site 499177007370 Response regulator receiver domain; Region: Response_reg; pfam00072 499177007371 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 499177007372 active site 499177007373 phosphorylation site [posttranslational modification] 499177007374 intermolecular recognition site; other site 499177007375 dimerization interface [polypeptide binding]; other site 499177007376 Chemotaxis phosphatase CheX; Region: CheX; cl15816 499177007377 Chemotaxis phosphatase CheX; Region: CheX; cl15816 499177007378 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 499177007379 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177007380 metal binding site [ion binding]; metal-binding site 499177007381 active site 499177007382 I-site; other site 499177007383 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 499177007384 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177007385 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 499177007386 diacylglycerol glucosyltransferase; Provisional; Region: PRK13609 499177007387 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 499177007388 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 499177007389 Pyruvate formate lyase 1; Region: PFL1; cd01678 499177007390 coenzyme A binding site [chemical binding]; other site 499177007391 active site 499177007392 catalytic residues [active] 499177007393 glycine loop; other site 499177007394 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 499177007395 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 499177007396 FeS/SAM binding site; other site 499177007397 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 499177007398 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 499177007399 ligand binding site [chemical binding]; other site 499177007400 flexible hinge region; other site 499177007401 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 499177007402 putative switch regulator; other site 499177007403 non-specific DNA interactions [nucleotide binding]; other site 499177007404 DNA binding site [nucleotide binding] 499177007405 sequence specific DNA binding site [nucleotide binding]; other site 499177007406 putative cAMP binding site [chemical binding]; other site 499177007407 threonine synthase; Reviewed; Region: PRK06721 499177007408 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 499177007409 homodimer interface [polypeptide binding]; other site 499177007410 pyridoxal 5'-phosphate binding site [chemical binding]; other site 499177007411 catalytic residue [active] 499177007412 homoserine kinase; Provisional; Region: PRK01212 499177007413 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 499177007414 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 499177007415 GDYXXLXY protein; Region: GDYXXLXY; cl02066 499177007416 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 499177007417 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 499177007418 Malic enzyme, N-terminal domain; Region: malic; pfam00390 499177007419 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 499177007420 putative NAD(P) binding site [chemical binding]; other site 499177007421 Predicted acetyltransferase [General function prediction only]; Region: COG3153 499177007422 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177007423 Coenzyme A binding pocket [chemical binding]; other site 499177007424 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 499177007425 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 499177007426 Uncharacterized protein, DegV family COG1307; Region: DegV; cl00577 499177007427 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 499177007428 Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Region: HTH_TipAL-Mta; cd01106 499177007429 DNA binding residues [nucleotide binding] 499177007430 dimer interface [polypeptide binding]; other site 499177007431 TipAS antibiotic-recognition domain; Region: TipAS; pfam07739 499177007432 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 499177007433 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 499177007434 dimer interface [polypeptide binding]; other site 499177007435 decamer (pentamer of dimers) interface [polypeptide binding]; other site 499177007436 catalytic triad [active] 499177007437 peroxidatic and resolving cysteines [active] 499177007438 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 499177007439 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 499177007440 dimer interface [polypeptide binding]; other site 499177007441 pyridoxal binding site [chemical binding]; other site 499177007442 ATP binding site [chemical binding]; other site 499177007443 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 499177007444 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 499177007445 ligand binding site [chemical binding]; other site 499177007446 dimerization interface [polypeptide binding]; other site 499177007447 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 499177007448 TM-ABC transporter signature motif; other site 499177007449 D-ribose transporter ATP binding protein; Provisional; Region: PRK10762 499177007450 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 499177007451 Walker A/P-loop; other site 499177007452 ATP binding site [chemical binding]; other site 499177007453 Q-loop/lid; other site 499177007454 ABC transporter signature motif; other site 499177007455 Walker B; other site 499177007456 D-loop; other site 499177007457 H-loop/switch region; other site 499177007458 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 499177007459 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 499177007460 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 499177007461 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 499177007462 substrate binding site [chemical binding]; other site 499177007463 dimer interface [polypeptide binding]; other site 499177007464 ATP binding site [chemical binding]; other site 499177007465 Transcriptional regulators [Transcription]; Region: PurR; COG1609 499177007466 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 499177007467 DNA binding site [nucleotide binding] 499177007468 domain linker motif; other site 499177007469 