-- dump date 20140619_021405 -- class Genbank::misc_feature -- table misc_feature_note -- id note 360107000001 Initiator Replication protein; Region: Rep_3; pfam01051 360107000002 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 360107000003 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 360107000004 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 360107000005 DnaA N-terminal domain; Region: DnaA_N; pfam11638 360107000006 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 360107000007 Walker A motif; other site 360107000008 ATP binding site [chemical binding]; other site 360107000009 Walker B motif; other site 360107000010 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 360107000011 arginine finger; other site 360107000012 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 360107000013 DnaA box-binding interface [nucleotide binding]; other site 360107000014 DNA polymerase III subunit beta; Validated; Region: PRK05643 360107000015 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 360107000016 putative DNA binding surface [nucleotide binding]; other site 360107000017 dimer interface [polypeptide binding]; other site 360107000018 beta-clamp/clamp loader binding surface; other site 360107000019 beta-clamp/translesion DNA polymerase binding surface; other site 360107000020 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 360107000021 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 360107000022 Mg2+ binding site [ion binding]; other site 360107000023 G-X-G motif; other site 360107000024 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 360107000025 anchoring element; other site 360107000026 dimer interface [polypeptide binding]; other site 360107000027 ATP binding site [chemical binding]; other site 360107000028 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 360107000029 active site 360107000030 putative metal-binding site [ion binding]; other site 360107000031 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 360107000032 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 360107000033 metal binding site [ion binding]; metal-binding site 360107000034 active site 360107000035 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 360107000036 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 360107000037 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 360107000038 HD domain; Region: HD_3; pfam13023 360107000039 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 360107000040 active site 360107000041 dimerization interface [polypeptide binding]; other site 360107000042 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 360107000043 Major Facilitator Superfamily; Region: MFS_1; pfam07690 360107000044 putative substrate translocation pore; other site 360107000045 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 360107000046 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 360107000047 dimer interface [polypeptide binding]; other site 360107000048 putative functional site; other site 360107000049 putative MPT binding site; other site 360107000050 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 360107000051 active site clefts [active] 360107000052 zinc binding site [ion binding]; other site 360107000053 dimer interface [polypeptide binding]; other site 360107000054 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 360107000055 Mechanosensitive ion channel; Region: MS_channel; pfam00924 360107000056 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional; Region: PRK11331 360107000057 trigger factor; Provisional; Region: tig; PRK01490 360107000058 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 360107000059 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 360107000060 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 360107000061 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 360107000062 oligomer interface [polypeptide binding]; other site 360107000063 active site residues [active] 360107000064 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 360107000065 active site 360107000066 catalytic residues [active] 360107000067 metal binding site [ion binding]; metal-binding site 360107000068 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 360107000069 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 360107000070 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 360107000071 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 360107000072 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 360107000073 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 360107000074 putative substrate binding site [chemical binding]; other site 360107000075 putative ATP binding site [chemical binding]; other site 360107000076 Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]; Region: PurN; COG0299 360107000077 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 360107000078 active site 360107000079 substrate binding site [chemical binding]; other site 360107000080 cosubstrate binding site; other site 360107000081 catalytic site [active] 360107000082 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 360107000083 Domain of unknown function DUF21; Region: DUF21; pfam01595 360107000084 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 360107000085 Transporter associated domain; Region: CorC_HlyC; smart01091 360107000086 fumarate hydratase; Provisional; Region: PRK06246 360107000087 Fumarase C-terminus; Region: Fumerase_C; cl00795 360107000088 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 360107000089 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 360107000090 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 360107000091 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 360107000092 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 360107000093 homopentamer interface [polypeptide binding]; other site 360107000094 active site 360107000095 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 360107000096 putative RNA binding site [nucleotide binding]; other site 360107000097 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 360107000098 active site 360107000099 dimer interface [polypeptide binding]; other site 360107000100 Peptidase family M48; Region: Peptidase_M48; pfam01435 360107000101 Predicted permeases [General function prediction only]; Region: COG0679 360107000102 putative transporter; Reviewed; Region: PRK12369 360107000103 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 360107000104 trimer interface [polypeptide binding]; other site 360107000105 dimer interface [polypeptide binding]; other site 360107000106 putative active site [active] 360107000107 Protein of unknown function (DUF493); Region: DUF493; cl01102 360107000108 V-type ATP synthase subunit I; Validated; Region: PRK05771 360107000109 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 360107000110 Helix-turn-helix domain; Region: HTH_17; pfam12728 360107000111 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 360107000112 homodecamer interface [polypeptide binding]; other site 360107000113 GTP cyclohydrolase I; Provisional; Region: PLN03044 360107000114 active site 360107000115 putative catalytic site residues [active] 360107000116 zinc binding site [ion binding]; other site 360107000117 GTP-CH-I/GFRP interaction surface; other site 360107000118 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 360107000119 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 360107000120 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 360107000121 catalytic residue [active] 360107000122 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 360107000123 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 360107000124 trimerization site [polypeptide binding]; other site 360107000125 active site 360107000126 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 360107000127 NifU-like domain; Region: NifU; cl00484 360107000128 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 360107000129 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 360107000130 putative ligand binding site [chemical binding]; other site 360107000131 putative NAD binding site [chemical binding]; other site 360107000132 catalytic site [active] 360107000133 coproporphyrinogen III oxidase; Provisional; Region: PRK08629 360107000134 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 360107000135 FeS/SAM binding site; other site 360107000136 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 360107000137 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 360107000138 active site 360107000139 HIGH motif; other site 360107000140 dimer interface [polypeptide binding]; other site 360107000141 KMSKS motif; other site 360107000142 shikimate kinase; Reviewed; Region: aroK; PRK00131 360107000143 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 360107000144 ADP binding site [chemical binding]; other site 360107000145 magnesium binding site [ion binding]; other site 360107000146 putative shikimate binding site; other site 360107000147 GTP-binding protein Der; Reviewed; Region: PRK00093 360107000148 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 360107000149 G1 box; other site 360107000150 GTP/Mg2+ binding site [chemical binding]; other site 360107000151 Switch I region; other site 360107000152 G2 box; other site 360107000153 Switch II region; other site 360107000154 G3 box; other site 360107000155 G4 box; other site 360107000156 G5 box; other site 360107000157 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 360107000158 G1 box; other site 360107000159 GTP/Mg2+ binding site [chemical binding]; other site 360107000160 Switch I region; other site 360107000161 G2 box; other site 360107000162 G3 box; other site 360107000163 Switch II region; other site 360107000164 G4 box; other site 360107000165 G5 box; other site 360107000166 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 360107000167 EamA-like transporter family; Region: EamA; cl17759 360107000168 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 360107000169 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 360107000170 cofactor binding site; other site 360107000171 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 360107000172 Shikimate / quinate 5-dehydrogenase; Region: Shikimate_DH; pfam01488 360107000173 Protein of unknown function DUF99; Region: DUF99; cl00704 360107000174 Protein of unknown function DUF262; Region: DUF262; pfam03235 360107000175 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 360107000176 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 360107000177 active site 360107000178 Adenine-specific methyltransferase EcoRI; Region: EcoRI_methylase; pfam13651 360107000179 Adenine-specific methyltransferase EcoRI; Region: EcoRI_methylase; pfam13651 360107000180 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 360107000181 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 360107000182 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 360107000183 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 360107000184 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 360107000185 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 360107000186 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 360107000187 FeS/SAM binding site; other site 360107000188 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 360107000189 classical (c) SDRs; Region: SDR_c; cd05233 360107000190 NAD(P) binding site [chemical binding]; other site 360107000191 active site 360107000192 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 360107000193 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 360107000194 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 360107000195 catalytic residue [active] 360107000196 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 360107000197 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 360107000198 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 360107000199 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 360107000200 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 360107000201 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 360107000202 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 360107000203 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 360107000204 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 360107000205 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 360107000206 putative translocon binding site; other site 360107000207 protein-rRNA interface [nucleotide binding]; other site 360107000208 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 360107000209 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 360107000210 G-X-X-G motif; other site 360107000211 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 360107000212 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 360107000213 23S rRNA interface [nucleotide binding]; other site 360107000214 5S rRNA interface [nucleotide binding]; other site 360107000215 putative antibiotic binding site [chemical binding]; other site 360107000216 L25 interface [polypeptide binding]; other site 360107000217 L27 interface [polypeptide binding]; other site 360107000218 50S ribosomal protein L29; Reviewed; Region: PRK00306 360107000219 trigger factor interaction site; other site 360107000220 23S rRNA interface [nucleotide binding]; other site 360107000221 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 360107000222 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 360107000223 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 360107000224 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 360107000225 RNA binding site [nucleotide binding]; other site 360107000226 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 360107000227 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 360107000228 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 360107000229 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 360107000230 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 360107000231 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 360107000232 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 360107000233 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 360107000234 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 360107000235 5S rRNA interface [nucleotide binding]; other site 360107000236 23S rRNA interface [nucleotide binding]; other site 360107000237 L5 interface [polypeptide binding]; other site 360107000238 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 360107000239 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 360107000240 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 360107000241 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 360107000242 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 360107000243 SecY translocase; Region: SecY; pfam00344 360107000244 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 360107000245 active site 360107000246 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 360107000247 putative deacylase active site [active] 360107000248 Methyltransferase domain; Region: Methyltransf_31; pfam13847 360107000249 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 360107000250 S-adenosylmethionine binding site [chemical binding]; other site 360107000251 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 360107000252 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 360107000253 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 360107000254 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 360107000255 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 360107000256 CoA-binding site [chemical binding]; other site 360107000257 ATP-binding [chemical binding]; other site 360107000258 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 360107000259 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 360107000260 dimerization interface [polypeptide binding]; other site 360107000261 putative ATP binding site [chemical binding]; other site 360107000262 SurA N-terminal domain; Region: SurA_N; pfam09312 360107000263 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 360107000264 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 360107000265 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 360107000266 active site 360107000267 HIGH motif; other site 360107000268 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 360107000269 active site 360107000270 KMSKS motif; other site 360107000271 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 360107000272 Malic enzyme, N-terminal domain; Region: malic; pfam00390 360107000273 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 360107000274 putative NAD(P) binding site [chemical binding]; other site 360107000275 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 360107000276 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 360107000277 active site 360107000278 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 360107000279 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 360107000280 Tetramer interface [polypeptide binding]; other site 360107000281 active site 360107000282 FMN-binding site [chemical binding]; other site 360107000283 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 360107000284 MoaE homodimer interface [polypeptide binding]; other site 360107000285 MoaD interaction [polypeptide binding]; other site 360107000286 active site residues [active] 360107000287 ThiS family; Region: ThiS; pfam02597 360107000288 charged pocket; other site 360107000289 hydrophobic patch; other site 360107000290 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 360107000291 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 360107000292 dimer interface [polypeptide binding]; other site 360107000293 active site 360107000294 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 360107000295 catalytic residues [active] 360107000296 substrate binding site [chemical binding]; other site 360107000297 UGMP family protein; Validated; Region: PRK09604 360107000298 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 360107000299 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 360107000300 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 360107000301 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 360107000302 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 360107000303 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 360107000304 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 360107000305 Domain of unknown function (DUF814); Region: DUF814; pfam05670 360107000306 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 360107000307 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 360107000308 substrate binding site [chemical binding]; other site 360107000309 ligand binding site [chemical binding]; other site 360107000310 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 360107000311 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 360107000312 GTP binding site; other site 360107000313 Phospholipase A1; Region: PLA1; pfam02253 360107000314 dimerization interface [polypeptide binding]; other site 360107000315 substrate binding site [chemical binding]; other site 360107000316 active site 360107000317 calcium binding site [ion binding]; other site 360107000318 Cytochrome c552; Region: Cytochrom_C552; pfam02335 360107000319 cytochrome c nitrate reductase, small subunit; Region: cytochr_NrfH; TIGR03153 360107000320 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 360107000321 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 360107000322 catalytic motif [active] 360107000323 Zn binding site [ion binding]; other site 360107000324 RibD C-terminal domain; Region: RibD_C; cl17279 360107000325 elongation factor P; Validated; Region: PRK00529 360107000326 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 360107000327 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 360107000328 RNA binding site [nucleotide binding]; other site 360107000329 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 360107000330 RNA binding site [nucleotide binding]; other site 360107000331 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 360107000332 DHH family; Region: DHH; pfam01368 360107000333 DHHA1 domain; Region: DHHA1; pfam02272 360107000334 CTP synthetase; Validated; Region: pyrG; PRK05380 360107000335 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 360107000336 Catalytic site [active] 360107000337 active site 360107000338 UTP binding site [chemical binding]; other site 360107000339 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 360107000340 active site 360107000341 putative oxyanion hole; other site 360107000342 catalytic triad [active] 360107000343 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 360107000344 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 360107000345 active site 360107000346 DNA binding site [nucleotide binding] 360107000347 Int/Topo IB signature motif; other site 360107000348 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 360107000349 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 360107000350 dimer interface [polypeptide binding]; other site 360107000351 ssDNA binding site [nucleotide binding]; other site 360107000352 tetramer (dimer of dimers) interface [polypeptide binding]; other site 360107000353 TrbM; Region: TrbM; pfam07424 360107000354 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 360107000355 Toprim-like; Region: Toprim_2; pfam13155 360107000356 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 360107000357 active site 360107000358 NTP binding site [chemical binding]; other site 360107000359 metal binding triad [ion binding]; metal-binding site 360107000360 antibiotic binding site [chemical binding]; other site 360107000361 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 360107000362 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 360107000363 DNA primase (bacterial type) [DNA replication, recombination, and repair]; Region: DnaG; COG0358 360107000364 CHC2 zinc finger; Region: zf-CHC2; cl17510 360107000365 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 360107000366 active site 360107000367 metal binding site [ion binding]; metal-binding site 360107000368 interdomain interaction site; other site 360107000369 Zeta toxin; Region: Zeta_toxin; pfam06414 360107000370 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 360107000371 Methyltransferase domain; Region: Methyltransf_26; pfam13659 360107000372 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 360107000373 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 360107000374 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 360107000375 ATP binding site [chemical binding]; other site 360107000376 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 360107000377 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 360107000378 nucleotide binding region [chemical binding]; other site 360107000379 ATP-binding site [chemical binding]; other site 360107000380 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 360107000381 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 360107000382 N-acetyl-D-glucosamine binding site [chemical binding]; other site 360107000383 catalytic residue [active] 360107000384 DNA topoisomerase III; Provisional; Region: PRK07726 360107000385 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 360107000386 active site 360107000387 putative interdomain interaction site [polypeptide binding]; other site 360107000388 putative metal-binding site [ion binding]; other site 360107000389 putative nucleotide binding site [chemical binding]; other site 360107000390 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; cl11986 360107000391 domain I; other site 360107000392 DNA binding groove [nucleotide binding] 360107000393 phosphate binding site [ion binding]; other site 360107000394 domain II; other site 360107000395 domain III; other site 360107000396 nucleotide binding site [chemical binding]; other site 360107000397 catalytic site [active] 360107000398 domain IV; other site 360107000399 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 360107000400 PcfJ-like protein; Region: PcfJ; pfam14284 360107000401 TrbM; Region: TrbM; pfam07424 360107000402 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 360107000403 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 360107000404 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 360107000405 Walker A motif; other site 360107000406 ATP binding site [chemical binding]; other site 360107000407 Walker B motif; other site 360107000408 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 360107000409 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 360107000410 ATP binding site [chemical binding]; other site 360107000411 Walker A motif; other site 360107000412 hexamer interface [polypeptide binding]; other site 360107000413 Walker B motif; other site 360107000414 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 360107000415 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 360107000416 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 360107000417 VirB7 interaction site; other site 360107000418 VirB8 protein; Region: VirB8; pfam04335 360107000419 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 360107000420 Type IV secretion system proteins; Region: T4SS; pfam07996 360107000421 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 360107000422 AAA-like domain; Region: AAA_10; pfam12846 360107000423 NADH dehydrogenase subunit A; Validated; Region: PRK08489 360107000424 NADH dehydrogenase subunit B; Validated; Region: PRK06411 360107000425 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 360107000426 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 360107000427 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 360107000428 NADH dehydrogenase subunit D; Validated; Region: PRK06075 360107000429 NADH dehydrogenase subunit G; Validated; Region: PRK08493 360107000430 NADH dehydrogenase subunit G; Validated; Region: PRK08493 360107000431 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 360107000432 catalytic loop [active] 360107000433 iron binding site [ion binding]; other site 360107000434 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 360107000435 4Fe-4S binding domain; Region: Fer4; pfam00037 360107000436 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 360107000437 molybdopterin cofactor binding site; other site 360107000438 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 360107000439 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 360107000440 Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]; Region: NuoI; COG1143 360107000441 4Fe-4S binding domain; Region: Fer4; pfam00037 360107000442 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 360107000443 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 360107000444 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 360107000445 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 360107000446 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 360107000447 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 360107000448 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 360107000449 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 360107000450 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 360107000451 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 360107000452 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 360107000453 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 360107000454 dimer interface [polypeptide binding]; other site 360107000455 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 360107000456 putative radical transfer pathway; other site 360107000457 diiron center [ion binding]; other site 360107000458 tyrosyl radical; other site 360107000459 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 360107000460 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 360107000461 S-adenosylmethionine binding site [chemical binding]; other site 360107000462 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 360107000463 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 360107000464 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 360107000465 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 360107000466 tetramerization interface [polypeptide binding]; other site 360107000467 active site 360107000468 hypothetical protein; Provisional; Region: PRK03762 360107000469 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 360107000470 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 360107000471 substrate binding pocket [chemical binding]; other site 360107000472 chain length determination region; other site 360107000473 substrate-Mg2+ binding site; other site 360107000474 catalytic residues [active] 360107000475 aspartate-rich region 1; other site 360107000476 active site lid residues [active] 360107000477 aspartate-rich region 2; other site 360107000478 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 360107000479 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 360107000480 TPP-binding site [chemical binding]; other site 360107000481 dimer interface [polypeptide binding]; other site 360107000482 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 360107000483 PYR/PP interface [polypeptide binding]; other site 360107000484 dimer interface [polypeptide binding]; other site 360107000485 TPP binding site [chemical binding]; other site 360107000486 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 360107000487 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 360107000488 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 360107000489 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 360107000490 alphaNTD homodimer interface [polypeptide binding]; other site 360107000491 alphaNTD - beta interaction site [polypeptide binding]; other site 360107000492 alphaNTD - beta' interaction site [polypeptide binding]; other site 360107000493 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 360107000494 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 360107000495 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 360107000496 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 360107000497 RNA binding surface [nucleotide binding]; other site 360107000498 30S ribosomal protein S11; Validated; Region: PRK05309 360107000499 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 360107000500 30S ribosomal protein S13; Region: bact_S13; TIGR03631 360107000501 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 360107000502 rRNA binding site [nucleotide binding]; other site 360107000503 predicted 30S ribosome binding site; other site 360107000504 seryl-tRNA synthetase; Provisional; Region: PRK05431 360107000505 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 360107000506 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 360107000507 dimer interface [polypeptide binding]; other site 360107000508 active site 360107000509 motif 1; other site 360107000510 motif 2; other site 360107000511 motif 3; other site 360107000512 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 360107000513 active site 360107000514 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 360107000515 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 360107000516 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 360107000517 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 360107000518 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 360107000519 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 360107000520 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 360107000521 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 360107000522 catalytic residues [active] 360107000523 hypothetical protein; Reviewed; Region: PRK12497 360107000524 homoserine dehydrogenase; Provisional; Region: PRK06349 360107000525 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 360107000526 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 360107000527 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 360107000528 aspartate aminotransferase; Provisional; Region: PRK08636 360107000529 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 360107000530 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107000531 homodimer interface [polypeptide binding]; other site 360107000532 catalytic residue [active] 360107000533 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 360107000534 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 360107000535 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 360107000536 Predicted methyltransferases [General function prediction only]; Region: COG0313 360107000537 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 360107000538 putative SAM binding site [chemical binding]; other site 360107000539 putative homodimer interface [polypeptide binding]; other site 360107000540 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 360107000541 BCCT family transporter; Region: BCCT; pfam02028 360107000542 Bacterial protein of unknown function (DUF839); Region: DUF839; pfam05787 360107000543 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 360107000544 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 360107000545 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 360107000546 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 360107000547 dimer interface [polypeptide binding]; other site 360107000548 active site 360107000549 acyl carrier protein; Provisional; Region: acpP; PRK00982 360107000550 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 360107000551 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 360107000552 NAD(P) binding site [chemical binding]; other site 360107000553 active site 360107000554 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 360107000555 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 360107000556 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 360107000557 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 360107000558 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 360107000559 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 360107000560 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 360107000561 RDD family; Region: RDD; pfam06271 360107000562 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 360107000563 Organic solvent tolerance protein; Region: OstA_C; pfam04453 360107000564 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cl00309 360107000565 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 360107000566 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 360107000567 oligomer interface [polypeptide binding]; other site 360107000568 RNA binding site [nucleotide binding]; other site 360107000569 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 360107000570 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 360107000571 RNase E interface [polypeptide binding]; other site 360107000572 trimer interface [polypeptide binding]; other site 360107000573 active site 360107000574 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 360107000575 putative nucleic acid binding region [nucleotide binding]; other site 360107000576 G-X-X-G motif; other site 360107000577 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 360107000578 RNA binding site [nucleotide binding]; other site 360107000579 domain interface; other site 360107000580 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 360107000581 Ligand Binding Site [chemical binding]; other site 360107000582 LysE type translocator; Region: LysE; pfam01810 360107000583 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 360107000584 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 360107000585 metal binding site [ion binding]; metal-binding site 360107000586 dimer interface [polypeptide binding]; other site 360107000587 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 360107000588 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 360107000589 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 360107000590 dimer interface [polypeptide binding]; other site 360107000591 ssDNA binding site [nucleotide binding]; other site 360107000592 tetramer (dimer of dimers) interface [polypeptide binding]; other site 360107000593 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 360107000594 endonuclease IV; Provisional; Region: PRK01060 360107000595 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 360107000596 AP (apurinic/apyrimidinic) site pocket; other site 360107000597 DNA interaction; other site 360107000598 Metal-binding active site; metal-binding site 360107000599 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 360107000600 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 360107000601 dimer interface [polypeptide binding]; other site 360107000602 FMN binding site [chemical binding]; other site 360107000603 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 360107000604 non-specific DNA binding site [nucleotide binding]; other site 360107000605 salt bridge; other site 360107000606 Predicted transcriptional regulator [Transcription]; Region: COG2932 360107000607 sequence-specific DNA binding site [nucleotide binding]; other site 360107000608 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 360107000609 Catalytic site [active] 360107000610 Helix-turn-helix domain; Region: HTH_28; pfam13518 360107000611 Winged helix-turn helix; Region: HTH_29; pfam13551 360107000612 Integrase core domain; Region: rve; pfam00665 360107000613 AAA domain; Region: AAA_22; pfam13401 360107000614 AAA domain; Region: AAA_30; pfam13604 360107000615 Bacteriophage Mu Gam like protein; Region: Phage_Mu_Gam; pfam07352 360107000616 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 360107000617 Domain of unknown function DUF1828; Region: DUF1828; pfam08861 360107000618 Domain of unknown function DUF1829; Region: DUF1829; pfam08862 360107000619 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 360107000620 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 360107000621 Protein of unknown function (DUF935); Region: DUF935; pfam06074 360107000622 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 360107000623 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 360107000624 DNA-binding interface [nucleotide binding]; DNA binding site 360107000625 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 360107000626 Lysozyme family protein [General function prediction only]; Region: zliS; COG3926 360107000627 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 360107000628 Phage-related minor tail protein [Function unknown]; Region: COG5281 360107000629 tape measure domain; Region: tape_meas_nterm; TIGR02675 360107000630 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 360107000631 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 360107000632 Putative phage tail protein; Region: Phage-tail_3; pfam13550 360107000633 Y-family of DNA polymerases; Region: PolY; cl12025 360107000634 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 360107000635 DNA binding site [nucleotide binding] 360107000636 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 360107000637 dimer interface [polypeptide binding]; other site 360107000638 substrate binding site [chemical binding]; other site 360107000639 metal binding sites [ion binding]; metal-binding site 360107000640 adenylate kinase; Reviewed; Region: adk; PRK00279 360107000641 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 360107000642 AMP-binding site [chemical binding]; other site 360107000643 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 360107000644 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 360107000645 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 360107000646 dimer interface [polypeptide binding]; other site 360107000647 anticodon binding site; other site 360107000648 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 360107000649 homodimer interface [polypeptide binding]; other site 360107000650 motif 1; other site 360107000651 active site 360107000652 motif 2; other site 360107000653 GAD domain; Region: GAD; pfam02938 360107000654 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 360107000655 active site 360107000656 motif 3; other site 360107000657 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: pnk; PRK14077 360107000658 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 360107000659 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 360107000660 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 360107000661 Walker A/P-loop; other site 360107000662 ATP binding site [chemical binding]; other site 360107000663 Q-loop/lid; other site 360107000664 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 360107000665 ABC transporter signature motif; other site 360107000666 Walker B; other site 360107000667 D-loop; other site 360107000668 H-loop/switch region; other site 360107000669 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 360107000670 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 360107000671 active site 360107000672 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 360107000673 N-acetyl-D-glucosamine binding site [chemical binding]; other site 360107000674 catalytic residue [active] 360107000675 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 360107000676 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 360107000677 Sporulation related domain; Region: SPOR; pfam05036 360107000678 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 360107000679 putative active site pocket [active] 360107000680 4-fold oligomerization interface [polypeptide binding]; other site 360107000681 metal binding residues [ion binding]; metal-binding site 360107000682 3-fold/trimer interface [polypeptide binding]; other site 360107000683 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 360107000684 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 360107000685 active site 360107000686 motif I; other site 360107000687 motif II; other site 360107000688 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 360107000689 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 360107000690 OstA-like protein; Region: OstA; pfam03968 360107000691 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 360107000692 G1 box; other site 360107000693 GTP/Mg2+ binding site [chemical binding]; other site 360107000694 Switch I region; other site 360107000695 G2 box; other site 360107000696 G3 box; other site 360107000697 Switch II region; other site 360107000698 G4 box; other site 360107000699 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 360107000700 Coenzyme A binding pocket [chemical binding]; other site 360107000701 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 360107000702 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 360107000703 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 360107000704 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 360107000705 Autotransporter beta-domain; Region: Autotransporter; smart00869 360107000706 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 360107000707 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 360107000708 dimer interface [polypeptide binding]; other site 360107000709 conserved gate region; other site 360107000710 putative PBP binding loops; other site 360107000711 ABC-ATPase subunit interface; other site 360107000712 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 360107000713 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 360107000714 Walker A/P-loop; other site 360107000715 ATP binding site [chemical binding]; other site 360107000716 Q-loop/lid; other site 360107000717 ABC transporter signature motif; other site 360107000718 Walker B; other site 360107000719 D-loop; other site 360107000720 H-loop/switch region; other site 360107000721 TOBE domain; Region: TOBE; pfam03459 360107000722 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 360107000723 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 360107000724 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 360107000725 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 360107000726 TOBE domain; Region: TOBE; cl01440 360107000727 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 360107000728 VacJ like lipoprotein; Region: VacJ; cl01073 360107000729 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 360107000730 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 360107000731 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 360107000732 Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small; Region: DSRD; cl00018 360107000733 non-heme iron binding site [ion binding]; other site 360107000734 dimer interface [polypeptide binding]; other site 360107000735 Rubrerythrin [Energy production and conversion]; Region: COG1592 360107000736 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 360107000737 binuclear metal center [ion binding]; other site 360107000738 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 360107000739 iron binding site [ion binding]; other site 360107000740 prenyltransferase; Reviewed; Region: ubiA; PRK12874 360107000741 UbiA prenyltransferase family; Region: UbiA; pfam01040 360107000742 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 360107000743 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 360107000744 FeS/SAM binding site; other site 360107000745 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 360107000746 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 360107000747 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 360107000748 FeS/SAM binding site; other site 360107000749 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 360107000750 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 360107000751 non-specific DNA binding site [nucleotide binding]; other site 360107000752 salt bridge; other site 360107000753 sequence-specific DNA binding site [nucleotide binding]; other site 360107000754 Abortive infection C-terminus; Region: Abi_C; pfam14355 360107000755 Superfamily II helicase [General function prediction only]; Region: COG1204 360107000756 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 360107000757 ATP binding site [chemical binding]; other site 360107000758 putative Mg++ binding site [ion binding]; other site 360107000759 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 360107000760 Domain of unknown function (DUF4298); Region: DUF4298; pfam14131 360107000761 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 360107000762 arsenical-resistance protein; Region: acr3; TIGR00832 360107000763 Predicted permeases [General function prediction only]; Region: COG0701 360107000764 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 360107000765 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 360107000766 Low molecular weight phosphatase family; Region: LMWPc; cl00105 360107000767 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 360107000768 catalytic residue [active] 360107000769 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 360107000770 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 360107000771 Menaquinone biosynthesis; Region: VitK2_biosynth; cl17475 360107000772 RDD family; Region: RDD; pfam06271 360107000773 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 360107000774 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 360107000775 active site 360107000776 nucleophile elbow; other site 360107000777 glutamate dehydrogenase; Provisional; Region: PRK09414 360107000778 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 360107000779 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 360107000780 NAD(P) binding site [chemical binding]; other site 360107000781 Menaquinone biosynthesis; Region: VitK2_biosynth; pfam02621 360107000782 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 360107000783 ligand binding site [chemical binding]; other site 360107000784 active site 360107000785 UGI interface [polypeptide binding]; other site 360107000786 catalytic site [active] 360107000787 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 360107000788 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 360107000789 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 360107000790 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 360107000791 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 360107000792 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 360107000793 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 360107000794 Walker A/P-loop; other site 360107000795 ATP binding site [chemical binding]; other site 360107000796 Q-loop/lid; other site 360107000797 ABC transporter signature motif; other site 360107000798 Walker B; other site 360107000799 D-loop; other site 360107000800 H-loop/switch region; other site 360107000801 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 360107000802 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 360107000803 Walker A/P-loop; other site 360107000804 ATP binding site [chemical binding]; other site 360107000805 Q-loop/lid; other site 360107000806 ABC transporter signature motif; other site 360107000807 Walker B; other site 360107000808 D-loop; other site 360107000809 H-loop/switch region; other site 360107000810 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 360107000811 HlyD family secretion protein; Region: HlyD_3; pfam13437 360107000812 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 360107000813 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 360107000814 Soluble P-type ATPase [General function prediction only]; Region: COG4087 360107000815 hypothetical protein; Provisional; Region: PRK14013 360107000816 ribosome recycling factor; Reviewed; Region: frr; PRK00083 360107000817 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 360107000818 hinge region; other site 360107000819 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 360107000820 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 360107000821 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 360107000822 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 360107000823 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 360107000824 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 360107000825 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 360107000826 Major Facilitator Superfamily; Region: MFS_1; pfam07690 360107000827 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 360107000828 Na2 binding site [ion binding]; other site 360107000829 putative substrate binding site 1 [chemical binding]; other site 360107000830 Na binding site 1 [ion binding]; other site 360107000831 putative substrate binding site 2 [chemical binding]; other site 360107000832 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 360107000833 DNA polymerase III subunit delta; Validated; Region: PRK08487 360107000834 RNB domain; Region: RNB; pfam00773 360107000835 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 360107000836 ketol-acid reductoisomerase; Provisional; Region: PRK05479 360107000837 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 360107000838 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 360107000839 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 360107000840 NodB motif; other site 360107000841 putative active site [active] 360107000842 putative catalytic site [active] 360107000843 Zn binding site [ion binding]; other site 360107000844 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 360107000845 DNA protecting protein DprA; Region: dprA; TIGR00732 360107000846 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 360107000847 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 360107000848 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 360107000849 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 360107000850 Domain of unknown function DUF83; Region: Cas_Cas4; pfam01930 360107000851 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 360107000852 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 360107000853 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 360107000854 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I; cl12040 360107000855 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 360107000856 DNA polymerase III PolC; Validated; Region: polC; PRK00448 360107000857 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 360107000858 M48 family peptidase; Provisional; Region: PRK03001 360107000859 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 360107000860 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 360107000861 dimer interface [polypeptide binding]; other site 360107000862 phosphorylation site [posttranslational modification] 360107000863 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 360107000864 ATP binding site [chemical binding]; other site 360107000865 Mg2+ binding site [ion binding]; other site 360107000866 G-X-G motif; other site 360107000867 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 360107000868 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107000869 active site 360107000870 phosphorylation site [posttranslational modification] 360107000871 intermolecular recognition site; other site 360107000872 dimerization interface [polypeptide binding]; other site 360107000873 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 360107000874 DNA binding site [nucleotide binding] 360107000875 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 360107000876 active site 360107000877 NTP binding site [chemical binding]; other site 360107000878 metal binding triad [ion binding]; metal-binding site 360107000879 antibiotic binding site [chemical binding]; other site 360107000880 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 360107000881 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 360107000882 Walker A/P-loop; other site 360107000883 ATP binding site [chemical binding]; other site 360107000884 Q-loop/lid; other site 360107000885 ABC transporter signature motif; other site 360107000886 Walker B; other site 360107000887 D-loop; other site 360107000888 H-loop/switch region; other site 360107000889 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 360107000890 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 360107000891 dimer interface [polypeptide binding]; other site 360107000892 conserved gate region; other site 360107000893 putative PBP binding loops; other site 360107000894 ABC-ATPase subunit interface; other site 360107000895 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 360107000896 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 360107000897 dimer interface [polypeptide binding]; other site 360107000898 conserved gate region; other site 360107000899 putative PBP binding loops; other site 360107000900 ABC-ATPase subunit interface; other site 360107000901 PBP superfamily domain; Region: PBP_like_2; cl17296 360107000902 PBP superfamily domain; Region: PBP_like_2; cl17296 360107000903 RNA methyltransferase, RsmE family; Region: TIGR00046 360107000904 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 360107000905 Tetratricopeptide repeat; Region: TPR_12; pfam13424 360107000906 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 360107000907 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 360107000908 active site 360107000909 substrate binding site [chemical binding]; other site 360107000910 metal binding site [ion binding]; metal-binding site 360107000911 Chain length determinant protein; Region: Wzz; pfam02706 360107000912 alanine racemase; Reviewed; Region: alr; PRK00053 360107000913 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 360107000914 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 360107000915 catalytic residue [active] 360107000916 Competence protein; Region: Competence; cl00471 360107000917 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 360107000918 ATP cone domain; Region: ATP-cone; pfam03477 360107000919 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 360107000920 ATP cone domain; Region: ATP-cone; pfam03477 360107000921 Class III ribonucleotide reductase; Region: RNR_III; cd01675 360107000922 effector binding site; other site 360107000923 active site 360107000924 Zn binding site [ion binding]; other site 360107000925 glycine loop; other site 360107000926 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 360107000927 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 360107000928 FeS/SAM binding site; other site 360107000929 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 360107000930 RNA/DNA hybrid binding site [nucleotide binding]; other site 360107000931 active site 360107000932 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 360107000933 AAA domain; Region: AAA_14; pfam13173 360107000934 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 360107000935 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 360107000936 dimer interface [polypeptide binding]; other site 360107000937 conserved gate region; other site 360107000938 putative PBP binding loops; other site 360107000939 ABC-ATPase subunit interface; other site 360107000940 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 360107000941 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 360107000942 Walker A/P-loop; other site 360107000943 ATP binding site [chemical binding]; other site 360107000944 Q-loop/lid; other site 360107000945 ABC transporter signature motif; other site 360107000946 Walker B; other site 360107000947 D-loop; other site 360107000948 H-loop/switch region; other site 360107000949 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 360107000950 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 360107000951 substrate binding pocket [chemical binding]; other site 360107000952 membrane-bound complex binding site; other site 360107000953 hinge residues; other site 360107000954 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 360107000955 thiamine phosphate binding site [chemical binding]; other site 360107000956 active site 360107000957 pyrophosphate binding site [ion binding]; other site 360107000958 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 360107000959 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 360107000960 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 360107000961 substrate binding pocket [chemical binding]; other site 360107000962 membrane-bound complex binding site; other site 360107000963 hinge residues; other site 360107000964 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 360107000965 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 360107000966 G1 box; other site 360107000967 GTP/Mg2+ binding site [chemical binding]; other site 360107000968 Switch I region; other site 360107000969 G2 box; other site 360107000970 G3 box; other site 360107000971 Switch II region; other site 360107000972 G4 box; other site 360107000973 G5 box; other site 360107000974 Nucleoside recognition; Region: Gate; pfam07670 360107000975 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 360107000976 Nucleoside recognition; Region: Gate; pfam07670 360107000977 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 360107000978 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 360107000979 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 360107000980 catalytic residues [active] 360107000981 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 360107000982 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 360107000983 Walker A/P-loop; other site 360107000984 ATP binding site [chemical binding]; other site 360107000985 Q-loop/lid; other site 360107000986 ABC transporter signature motif; other site 360107000987 Walker B; other site 360107000988 D-loop; other site 360107000989 H-loop/switch region; other site 360107000990 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 360107000991 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 360107000992 FtsX-like permease family; Region: FtsX; pfam02687 360107000993 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 360107000994 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 360107000995 FtsX-like permease family; Region: FtsX; pfam02687 360107000996 Predicted membrane protein [Function unknown]; Region: COG4393 360107000997 Predicted membrane protein (DUF2318); Region: DUF2318; pfam10080 360107000998 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 360107000999 Fe2+ transport protein; Region: Iron_transport; pfam10634 360107001000 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 360107001001 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 360107001002 aspartate racemase; Region: asp_race; TIGR00035 360107001003 competence protein ComEA helix-hairpin-helix repeat region; Region: TIGR00426 360107001004 Helix-hairpin-helix motif; Region: HHH; pfam00633 360107001005 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 360107001006 minor groove reading motif; other site 360107001007 helix-hairpin-helix signature motif; other site 360107001008 active site 360107001009 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 360107001010 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 360107001011 putative active site [active] 360107001012 metal binding site [ion binding]; metal-binding site 360107001013 homodimer binding site [polypeptide binding]; other site 360107001014 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 360107001015 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 360107001016 Walker A motif; other site 360107001017 ATP binding site [chemical binding]; other site 360107001018 Walker B motif; other site 360107001019 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 360107001020 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 360107001021 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 360107001022 ATP binding site [chemical binding]; other site 360107001023 putative Mg++ binding site [ion binding]; other site 360107001024 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 360107001025 nucleotide binding region [chemical binding]; other site 360107001026 ATP-binding site [chemical binding]; other site 360107001027 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 360107001028 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 360107001029 Peptidase family M23; Region: Peptidase_M23; pfam01551 360107001030 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 360107001031 Lipopolysaccharide-assembly; Region: LptE; pfam04390 360107001032 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 360107001033 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 360107001034 HIGH motif; other site 360107001035 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 360107001036 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 360107001037 active site 360107001038 KMSKS motif; other site 360107001039 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 360107001040 tRNA binding surface [nucleotide binding]; other site 360107001041 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 360107001042 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 360107001043 Protein export membrane protein; Region: SecD_SecF; pfam02355 360107001044 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 360107001045 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 360107001046 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 360107001047 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 360107001048 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 360107001049 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 360107001050 active site 360107001051 catalytic triad [active] 360107001052 isocitrate dehydrogenase; Validated; Region: PRK07362 360107001053 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 360107001054 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 360107001055 ligand binding site [chemical binding]; other site 360107001056 NAD binding site [chemical binding]; other site 360107001057 dimerization interface [polypeptide binding]; other site 360107001058 catalytic site [active] 360107001059 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 360107001060 putative L-serine binding site [chemical binding]; other site 360107001061 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 360107001062 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 360107001063 RNA binding site [nucleotide binding]; other site 360107001064 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 360107001065 RNA binding site [nucleotide binding]; other site 360107001066 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 360107001067 RNA binding site [nucleotide binding]; other site 360107001068 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 360107001069 RNA binding site [nucleotide binding]; other site 360107001070 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 360107001071 RNA binding site [nucleotide binding]; other site 360107001072 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 360107001073 RNA binding site [nucleotide binding]; other site 360107001074 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 360107001075 LytB protein; Region: LYTB; pfam02401 360107001076 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 360107001077 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 360107001078 hinge; other site 360107001079 active site 360107001080 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 360107001081 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 360107001082 putative tRNA-binding site [nucleotide binding]; other site 360107001083 B3/4 domain; Region: B3_4; pfam03483 360107001084 tRNA synthetase B5 domain; Region: B5; smart00874 360107001085 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 360107001086 motif 1; other site 360107001087 dimer interface [polypeptide binding]; other site 360107001088 active site 360107001089 motif 2; other site 360107001090 motif 3; other site 360107001091 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 360107001092 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 360107001093 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 360107001094 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 360107001095 dimer interface [polypeptide binding]; other site 360107001096 motif 1; other site 360107001097 active site 