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 499177007470 dimerization interface [polypeptide binding]; other site 499177007471 ligand binding site [chemical binding]; other site 499177007472 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 499177007473 Helix-turn-helix domains; Region: HTH; cl00088 499177007474 Integrase core domain; Region: rve; cl01316 499177007475 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 499177007476 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177007477 metal binding site [ion binding]; metal-binding site 499177007478 active site 499177007479 I-site; other site 499177007480 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 499177007481 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177007482 EamA-like transporter family; Region: EamA; cl01037 499177007483 Threonine/homoserine efflux transporter [Amino acid transport and metabolism]; Region: rhtA; COG5006 499177007484 aspartyl-tRNA synthetase; Provisional; Region: aspC; PRK05159 499177007485 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 499177007486 Dimer interface [polypeptide binding]; other site 499177007487 anticodon binding site; other site 499177007488 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 499177007489 homodimer interface [polypeptide binding]; other site 499177007490 motif 1; other site 499177007491 motif 2; other site 499177007492 active site 499177007493 motif 3; other site 499177007494 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 499177007495 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 499177007496 active site residue [active] 499177007497 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 499177007498 active site residue [active] 499177007499 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 499177007500 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 499177007501 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 499177007502 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 499177007503 catalytic site [active] 499177007504 subunit interface [polypeptide binding]; other site 499177007505 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 499177007506 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 499177007507 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177007508 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 499177007509 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 499177007510 ATP-grasp domain; Region: ATP-grasp_4; cl03087 499177007511 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 499177007512 IMP binding site; other site 499177007513 dimer interface [polypeptide binding]; other site 499177007514 interdomain contacts; other site 499177007515 partial ornithine binding site; other site 499177007516 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_IV; cd01994 499177007517 Ligand Binding Site [chemical binding]; other site 499177007518 D-aminoacyl-tRNA deacylase; Region: tRNA_deacylase; cl00716 499177007519 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 499177007520 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; cd00640 499177007521 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177007522 catalytic residue [active] 499177007523 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 499177007524 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 499177007525 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 499177007526 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 499177007527 Zn2+ binding site [ion binding]; other site 499177007528 Mg2+ binding site [ion binding]; other site 499177007529 Cache domain; Region: Cache_1; pfam02743 499177007530 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 499177007531 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 499177007532 dimer interface [polypeptide binding]; other site 499177007533 phosphorylation site [posttranslational modification] 499177007534 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 499177007535 ATP binding site [chemical binding]; other site 499177007536 Mg2+ binding site [ion binding]; other site 499177007537 G-X-G motif; other site 499177007538 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177007539 dimer interface [polypeptide binding]; other site 499177007540 putative CheW interface [polypeptide binding]; other site 499177007541 Cache domain; Region: Cache_1; pfam02743 499177007542 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 499177007543 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 499177007544 dimer interface [polypeptide binding]; other site 499177007545 putative CheW interface [polypeptide binding]; other site 499177007546 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 499177007547 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 499177007548 substrate binding pocket [chemical binding]; other site 499177007549 membrane-bound complex binding site; other site 499177007550 hinge residues; other site 499177007551 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 499177007552 dimer interface [polypeptide binding]; other site 499177007553 conserved gate region; other site 499177007554 putative PBP binding loops; other site 499177007555 ABC-ATPase subunit interface; other site 499177007556 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 499177007557 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 499177007558 Walker A/P-loop; other site 499177007559 ATP binding site [chemical binding]; other site 499177007560 Q-loop/lid; other site 499177007561 ABC transporter signature motif; other site 499177007562 Walker B; other site 499177007563 D-loop; other site 499177007564 H-loop/switch region; other site 499177007565 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 499177007566 non-specific DNA binding site [nucleotide binding]; other site 499177007567 salt bridge; other site 499177007568 sequence-specific DNA binding site [nucleotide binding]; other site 499177007569 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 499177007570 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 499177007571 putative substrate translocation pore; other site 499177007572 Uncharacterized conserved protein (DUF2294); Region: DUF2294; cl02390 499177007573 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 499177007574 catalytic residues [active] 499177007575 dimer interface [polypeptide binding]; other site 499177007576 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 499177007577 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 499177007578 conserved cys residue [active] 499177007579 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177007580 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177007581 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 499177007582 non-specific DNA binding site [nucleotide binding]; other site 499177007583 salt bridge; other site 499177007584 sequence-specific DNA binding site [nucleotide binding]; other site 499177007585 desulfoferrodoxin; Region: dfx_rbo; TIGR00320 499177007586 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 499177007587 non-heme iron binding site [ion binding]; other site 499177007588 GIY-YIG domain of LuxR and ArsR family transcriptional regulators, and uncharacterized hypothetical proteins found in bacteria; Region: GIY-YIG_LuxR_like; cd10451 499177007589 GIY-YIG motif/motif A; other site 499177007590 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 499177007591 Cadherin repeat-like domain; Region: CA_like; cl15786 499177007592 S-layer homology domain; Region: SLH; pfam00395 499177007593 S-layer homology domain; Region: SLH; pfam00395 499177007594 S-layer homology domain; Region: SLH; pfam00395 499177007595 Phage Tail Collar Domain; Region: Collar; pfam07484 499177007596 Phage Tail Collar Domain; Region: Collar; pfam07484 499177007597 Phage Tail Collar Domain; Region: Collar; pfam07484 499177007598 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 499177007599 hypothetical protein; Provisional; Region: PRK10220 499177007600 PhnA protein; Region: PhnA; pfam03831 499177007601 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 499177007602 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 499177007603 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 499177007604 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007605 ABC transporter; Region: ABC_tran_2; pfam12848 499177007606 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 499177007607 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 499177007608 NodB motif; other site 499177007609 active site 499177007610 catalytic site [active] 499177007611 metal binding site [ion binding]; metal-binding site 499177007612 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 499177007613 FMN binding site [chemical binding]; other site 499177007614 dimer interface [polypeptide binding]; other site 499177007615 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 499177007616 dimer interface [polypeptide binding]; other site 499177007617 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 499177007618 ABC-ATPase subunit interface; other site 499177007619 dimer interface [polypeptide binding]; other site 499177007620 putative PBP binding regions; other site 499177007621 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 499177007622 ABC-ATPase subunit interface; other site 499177007623 dimer interface [polypeptide binding]; other site 499177007624 putative PBP binding regions; other site 499177007625 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 499177007626 Periplasmic binding protein FeuA. These proteins have predicted to function as initial receptors in ABC transport of metal ions in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct...; Region: FeuA; cd01138 499177007627 putative ligand binding residues [chemical binding]; other site 499177007628 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 499177007629 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 499177007630 Walker A/P-loop; other site 499177007631 ATP binding site [chemical binding]; other site 499177007632 Q-loop/lid; other site 499177007633 ABC transporter signature motif; other site 499177007634 Walker B; other site 499177007635 D-loop; other site 499177007636 H-loop/switch region; other site 499177007637 Flavin Reductases; Region: FlaRed; cl00801 499177007638 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 499177007639 B12 binding site [chemical binding]; other site 499177007640 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 499177007641 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 499177007642 FeS/SAM binding site; other site 499177007643 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 499177007644 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 499177007645 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 499177007646 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 499177007647 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177007648 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 499177007649 The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme...; Region: ABC_BcrA_bacitracin_resist; cd03268 499177007650 Walker A/P-loop; other site 499177007651 ATP binding site [chemical binding]; other site 499177007652 Q-loop/lid; other site 499177007653 ABC transporter signature motif; other site 499177007654 Walker B; other site 499177007655 D-loop; other site 499177007656 H-loop/switch region; other site 499177007657 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 499177007658 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 499177007659 active site 499177007660 Chromate transporter; Region: Chromate_transp; pfam02417 499177007661 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 499177007662 Chromate transporter; Region: Chromate_transp; pfam02417 499177007663 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 499177007664 dimerization interface [polypeptide binding]; other site 499177007665 active site 499177007666 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 499177007667 folate binding site [chemical binding]; other site 499177007668 NADP+ binding site [chemical binding]; other site 499177007669 AAA domain; Region: AAA_21; pfam13304 499177007670 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177007671 Walker A/P-loop; other site 499177007672 ATP binding site [chemical