360107001098 motif 2; other site 360107001099 motif 3; other site 360107001100 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 360107001101 nucleotide binding site/active site [active] 360107001102 HIT family signature motif; other site 360107001103 catalytic residue [active] 360107001104 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 360107001105 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 360107001106 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 360107001107 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 360107001108 Walker A motif; other site 360107001109 ATP binding site [chemical binding]; other site 360107001110 Walker B motif; other site 360107001111 arginine finger; other site 360107001112 Peptidase family M41; Region: Peptidase_M41; pfam01434 360107001113 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 360107001114 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 360107001115 2-isopropylmalate synthase; Validated; Region: PRK00915 360107001116 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 360107001117 active site 360107001118 catalytic residues [active] 360107001119 metal binding site [ion binding]; metal-binding site 360107001120 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 360107001121 diaminopimelate epimerase; Region: PLN02536 360107001122 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 360107001123 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 360107001124 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 360107001125 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 360107001126 23S rRNA binding site [nucleotide binding]; other site 360107001127 L21 binding site [polypeptide binding]; other site 360107001128 L13 binding site [polypeptide binding]; other site 360107001129 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 360107001130 Sel1-like repeats; Region: SEL1; smart00671 360107001131 peptide chain release factor 2; Validated; Region: prfB; PRK00578 360107001132 This domain is found in peptide chain release factors; Region: PCRF; smart00937 360107001133 RF-1 domain; Region: RF-1; pfam00472 360107001134 pantoate--beta-alanine ligase; Region: panC; TIGR00018 360107001135 Pantoate-beta-alanine ligase; Region: PanC; cd00560 360107001136 active site 360107001137 ATP-binding site [chemical binding]; other site 360107001138 pantoate-binding site; other site 360107001139 HXXH motif; other site 360107001140 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 360107001141 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 360107001142 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 360107001143 FeS/SAM binding site; other site 360107001144 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 360107001145 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 360107001146 Ligand Binding Site [chemical binding]; other site 360107001147 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 360107001148 putative acyl-acceptor binding pocket; other site 360107001149 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 360107001150 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 360107001151 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 360107001152 FeS/SAM binding site; other site 360107001153 TRAM domain; Region: TRAM; cl01282 360107001154 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 360107001155 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 360107001156 NusA N-terminal domain; Region: NusA_N; pfam08529 360107001157 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 360107001158 RNA binding site [nucleotide binding]; other site 360107001159 homodimer interface [polypeptide binding]; other site 360107001160 NusA-like KH domain; Region: KH_5; pfam13184 360107001161 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 360107001162 G-X-X-G motif; other site 360107001163 NosL; Region: NosL; cl01769 360107001164 NosL; Region: NosL; cl01769 360107001165 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 360107001166 FtsX-like permease family; Region: FtsX; pfam02687 360107001167 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 360107001168 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 360107001169 Walker A/P-loop; other site 360107001170 ATP binding site [chemical binding]; other site 360107001171 Q-loop/lid; other site 360107001172 ABC transporter signature motif; other site 360107001173 Walker B; other site 360107001174 D-loop; other site 360107001175 H-loop/switch region; other site 360107001176 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 360107001177 S-adenosylmethionine binding site [chemical binding]; other site 360107001178 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 360107001179 metal binding site 2 [ion binding]; metal-binding site 360107001180 putative DNA binding helix; other site 360107001181 metal binding site 1 [ion binding]; metal-binding site 360107001182 structural Zn2+ binding site [ion binding]; other site 360107001183 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 360107001184 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 360107001185 intersubunit interface [polypeptide binding]; other site 360107001186 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 360107001187 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 360107001188 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 360107001189 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 360107001190 dimer interface [polypeptide binding]; other site 360107001191 putative PBP binding regions; other site 360107001192 ABC-ATPase subunit interface; other site 360107001193 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 360107001194 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 360107001195 catalytic triad [active] 360107001196 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 360107001197 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 360107001198 substrate binding pocket [chemical binding]; other site 360107001199 membrane-bound complex binding site; other site 360107001200 hinge residues; other site 360107001201 glucose-6-phosphate isomerase; Provisional; Region: PRK03868 360107001202 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 360107001203 dimer interface [polypeptide binding]; other site 360107001204 active site 360107001205 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 360107001206 dimer interface [polypeptide binding]; other site 360107001207 active site 360107001208 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 360107001209 active site 360107001210 tetramer interface; other site 360107001211 Uncharacterized conserved protein [Function unknown]; Region: COG1739 360107001212 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 360107001213 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 360107001214 putative amphipathic alpha helix; other site 360107001215 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 360107001216 Peptidase family M23; Region: Peptidase_M23; pfam01551 360107001217 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 360107001218 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 360107001219 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107001220 active site 360107001221 phosphorylation site [posttranslational modification] 360107001222 intermolecular recognition site; other site 360107001223 dimerization interface [polypeptide binding]; other site 360107001224 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; cl17355 360107001225 DNA binding site [nucleotide binding] 360107001226 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 360107001227 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 360107001228 dimer interface [polypeptide binding]; other site 360107001229 phosphorylation site [posttranslational modification] 360107001230 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 360107001231 ATP binding site [chemical binding]; other site 360107001232 Mg2+ binding site [ion binding]; other site 360107001233 G-X-G motif; other site 360107001234 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 360107001235 putative substrate binding site 2 [chemical binding]; other site 360107001236 putative substrate binding site 1 [chemical binding]; other site 360107001237 Na binding site 1 [ion binding]; other site 360107001238 Na2 binding site [ion binding]; other site 360107001239 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 360107001240 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 360107001241 FMN binding site [chemical binding]; other site 360107001242 active site 360107001243 catalytic residues [active] 360107001244 substrate binding site [chemical binding]; other site 360107001245 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 360107001246 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 360107001247 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 360107001248 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 360107001249 RNA polymerase subunit 9; Region: RPOL9; smart00661 360107001250 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 360107001251 TRAP-type uncharacterized transport system, fused permease components [General function prediction only]; Region: COG4666 360107001252 DctM-like transporters; Region: DctM; pfam06808 360107001253 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 360107001254 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 360107001255 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 360107001256 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 360107001257 Walker A/P-loop; other site 360107001258 ATP binding site [chemical binding]; other site 360107001259 Q-loop/lid; other site 360107001260 ABC transporter signature motif; other site 360107001261 Walker B; other site 360107001262 D-loop; other site 360107001263 H-loop/switch region; other site 360107001264 Cobalt transport protein; Region: CbiQ; cl00463 360107001265 cobalt transport protein CbiM; Validated; Region: PRK06265 360107001266 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 360107001267 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 360107001268 S-ribosylhomocysteinase; Provisional; Region: PRK02260 360107001269 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3787; cl17897 360107001270 dUTPase; Region: dUTPase_2; pfam08761 360107001271 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in dimeric 2-Deoxyuridine 5'-triphosphate nucleotidohydrolase and similar proteins; Region: NTP-PPase_dUTPase; cd11527 360107001272 active site 360107001273 homodimer interface [polypeptide binding]; other site 360107001274 metal binding site [ion binding]; metal-binding site 360107001275 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 360107001276 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 360107001277 Walker A motif; other site 360107001278 ATP binding site [chemical binding]; other site 360107001279 Walker B motif; other site 360107001280 arginine finger; other site 360107001281 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 360107001282 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 360107001283 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 360107001284 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 360107001285 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 360107001286 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 360107001287 30S subunit binding site; other site 360107001288 signal recognition particle protein; Provisional; Region: PRK10867 360107001289 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 360107001290 P loop; other site 360107001291 GTP binding site [chemical binding]; other site 360107001292 Signal peptide binding domain; Region: SRP_SPB; pfam02978 360107001293 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 360107001294 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 360107001295 KH domain; Region: KH_4; pfam13083 360107001296 RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Region: RimM; COG0806 360107001297 RimM N-terminal domain; Region: RimM; pfam01782 360107001298 PRC-barrel domain; Region: PRC; pfam05239 360107001299 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 360107001300 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 360107001301 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 360107001302 active site 360107001303 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 360107001304 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 360107001305 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 360107001306 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 360107001307 HlyD family secretion protein; Region: HlyD_3; pfam13437 360107001308 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 360107001309 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 360107001310 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 360107001311 oligomerisation interface [polypeptide binding]; other site 360107001312 mobile loop; other site 360107001313 roof hairpin; other site 360107001314 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 360107001315 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 360107001316 ring oligomerisation interface [polypeptide binding]; other site 360107001317 ATP/Mg binding site [chemical binding]; other site 360107001318 stacking interactions; other site 360107001319 hinge regions; other site 360107001320 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 360107001321 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 360107001322 ATP-grasp domain; Region: ATP-grasp_4; cl17255 360107001323 Holliday junction DNA helicase RuvA; Provisional; Region: ruvA; PRK14601 360107001324 RuvA N terminal domain; Region: RuvA_N; pfam01330 360107001325 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 360107001326 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 360107001327 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 360107001328 mce related protein; Region: MCE; pfam02470 360107001329 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 360107001330 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 360107001331 Walker A/P-loop; other site 360107001332 ATP binding site [chemical binding]; other site 360107001333 Q-loop/lid; other site 360107001334 ABC transporter signature motif; other site 360107001335 Walker B; other site 360107001336 D-loop; other site 360107001337 H-loop/switch region; other site 360107001338 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 360107001339 Permease; Region: Permease; pfam02405 360107001340 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 360107001341 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 360107001342 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 360107001343 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 360107001344 active site 360107001345 HIGH motif; other site 360107001346 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 360107001347 KMSKS motif; other site 360107001348 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 360107001349 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 360107001350 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 360107001351 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 360107001352 Walker A/P-loop; other site 360107001353 ATP binding site [chemical binding]; other site 360107001354 Q-loop/lid; other site 360107001355 ABC transporter signature motif; other site 360107001356 Walker B; other site 360107001357 D-loop; other site 360107001358 H-loop/switch region; other site 360107001359 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 360107001360 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 360107001361 quinone interaction residues [chemical binding]; other site 360107001362 active site 360107001363 catalytic residues [active] 360107001364 FMN binding site [chemical binding]; other site 360107001365 substrate binding site [chemical binding]; other site 360107001366 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 360107001367 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 360107001368 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 360107001369 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 360107001370 dihydrodipicolinate synthase; Region: dapA; TIGR00674 360107001371 dimer interface [polypeptide binding]; other site 360107001372 active site 360107001373 catalytic residue [active] 360107001374 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 360107001375 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 360107001376 NAD(P) binding site [chemical binding]; other site 360107001377 active site 360107001378 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 360107001379 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12694 360107001380 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 360107001381 DNA polymerase (pol2); Region: pol2; TIGR00592 360107001382 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 360107001383 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 360107001384 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 360107001385 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 360107001386 active site 360107001387 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 360107001388 protein binding site [polypeptide binding]; other site 360107001389 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 360107001390 putative substrate binding region [chemical binding]; other site 360107001391 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 360107001392 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 360107001393 catalytic residue [active] 360107001394 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 360107001395 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 360107001396 putative dimer interface [polypeptide binding]; other site 360107001397 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 360107001398 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 360107001399 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 360107001400 active site 360107001401 dimer interface [polypeptide binding]; other site 360107001402 motif 1; other site 360107001403 motif 2; other site 360107001404 motif 3; other site 360107001405 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 360107001406 anticodon binding site; other site 360107001407 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 360107001408 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 360107001409 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 360107001410 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 360107001411 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 360107001412 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_2; cd10034 360107001413 putative uracil binding site [chemical binding]; other site 360107001414 putative active site [active] 360107001415 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 360107001416 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 360107001417 S-adenosylmethionine binding site [chemical binding]; other site 360107001418 Peptidase family M48; Region: Peptidase_M48; pfam01435 360107001419 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 360107001420 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 360107001421 Walker A/P-loop; other site 360107001422 ATP binding site [chemical binding]; other site 360107001423 Q-loop/lid; other site 360107001424 ABC transporter signature motif; other site 360107001425 Walker B; other site 360107001426 D-loop; other site 360107001427 H-loop/switch region; other site 360107001428 ABC transporter; Region: ABC_tran_2; pfam12848 360107001429 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 360107001430 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 360107001431 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 360107001432 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 360107001433 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 360107001434 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 360107001435 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 360107001436 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 360107001437 putative active site [active] 360107001438 putative metal binding site [ion binding]; other site 360107001439 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 360107001440 Helix-turn-helix domain; Region: HTH_18; pfam12833 360107001441 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 360107001442 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 360107001443 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 360107001444 Walker A/P-loop; other site 360107001445 ATP binding site [chemical binding]; other site 360107001446 Q-loop/lid; other site 360107001447 ABC transporter signature motif; other site 360107001448 Walker B; other site 360107001449 D-loop; other site 360107001450 H-loop/switch region; other site 360107001451 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 360107001452 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 360107001453 Walker A/P-loop; other site 360107001454 ATP binding site [chemical binding]; other site 360107001455 Q-loop/lid; other site 360107001456 ABC transporter signature motif; other site 360107001457 Walker B; other site 360107001458 D-loop; other site 360107001459 H-loop/switch region; other site 360107001460 AAA ATPase domain; Region: AAA_15; pfam13175 360107001461 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 360107001462 Walker A/P-loop; other site 360107001463 ATP binding site [chemical binding]; other site 360107001464 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 360107001465 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 360107001466 GMP synthase; Reviewed; Region: guaA; PRK00074 360107001467 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 360107001468 AMP/PPi binding site [chemical binding]; other site 360107001469 candidate oxyanion hole; other site 360107001470 catalytic triad [active] 360107001471 potential glutamine specificity residues [chemical binding]; other site 360107001472 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 360107001473 ATP Binding subdomain [chemical binding]; other site 360107001474 Ligand Binding sites [chemical binding]; other site 360107001475 Dimerization subdomain; other site 360107001476 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 360107001477 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 360107001478 GIY-YIG motif/motif A; other site 360107001479 active site 360107001480 catalytic site [active] 360107001481 putative DNA binding site [nucleotide binding]; other site 360107001482 metal binding site [ion binding]; metal-binding site 360107001483 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 360107001484 Nitrate and nitrite sensing; Region: NIT; pfam08376 360107001485 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 360107001486 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 360107001487 dimer interface [polypeptide binding]; other site 360107001488 phosphorylation site [posttranslational modification] 360107001489 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 360107001490 ATP binding site [chemical binding]; other site 360107001491 Mg2+ binding site [ion binding]; other site 360107001492 G-X-G motif; other site 360107001493 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 360107001494 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107001495 active site 360107001496 phosphorylation site [posttranslational modification] 360107001497 intermolecular recognition site; other site 360107001498 dimerization interface [polypeptide binding]; other site 360107001499 Response regulator receiver domain; Region: Response_reg; pfam00072 360107001500 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107001501 active site 360107001502 phosphorylation site [posttranslational modification] 360107001503 intermolecular recognition site; other site 360107001504 dimerization interface [polypeptide binding]; other site 360107001505 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 360107001506 Protein of unknown function DUF45; Region: DUF45; pfam01863 360107001507 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 360107001508 putative efflux protein, MATE family; Region: matE; TIGR00797 360107001509 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 360107001510 Ribonuclease P; Region: Ribonuclease_P; pfam00825 360107001511 Haemolytic domain; Region: Haemolytic; pfam01809 360107001512 membrane protein insertase; Provisional; Region: PRK01318 360107001513 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 360107001514 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 360107001515 KH domain; Region: KH_4; pfam13083 360107001516 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 360107001517 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 360107001518 trmE is a tRNA modification GTPase; Region: trmE; cd04164 360107001519 G1 box; other site 360107001520 GTP/Mg2+ binding site [chemical binding]; other site 360107001521 Switch I region; other site 360107001522 G2 box; other site 360107001523 Switch II region; other site 360107001524 G3 box; other site 360107001525 G4 box; other site 360107001526 G5 box; other site 360107001527 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 360107001528 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 360107001529 putative acyl-acceptor binding pocket; other site 360107001530 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 360107001531 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 360107001532 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 360107001533 putative ADP-binding pocket [chemical binding]; other site 360107001534 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 360107001535 O-antigen ligase like membrane protein; Region: O-antigen_lig; pfam13425 360107001536 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 360107001537 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 360107001538 putative active site [active] 360107001539 putative metal binding site [ion binding]; other site 360107001540 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 360107001541 UDP-D-galactose:(glucosyl)lipopolysaccharide-1, 6-D-galactosyltransferase; Provisional; Region: PRK09922 360107001542 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 360107001543 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 360107001544 putative ADP-binding pocket [chemical binding]; other site 360107001545 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 360107001546 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 360107001547 putative active site [active] 360107001548 putative metal binding site [ion binding]; other site 360107001549 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 360107001550 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 360107001551 putative metal binding site; other site 360107001552 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 360107001553 Sulfatase; Region: Sulfatase; cl17466 360107001554 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 360107001555 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 360107001556 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 360107001557 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 360107001558 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 360107001559 dimerization interface [polypeptide binding]; other site 360107001560 ATP binding site [chemical binding]; other site 360107001561 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 360107001562 dimerization interface [polypeptide binding]; other site 360107001563 ATP binding site [chemical binding]; other site 360107001564 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 360107001565 putative metal binding site [ion binding]; other site 360107001566 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 360107001567 HSP70 interaction site [polypeptide binding]; other site 360107001568 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 360107001569 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 360107001570 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 360107001571 purine monophosphate binding site [chemical binding]; other site 360107001572 dimer interface [polypeptide binding]; other site 360107001573 putative catalytic residues [active] 360107001574 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 360107001575 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 360107001576 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 360107001577 ThiC family; Region: ThiC; pfam01964 360107001578 thiamine biosynthesis protein ThiC; Region: thiC; TIGR00190 360107001579 Domain of unknown function DUF59; Region: DUF59; cl00941 360107001580 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 360107001581 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 360107001582 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 360107001583 active site 360107001584 GTPase CgtA; Reviewed; Region: obgE; PRK12299 360107001585 GTP1/OBG; Region: GTP1_OBG; pfam01018 360107001586 Obg GTPase; Region: Obg; cd01898 360107001587 G1 box; other site 360107001588 GTP/Mg2+ binding site [chemical binding]; other site 360107001589 Switch I region; other site 360107001590 G2 box; other site 360107001591 G3 box; other site 360107001592 Switch II region; other site 360107001593 G4 box; other site 360107001594 G5 box; other site 360107001595 Glutamate 5-kinase [Amino acid transport and metabolism]; Region: ProB; COG0263 360107001596 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 360107001597 nucleotide binding site [chemical binding]; other site 360107001598 homotetrameric interface [polypeptide binding]; other site 360107001599 putative phosphate binding site [ion binding]; other site 360107001600 putative allosteric binding site; other site 360107001601 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 360107001602 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 360107001603 putative active site [active] 360107001604 substrate binding site [chemical binding]; other site 360107001605 putative cosubstrate binding site; other site 360107001606 catalytic site [active] 360107001607 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 360107001608 substrate binding site [chemical binding]; other site 360107001609 biotin--protein ligase; Provisional; Region: PRK08477 360107001610 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 360107001611 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 360107001612 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 360107001613 P-loop; other site 360107001614 Magnesium ion binding site [ion binding]; other site 360107001615 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 360107001616 Magnesium ion binding site [ion binding]; other site 360107001617 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 360107001618 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 360107001619 ParB-like nuclease domain; Region: ParB; smart00470 360107001620 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 360107001621 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 360107001622 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 360107001623 ATP synthase B/B' CF(0); Region: ATP-synt_B; pfam00430 360107001624 F0F1 ATP synthase subunit delta; Validated; Region: PRK08474 360107001625 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 360107001626 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 360107001627 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 360107001628 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 360107001629 beta subunit interaction interface [polypeptide binding]; other site 360107001630 Walker A motif; other site 360107001631 ATP binding site [chemical binding]; other site 360107001632 Walker B motif; other site 360107001633 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 360107001634 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 360107001635 core domain interface [polypeptide binding]; other site 360107001636 delta subunit interface [polypeptide binding]; other site 360107001637 epsilon subunit interface [polypeptide binding]; other site 360107001638 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 360107001639 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 360107001640 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 360107001641 alpha subunit interaction interface [polypeptide binding]; other site 360107001642 Walker A motif; other site 360107001643 ATP binding site [chemical binding]; other site 360107001644 Walker B motif; other site 360107001645 inhibitor binding site; inhibition site 360107001646 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 360107001647 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 360107001648 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 360107001649 gamma subunit interface [polypeptide binding]; other site 360107001650 epsilon subunit interface [polypeptide binding]; other site 360107001651 LBP interface [polypeptide binding]; other site 360107001652 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 360107001653 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 360107001654 TolR protein; Region: tolR; TIGR02801 360107001655 TonB C terminal; Region: TonB_2; pfam13103 360107001656 translocation protein TolB; Provisional; Region: tolB; PRK04043 360107001657 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 360107001658 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 360107001659 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 360107001660 ligand binding site [chemical binding]; other site 360107001661 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 360107001662 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 360107001663 binding surface 360107001664 TPR motif; other site 360107001665 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 360107001666 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 360107001667 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 360107001668 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 360107001669 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 360107001670 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 360107001671 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 360107001672 Ligand Binding Site [chemical binding]; other site 360107001673 AAA domain; Region: AAA_26; pfam13500 360107001674 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 360107001675 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 360107001676 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 360107001677 inhibitor-cofactor binding pocket; inhibition site 360107001678 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107001679 catalytic residue [active] 360107001680 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 360107001681 Na binding site [ion binding]; other site 360107001682 thiamine monophosphate kinase; Provisional; Region: PRK05731 360107001683 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 360107001684 ATP binding site [chemical binding]; other site 360107001685 dimerization interface [polypeptide binding]; other site 360107001686 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 360107001687 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 360107001688 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 360107001689 active site 360107001690 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 360107001691 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 360107001692 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 360107001693 Putative zinc ribbon domain; Region: DUF164; pfam02591 360107001694 Uncharacterized conserved protein [Function unknown]; Region: COG0327 360107001695 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 360107001696 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 360107001697 dimer interface [polypeptide binding]; other site 360107001698 motif 1; other site 360107001699 active site 360107001700 motif 2; other site 360107001701 motif 3; other site 360107001702 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 360107001703 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 360107001704 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 360107001705 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 360107001706 biotin synthase; Region: bioB; TIGR00433 360107001707 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 360107001708 FeS/SAM binding site; other site 360107001709 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 360107001710 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 360107001711 Lumazine binding domain; Region: Lum_binding; pfam00677 360107001712 Lumazine binding domain; Region: Lum_binding; pfam00677 360107001713 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 360107001714 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 360107001715 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 360107001716 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 360107001717 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 360107001718 DNA binding residues [nucleotide binding] 360107001719 Predicted membrane protein [Function unknown]; Region: COG2860 360107001720 UPF0126 domain; Region: UPF0126; pfam03458 360107001721 UPF0126 domain; Region: UPF0126; pfam03458 360107001722 acetylornithine aminotransferase; Provisional; Region: PRK02627 360107001723 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 360107001724 inhibitor-cofactor binding pocket; inhibition site 360107001725 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107001726 catalytic residue [active] 360107001727 Uncharacterized conserved protein [Function unknown]; Region: COG1565 360107001728 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 360107001729 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 360107001730 S-adenosylmethionine binding site [chemical binding]; other site 360107001731 Protein of unknown function (DUF2400); Region: DUF2400; pfam09674 360107001732 hypothetical protein; Provisional; Region: PRK10621 360107001733 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 360107001734 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 360107001735 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 360107001736 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 360107001737 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 360107001738 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 360107001739 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 360107001740 active site 360107001741 HIGH motif; other site 360107001742 KMSKS motif; other site 360107001743 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 360107001744 tRNA binding surface [nucleotide binding]; other site 360107001745 anticodon binding site; other site 360107001746 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 360107001747 dimer interface [polypeptide binding]; other site 360107001748 putative tRNA-binding site [nucleotide binding]; other site 360107001749 fructose-1,6-bisphosphatase; Provisional; Region: PRK09293 360107001750 active site 360107001751 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 360107001752 Walker A motif; other site 360107001753 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 360107001754 putative amphipathic alpha helix; other site 360107001755 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 360107001756 active site 360107001757 oligomerization interface [polypeptide binding]; other site 360107001758 metal binding site [ion binding]; metal-binding site 360107001759 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 360107001760 Sel1-like repeats; Region: SEL1; smart00671 360107001761 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 360107001762 binding surface 360107001763 TPR motif; other site 360107001764 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 360107001765 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 360107001766 Walker A motif; other site 360107001767 ATP binding site [chemical binding]; other site 360107001768 Walker B motif; other site 360107001769 arginine finger; other site 360107001770 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 360107001771 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 360107001772 Domain of unknown function DUF20; Region: UPF0118; pfam01594 360107001773 metal-binding heat shock protein; Provisional; Region: PRK00016 360107001774 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 360107001775 Ligand Binding Site [chemical binding]; other site 360107001776 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 360107001777 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107001778 active site 360107001779 phosphorylation site [posttranslational modification] 360107001780 intermolecular recognition site; other site 360107001781 dimerization interface [polypeptide binding]; other site 360107001782 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 360107001783 DNA binding site [nucleotide binding] 360107001784 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 360107001785 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 360107001786 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 360107001787 dimer interface [polypeptide binding]; other site 360107001788 phosphorylation site [posttranslational modification] 360107001789 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 360107001790 ATP binding site [chemical binding]; other site 360107001791 Mg2+ binding site [ion binding]; other site 360107001792 G-X-G motif; other site 360107001793 benzoyl-CoA oxygenase/reductase, BoxA protein; Region: benzo_boxA; TIGR03224 360107001794 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 360107001795 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 360107001796 nucleotide binding site [chemical binding]; other site 360107001797 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 360107001798 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 360107001799 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 360107001800 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 360107001801 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 360107001802 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 360107001803 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 360107001804 NAD(P) binding site [chemical binding]; other site 360107001805 homodimer interface [polypeptide binding]; other site 360107001806 substrate binding site [chemical binding]; other site 360107001807 active site 360107001808 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 360107001809 active site 360107001810 DNA binding site [nucleotide binding] 360107001811 Int/Topo IB signature motif; other site 360107001812 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 360107001813 L-seryl-tRNA selenium transferase; Region: SelA; pfam03841 360107001814 Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]; Region: SelB; COG3276 360107001815 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 360107001816 G1 box; other site 360107001817 putative GEF interaction site [polypeptide binding]; other site 360107001818 GTP/Mg2+ binding site [chemical binding]; other site 360107001819 Switch I region; other site 360107001820 G2 box; other site 360107001821 G3 box; other site 360107001822 Switch II region; other site 360107001823 G4 box; other site 360107001824 G5 box; other site 360107001825 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 360107001826 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 360107001827 GTP-binding protein LepA; Provisional; Region: PRK05433 360107001828 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 360107001829 G1 box; other site 360107001830 putative GEF interaction site [polypeptide binding]; other site 360107001831 GTP/Mg2+ binding site [chemical binding]; other site 360107001832 Switch I region; other site 360107001833 G2 box; other site 360107001834 G3 box; other site 360107001835 Switch II region; other site 360107001836 G4 box; other site 360107001837 G5 box; other site 360107001838 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 360107001839 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 360107001840 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 360107001841 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 360107001842 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 360107001843 active site 360107001844 catalytic site [active] 360107001845 substrate binding site [chemical binding]; other site 360107001846 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 360107001847 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 360107001848 substrate binding site [chemical binding]; other site 360107001849 hexamer interface [polypeptide binding]; other site 360107001850 metal binding site [ion binding]; metal-binding site 360107001851 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 360107001852 Ion channel; Region: Ion_trans_2; pfam07885 360107001853 TrkA-N domain; Region: TrkA_N; pfam02254 360107001854 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 360107001855 TrkA-C domain; Region: TrkA_C; pfam02080 360107001856 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 360107001857 heterotetramer interface [polypeptide binding]; other site 360107001858 active site pocket [active] 360107001859 cleavage site 360107001860 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 360107001861 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 360107001862 trimer interface [polypeptide binding]; other site 360107001863 putative metal binding site [ion binding]; other site 360107001864 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 360107001865 Sulfatase; Region: Sulfatase; cl17466 360107001866 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 360107001867 Na2 binding site [ion binding]; other site 360107001868 putative substrate binding site 1 [chemical binding]; other site 360107001869 Na binding site 1 [ion binding]; other site 360107001870 putative substrate binding site 2 [chemical binding]; other site 360107001871 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 360107001872 active site 360107001873 (T/H)XGH motif; other site 360107001874 Oligomerisation domain; Region: Oligomerisation; pfam02410 360107001875 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 360107001876 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 360107001877 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 360107001878 Phosphoglycerate kinase; Region: PGK; pfam00162 360107001879 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 360107001880 substrate binding site [chemical binding]; other site 360107001881 hinge regions; other site 360107001882 ADP binding site [chemical binding]; other site 360107001883 catalytic site [active] 360107001884 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 360107001885 triosephosphate isomerase; Provisional; Region: PRK14565 360107001886 substrate binding site [chemical binding]; other site 360107001887 dimer interface [polypeptide binding]; other site 360107001888 catalytic triad [active] 360107001889 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 360107001890 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 360107001891 NAD binding site [chemical binding]; other site 360107001892 homotetramer interface [polypeptide binding]; other site 360107001893 homodimer interface [polypeptide binding]; other site 360107001894 substrate binding site [chemical binding]; other site 360107001895 active site 360107001896 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 360107001897 active site 360107001898 catalytic site [active] 360107001899 substrate binding site [chemical binding]; other site 360107001900 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 360107001901 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 360107001902 DNA binding site [nucleotide binding] 360107001903 DNA polymerase LigD, ligase domain; Region: NHEJ_ligase_lig; TIGR02779 360107001904 active site 360107001905 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 360107001906 DNA binding site [nucleotide binding] 360107001907 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 360107001908 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 360107001909 NAD binding site [chemical binding]; other site 360107001910 homodimer interface [polypeptide binding]; other site 360107001911 active site 360107001912 substrate binding site [chemical binding]; other site 360107001913 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 360107001914 Dynamin family; Region: Dynamin_N; pfam00350 360107001915 G1 box; other site 360107001916 GTP/Mg2+ binding site [chemical binding]; other site 360107001917 G2 box; other site 360107001918 Switch I region; other site 360107001919 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 360107001920 G3 box; other site 360107001921 Switch II region; other site 360107001922 GTP/Mg2+ binding site [chemical binding]; other site 360107001923 G4 box; other site 360107001924 G5 box; other site 360107001925 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 360107001926 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 360107001927 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 360107001928 trimer interface [polypeptide binding]; other site 360107001929 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 360107001930 trimer interface [polypeptide binding]; other site 360107001931 Haemagglutinin; Region: HIM; pfam05662 360107001932 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 360107001933 trimer interface [polypeptide binding]; other site 360107001934 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 360107001935 trimer interface [polypeptide binding]; other site 360107001936 Haemagglutinin; Region: HIM; pfam05662 360107001937 Autotransporter adhesin [Intracellular trafficking and secretion / Extracellular structures]; Region: Hia; COG5295 360107001938 YadA-like C-terminal region; Region: YadA; pfam03895 360107001939 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 360107001940 IHF dimer interface [polypeptide binding]; other site 360107001941 IHF - DNA interface [nucleotide binding]; other site 360107001942 Protein of unknown function (DUF328); Region: DUF328; cl01143 360107001943 acetyl-CoA carboxylase subunit A; Validated; Region: PRK08463 360107001944 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 360107001945 ATP-grasp domain; Region: ATP-grasp_4; cl17255 360107001946 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 360107001947 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 360107001948 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 360107001949 ATP-binding site [chemical binding]; other site 360107001950 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 360107001951 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 360107001952 transmembrane helices; other site 360107001953 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 360107001954 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 360107001955 metal binding site [ion binding]; metal-binding site 360107001956 Methyltransferase domain; Region: Methyltransf_23; pfam13489 360107001957 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 360107001958 S-adenosylmethionine binding site [chemical binding]; other site 360107001959 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 360107001960 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 360107001961 substrate binding pocket [chemical binding]; other site 360107001962 membrane-bound complex binding site; other site 360107001963 hinge residues; other site 360107001964 MraW methylase family; Region: Methyltransf_5; cl17771 360107001965 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 360107001966 hypothetical protein; Provisional; Region: PRK05834 360107001967 intersubunit interface [polypeptide binding]; other site 360107001968 active site 360107001969 Zn2+ binding site [ion binding]; other site 360107001970 SurA N-terminal domain; Region: SurA_N_3; cl07813 360107001971 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 360107001972 cell division protein FtsA; Region: ftsA; TIGR01174 360107001973 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 360107001974 nucleotide binding site [chemical binding]; other site 360107001975 Cell division protein FtsA; Region: FtsA; pfam14450 360107001976 cell division protein FtsZ; Validated; Region: PRK09330 360107001977 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 360107001978 nucleotide binding site [chemical binding]; other site 360107001979 SulA interaction site; other site 360107001980 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 360107001981 recombination factor protein RarA; Reviewed; Region: PRK13342 360107001982 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 360107001983 Walker A motif; other site 360107001984 ATP binding site [chemical binding]; other site 360107001985 Walker B motif; other site 360107001986 arginine finger; other site 360107001987 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 360107001988 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 360107001989 putative active site [active] 360107001990 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 360107001991 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 360107001992 glutaminase active site [active] 360107001993 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 360107001994 dimer interface [polypeptide binding]; other site 360107001995 active site 360107001996 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 360107001997 dimer interface [polypeptide binding]; other site 360107001998 active site 360107001999 hypothetical protein; Provisional; Region: PRK08444 360107002000 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 360107002001 FeS/SAM binding site; other site 360107002002 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 360107002003 active site 360107002004 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 360107002005 Major Facilitator Superfamily; Region: MFS_1; pfam07690 360107002006 putative substrate translocation pore; other site 360107002007 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 360107002008 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 360107002009 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 360107002010 Coenzyme A binding pocket [chemical binding]; other site 360107002011 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 360107002012 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 360107002013 Walker A/P-loop; other site 360107002014 ATP binding site [chemical binding]; other site 360107002015 Q-loop/lid; other site 360107002016 ABC transporter signature motif; other site 360107002017 Walker B; other site 360107002018 D-loop; other site 360107002019 H-loop/switch region; other site 360107002020 elongation factor Ts; Provisional; Region: tsf; PRK09377 360107002021 UBA/TS-N domain; Region: UBA; pfam00627 360107002022 Elongation factor TS; Region: EF_TS; pfam00889 360107002023 Elongation factor TS; Region: EF_TS; pfam00889 360107002024 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 360107002025 rRNA interaction site [nucleotide binding]; other site 360107002026 S8 interaction site; other site 360107002027 putative laminin-1 binding site; other site 360107002028 Acyltransferase family; Region: Acyl_transf_3; pfam01757 360107002029 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 360107002030 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 360107002031 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 360107002032 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 360107002033 putative acyl-acceptor binding pocket; other site 360107002034 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 360107002035 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 360107002036 putative active site [active] 360107002037 catalytic triad [active] 360107002038 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; pfam02700 360107002039 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 360107002040 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 360107002041 ATP binding site [chemical binding]; other site 360107002042 active site 360107002043 substrate binding site [chemical binding]; other site 360107002044 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 360107002045 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 360107002046 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 360107002047 protein binding site [polypeptide binding]; other site 360107002048 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 360107002049 Catalytic dyad [active] 360107002050 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 360107002051 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 360107002052 Walker A motif; other site 360107002053 ATP binding site [chemical binding]; other site 360107002054 Walker B motif; other site 360107002055 arginine finger; other site 360107002056 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 360107002057 Walker A motif; other site 360107002058 ATP binding site [chemical binding]; other site 360107002059 Walker B motif; other site 360107002060 arginine finger; other site 360107002061 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 360107002062 Predicted permeases [General function prediction only]; Region: RarD; COG2962 360107002063 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 360107002064 EamA-like transporter family; Region: EamA; pfam00892 360107002065 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 360107002066 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 360107002067 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 360107002068 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 360107002069 Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR; Region: SQR_QFR_TM; cl00881 360107002070 Iron-sulfur protein interface; other site 360107002071 proximal heme binding site [chemical binding]; other site 360107002072 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 360107002073 L-aspartate oxidase; Provisional; Region: PRK06175 360107002074 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 360107002075 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 360107002076 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 360107002077 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 360107002078 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 360107002079 Dynamin family; Region: Dynamin_N; pfam00350 360107002080 G1 box; other site 360107002081 GTP/Mg2+ binding site [chemical binding]; other site 360107002082 G2 box; other site 360107002083 Switch I region; other site 360107002084 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 360107002085 G3 box; other site 360107002086 Switch II region; other site 360107002087 GTP/Mg2+ binding site [chemical binding]; other site 360107002088 G4 box; other site 360107002089 G5 box; other site 360107002090 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 360107002091 Dynamin family; Region: Dynamin_N; pfam00350 360107002092 G1 box; other site 360107002093 GTP/Mg2+ binding site [chemical binding]; other site 360107002094 G2 box; other site 360107002095 Switch I region; other site 360107002096 G3 box; other site 360107002097 Switch II region; other site 360107002098 G4 box; other site 360107002099 G5 box; other site 360107002100 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 360107002101 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 360107002102 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 360107002103 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 360107002104 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 360107002105 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 360107002106 putative substrate-binding site; other site 360107002107 nickel binding site [ion binding]; other site 360107002108 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 360107002109 Acylphosphatase; Region: Acylphosphatase; pfam00708 360107002110 HypF finger; Region: zf-HYPF; pfam07503 360107002111 HypF finger; Region: zf-HYPF; pfam07503 360107002112 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 360107002113 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 360107002114 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 360107002115 nickel responsive regulator; Provisional; Region: PRK00630 360107002116 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]; Region: COG3609 360107002117 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 360107002118 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 360107002119 HupF/HypC family; Region: HupF_HypC; pfam01455 360107002120 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 360107002121 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 360107002122 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 360107002123 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 360107002124 metal-binding site [ion binding] 360107002125 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 360107002126 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 360107002127 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 360107002128 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 360107002129 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypE; COG0309 360107002130 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 360107002131 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 360107002132 dimerization interface [polypeptide binding]; other site 360107002133 ATP binding site [chemical binding]; other site 360107002134 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 360107002135 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 360107002136 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 360107002137 TPR motif; other site 360107002138 binding surface 360107002139 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 360107002140 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 360107002141 dimer interface [polypeptide binding]; other site 360107002142 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107002143 catalytic residue [active] 360107002144 Rrf2 family protein; Region: rrf2_super; TIGR00738 360107002145 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 360107002146 putative Zn2+ binding site [ion binding]; other site 360107002147 putative DNA binding site [nucleotide binding]; other site 360107002148 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 360107002149 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 360107002150 homodimer interface [polypeptide binding]; other site 360107002151 substrate-cofactor binding pocket; other site 360107002152 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107002153 catalytic residue [active] 360107002154 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 360107002155 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 360107002156 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 360107002157 motif II; other site 360107002158 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 360107002159 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 360107002160 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 360107002161 substrate binding pocket [chemical binding]; other site 360107002162 chain length determination region; other site 360107002163 substrate-Mg2+ binding site; other site 360107002164 catalytic residues [active] 360107002165 aspartate-rich region 1; other site 360107002166 active site lid residues [active] 360107002167 aspartate-rich region 2; other site 360107002168 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 360107002169 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 360107002170 tRNA; other site 360107002171 putative tRNA binding site [nucleotide binding]; other site 360107002172 putative NADP binding site [chemical binding]; other site 360107002173 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 360107002174 prolyl-tRNA synthetase; Provisional; Region: PRK09194 360107002175 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 360107002176 dimer interface [polypeptide binding]; other site 360107002177 motif 1; other site 360107002178 active site 360107002179 motif 2; other site 360107002180 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 360107002181 putative deacylase active site [active] 360107002182 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 360107002183 active site 360107002184 motif 3; other site 360107002185 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 360107002186 anticodon binding site; other site 360107002187 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 360107002188 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 360107002189 domain interfaces; other site 360107002190 active site 360107002191 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 360107002192 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 360107002193 Competence-damaged protein; Region: CinA; pfam02464 360107002194 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 360107002195 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 360107002196 active site 360107002197 HIGH motif; other site 360107002198 nucleotide binding site [chemical binding]; other site 360107002199 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 360107002200 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 360107002201 active site 360107002202 KMSKS motif; other site 360107002203 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 360107002204 tRNA binding surface [nucleotide binding]; other site 360107002205 anticodon binding site; other site 360107002206 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 360107002207 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 360107002208 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 360107002209 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 360107002210 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 360107002211 