binding]; other site 499177007673 Q-loop/lid; other site 499177007674 ABC transporter signature motif; other site 499177007675 Walker B; other site 499177007676 D-loop; other site 499177007677 H-loop/switch region; other site 499177007678 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 499177007679 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 499177007680 catalytic triad [active] 499177007681 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 499177007682 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177007683 Coenzyme A binding pocket [chemical binding]; other site 499177007684 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177007685 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 499177007686 nudix motif; other site 499177007687 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 499177007688 Isochorismatase family; Region: Isochorismatase; pfam00857 499177007689 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 499177007690 catalytic triad [active] 499177007691 conserved cis-peptide bond; other site 499177007692 ribose-phosphate pyrophosphokinase; Region: ribP_PPkin; TIGR01251 499177007693 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 499177007694 active site 499177007695 putative nicotinate phosphoribosyltransferase; Provisional; Region: PRK09198 499177007696 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 499177007697 active site 499177007698 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 499177007699 NAD synthase; Region: NAD_synthase; pfam02540 499177007700 homodimer interface [polypeptide binding]; other site 499177007701 NAD binding pocket [chemical binding]; other site 499177007702 ATP binding pocket [chemical binding]; other site 499177007703 Mg binding site [ion binding]; other site 499177007704 active-site loop [active] 499177007705 Fic family protein [Function unknown]; Region: COG3177 499177007706 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 499177007707 Fic/DOC family; Region: Fic; cl00960 499177007708 ABC-2 type transporter; Region: ABC2_membrane; cl11417 499177007709 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 499177007710 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 499177007711 Walker A/P-loop; other site 499177007712 ATP binding site [chemical binding]; other site 499177007713 Q-loop/lid; other site 499177007714 ABC transporter signature motif; other site 499177007715 Walker B; other site 499177007716 D-loop; other site 499177007717 H-loop/switch region; other site 499177007718 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 499177007719 DNA binding residues [nucleotide binding] 499177007720 Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Region: HTH_MerR-like; cd00592 499177007721 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 499177007722 DNA binding residues [nucleotide binding] 499177007723 dimer interface [polypeptide binding]; other site 499177007724 Scramblase; Region: Scramblase; cl02043 499177007725 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 499177007726 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177007727 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 499177007728 non-specific DNA binding site [nucleotide binding]; other site 499177007729 salt bridge; other site 499177007730 sequence-specific DNA binding site [nucleotide binding]; other site 499177007731 Uncharacterized protein conserved in bacteria (DUF2200); Region: DUF2200; cl02047 499177007732 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 499177007733 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 499177007734 Walker A/P-loop; other site 499177007735 ATP binding site [chemical binding]; other site 499177007736 Q-loop/lid; other site 499177007737 ABC transporter signature motif; other site 499177007738 Walker B; other site 499177007739 D-loop; other site 499177007740 H-loop/switch region; other site 499177007741 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 499177007742 FtsX-like permease family; Region: FtsX; cl15850 499177007743 H+ Antiporter protein; Region: 2A0121; TIGR00900 499177007744 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 499177007745 putative substrate translocation pore; other site 499177007746 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 499177007747 Helix-turn-helix domains; Region: HTH; cl00088 499177007748 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 499177007749 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177007750 Coenzyme A binding pocket [chemical binding]; other site 499177007751 Protein of unknown function (DUF1706); Region: DUF1706; cl01748 499177007752 Protein of unknown function (DUF3810); Region: DUF3810; pfam12725 499177007753 8-oxoguanine DNA glycosylase, N-terminal domain; Region: OGG_N; pfam07934 499177007754 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 499177007755 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 499177007756 minor groove reading motif; other site 499177007757 helix-hairpin-helix signature motif; other site 499177007758 substrate binding pocket [chemical binding]; other site 499177007759 active site 499177007760 Protein of unknown function (DUF805); Region: DUF805; cl01224 499177007761 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 499177007762 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 499177007763 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 499177007764 ATP binding site [chemical binding]; other site 499177007765 putative Mg++ binding site [ion binding]; other site 499177007766 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 499177007767 nucleotide binding region [chemical binding]; other site 499177007768 ATP-binding site [chemical binding]; other site 499177007769 RQC domain; Region: RQC; cl09632 499177007770 HRDC domain; Region: HRDC; cl02578 499177007771 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 499177007772 Fic family protein [Function unknown]; Region: COG3177 499177007773 Fic/DOC family; Region: Fic; cl00960 499177007774 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 499177007775 Coenzyme A binding pocket [chemical binding]; other site 499177007776 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177007777 