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 360107002212 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 360107002213 active site 360107002214 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 360107002215 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 360107002216 Exonuclease VII small subunit; Region: Exonuc_VII_S; pfam02609 360107002217 Predicted amidohydrolase [General function prediction only]; Region: COG0388 360107002218 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 360107002219 active site 360107002220 catalytic triad [active] 360107002221 dimer interface [polypeptide binding]; other site 360107002222 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 360107002223 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 360107002224 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_4; pfam14281 360107002225 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 360107002226 catalytic core [active] 360107002227 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 360107002228 dinuclear metal binding motif [ion binding]; other site 360107002229 Rhomboid family; Region: Rhomboid; pfam01694 360107002230 NlpC/P60 family; Region: NLPC_P60; cl17555 360107002231 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 360107002232 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 360107002233 hinge; other site 360107002234 active site 360107002235 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 360107002236 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 360107002237 dimer interface [polypeptide binding]; other site 360107002238 putative functional site; other site 360107002239 putative MPT binding site; other site 360107002240 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 360107002241 Flavoprotein; Region: Flavoprotein; pfam02441 360107002242 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 360107002243 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 360107002244 active site 360107002245 (T/H)XGH motif; other site 360107002246 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 360107002247 thymidylate kinase; Validated; Region: tmk; PRK00698 360107002248 TMP-binding site; other site 360107002249 ATP-binding site [chemical binding]; other site 360107002250 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 360107002251 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 360107002252 dimer interface [polypeptide binding]; other site 360107002253 motif 1; other site 360107002254 active site 360107002255 motif 2; other site 360107002256 motif 3; other site 360107002257 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 360107002258 anticodon binding site; other site 360107002259 arginine decarboxylase; Provisional; Region: PRK05354 360107002260 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 360107002261 dimer interface [polypeptide binding]; other site 360107002262 active site 360107002263 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 360107002264 catalytic residues [active] 360107002265 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 360107002266 serine O-acetyltransferase; Region: cysE; TIGR01172 360107002267 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 360107002268 trimer interface [polypeptide binding]; other site 360107002269 active site 360107002270 substrate binding site [chemical binding]; other site 360107002271 CoA binding site [chemical binding]; other site 360107002272 aspartate aminotransferase; Provisional; Region: PRK05764 360107002273 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 360107002274 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107002275 homodimer interface [polypeptide binding]; other site 360107002276 catalytic residue [active] 360107002277 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 360107002278 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 360107002279 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 360107002280 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 360107002281 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 360107002282 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 360107002283 substrate binding site; other site 360107002284 dimer interface; other site 360107002285 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 360107002286 homotrimer interaction site [polypeptide binding]; other site 360107002287 zinc binding site [ion binding]; other site 360107002288 CDP-binding sites; other site 360107002289 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 360107002290 DHH family; Region: DHH; pfam01368 360107002291 Rrf2 family protein; Region: rrf2_super; TIGR00738 360107002292 Transcriptional regulator; Region: Rrf2; pfam02082 360107002293 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 360107002294 16S/18S rRNA binding site [nucleotide binding]; other site 360107002295 S13e-L30e interaction site [polypeptide binding]; other site 360107002296 25S rRNA binding site [nucleotide binding]; other site 360107002297 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 360107002298 DEAD/DEAH box helicase; Region: DEAD; pfam00270 360107002299 ATP binding site [chemical binding]; other site 360107002300 putative Mg++ binding site [ion binding]; other site 360107002301 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 360107002302 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 360107002303 nucleotide binding region [chemical binding]; other site 360107002304 ATP-binding site [chemical binding]; other site 360107002305 SEC-C motif; Region: SEC-C; pfam02810 360107002306 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 360107002307 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 360107002308 FtsX-like permease family; Region: FtsX; pfam02687 360107002309 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 360107002310 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 360107002311 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 360107002312 NlpC/P60 family; Region: NLPC_P60; cl17555 360107002313 AAA domain; Region: AAA_30; pfam13604 360107002314 Family description; Region: UvrD_C_2; pfam13538 360107002315 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 360107002316 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 360107002317 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 360107002318 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 360107002319 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 360107002320 GatB domain; Region: GatB_Yqey; smart00845 360107002321 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 360107002322 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 360107002323 catalytic residues [active] 360107002324 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 360107002325 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 360107002326 putative active site [active] 360107002327 oxyanion strand; other site 360107002328 catalytic triad [active] 360107002329 Cache domain; Region: Cache_1; pfam02743 360107002330 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 360107002331 CoA binding domain; Region: CoA_binding; cl17356 360107002332 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 360107002333 NAD(P) binding site [chemical binding]; other site 360107002334 homodimer interface [polypeptide binding]; other site 360107002335 substrate binding site [chemical binding]; other site 360107002336 active site 360107002337 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 360107002338 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 360107002339 inhibitor-cofactor binding pocket; inhibition site 360107002340 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107002341 catalytic residue [active] 360107002342 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 360107002343 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 360107002344 putative trimer interface [polypeptide binding]; other site 360107002345 putative CoA binding site [chemical binding]; other site 360107002346 Bacterial sugar transferase; Region: Bac_transf; pfam02397 360107002347 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 360107002348 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 360107002349 putative ADP-binding pocket [chemical binding]; other site 360107002350 Oligosaccharyl transferase STT3 subunit; Region: STT3; pfam02516 360107002351 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 360107002352 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 360107002353 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 360107002354 putative ADP-binding pocket [chemical binding]; other site 360107002355 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 360107002356 This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be...; Region: GT1_amsD_like; cd03820 360107002357 putative ADP-binding pocket [chemical binding]; other site 360107002358 putative glycosyl transferase; Provisional; Region: PRK10073 360107002359 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 360107002360 active site 360107002361 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 360107002362 This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be...; Region: GT1_amsD_like; cd03820 360107002363 putative ADP-binding pocket [chemical binding]; other site 360107002364 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 360107002365 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 360107002366 active site 360107002367 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 360107002368 4Fe-4S binding domain; Region: Fer4; pfam00037 360107002369 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 360107002370 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; Region: FrhB_FdhB_C; pfam04432 360107002371 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 360107002372 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 360107002373 Ecotin; Region: Ecotin; pfam03974 360107002374 secondary substrate binding site; other site 360107002375 primary substrate binding site; other site 360107002376 inhibition loop; other site 360107002377 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 360107002378 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 360107002379 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 360107002380 dihydroorotase; Validated; Region: pyrC; PRK09357 360107002381 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 360107002382 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 360107002383 active site 360107002384 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 360107002385 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 360107002386 Substrate binding site; other site 360107002387 Mg++ binding site; other site 360107002388 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 360107002389 active site 360107002390 substrate binding site [chemical binding]; other site 360107002391 CoA binding site [chemical binding]; other site 360107002392 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 360107002393 Flavoprotein; Region: Flavoprotein; pfam02441 360107002394 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 360107002395 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 360107002396 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 360107002397 catalytic residue [active] 360107002398 putative FPP diphosphate binding site; other site 360107002399 putative FPP binding hydrophobic cleft; other site 360107002400 dimer interface [polypeptide binding]; other site 360107002401 putative IPP diphosphate binding site; other site 360107002402 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 360107002403 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 360107002404 Predicted permeases [General function prediction only]; Region: COG0795 360107002405 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 360107002406 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 360107002407 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 360107002408 active site 360107002409 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 360107002410 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 360107002411 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 360107002412 TrkA-N domain; Region: TrkA_N; pfam02254 360107002413 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 360107002414 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 360107002415 DNA binding residues [nucleotide binding] 360107002416 putative dimer interface [polypeptide binding]; other site 360107002417 chaperone protein DnaJ; Provisional; Region: PRK14299 360107002418 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 360107002419 HSP70 interaction site [polypeptide binding]; other site 360107002420 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 360107002421 substrate binding site [polypeptide binding]; other site 360107002422 dimer interface [polypeptide binding]; other site 360107002423 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 360107002424 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 360107002425 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 360107002426 protein binding site [polypeptide binding]; other site 360107002427 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 360107002428 protein binding site [polypeptide binding]; other site 360107002429 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 360107002430 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107002431 active site 360107002432 phosphorylation site [posttranslational modification] 360107002433 intermolecular recognition site; other site 360107002434 dimerization interface [polypeptide binding]; other site 360107002435 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 360107002436 DNA binding site [nucleotide binding] 360107002437 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 360107002438 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 360107002439 dimer interface [polypeptide binding]; other site 360107002440 phosphorylation site [posttranslational modification] 360107002441 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 360107002442 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 360107002443 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 360107002444 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 360107002445 DsbD alpha interface [polypeptide binding]; other site 360107002446 catalytic residues [active] 360107002447 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 360107002448 Transglycosylase; Region: Transgly; pfam00912 360107002449 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 360107002450 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 360107002451 Maf-like protein; Region: Maf; pfam02545 360107002452 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 360107002453 active site 360107002454 dimer interface [polypeptide binding]; other site 360107002455 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 360107002456 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 360107002457 motif 1; other site 360107002458 active site 360107002459 motif 2; other site 360107002460 motif 3; other site 360107002461 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 360107002462 DHHA1 domain; Region: DHHA1; pfam02272 360107002463 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 360107002464 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 360107002465 ferrochelatase; Reviewed; Region: hemH; PRK00035 360107002466 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 360107002467 C-terminal domain interface [polypeptide binding]; other site 360107002468 active site 360107002469 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 360107002470 active site 360107002471 N-terminal domain interface [polypeptide binding]; other site 360107002472 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 360107002473 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 360107002474 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 360107002475 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 360107002476 Part of AAA domain; Region: AAA_19; pfam13245 360107002477 Family description; Region: UvrD_C_2; pfam13538 360107002478 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 360107002479 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 360107002480 dimerization interface [polypeptide binding]; other site 360107002481 DPS ferroxidase diiron center [ion binding]; other site 360107002482 ion pore; other site 360107002483 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 360107002484 tetramer interfaces [polypeptide binding]; other site 360107002485 binuclear metal-binding site [ion binding]; other site 360107002486 replicative DNA helicase; Provisional; Region: PRK08506 360107002487 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 360107002488 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 360107002489 Walker A motif; other site 360107002490 ATP binding site [chemical binding]; other site 360107002491 Walker B motif; other site 360107002492 DNA binding loops [nucleotide binding] 360107002493 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 360107002494 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 360107002495 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 360107002496 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 360107002497 FeS/SAM binding site; other site 360107002498 HemN C-terminal domain; Region: HemN_C; pfam06969 360107002499 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 360107002500 putative active site [active] 360107002501 Ap4A binding site [chemical binding]; other site 360107002502 nudix motif; other site 360107002503 putative metal binding site [ion binding]; other site 360107002504 aspartate kinase; Reviewed; Region: PRK06635 360107002505 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 360107002506 putative nucleotide binding site [chemical binding]; other site 360107002507 putative catalytic residues [active] 360107002508 putative Mg ion binding site [ion binding]; other site 360107002509 putative aspartate binding site [chemical binding]; other site 360107002510 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 360107002511 putative allosteric regulatory site; other site 360107002512 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 360107002513 DNA replication regulator; Region: HobA; pfam12163 360107002514 DNA polymerase III subunit delta'; Validated; Region: PRK08485 360107002515 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 360107002516 dihydropteroate synthase; Region: DHPS; TIGR01496 360107002517 substrate binding pocket [chemical binding]; other site 360107002518 dimer interface [polypeptide binding]; other site 360107002519 inhibitor binding site; inhibition site 360107002520 KWG Leptospira; Region: KWG; pfam07656 360107002521 Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly...; Region: Macro; cl00019 360107002522 ADP-ribose binding site [chemical binding]; other site 360107002523 heat shock protein 90; Provisional; Region: PRK05218 360107002524 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 360107002525 ATP binding site [chemical binding]; other site 360107002526 Mg2+ binding site [ion binding]; other site 360107002527 G-X-G motif; other site 360107002528 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 360107002529 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 360107002530 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 360107002531 Permutation of conserved domain; other site 360107002532 active site 360107002533 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 360107002534 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 360107002535 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 360107002536 dimer interface [polypeptide binding]; other site 360107002537 decamer (pentamer of dimers) interface [polypeptide binding]; other site 360107002538 catalytic triad [active] 360107002539 peroxidatic and resolving cysteines [active] 360107002540 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 360107002541 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 360107002542 S-adenosylmethionine binding site [chemical binding]; other site 360107002543 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 360107002544 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 360107002545 active site 360107002546 nucleotide binding site [chemical binding]; other site 360107002547 HIGH motif; other site 360107002548 KMSKS motif; other site 360107002549 Riboflavin kinase; Region: Flavokinase; smart00904 360107002550 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 360107002551 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 360107002552 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 360107002553 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 360107002554 RNA binding surface [nucleotide binding]; other site 360107002555 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 360107002556 S-adenosylmethionine binding site [chemical binding]; other site 360107002557 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 360107002558 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 360107002559 nucleotide binding pocket [chemical binding]; other site 360107002560 K-X-D-G motif; other site 360107002561 catalytic site [active] 360107002562 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 360107002563 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 360107002564 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 360107002565 Dimer interface [polypeptide binding]; other site 360107002566 BRCT sequence motif; other site 360107002567 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 360107002568 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 360107002569 Ligand binding site; other site 360107002570 oligomer interface; other site 360107002571 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 360107002572 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 360107002573 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107002574 catalytic residue [active] 360107002575 DNA methylase; Region: N6_N4_Mtase; pfam01555 360107002576 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 360107002577 feedback inhibition sensing region; other site 360107002578 homohexameric interface [polypeptide binding]; other site 360107002579 nucleotide binding site [chemical binding]; other site 360107002580 N-acetyl-L-glutamate binding site [chemical binding]; other site 360107002581 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 360107002582 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 360107002583 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 360107002584 NAD synthase; Region: NAD_synthase; pfam02540 360107002585 NAD binding pocket [chemical binding]; other site 360107002586 ATP binding pocket [chemical binding]; other site 360107002587 Mg binding site [ion binding]; other site 360107002588 active-site loop [active] 360107002589 homodimer interface [polypeptide binding]; other site 360107002590 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 360107002591 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 360107002592 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 360107002593 generic binding surface II; other site 360107002594 ssDNA binding site; other site 360107002595 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 360107002596 ATP binding site [chemical binding]; other site 360107002597 putative Mg++ binding site [ion binding]; other site 360107002598 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 360107002599 nucleotide binding region [chemical binding]; other site 360107002600 ATP-binding site [chemical binding]; other site 360107002601 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 360107002602 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 360107002603 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 360107002604 hypothetical protein; Provisional; Region: PRK08445 360107002605 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 360107002606 FeS/SAM binding site; other site 360107002607 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 360107002608 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 360107002609 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 360107002610 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 360107002611 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 360107002612 inhibitor-cofactor binding pocket; inhibition site 360107002613 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107002614 catalytic residue [active] 360107002615 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 360107002616 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 360107002617 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 360107002618 homodimer interface [polypeptide binding]; other site 360107002619 NADP binding site [chemical binding]; other site 360107002620 substrate binding site [chemical binding]; other site 360107002621 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 360107002622 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 360107002623 Catalytic site [active] 360107002624 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 360107002625 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 360107002626 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 360107002627 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 360107002628 active site 360107002629 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 360107002630 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 360107002631 multifunctional aminopeptidase A; Provisional; Region: PRK00913 360107002632 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 360107002633 interface (dimer of trimers) [polypeptide binding]; other site 360107002634 Substrate-binding/catalytic site; other site 360107002635 Zn-binding sites [ion binding]; other site 360107002636 GTP-binding protein YchF; Reviewed; Region: PRK09601 360107002637 YchF GTPase; Region: YchF; cd01900 360107002638 G1 box; other site 360107002639 GTP/Mg2+ binding site [chemical binding]; other site 360107002640 Switch I region; other site 360107002641 G2 box; other site 360107002642 Switch II region; other site 360107002643 G3 box; other site 360107002644 G4 box; other site 360107002645 G5 box; other site 360107002646 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 360107002647 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 360107002648 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 360107002649 active site 360107002650 homodimer interface [polypeptide binding]; other site 360107002651 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 360107002652 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 360107002653 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 360107002654 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 360107002655 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 360107002656 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 360107002657 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 360107002658 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 360107002659 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 360107002660 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 360107002661 Walker A motif; other site 360107002662 ATP binding site [chemical binding]; other site 360107002663 Walker B motif; other site 360107002664 AAA ATPase domain; Region: AAA_16; pfam13191 360107002665 AAA domain; Region: AAA_22; pfam13401 360107002666 Walker A motif; other site 360107002667 ATP binding site [chemical binding]; other site 360107002668 Walker B motif; other site 360107002669 arginine finger; other site 360107002670 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 360107002671 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 360107002672 GTPase Era; Reviewed; Region: era; PRK00089 360107002673 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 360107002674 G1 box; other site 360107002675 GTP/Mg2+ binding site [chemical binding]; other site 360107002676 Switch I region; other site 360107002677 G2 box; other site 360107002678 Switch II region; other site 360107002679 G3 box; other site 360107002680 G4 box; other site 360107002681 G5 box; other site 360107002682 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 360107002683 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 360107002684 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 360107002685 Walker A motif; other site 360107002686 ATP binding site [chemical binding]; other site 360107002687 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 360107002688 Walker B motif; other site 360107002689 arginine finger; other site 360107002690 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 360107002691 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 360107002692 active site 360107002693 HslU subunit interaction site [polypeptide binding]; other site 360107002694 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 360107002695 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 360107002696 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 360107002697 argininosuccinate synthase; Provisional; Region: PRK13820 360107002698 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 360107002699 ANP binding site [chemical binding]; other site 360107002700 Substrate Binding Site II [chemical binding]; other site 360107002701 Substrate Binding Site I [chemical binding]; other site 360107002702 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 360107002703 DNA methylase; Region: N6_N4_Mtase; cl17433 360107002704 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 360107002705 RNA binding surface [nucleotide binding]; other site 360107002706 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 360107002707 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 360107002708 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 360107002709 Walker A/P-loop; other site 360107002710 ATP binding site [chemical binding]; other site 360107002711 Q-loop/lid; other site 360107002712 ABC transporter signature motif; other site 360107002713 Walker B; other site 360107002714 D-loop; other site 360107002715 H-loop/switch region; other site 360107002716 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 360107002717 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 360107002718 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 360107002719 MPT binding site; other site 360107002720 trimer interface [polypeptide binding]; other site 360107002721 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 360107002722 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 360107002723 Walker A motif; other site 360107002724 ATP binding site [chemical binding]; other site 360107002725 Walker B motif; other site 360107002726 arginine finger; other site 360107002727 Peptidase family M41; Region: Peptidase_M41; pfam01434 360107002728 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 360107002729 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 360107002730 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 360107002731 FeS/SAM binding site; other site 360107002732 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 360107002733 Mechanosensitive ion channel; Region: MS_channel; pfam00924 360107002734 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 360107002735 active site 360107002736 dimer interface [polypeptide binding]; other site 360107002737 metal binding site [ion binding]; metal-binding site 360107002738 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 360107002739 TrkA-C domain; Region: TrkA_C; pfam02080 360107002740 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 360107002741 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 360107002742 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 360107002743 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 360107002744 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 360107002745 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 360107002746 active site 360107002747 metal binding site [ion binding]; metal-binding site 360107002748 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 360107002749 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 360107002750 HlyD family secretion protein; Region: HlyD_3; pfam13437 360107002751 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 360107002752 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 360107002753 Walker A/P-loop; other site 360107002754 ATP binding site [chemical binding]; other site 360107002755 Q-loop/lid; other site 360107002756 ABC transporter signature motif; other site 360107002757 Walker B; other site 360107002758 D-loop; other site 360107002759 H-loop/switch region; other site 360107002760 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 360107002761 FtsX-like permease family; Region: FtsX; pfam02687 360107002762 Outer membrane efflux protein; Region: OEP; pfam02321 360107002763 Outer membrane efflux protein; Region: OEP; pfam02321 360107002764 