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 499177007778 active site 499177007779 NTP binding site [chemical binding]; other site 499177007780 metal binding triad [ion binding]; metal-binding site 499177007781 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 499177007782 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 499177007783 sporadically distributed protein, TIGR04141 family; Region: TIGR04141 499177007784 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 499177007785 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 499177007786 catalytic residues [active] 499177007787 catalytic nucleophile [active] 499177007788 Recombinase; Region: Recombinase; pfam07508 499177007789 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 499177007790 Domain of unknown function (DUF927); Region: DUF927; cl12098 499177007791 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 499177007792 non-specific DNA binding site [nucleotide binding]; other site 499177007793 salt bridge; other site 499177007794 sequence-specific DNA binding site [nucleotide binding]; other site 499177007795 Protein of unknown function (DUF1643); Region: DUF1643; cl01787 499177007796 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 499177007797 MPN+ (JAMM) motif; other site 499177007798 Zinc-binding site [ion binding]; other site 499177007799 Protein of unknown function DUF262; Region: DUF262; cl14890 499177007800 Protein of unknown function DUF262; Region: DUF262; cl14890 499177007801 BsuBI/PstI restriction endonuclease C-terminus; Region: BsuBI_PstI_RE; pfam06616 499177007802 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family; Region: met_A_Alw26; TIGR02987 499177007803 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007804 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007805 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 499177007806 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 499177007807 H+ Antiporter protein; Region: 2A0121; TIGR00900 499177007808 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 499177007809 putative substrate translocation pore; other site 499177007810 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 499177007811 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 499177007812 DNA binding residues [nucleotide binding] 499177007813 Trm112p-like protein; Region: Trm112p; cl01066 499177007814 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007815 FMN-binding domain; Region: FMN_bind; cl01081 499177007816 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177007817 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 499177007818 Helix-turn-helix domains; Region: HTH; cl00088 499177007819 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 499177007820 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 499177007821 Protein of unknown function, DUF606; Region: DUF606; cl01273 499177007822 Protein of unknown function, DUF606; Region: DUF606; cl01273 499177007823 Predicted transcriptional regulator [Transcription]; Region: COG2378 499177007824 Helix-turn-helix domains; Region: HTH; cl00088 499177007825 WYL domain; Region: WYL; cl14852 499177007826 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 499177007827 EamA-like transporter family; Region: EamA; cl01037 499177007828 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 499177007829 EamA-like transporter family; Region: EamA; cl01037 499177007830 ParB-like nuclease domain; Region: ParBc; cl02129 499177007831 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 499177007832 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 499177007833 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 499177007834 P-loop; other site 499177007835 Magnesium ion binding site [ion binding]; other site 499177007836 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 499177007837 Magnesium ion binding site [ion binding]; other site 499177007838 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 499177007839 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 499177007840 Walker A/P-loop; other site 499177007841 ATP binding site [chemical binding]; other site 499177007842 Q-loop/lid; other site 499177007843 ABC transporter signature motif; other site 499177007844 Walker B; other site 499177007845 D-loop; other site 499177007846 H-loop/switch region; other site 499177007847 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 499177007848 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 499177007849 FtsX-like permease family; Region: FtsX; cl15850 499177007850 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 499177007851 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 499177007852 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 499177007853 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 499177007854 protein binding site [polypeptide binding]; other site 499177007855 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 499177007856 YycH protein; Region: YycI; cl02015 499177007857 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 499177007858 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 499177007859 dimerization interface [polypeptide binding]; other site 499177007860 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 499177007861 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 499177007862 dimer interface [polypeptide binding]; other site 499177007863 phosphorylation site [posttranslational modification] 499177007864 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 499177007865 ATP binding site [chemical binding]; other site 499177007866 Mg2+ binding site [ion binding]; other site 499177007867 G-X-G motif; other site 499177007868 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 499177007869 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 499177007870 active site 499177007871 phosphorylation site [posttranslational modification] 499177007872 intermolecular recognition site; other site 499177007873 dimerization interface [polypeptide binding]; other site 499177007874 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 499177007875 DNA binding site [nucleotide binding] 499177007876 