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 360107002765 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 360107002766 homodimer interface [polypeptide binding]; other site 360107002767 substrate-cofactor binding pocket; other site 360107002768 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107002769 catalytic residue [active] 360107002770 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 360107002771 methionine sulfoxide reductase B; Provisional; Region: PRK00222 360107002772 SelR domain; Region: SelR; pfam01641 360107002773 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 360107002774 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 360107002775 chorismate binding enzyme; Region: Chorismate_bind; cl10555 360107002776 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 360107002777 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 360107002778 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 360107002779 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 360107002780 sec-independent translocase; Provisional; Region: PRK04098 360107002781 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 360107002782 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 360107002783 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 360107002784 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 360107002785 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 360107002786 sequence-specific DNA binding site [nucleotide binding]; other site 360107002787 salt bridge; other site 360107002788 S-adenosylmethionine synthetase; Validated; Region: PRK05250 360107002789 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 360107002790 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 360107002791 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 360107002792 serine/threonine transporter SstT; Provisional; Region: PRK13628 360107002793 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 360107002794 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 360107002795 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 360107002796 active site 360107002797 Zn binding site [ion binding]; other site 360107002798 Na/Pi-cotransporter; Region: NaPi_cotrn_rel; TIGR00704 360107002799 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 360107002800 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 360107002801 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 360107002802 Part of AAA domain; Region: AAA_19; pfam13245 360107002803 Family description; Region: UvrD_C_2; pfam13538 360107002804 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK04099 360107002805 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 360107002806 active site 360107002807 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 360107002808 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 360107002809 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 360107002810 SmpB-tmRNA interface; other site 360107002811 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 360107002812 Uncharacterized conserved protein [Function unknown]; Region: COG2127 360107002813 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 360107002814 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 360107002815 Walker A motif; other site 360107002816 ATP binding site [chemical binding]; other site 360107002817 Walker B motif; other site 360107002818 arginine finger; other site 360107002819 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 360107002820 Walker A motif; other site 360107002821 ATP binding site [chemical binding]; other site 360107002822 Walker B motif; other site 360107002823 arginine finger; other site 360107002824 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 360107002825 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 360107002826 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 360107002827 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 360107002828 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 360107002829 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 360107002830 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 360107002831 metal-binding site [ion binding] 360107002832 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 360107002833 Soluble P-type ATPase [General function prediction only]; Region: COG4087 360107002834 Domain of unknown function DUF20; Region: UPF0118; pfam01594 360107002835 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 360107002836 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 360107002837 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 360107002838 nucleotide binding site [chemical binding]; other site 360107002839 NEF interaction site [polypeptide binding]; other site 360107002840 SBD interface [polypeptide binding]; other site 360107002841 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 360107002842 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 360107002843 dimer interface [polypeptide binding]; other site 360107002844 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 360107002845 heat-inducible transcription repressor; Provisional; Region: PRK03911 360107002846 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 360107002847 Na2 binding site [ion binding]; other site 360107002848 putative substrate binding site 1 [chemical binding]; other site 360107002849 Na binding site 1 [ion binding]; other site 360107002850 putative substrate binding site 2 [chemical binding]; other site 360107002851 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 360107002852 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 360107002853 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 360107002854 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 360107002855 putative active site; other site 360107002856 catalytic triad [active] 360107002857 putative dimer interface [polypeptide binding]; other site 360107002858 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 360107002859 Domain of unknown function (DUF4410); Region: DUF4410; pfam14366 360107002860 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 360107002861 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 360107002862 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 360107002863 active site 360107002864 DNA binding site [nucleotide binding] 360107002865 Int/Topo IB signature motif; other site 360107002866 Protein of unknown function; Region: DUF3971; pfam13116 360107002867 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 360107002868 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 360107002869 proteins similar to Escherichia coli yceG; Region: yceG_like; cl17666 360107002870 dimerization interface [polypeptide binding]; other site 360107002871 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 360107002872 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 360107002873 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 360107002874 LDH/MDH dimer interface [polypeptide binding]; other site 360107002875 malate dehydrogenase; Reviewed; Region: PRK06223 360107002876 NAD(P) binding site [chemical binding]; other site 360107002877 substrate binding site [chemical binding]; other site 360107002878 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 360107002879 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 360107002880 CoA-ligase; Region: Ligase_CoA; pfam00549 360107002881 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 360107002882 CoA binding domain; Region: CoA_binding; smart00881 360107002883 CoA-ligase; Region: Ligase_CoA; pfam00549 360107002884 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 360107002885 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 360107002886 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 360107002887 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 360107002888 dimer interface [polypeptide binding]; other site 360107002889 PYR/PP interface [polypeptide binding]; other site 360107002890 TPP binding site [chemical binding]; other site 360107002891 substrate binding site [chemical binding]; other site 360107002892 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 360107002893 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 360107002894 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 360107002895 TPP-binding site [chemical binding]; other site 360107002896 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 360107002897 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 360107002898 recombination protein RecR; Reviewed; Region: recR; PRK00076 360107002899 RecR protein; Region: RecR; pfam02132 360107002900 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 360107002901 putative active site [active] 360107002902 putative metal-binding site [ion binding]; other site 360107002903 tetramer interface [polypeptide binding]; other site 360107002904 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 360107002905 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 360107002906 dimerization interface [polypeptide binding]; other site 360107002907 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 360107002908 dimer interface [polypeptide binding]; other site 360107002909 phosphorylation site [posttranslational modification] 360107002910 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 360107002911 ATP binding site [chemical binding]; other site 360107002912 Mg2+ binding site [ion binding]; other site 360107002913 G-X-G motif; other site 360107002914 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 360107002915 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107002916 active site 360107002917 phosphorylation site [posttranslational modification] 360107002918 intermolecular recognition site; other site 360107002919 dimerization interface [polypeptide binding]; other site 360107002920 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 360107002921 DNA binding site [nucleotide binding] 360107002922 chaperone protein DnaJ; Provisional; Region: PRK10767 360107002923 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 360107002924 HSP70 interaction site [polypeptide binding]; other site 360107002925 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 360107002926 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 360107002927 dimer interface [polypeptide binding]; other site 360107002928 Autotransporter beta-domain; Region: Autotransporter; smart00869 360107002929 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 360107002930 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 360107002931 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 360107002932 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 360107002933 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 360107002934 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 360107002935 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 360107002936 propionate/acetate kinase; Provisional; Region: PRK12379 360107002937 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 360107002938 DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]; Region: ComEA; COG1555 360107002939 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK08527 360107002940 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 360107002941 PYR/PP interface [polypeptide binding]; other site 360107002942 dimer interface [polypeptide binding]; other site 360107002943 TPP binding site [chemical binding]; other site 360107002944 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 360107002945 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 360107002946 TPP-binding site [chemical binding]; other site 360107002947 dimer interface [polypeptide binding]; other site 360107002948 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 360107002949 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 360107002950 putative valine binding site [chemical binding]; other site 360107002951 dimer interface [polypeptide binding]; other site 360107002952 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 360107002953 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 360107002954 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 360107002955 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 360107002956 trimer interface [polypeptide binding]; other site 360107002957 active site 360107002958 UDP-GlcNAc binding site [chemical binding]; other site 360107002959 lipid binding site [chemical binding]; lipid-binding site 360107002960 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 360107002961 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 360107002962 active site 360107002963 NLPA lipoprotein; Region: Lipoprotein_9; cl17547 360107002964 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 360107002965 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 360107002966 substrate binding site [chemical binding]; other site 360107002967 THF binding site; other site 360107002968 zinc-binding site [ion binding]; other site 360107002969 OsmC-like protein; Region: OsmC; pfam02566 360107002970 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 360107002971 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 360107002972 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 360107002973 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 360107002974 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 360107002975 thiamine phosphate binding site [chemical binding]; other site 360107002976 active site 360107002977 pyrophosphate binding site [ion binding]; other site 360107002978 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 360107002979 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 360107002980 FeS/SAM binding site; other site 360107002981 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 360107002982 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 360107002983 ThiS interaction site; other site 360107002984 putative active site [active] 360107002985 tetramer interface [polypeptide binding]; other site 360107002986 ThiS-like ubiquitin; Region: ThiS-like; pfam14453 360107002987 thiamine biosynthesis protein ThiF; Provisional; Region: PRK08644 360107002988 E1_ThiF_like. Member of superfamily of activating enzymes (E1) of the ubiquitin-like proteins. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on...; Region: E1_ThiF_like; cd01487 360107002989 putative ATP binding site [chemical binding]; other site 360107002990 putative substrate interface [chemical binding]; other site 360107002991 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 360107002992 thiS-thiF/thiG interaction site; other site 360107002993 Uncharacterized conserved protein [Function unknown]; Region: COG1432 360107002994 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 360107002995 putative metal binding site [ion binding]; other site 360107002996 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 360107002997 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 360107002998 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 360107002999 putative trimer interface [polypeptide binding]; other site 360107003000 putative CoA binding site [chemical binding]; other site 360107003001 Branched-chain amino acid transport protein; Region: Branch_AA_trans; pfam05525 360107003002 DNA repair protein RadA; Provisional; Region: PRK11823 360107003003 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 360107003004 Walker A motif; other site 360107003005 ATP binding site [chemical binding]; other site 360107003006 Walker B motif; other site 360107003007 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 360107003008 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 360107003009 lipoprotein NlpI; Provisional; Region: PRK11189 360107003010 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 360107003011 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 360107003012 nucleophilic elbow; other site 360107003013 catalytic triad; other site 360107003014 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 360107003015 nucleophilic elbow; other site 360107003016 catalytic triad; other site 360107003017 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 360107003018 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 360107003019 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 360107003020 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 360107003021 Ligand Binding Site [chemical binding]; other site 360107003022 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 360107003023 AAA domain; Region: AAA_31; pfam13614 360107003024 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 360107003025 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 360107003026 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 360107003027 catalytic center binding site [active] 360107003028 ATP binding site [chemical binding]; other site 360107003029 methionine aminopeptidase; Provisional; Region: PRK12318 360107003030 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 360107003031 active site 360107003032 Dehydroquinase class II; Region: DHquinase_II; pfam01220 360107003033 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 360107003034 trimer interface [polypeptide binding]; other site 360107003035 active site 360107003036 dimer interface [polypeptide binding]; other site 360107003037 chlorohydrolase; Provisional; Region: PRK08418 360107003038 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 360107003039 active site 360107003040 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 360107003041 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 360107003042 tandem repeat interface [polypeptide binding]; other site 360107003043 oligomer interface [polypeptide binding]; other site 360107003044 active site residues [active] 360107003045 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 360107003046 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 360107003047 active site 360107003048 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 360107003049 histidinol dehydrogenase; Region: hisD; TIGR00069 360107003050 NAD binding site [chemical binding]; other site 360107003051 dimerization interface [polypeptide binding]; other site 360107003052 product binding site; other site 360107003053 substrate binding site [chemical binding]; other site 360107003054 zinc binding site [ion binding]; other site 360107003055 catalytic residues [active] 360107003056 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 360107003057 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 360107003058 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 360107003059 catalytic residue [active] 360107003060 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 360107003061 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 360107003062 ligand binding site [chemical binding]; other site 360107003063 AAA domain; Region: AAA_13; pfam13166 360107003064 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 360107003065 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 360107003066 active site 360107003067 intersubunit interface [polypeptide binding]; other site 360107003068 zinc binding site [ion binding]; other site 360107003069 Na+ binding site [ion binding]; other site 360107003070 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 360107003071 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 360107003072 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 360107003073 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 360107003074 minor groove reading motif; other site 360107003075 helix-hairpin-helix signature motif; other site 360107003076 substrate binding pocket [chemical binding]; other site 360107003077 active site 360107003078 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 360107003079 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 360107003080 PAS fold; Region: PAS_3; pfam08447 360107003081 putative active site [active] 360107003082 heme pocket [chemical binding]; other site 360107003083 Transglycosylase; Region: Transgly; pfam00912 360107003084 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 360107003085 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 360107003086 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 360107003087 MG2 domain; Region: A2M_N; pfam01835 360107003088 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 360107003089 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 360107003090 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 360107003091 active site 360107003092 HIGH motif; other site 360107003093 nucleotide binding site [chemical binding]; other site 360107003094 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 360107003095 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 360107003096 active site 360107003097 KMSKS motif; other site 360107003098 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 360107003099 tRNA binding surface [nucleotide binding]; other site 360107003100 anticodon binding site; other site 360107003101 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 360107003102 DpnII restriction endonuclease; Region: DpnII; pfam04556 360107003103 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 360107003104 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 360107003105 DNA methylase; Region: N6_N4_Mtase; pfam01555 360107003106 Protein of unknown function, DUF486; Region: DUF486; cl01236 360107003107 ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]; Region: AbcC; COG1135 360107003108 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 360107003109 Walker A/P-loop; other site 360107003110 ATP binding site [chemical binding]; other site 360107003111 Q-loop/lid; other site 360107003112 ABC transporter signature motif; other site 360107003113 Walker B; other site 360107003114 D-loop; other site 360107003115 H-loop/switch region; other site 360107003116 NIL domain; Region: NIL; pfam09383 360107003117 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 360107003118 ABC-ATPase subunit interface; other site 360107003119 Cytochrome c; Region: Cytochrom_C; cl11414 360107003120 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 360107003121 Cytochrome c; Region: Cytochrom_C; pfam00034 360107003122 Cytochrome c; Region: Cytochrom_C; cl11414 360107003123 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 360107003124 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 360107003125 intrachain domain interface; other site 360107003126 interchain domain interface [polypeptide binding]; other site 360107003127 heme bH binding site [chemical binding]; other site 360107003128 Qi binding site; other site 360107003129 heme bL binding site [chemical binding]; other site 360107003130 Qo binding site; other site 360107003131 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cl00193 360107003132 interchain domain interface [polypeptide binding]; other site 360107003133 intrachain domain interface; other site 360107003134 Qi binding site; other site 360107003135 Qo binding site; other site 360107003136 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 360107003137 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 360107003138 iron-sulfur cluster [ion binding]; other site 360107003139 [2Fe-2S] cluster binding site [ion binding]; other site 360107003140 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 360107003141 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 360107003142 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 360107003143 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 360107003144 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 360107003145 DNA gyrase subunit A; Validated; Region: PRK05560 360107003146 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 360107003147 CAP-like domain; other site 360107003148 active site 360107003149 primary dimer interface [polypeptide binding]; other site 360107003150 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 360107003151 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 360107003152 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 360107003153 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 360107003154 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 360107003155 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 360107003156 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 360107003157 substrate binding pocket [chemical binding]; other site 360107003158 membrane-bound complex binding site; other site 360107003159 hinge residues; other site 360107003160 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 360107003161 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 360107003162 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 360107003163 putative catalytic site [active] 360107003164 putative metal binding site [ion binding]; other site 360107003165 putative phosphate binding site [ion binding]; other site 360107003166 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 360107003167 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 360107003168 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 360107003169 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 360107003170 putative active site [active] 360107003171 putative substrate binding site [chemical binding]; other site 360107003172 putative cosubstrate binding site; other site 360107003173 catalytic site [active] 360107003174 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 360107003175 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 360107003176 catalytic site [active] 360107003177 G-X2-G-X-G-K; other site 360107003178 twin arginine-targeting protein translocase, TatA/E family; Region: tatAE; TIGR01411 360107003179 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 360107003180 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 360107003181 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 360107003182 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 360107003183 active site 360107003184 HIGH motif; other site 360107003185 KMSK motif region; other site 360107003186 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 360107003187 tRNA binding surface [nucleotide binding]; other site 360107003188 anticodon binding site; other site 360107003189 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 360107003190 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 360107003191 Walker A motif; other site 360107003192 ATP binding site [chemical binding]; other site 360107003193 Walker B motif; other site 360107003194 arginine finger; other site 360107003195 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 360107003196 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 360107003197 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 360107003198 active site 360107003199 putative recombination protein RecO; Provisional; Region: PRK13908 360107003200 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 360107003201 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 360107003202 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 360107003203 active site 360107003204 NTP binding site [chemical binding]; other site 360107003205 metal binding triad [ion binding]; metal-binding site 360107003206 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 360107003207 tartrate dehydrogenase; Region: TTC; TIGR02089 360107003208 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 360107003209 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 360107003210 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 360107003211 substrate binding site [chemical binding]; other site 360107003212 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 360107003213 Domain of unknown function (DUF4405); Region: DUF4405; pfam14358 360107003214 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 360107003215 substrate binding site [chemical binding]; other site 360107003216 active site 360107003217 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 360107003218 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 360107003219 FeS/SAM binding site; other site 360107003220 flavodoxin FldA; Validated; Region: PRK09267 360107003221 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4378 360107003222 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 360107003223 active site 360107003224 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 360107003225 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 360107003226 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107003227 catalytic residue [active] 360107003228 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 360107003229 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 360107003230 substrate binding site [chemical binding]; other site 360107003231 active site 360107003232 catalytic residues [active] 360107003233 heterodimer interface [polypeptide binding]; other site 360107003234 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 360107003235 Uncharacterized conserved protein [Function unknown]; Region: COG4121 360107003236 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 360107003237 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 360107003238 active site 360107003239 metal binding site [ion binding]; metal-binding site 360107003240 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 360107003241 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 360107003242 FMN binding site [chemical binding]; other site 360107003243 substrate binding site [chemical binding]; other site 360107003244 putative catalytic residue [active] 360107003245 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 360107003246 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 360107003247 active site 360107003248 HIGH motif; other site 360107003249 dimer interface [polypeptide binding]; other site 360107003250 KMSKS motif; other site 360107003251 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 360107003252 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 360107003253 Zn2+ binding site [ion binding]; other site 360107003254 Mg2+ binding site [ion binding]; other site 360107003255 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 360107003256 synthetase active site [active] 360107003257 NTP binding site [chemical binding]; other site 360107003258 metal binding site [ion binding]; metal-binding site 360107003259 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 360107003260 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 360107003261 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 360107003262 putative nucleotide binding site [chemical binding]; other site 360107003263 uridine monophosphate binding site [chemical binding]; other site 360107003264 homohexameric interface [polypeptide binding]; other site 360107003265 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 360107003266 Peptidase family M23; Region: Peptidase_M23; pfam01551 360107003267 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 360107003268 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 360107003269 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 360107003270 Walker A/P-loop; other site 360107003271 ATP binding site [chemical binding]; other site 360107003272 Q-loop/lid; other site 360107003273 ABC transporter signature motif; other site 360107003274 Walker B; other site 360107003275 D-loop; other site 360107003276 H-loop/switch region; other site 360107003277 tRNA (guanine-N(7)-)-methyltransferase; Provisional; Region: PRK14121 360107003278 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 360107003279 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 360107003280 Interdomain contacts; other site 360107003281 Cytokine receptor motif; other site 360107003282 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 360107003283 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 360107003284 RNA binding surface [nucleotide binding]; other site 360107003285 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 360107003286 active site 360107003287 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 360107003288 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 360107003289 HIT family signature motif; other site 360107003290 catalytic residue [active] 360107003291 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 360107003292 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 360107003293 catalytic residue [active] 360107003294 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 360107003295 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 360107003296 generic binding surface I; other site 360107003297 generic binding surface II; other site 360107003298 ubiquinone/menaquinone biosynthesis methyltransferase; Reviewed; Region: ubiE; PRK00216 360107003299 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 360107003300 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 360107003301 metal binding site 2 [ion binding]; metal-binding site 360107003302 putative DNA binding helix; other site 360107003303 metal binding site 1 [ion binding]; metal-binding site 360107003304 structural Zn2+ binding