Replication initiation and membrane attachment; Region: DnaB_2; cl12121 499177007877 Replication initiation and membrane attachment; Region: DnaB_2; cl12121 499177007878 DNA replication protein DnaC; Validated; Region: PRK06835 499177007879 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 499177007880 Walker A motif; other site 499177007881 ATP binding site [chemical binding]; other site 499177007882 Walker B motif; other site 499177007883 arginine finger; other site 499177007884 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 499177007885 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 499177007886 FOG: CBS domain [General function prediction only]; Region: COG0517 499177007887 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 499177007888 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 499177007889 metal binding site [ion binding]; metal-binding site 499177007890 active site 499177007891 I-site; other site 499177007892 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 499177007893 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 499177007894 GDP-binding site [chemical binding]; other site 499177007895 ACT binding site; other site 499177007896 IMP binding site; other site 499177007897 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 499177007898 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 499177007899 replicative DNA helicase; Region: DnaB; TIGR00665 499177007900 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 499177007901 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 499177007902 Walker A motif; other site 499177007903 ATP binding site [chemical binding]; other site 499177007904 Walker B motif; other site 499177007905 DNA binding loops [nucleotide binding] 499177007906 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 499177007907 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 499177007908 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 499177007909 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]; Region: COG3887 499177007910 DHH family; Region: DHH; pfam01368 499177007911 DHHA1 domain; Region: DHHA1; pfam02272 499177007912 Predicted membrane protein (DUF2232); Region: DUF2232; cl01728 499177007913 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 499177007914 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 499177007915 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 499177007916 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 499177007917 dimer interface [polypeptide binding]; other site 499177007918 ssDNA binding site [nucleotide binding]; other site 499177007919 tetramer (dimer of dimers) interface [polypeptide binding]; other site 499177007920 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 499177007921 Bacterial protein of unknown function (DUF951); Region: DUF951; cl01864 499177007922 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 499177007923 SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response...; Region: SirA_like_N; cd03421 499177007924 selenium metabolism protein YedF; Region: selenium_YedF; TIGR03527 499177007925 CPxP motif; other site 499177007926 Colicin V production protein; Region: Colicin_V; cl00567 499177007927 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 499177007928 non-specific DNA binding site [nucleotide binding]; other site 499177007929 salt bridge; other site 499177007930 sequence-specific DNA binding site [nucleotide binding]; other site 499177007931 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 499177007932 Tetratricopeptide repeat; Region: TPR_12; pfam13424 499177007933 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 499177007934 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 499177007935 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 499177007936 catalytic residue [active] 499177007937 ParB-like partition proteins; Region: parB_part; TIGR00180 499177007938 ParB-like nuclease domain; Region: ParBc; cl02129 499177007939 Methyltransferase domain; Region: Methyltransf_31; pfam13847 499177007940 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 499177007941 S-adenosylmethionine binding site [chemical binding]; other site 499177007942 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 499177007943 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 499177007944 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 499177007945 Predicted transcriptional regulators [Transcription]; Region: COG1725 499177007946 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 499177007947 DNA-binding site [nucleotide binding]; DNA binding site 499177007948 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 499177007949 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 499177007950 Walker A/P-loop; other site 499177007951 ATP binding site [chemical binding]; other site 499177007952 Q-loop/lid; other site 499177007953 ABC transporter signature motif; other site 499177007954 Walker B; other site 499177007955 D-loop; other site 499177007956 H-loop/switch region; other site 499177007957 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 499177007958 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 499177007959 trmE is a tRNA modification GTPase; Region: trmE; cd04164 499177007960 G1 box; other site 499177007961 GTP/Mg2+ binding site [chemical binding]; other site 499177007962 Switch I region; other site 499177007963 G2 box; other site 499177007964 Switch II region; other site 499177007965 G3 box; other site 499177007966 G4 box; other site 499177007967 G5 box; other site 499177007968 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 499177007969 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 499177007970 jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta...; Region: jag_KH; cd02414 499177007971 G-X-X-G motif; other site 499177007972 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 499177007973 RxxxH motif; other site 499177007974 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 499177007975 Haemolytic domain; Region: Haemolytic; cl00506 499177007976 Ribonuclease P; Region: Ribonuclease_P; cl00457 499177007977 Ribosomal protein L34; Region: Ribosomal_L34; cl00370