site [ion binding]; other site 360107003305 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 360107003306 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 360107003307 TPP-binding site; other site 360107003308 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 360107003309 PYR/PP interface [polypeptide binding]; other site 360107003310 dimer interface [polypeptide binding]; other site 360107003311 TPP binding site [chemical binding]; other site 360107003312 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 360107003313 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 360107003314 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 360107003315 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107003316 homodimer interface [polypeptide binding]; other site 360107003317 catalytic residue [active] 360107003318 Chorismate mutase type II; Region: CM_2; smart00830 360107003319 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 360107003320 Prephenate dehydratase; Region: PDT; pfam00800 360107003321 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 360107003322 putative L-Phe binding site [chemical binding]; other site 360107003323 Haloacid Dehalogenase Superfamily Class (subfamily) IIA; Region: HAD-SF-IIA; TIGR01460 360107003324 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 360107003325 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 360107003326 diaminopimelate decarboxylase; Region: lysA; TIGR01048 360107003327 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 360107003328 active site 360107003329 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 360107003330 substrate binding site [chemical binding]; other site 360107003331 catalytic residues [active] 360107003332 dimer interface [polypeptide binding]; other site 360107003333 Predicted permeases [General function prediction only]; Region: COG0795 360107003334 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 360107003335 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 360107003336 putative active site [active] 360107003337 catalytic residue [active] 360107003338 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 360107003339 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 360107003340 5S rRNA interface [nucleotide binding]; other site 360107003341 CTC domain interface [polypeptide binding]; other site 360107003342 L16 interface [polypeptide binding]; other site 360107003343 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 360107003344 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 360107003345 Walker A motif; other site 360107003346 ATP binding site [chemical binding]; other site 360107003347 Walker B motif; other site 360107003348 Class I aldolases; Region: Aldolase_Class_I; cl17187 360107003349 transaldolase; Provisional; Region: PRK03903 360107003350 catalytic residue [active] 360107003351 phosphoserine phosphatase SerB; Region: serB; TIGR00338 360107003352 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 360107003353 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 360107003354 motif II; other site 360107003355 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 360107003356 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 360107003357 putative active site [active] 360107003358 putative metal binding site [ion binding]; other site 360107003359 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 360107003360 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 360107003361 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 360107003362 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 360107003363 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 360107003364 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 360107003365 Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]; Region: LpxB; COG0763 360107003366 Stage III sporulation protein AE (spore_III_AE); Region: Spore_III_AE; cl09771 360107003367 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 360107003368 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 360107003369 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cl17196 360107003370 ATP binding site [chemical binding]; other site 360107003371 substrate interface [chemical binding]; other site 360107003372 Undecaprenyl-phosphate galactose phosphotransferase, WbaP; Region: WbaP_sugtrans; TIGR03022 360107003373 Bacterial sugar transferase; Region: Bac_transf; pfam02397 360107003374 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 360107003375 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 360107003376 putative catalytic cysteine [active] 360107003377 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 360107003378 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 360107003379 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 360107003380 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 360107003381 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 360107003382 S-adenosylmethionine binding site [chemical binding]; other site 360107003383 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 360107003384 binding surface 360107003385 TPR motif; other site 360107003386 TPR repeat; Region: TPR_11; pfam13414 360107003387 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 360107003388 active site 360107003389 ribulose/triose binding site [chemical binding]; other site 360107003390 phosphate binding site [ion binding]; other site 360107003391 substrate (anthranilate) binding pocket [chemical binding]; other site 360107003392 product (indole) binding pocket [chemical binding]; other site 360107003393 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 360107003394 nucleotide binding site/active site [active] 360107003395 HIT family signature motif; other site 360107003396 catalytic residue [active] 360107003397 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 360107003398 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 360107003399 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 360107003400 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 360107003401 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 360107003402 P loop; other site 360107003403 GTP binding site [chemical binding]; other site 360107003404 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 360107003405 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 360107003406 catalytic residues [active] 360107003407 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 360107003408 phosphodiesterase; Provisional; Region: PRK12704 360107003409 KH domain; Region: KH_1; pfam00013 360107003410 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 360107003411 Zn2+ binding site [ion binding]; other site 360107003412 Mg2+ binding site [ion binding]; other site 360107003413 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 360107003414 putative amphipathic alpha helix; other site 360107003415 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 360107003416 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 360107003417 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 360107003418 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 360107003419 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 360107003420 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 360107003421 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 360107003422 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 360107003423 transcription termination factor Rho; Provisional; Region: rho; PRK09376 360107003424 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 360107003425 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 360107003426 RNA binding site [nucleotide binding]; other site 360107003427 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 360107003428 multimer interface [polypeptide binding]; other site 360107003429 Walker A motif; other site 360107003430 ATP binding site [chemical binding]; other site 360107003431 Walker B motif; other site 360107003432 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 360107003433 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 360107003434 substrate binding pocket [chemical binding]; other site 360107003435 membrane-bound complex binding site; other site 360107003436 hinge residues; other site 360107003437 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 360107003438 4Fe-4S binding domain; Region: Fer4_5; pfam12801 360107003439 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 360107003440 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 360107003441 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 360107003442 Autotransporter beta-domain; Region: Autotransporter; smart00869 360107003443 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 360107003444 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 360107003445 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 360107003446 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 360107003447 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 360107003448 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 360107003449 ATP-grasp domain; Region: ATP-grasp_4; cl17255 360107003450 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 360107003451 IMP binding site; other site 360107003452 dimer interface [polypeptide binding]; other site 360107003453 interdomain contacts; other site 360107003454 partial ornithine binding site; other site 360107003455 rod shape-determining protein MreC; Provisional; Region: PRK13922 360107003456 rod shape-determining protein MreC; Region: MreC; pfam04085 360107003457 rod shape-determining protein MreB; Provisional; Region: PRK13927 360107003458 MreB and similar proteins; Region: MreB_like; cd10225 360107003459 nucleotide binding site [chemical binding]; other site 360107003460 Mg binding site [ion binding]; other site 360107003461 putative protofilament interaction site [polypeptide binding]; other site 360107003462 RodZ interaction site [polypeptide binding]; other site 360107003463 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 360107003464 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 360107003465 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 360107003466 Walker A motif; other site 360107003467 ATP binding site [chemical binding]; other site 360107003468 Walker B motif; other site 360107003469 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 360107003470 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 360107003471 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 360107003472 putative trimer interface [polypeptide binding]; other site 360107003473 putative CoA binding site [chemical binding]; other site 360107003474 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 360107003475 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group; Region: Alpha_ANH_like; cd01986 360107003476 Ligand Binding Site [chemical binding]; other site 360107003477 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 360107003478 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 360107003479 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 360107003480 dihydrodipicolinate reductase; Provisional; Region: PRK00048 360107003481 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 360107003482 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 360107003483 amidophosphoribosyltransferase; Provisional; Region: PRK08525 360107003484 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 360107003485 active site 360107003486 tetramer interface [polypeptide binding]; other site 360107003487 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 360107003488 active site 360107003489 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 360107003490 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107003491 active site 360107003492 phosphorylation site [posttranslational modification] 360107003493 intermolecular recognition site; other site 360107003494 dimerization interface [polypeptide binding]; other site 360107003495 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 360107003496 DNA binding site [nucleotide binding] 360107003497 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 360107003498 PAS domain; Region: PAS_9; pfam13426 360107003499 putative active site [active] 360107003500 heme pocket [chemical binding]; other site 360107003501 Protein of unknown function (DUF2869); Region: DUF2869; pfam11068 360107003502 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 360107003503 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 360107003504 dimer interface [polypeptide binding]; other site 360107003505 phosphorylation site [posttranslational modification] 360107003506 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 360107003507 ATP binding site [chemical binding]; other site 360107003508 Mg2+ binding site [ion binding]; other site 360107003509 G-X-G motif; other site 360107003510 Family description; Region: DsbD_2; pfam13386 360107003511 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 360107003512 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 360107003513 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 360107003514 catalytic site [active] 360107003515 subunit interface [polypeptide binding]; other site 360107003516 Protein of unknown function (DUF507); Region: DUF507; pfam04368 360107003517 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12293 360107003518 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 360107003519 motif 1; other site 360107003520 dimer interface [polypeptide binding]; other site 360107003521 active site 360107003522 motif 2; other site 360107003523 motif 3; other site 360107003524 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 360107003525 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 360107003526 GDP-binding site [chemical binding]; other site 360107003527 ACT binding site; other site 360107003528 IMP binding site; other site 360107003529 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 360107003530 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 360107003531 threonine dehydratase; Provisional; Region: PRK08526 360107003532 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 360107003533 tetramer interface [polypeptide binding]; other site 360107003534 pyridoxal 5'-phosphate binding site [chemical binding]; other site 360107003535 catalytic residue [active] 360107003536 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 360107003537 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 360107003538 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 360107003539 S-adenosylmethionine binding site [chemical binding]; other site 360107003540 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 360107003541 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 360107003542 malonic semialdehyde reductase; Provisional; Region: PRK10538 360107003543 putative NAD(P) binding site [chemical binding]; other site 360107003544 homotetramer interface [polypeptide binding]; other site 360107003545 homodimer interface [polypeptide binding]; other site 360107003546 active site 360107003547 hydroxylamine reductase; Provisional; Region: PRK12310 360107003548 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 360107003549 ACS interaction site; other site 360107003550 CODH interaction site; other site 360107003551 metal cluster binding site [ion binding]; other site 360107003552 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 360107003553 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 360107003554 N-acetyl-D-glucosamine binding site [chemical binding]; other site 360107003555 catalytic residue [active] 360107003556 YGGT family; Region: YGGT; pfam02325 360107003557 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 360107003558 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 360107003559 active site 360107003560 HIGH motif; other site 360107003561 nucleotide binding site [chemical binding]; other site 360107003562 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 360107003563 active site 360107003564 KMSKS motif; other site 360107003565 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 360107003566 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 360107003567 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 360107003568 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 360107003569 ligand binding site [chemical binding]; other site 360107003570 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 360107003571 putative switch regulator; other site 360107003572 non-specific DNA interactions [nucleotide binding]; other site 360107003573 DNA binding site [nucleotide binding] 360107003574 sequence specific DNA binding site [nucleotide binding]; other site 360107003575 putative cAMP binding site [chemical binding]; other site 360107003576 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 360107003577 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 360107003578 putative active site [active] 360107003579 putative metal binding site [ion binding]; other site 360107003580 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 360107003581 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 360107003582 primosome assembly protein PriA; Validated; Region: PRK05580 360107003583 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 360107003584 ATP binding site [chemical binding]; other site 360107003585 putative Mg++ binding site [ion binding]; other site 360107003586 helicase superfamily c-terminal domain; Region: HELICc; smart00490 360107003587 ATP-binding site [chemical binding]; other site 360107003588 putative recombination protein RecB; Provisional; Region: PRK13909 360107003589 Part of AAA domain; Region: AAA_19; pfam13245 360107003590 Family description; Region: UvrD_C_2; pfam13538 360107003591 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 360107003592 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 360107003593 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 360107003594 Filamin/ABP280 repeat; Region: Filamin; pfam00630 360107003595 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 360107003596 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 360107003597 Cytochrome c; Region: Cytochrom_C; pfam00034 360107003598 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 360107003599 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 360107003600 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 360107003601 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 360107003602 cbb3-type cytochrome c oxidase subunit I; Provisional; Region: PRK14488 360107003603 Low-spin heme binding site [chemical binding]; other site 360107003604 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 360107003605 D-pathway; other site 360107003606 Putative water exit pathway; other site 360107003607 Binuclear center (active site) [active] 360107003608 K-pathway; other site 360107003609 Putative proton exit pathway; other site 360107003610 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 360107003611 trimer interface [polypeptide binding]; other site 360107003612 Autotransporter adhesin [Intracellular trafficking and secretion / Extracellular structures]; Region: Hia; COG5295 360107003613 YadA-like C-terminal region; Region: YadA; pfam03895 360107003614 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 360107003615 trimer interface [polypeptide binding]; other site 360107003616 Fic family protein [Function unknown]; Region: COG3177 360107003617 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 360107003618 Fic/DOC family; Region: Fic; pfam02661 360107003619 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 360107003620 Domain of unknown function (DUF4325); Region: DUF4325; pfam14213 360107003621 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 360107003622 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 360107003623 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 360107003624 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 360107003625 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 360107003626 substrate binding site [chemical binding]; other site 360107003627 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 360107003628 substrate binding site [chemical binding]; other site 360107003629 ligand binding site [chemical binding]; other site 360107003630 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 360107003631 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 360107003632 DNA binding site [nucleotide binding] 360107003633 active site 360107003634 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 360107003635 metal-binding site [ion binding] 360107003636 hypothetical protein; Provisional; Region: PRK12378 360107003637 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 360107003638 active site 360107003639 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 360107003640 Protein of unknown function (DUF805); Region: DUF805; pfam05656 360107003641 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 360107003642 Protein of unknown function (DUF2974); Region: DUF2974; pfam11187 360107003643 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 360107003644 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 360107003645 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 360107003646 Outer membrane efflux protein; Region: OEP; pfam02321 360107003647 Transglycosylase; Region: Transgly; pfam00912 360107003648 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 360107003649 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 360107003650 HlyD family secretion protein; Region: HlyD_3; pfam13437 360107003651 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 360107003652 putative active site [active] 360107003653 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 360107003654 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 360107003655 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 360107003656 Walker A/P-loop; other site 360107003657 ATP binding site [chemical binding]; other site 360107003658 Q-loop/lid; other site 360107003659 ABC transporter signature motif; other site 360107003660 Walker B; other site 360107003661 D-loop; other site 360107003662 H-loop/switch region; other site 360107003663 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 360107003664 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 360107003665 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 360107003666 metal binding site [ion binding]; metal-binding site 360107003667 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 360107003668 SPFH domain / Band 7 family; Region: Band_7; pfam01145 360107003669 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 360107003670 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 360107003671 homodimer interface [polypeptide binding]; other site 360107003672 substrate-cofactor binding pocket; other site 360107003673 catalytic residue [active] 360107003674 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 360107003675 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 360107003676 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 360107003677 integrase; Provisional; Region: PRK09692 360107003678 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 360107003679 active site 360107003680 DNA binding site [nucleotide binding] 360107003681 Int/Topo IB signature motif; other site 360107003682 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 360107003683 DNA binding residues [nucleotide binding] 360107003684 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; pfam09669 360107003685 YcfA-like protein; Region: YcfA; cl00752 360107003686 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 360107003687 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 360107003688 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 360107003689 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 360107003690 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 360107003691 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 360107003692 D-glucuronyl C5-epimerase C-terminus; Region: C5-epim_C; pfam06662 360107003693 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 360107003694 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 360107003695 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 360107003696 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 360107003697 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 360107003698 active site 360107003699 homodimer interface [polypeptide binding]; other site 360107003700 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 360107003701 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 360107003702 active site 360107003703 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 360107003704 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 360107003705 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 360107003706 S-adenosylmethionine binding site [chemical binding]; other site 360107003707 Predicted methyltransferase regulatory domain; Region: MethyTransf_Reg; pfam10119 360107003708 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 360107003709 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 360107003710 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 360107003711 active site 360107003712 argininosuccinate lyase; Provisional; Region: PRK00855 360107003713 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 360107003714 active sites [active] 360107003715 tetramer interface [polypeptide binding]; other site 360107003716 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 360107003717 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 360107003718 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 360107003719 active site 360107003720 substrate-binding site [chemical binding]; other site 360107003721 metal-binding site [ion binding] 360107003722 ATP binding site [chemical binding]; other site 360107003723 Ferredoxin [Energy production and conversion]; Region: COG1146 360107003724 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 360107003725 active site 360107003726 multimer interface [polypeptide binding]; other site 360107003727 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 360107003728 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 360107003729 putative phosphate acyltransferase; Provisional; Region: PRK05331 360107003730 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 360107003731 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 360107003732 dimer interface [polypeptide binding]; other site 360107003733 active site 360107003734 CoA binding pocket [chemical binding]; other site 360107003735 Curli production assembly/transport component CsgG; Region: CsgG; pfam03783 360107003736 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4259 360107003737 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 360107003738 Putative bacterial lipoprotein (DUF799); Region: DUF799; cl01813 360107003739 Enterobacterial TraT complement resistance protein; Region: TraT; pfam05818 360107003740 succinic semialdehyde dehydrogenase; Region: PLN02278 360107003741 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 360107003742 tetramerization interface [polypeptide binding]; other site 360107003743 NAD(P) binding site [chemical binding]; other site 360107003744 catalytic residues [active] 360107003745 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 360107003746 substrate binding site [chemical binding]; other site 360107003747 dimer interface [polypeptide binding]; other site 360107003748 ATP binding site [chemical binding]; other site 360107003749 High-affinity nickel-transport protein; Region: NicO; cl00964 360107003750 AIR carboxylase; Region: AIRC; smart01001 360107003751 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 360107003752 Peptidase family U32; Region: Peptidase_U32; pfam01136 360107003753 histidinol-phosphatase; Provisional; Region: PRK07328 360107003754 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Region: PHP_HisPPase_Hisj_like; cd12110 360107003755 active site 360107003756 dimer interface [polypeptide binding]; other site 360107003757 Dihydroneopterin aldolase; Region: FolB; pfam02152 360107003758 active site 360107003759 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 360107003760 Domain of unknown function DUF87; Region: DUF87; pfam01935 360107003761 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1; cd01653 360107003762 conserved cys residue [active] 360107003763 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 360107003764 H+ Antiporter protein; Region: 2A0121; TIGR00900 360107003765 putative substrate translocation pore; other site 360107003766 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14454 360107003767 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 360107003768 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 360107003769 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 360107003770 molybdopterin cofactor binding site [chemical binding]; other site 360107003771 substrate binding site [chemical binding]; other site 360107003772 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 360107003773 molybdopterin cofactor binding site; other site 360107003774 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 360107003775 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 360107003776 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 360107003777 haemagglutination activity domain; Region: Haemagg_act; pfam05860 360107003778 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 360107003779 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 360107003780 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 360107003781 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 360107003782 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 360107003783 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 360107003784 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 360107003785 active site 360107003786 PHP Thumb interface [polypeptide binding]; other site 360107003787 metal binding site [ion binding]; metal-binding site 360107003788 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 360107003789 dimerization interface [polypeptide binding]; other site 360107003790 putative DNA binding site [nucleotide binding]; other site 360107003791 putative Zn2+ binding site [ion binding]; other site 360107003792 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 360107003793 CPxP motif; other site 360107003794 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 360107003795 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 360107003796 active site 360107003797 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A; Region: CS_ACL-C_CCL; cl00416 360107003798 Citrate synthase; Region: Citrate_synt; pfam00285 360107003799 oxalacetate binding site [chemical binding]; other site 360107003800 citrylCoA binding site [chemical binding]; other site 360107003801 coenzyme A binding site [chemical binding]; other site 360107003802 catalytic triad [active] 360107003803 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 360107003804 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 360107003805 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 360107003806 active site 360107003807 metal binding site [ion binding]; metal-binding site 360107003808 homotetramer interface [polypeptide binding]; other site 360107003809 DNA topoisomerase I; Validated; Region: PRK05582 360107003810 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 360107003811 active site 360107003812 interdomain interaction site; other site 360107003813 putative metal-binding site [ion binding]; other site 360107003814 nucleotide binding site [chemical binding]; other site 360107003815 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 360107003816 domain I; other site 360107003817 DNA binding groove [nucleotide binding] 360107003818 phosphate binding site [ion binding]; other site 360107003819 domain II; other site 360107003820 domain III; other site 360107003821 nucleotide binding site [chemical binding]; other site 360107003822 catalytic site [active] 360107003823 domain IV; other site 360107003824 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 360107003825 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 360107003826 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 360107003827 trimer interface [polypeptide binding]; other site 360107003828 active site 360107003829 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 360107003830 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 360107003831 carboxyltransferase (CT) interaction site; other site 360107003832 biotinylation site [posttranslational modification]; other site 360107003833 biotin carboxylase; Validated; Region: PRK08462 360107003834 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 360107003835 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 360107003836 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 360107003837 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 360107003838 Aspartase; Region: Aspartase; cd01357 360107003839 active sites [active] 360107003840 tetramer interface [polypeptide binding]; other site 360107003841 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 360107003842 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK09412 360107003843 Sulfatase; Region: Sulfatase; cl17466 360107003844 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 360107003845 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 360107003846 active site 360107003847 DNA binding site [nucleotide binding] 360107003848 Int/Topo IB signature motif; other site 360107003849 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated; Region: PRK05778 360107003850 Transposase; Region: DEDD_Tnp_IS110; pfam01548 360107003851 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 360107003852 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 360107003853 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 360107003854 Glycosyl hydrolase 108; Region: Glyco_hydro_108; pfam05838 360107003855 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 360107003856 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 360107003857 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 360107003858 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 360107003859 phosphoglyceromutase; Provisional; Region: PRK05434 360107003860 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 360107003861 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 360107003862 Mg++ binding site [ion binding]; other site 360107003863 putative catalytic motif [active] 360107003864 putative substrate binding site [chemical binding]; other site 360107003865 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 360107003866 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 360107003867 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 360107003868 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 360107003869 23S rRNA interface [nucleotide binding]; other site 360107003870 L3 interface [polypeptide binding]; other site 360107003871 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 360107003872 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 360107003873 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 360107003874 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 360107003875 ligand binding site [chemical binding]; other site 360107003876 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 360107003877 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 360107003878 motif II; other site 360107003879 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 360107003880 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 360107003881 dimer interface [polypeptide binding]; other site 360107003882 PYR/PP interface [polypeptide binding]; other site 360107003883 TPP binding site [chemical binding]; other site 360107003884 substrate binding site [chemical binding]; other site 360107003885 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 360107003886 Domain of unknown function; Region: EKR; smart00890 360107003887 4Fe-4S binding domain; Region: Fer4_6; pfam12837 360107003888 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 360107003889 TPP-binding site [chemical binding]; other site 360107003890 dimer interface [polypeptide binding]; other site 360107003891 Cytochrome c; Region: Cytochrom_C; cl11414 360107003892 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 360107003893 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 360107003894 Ligand Binding Site [chemical binding]; other site 360107003895 DNA primase; Validated; Region: dnaG; PRK05667 360107003896 CHC2 zinc finger; Region: zf-CHC2; pfam01807 360107003897 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 360107003898 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 360107003899 active site 360107003900 metal binding site [ion binding]; metal-binding site 360107003901 interdomain interaction site; other site 360107003902 Tetratricopeptide repeat; Region: TPR_12; pfam13424 360107003903 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 360107003904 TPR motif; other site 360107003905 binding surface 360107003906 Tetratricopeptide repeat; Region: TPR_16; pfam13432 360107003907 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 360107003908 RNA/DNA hybrid binding site [nucleotide binding]; other site 360107003909 active site 360107003910 ribonuclease III; Reviewed; Region: rnc; PRK00102 360107003911 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 360107003912 dimerization interface [polypeptide binding]; other site 360107003913 active site 360107003914 metal binding site [ion binding]; metal-binding site 360107003915 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 360107003916 FAD binding domain; Region: FAD_binding_4; pfam01565 360107003917 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 360107003918 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 360107003919 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 360107003920 Cysteine-rich domain; Region: CCG; pfam02754 360107003921 Cysteine-rich domain; Region: CCG; pfam02754 360107003922 EamA-like transporter family; Region: EamA; pfam00892 360107003923 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 360107003924 EamA-like transporter family; Region: EamA; pfam00892 360107003925 peptide chain release factor 1; Validated; Region: prfA; PRK00591 360107003926 This domain is found in peptide chain release factors; Region: PCRF; smart00937 360107003927 RF-1 domain; Region: RF-1; pfam00472 360107003928 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 360107003929 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]; Region: COG5016 360107003930 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 360107003931 active site 360107003932 catalytic residues [active] 360107003933 metal binding site [ion binding]; metal-binding site 360107003934 homodimer binding site [polypeptide binding]; other site 360107003935 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK05641 360107003936 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 360107003937 carboxyltransferase (CT) interaction site; other site 360107003938 biotinylation site [posttranslational modification]; other site 360107003939 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 360107003940 DctM-like transporters; Region: DctM; pfam06808 360107003941 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 360107003942 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 360107003943 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 360107003944 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 360107003945 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 360107003946 dimer interface [polypeptide binding]; other site 360107003947 ADP-ribose binding site [chemical binding]; other site 360107003948 active site 360107003949 nudix motif; other site 360107003950 metal binding site [ion binding]; metal-binding site 360107003951 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 360107003952 MgtE intracellular N domain; Region: MgtE_N; pfam03448 360107003953 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 360107003954 Divalent cation transporter; Region: MgtE; pfam01769 360107003955 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 360107003956 Peptidase family M23; Region: Peptidase_M23; pfam01551 360107003957 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 360107003958 putative catalytic site [active] 360107003959 putative metal binding site [ion binding]; other site 360107003960 putative phosphate binding site [ion binding]; other site 360107003961 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 360107003962 Ligand Binding Site [chemical binding]; other site 360107003963 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 360107003964 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 360107003965 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 360107003966 DJ-1 family protein; Region: not_thiJ; TIGR01383 360107003967 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 360107003968 conserved cys residue [active] 360107003969 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 360107003970 Predicted dehydrogenase [General function prediction only]; Region: COG0579 360107003971 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 360107003972 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 360107003973 domain interfaces; other site 360107003974 active site 360107003975 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 360107003976 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 360107003977 pantothenate kinase; Reviewed; Region: PRK13333 360107003978 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 360107003979 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 360107003980 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 360107003981 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 360107003982 Walker A motif; other site 360107003983 ATP binding site [chemical binding]; other site 360107003984 Walker B motif; other site 360107003985 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 360107003986 Colicin V production protein; Region: Colicin_V; pfam02674 360107003987 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 360107003988 metal binding site 2 [ion binding]; metal-binding site 360107003989 putative DNA binding helix; other site 360107003990 metal binding site 1 [ion binding]; metal-binding site 360107003991 dimer interface [polypeptide binding]; other site 360107003992 structural Zn2+ binding site [ion binding]; other site 360107003993 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 360107003994 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 360107003995 dimer interface [polypeptide binding]; other site 360107003996 putative anticodon binding site; other site 360107003997 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 360107003998 motif 1; other site 360107003999 active site 360107004000 motif 2; other site 360107004001 motif 3; other site 360107004002 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 360107004003 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 360107004004 dimer interface [polypeptide binding]; other site 360107004005 active site 360107004006 glycine-pyridoxal phosphate binding site [chemical binding]; other site 360107004007 folate binding site [chemical binding]; other site 360107004008 Sporulation related domain; Region: SPOR; pfam05036 360107004009 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 360107004010 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 360107004011 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 360107004012 shikimate binding site; other site 360107004013 NAD(P) binding site [chemical binding]; other site 360107004014 Predicted membrane protein [Function unknown]; Region: COG1971 360107004015 Domain of unknown function DUF; Region: DUF204; pfam02659 360107004016 Domain of unknown function DUF; Region: DUF204; pfam02659 360107004017 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 360107004018 active site 360107004019 homotetramer interface [polypeptide binding]; other site 360107004020 homodimer interface [polypeptide binding]; other site 360107004021 elongation factor G; Reviewed; Region: PRK00007 360107004022 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 360107004023 G1 box; other site 360107004024 putative GEF interaction site [polypeptide binding]; other site 360107004025 GTP/Mg2+ binding site [chemical binding]; other site 360107004026 Switch I region; other site 360107004027 G2 box; other site 360107004028 G3 box; other site 360107004029 Switch II region; other site 360107004030 G4 box; other site 360107004031 G5 box; other site 360107004032 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 360107004033 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 360107004034 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 360107004035 30S ribosomal protein S7; Validated; Region: PRK05302 360107004036 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 360107004037 S17 interaction site [polypeptide binding]; other site 360107004038 S8 interaction site; other site 360107004039 16S rRNA interaction site [nucleotide binding]; other site 360107004040 streptomycin interaction site [chemical binding]; other site 360107004041 23S rRNA interaction site [nucleotide binding]; other site 360107004042 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 360107004043 Predicted membrane protein [Function unknown]; Region: COG2259 360107004044 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 360107004045 L11 interface [polypeptide binding]; other site 360107004046 putative EF-Tu interaction site [polypeptide binding]; other site 360107004047 putative EF-G interaction site [polypeptide binding]; other site 360107004048 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 360107004049 23S rRNA interface [nucleotide binding]; other site 360107004050 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 360107004051 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 360107004052 mRNA/rRNA interface [nucleotide binding]; other site 360107004053 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 360107004054 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 360107004055 23S rRNA interface [nucleotide binding]; other site 360107004056 L7/L12 interface [polypeptide binding]; other site 360107004057 putative thiostrepton binding site; other site 360107004058 L25 interface [polypeptide binding]; other site 360107004059 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 360107004060 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 360107004061 putative homodimer interface [polypeptide binding]; other site 360107004062 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 360107004063 heterodimer interface [polypeptide binding]; other site 360107004064 homodimer interface [polypeptide binding]; other site 360107004065 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 360107004066 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 360107004067 elongation factor Tu; Reviewed; Region: PRK00049 360107004068 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 360107004069 G1 box; other site 360107004070 GEF interaction site [polypeptide binding]; other site 360107004071 GTP/Mg2+ binding site [chemical binding]; other site 360107004072 Switch I region; other site 360107004073 G2 box; other site 360107004074 G3 box; other site 360107004075 Switch II region; other site 360107004076 G4 box; other site 360107004077 G5 box; other site 360107004078 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 360107004079 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 360107004080 Antibiotic Binding Site [chemical binding]; other site 360107004081 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 360107004082 Sm and related proteins; Region: Sm_like; cl00259 360107004083 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 360107004084 putative oligomer interface [polypeptide binding]; other site 360107004085 putative RNA binding site [nucleotide binding]; other site 360107004086 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 360107004087 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 360107004088 translation initiation factor IF-2; Region: IF-2; TIGR00487 360107004089 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 360107004090 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 360107004091 G1 box; other site 360107004092 putative GEF interaction site [polypeptide binding]; other site 360107004093 GTP/Mg2+ binding site [chemical binding]; other site 360107004094 Switch I region; other site 360107004095 G2 box; other site 360107004096 G3 box; other site 360107004097 Switch II region; other site 360107004098 G4 box; other site 360107004099 G5 box; other site 360107004100 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 360107004101 Translation-initiation factor 2; Region: IF-2; pfam11987 360107004102 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 360107004103 homoserine kinase; Provisional; Region: PRK01212 360107004104 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 360107004105 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 360107004106 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 360107004107 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 360107004108 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 360107004109 Peptidase family M23; Region: Peptidase_M23; pfam01551 360107004110 prephenate dehydrogenase; Validated; Region: PRK08507 360107004111 Prephenate dehydrogenase; Region: PDH; pfam02153 360107004112 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 360107004113 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 360107004114 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 360107004115 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 360107004116 Surface antigen; Region: Bac_surface_Ag; pfam01103 360107004117 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 360107004118 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 360107004119 Walker A/P-loop; other site 360107004120 ATP binding site [chemical binding]; other site 360107004121 Q-loop/lid; other site 360107004122 ABC transporter signature motif; other site 360107004123 Walker B; other site 360107004124 D-loop; other site 360107004125 H-loop/switch region; other site 360107004126 Smr domain; Region: Smr; pfam01713 360107004127 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 360107004128 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 360107004129 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 360107004130 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 360107004131 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 360107004132 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 360107004133 Sel1 repeat; Region: Sel1; cl02723 360107004134 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 360107004135 Sel1-like repeats; Region: SEL1; smart00671 360107004136 Sel1-like repeats; Region: SEL1; smart00671 360107004137 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 360107004138 homotrimer interaction site [polypeptide binding]; other site 360107004139 putative active site [active] 360107004140 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 360107004141 HemN C-terminal domain; Region: HemN_C; pfam06969 360107004142 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 360107004143 ornithine carbamoyltransferase; Provisional; Region: PRK00779 360107004144 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 360107004145 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 360107004146 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 360107004147 dimer interface [polypeptide binding]; other site 360107004148 active site 360107004149 Schiff base residues; other site 360107004150 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 360107004151 dimerization interface [polypeptide binding]; other site 360107004152 active site 360107004153 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 360107004154 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; cl17726 360107004155 excinuclease ABC subunit B; Provisional; Region: PRK05298 360107004156 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 360107004157 ATP binding site [chemical binding]; other site 360107004158 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 360107004159 nucleotide binding region [chemical binding]; other site 360107004160 ATP-binding site [chemical binding]; other site 360107004161 Ultra-violet resistance protein B; Region: UvrB; pfam12344 360107004162 UvrB/uvrC motif; Region: UVR; pfam02151 360107004163 Campylobacter major outer membrane protein; Region: Campylo_MOMP; pfam05538 360107004164 Cytochrome c; Region: Cytochrom_C; pfam00034 360107004165 glutamine synthetase, type I; Region: GlnA; TIGR00653 360107004166 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 360107004167 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 360107004168 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 360107004169 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 360107004170 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 360107004171 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 360107004172 Yqey-like protein; Region: YqeY; pfam09424 360107004173 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 360107004174 exopolyphosphatase; Region: exo_poly_only; TIGR03706 360107004175 nucleotide binding site [chemical binding]; other site 360107004176 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 360107004177 active site 360107004178 hydrophilic channel; other site 360107004179 dimerization interface [polypeptide binding]; other site 360107004180 catalytic residues [active] 360107004181 active site lid [active] 360107004182 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 360107004183 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 360107004184 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 360107004185 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 360107004186 molybdopterin cofactor binding site; other site 360107004187 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 360107004188 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 360107004189 molybdopterin cofactor binding site; other site 360107004190 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 360107004191 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 360107004192 4Fe-4S binding domain; Region: Fer4_5; pfam12801 360107004193 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 360107004194 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 360107004195 ferredoxin-type protein; Provisional; Region: PRK10194 360107004196 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 360107004197 FOG: WD40 repeat [General function prediction only]; Region: COG2319 360107004198 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 360107004199 structural tetrad; other site 360107004200 NapD protein; Region: NapD; cl01163 360107004201 polyphosphate kinase; Provisional; Region: PRK05443 360107004202 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 360107004203 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 360107004204 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 360107004205 putative domain interface [polypeptide binding]; other site 360107004206 putative active site [active] 360107004207 catalytic site [active] 360107004208 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 360107004209 putative domain interface [polypeptide binding]; other site 360107004210 putative active site [active] 360107004211 catalytic site [active] 360107004212 DNA polymerase I; Provisional; Region: PRK05755 360107004213 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 360107004214 active site 360107004215 metal binding site 1 [ion binding]; metal-binding site 360107004216 putative 5' ssDNA interaction site; other site 360107004217 metal binding site 3; metal-binding site 360107004218 metal binding site 2 [ion binding]; metal-binding site 360107004219 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 360107004220 putative DNA binding site [nucleotide binding]; other site 360107004221 putative metal binding site [ion binding]; other site 360107004222 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 360107004223 active site 360107004224 catalytic site [active] 360107004225 substrate binding site [chemical binding]; other site 360107004226 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 360107004227 active site 360107004228 DNA binding site [nucleotide binding] 360107004229 catalytic site [active] 360107004230 2-acyl-glycerophospho-ethanolamine acyltransferase; Validated; Region: PRK08633 360107004231 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 360107004232 putative acyl-acceptor binding pocket; other site 360107004233 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 360107004234 acyl-activating enzyme (AAE) consensus motif; other site 360107004235 AMP binding site [chemical binding]; other site 360107004236 active site 360107004237 CoA binding site [chemical binding]; other site 360107004238 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 360107004239 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 360107004240 substrate binding pocket [chemical binding]; other site 360107004241 membrane-bound complex binding site; other site 360107004242 hinge residues; other site 360107004243 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 360107004244 ATP cone domain; Region: ATP-cone; pfam03477 360107004245 Class I ribonucleotide reductase; Region: RNR_I; cd01679 360107004246 active site 360107004247 dimer interface [polypeptide binding]; other site 360107004248 catalytic residues [active] 360107004249 effector binding site; other site 360107004250 R2 peptide binding site; other site 360107004251 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 360107004252 Na binding site [ion binding]; other site 360107004253 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 360107004254 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 360107004255 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 360107004256 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 360107004257 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 360107004258 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 360107004259 adenylosuccinate lyase; Provisional; Region: PRK08470 360107004260 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 360107004261 tetramer interface [polypeptide binding]; other site 360107004262 active site 360107004263 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 360107004264 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 360107004265 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 360107004266 active site 360107004267 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 360107004268 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 360107004269 FeS/SAM binding site; other site 360107004270 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 360107004271 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 360107004272 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 360107004273 substrate binding site [chemical binding]; other site 360107004274 glutamase interaction surface [polypeptide binding]; other site 360107004275 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 360107004276 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 360107004277 S-adenosylmethionine binding site [chemical binding]; other site 360107004278 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 360107004279 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 360107004280 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 360107004281 Protein of unknown function (DUF511); Region: DUF511; pfam04373 360107004282 KpsF/GutQ family protein; Region: kpsF; TIGR00393 360107004283 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 360107004284 putative active site [active] 360107004285 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 360107004286 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 360107004287 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 360107004288 RNA binding surface [nucleotide binding]; other site 360107004289 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 360107004290 active site 360107004291 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 360107004292 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 360107004293 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 360107004294 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 360107004295 G1 box; other site 360107004296 putative GEF interaction site [polypeptide binding]; other site 360107004297 GTP/Mg2+ binding site [chemical binding]; other site 360107004298 Switch I region; other site 360107004299 G2 box; other site 360107004300 G3 box; other site 360107004301 Switch II region; other site 360107004302 G4 box; other site 360107004303 G5 box; other site 360107004304 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 360107004305 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 360107004306 Predicted permease [General function prediction only]; Region: COG2056 360107004307 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 360107004308 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; cl17322 360107004309 Uncharacterized Staphylococcus aureus AldA1 (SACOL0154) aldehyde dehydrogenase-like; Region: ALDH_StaphAldA1; cd07117 360107004310 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 360107004311 NAD(P) binding site [chemical binding]; other site 360107004312 catalytic residues [active] 360107004313 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 360107004314 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 360107004315 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 360107004316 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 360107004317 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 360107004318 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 360107004319 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 360107004320 active site 360107004321 phosphorylation site [posttranslational modification] 360107004322 intermolecular recognition site; other site 360107004323 dimerization interface [polypeptide binding]; other site 360107004324 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 360107004325 DNA binding site [nucleotide binding] 360107004326 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 360107004327 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 360107004328 dimer interface [polypeptide binding]; other site 360107004329 phosphorylation site [posttranslational modification] 360107004330 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 360107004331 ATP binding site [chemical binding]; other site 360107004332 Mg2+ binding site [ion binding]; other site 360107004333 G-X-G motif; other site 360107004334 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 360107004335 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 360107004336 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 360107004337 Sulfatase; Region: Sulfatase; cl17466 360107004338 Selenophosphate synthase [Amino acid transport and metabolism]; Region: SelD; COG0709 360107004339 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 360107004340 dimerization interface [polypeptide binding]; other site 360107004341 putative ATP binding site [chemical binding]; other site 360107004342 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 360107004343 selenium metabolism protein YedF; Region: selenium_YedF; TIGR03527 360107004344 CPxP motif; other site 360107004345 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 360107004346 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 360107004347 NifU-like domain; Region: NifU; pfam01106 360107004348 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 360107004349 dimer interface [polypeptide binding]; other site 360107004350 catalytic triad [active] 360107004351 peroxidatic and resolving cysteines [active] 360107004352 enolase; Provisional; Region: eno; PRK00077 360107004353 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 360107004354 dimer interface [polypeptide binding]; other site 360107004355 metal binding site [ion binding]; metal-binding site 360107004356 substrate binding pocket [chemical binding]; other site 360107004357 recombinase A; Provisional; Region: recA; PRK09354 360107004358 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 360107004359 hexamer interface [polypeptide binding]; other site 360107004360 Walker A motif; other site 360107004361 ATP binding site [chemical binding]; other site 360107004362 Walker B motif; other site 360107004363 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 360107004364 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 360107004365 active site 360107004366 substrate binding site [chemical binding]; other site 360107004367 metal binding site [ion binding]; metal-binding site 360107004368 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 360107004369 TM2 domain; Region: TM2; pfam05154 360107004370 Short C-terminal domain; Region: SHOCT; pfam09851 360107004371 Isochorismatase family; Region: Isochorismatase; pfam00857 360107004372 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 360107004373 catalytic triad [active] 360107004374 conserved cis-peptide bond; other site 360107004375 Predicted amidohydrolase [General function prediction only]; Region: COG0388 360107004376 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 360107004377 active site 360107004378 catalytic triad [active] 360107004379 dimer interface [polypeptide binding]; other site 360107004380 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 360107004381 active site 360107004382 putative DNA-binding cleft [nucleotide binding]; other site 360107004383 dimer interface [polypeptide binding]; other site