-- dump date 20120504_160707 -- class Genbank::misc_feature -- table misc_feature_note -- id note 392021000001 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 392021000002 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 392021000003 catalytic residues [active] 392021000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 392021000005 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and...; Region: ABC_KpsT_Wzt; cd03220 392021000006 Walker A/P-loop; other site 392021000007 ATP binding site [chemical binding]; other site 392021000008 Q-loop/lid; other site 392021000009 ABC transporter signature motif; other site 392021000010 Walker B; other site 392021000011 D-loop; other site 392021000012 H-loop/switch region; other site 392021000013 ABC-2 type transporter; Region: ABC2_membrane; cl11417 392021000014 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 392021000015 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 392021000016 FAD binding pocket [chemical binding]; other site 392021000017 FAD binding motif [chemical binding]; other site 392021000018 phosphate binding motif [ion binding]; other site 392021000019 beta-alpha-beta structure motif; other site 392021000020 NAD binding pocket [chemical binding]; other site 392021000021 Iron coordination center [ion binding]; other site 392021000022 PemK-like protein; Region: PemK; cl00995 392021000023 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 392021000024 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 392021000025 active site 392021000026 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 392021000027 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 392021000028 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 392021000029 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 392021000030 trimer interface [polypeptide binding]; other site 392021000031 active site 392021000032 UDP-GlcNAc binding site [chemical binding]; other site 392021000033 lipid binding site [chemical binding]; lipid-binding site 392021000034 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 392021000035 active site 392021000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 392021000037 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 392021000038 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 392021000039 FMN binding site [chemical binding]; other site 392021000040 active site 392021000041 catalytic residues [active] 392021000042 substrate binding site [chemical binding]; other site 392021000043 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 392021000044 NodB motif; other site 392021000045 putative active site [active] 392021000046 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 392021000047 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 392021000048 intersubunit interface [polypeptide binding]; other site 392021000049 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 392021000050 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 392021000051 active site 392021000052 NTP binding site [chemical binding]; other site 392021000053 metal binding triad [ion binding]; metal-binding site 392021000054 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 392021000055 Competence protein; Region: Competence; cl00471 392021000056 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein; Reviewed; Region: PRK11907 392021000057 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021000058 AAA domain; Region: AAA_22; pfam13401 392021000059 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 392021000060 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 392021000061 Plant ATP synthase F0; Region: YMF19; cl07975 392021000062 Plant ATP synthase F0; Region: YMF19; cl07975 392021000063 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 392021000064 ATP synthase subunit C; Region: ATP-synt_C; cl00466 392021000065 ATP synthase A chain; Region: ATP-synt_A; cl00413 392021000066 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 392021000067 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 392021000068 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 392021000069 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 392021000070 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 392021000071 S-adenosylmethionine binding site [chemical binding]; other site 392021000072 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 392021000073 recombination protein F; Reviewed; Region: recF; PRK00064 392021000074 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021000075 Walker A/P-loop; other site 392021000076 ATP binding site [chemical binding]; other site 392021000077 Q-loop/lid; other site 392021000078 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021000079 ABC transporter signature motif; other site 392021000080 Walker B; other site 392021000081 D-loop; other site 392021000082 H-loop/switch region; other site 392021000083 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 392021000084 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 392021000085 folate binding site [chemical binding]; other site 392021000086 NADP+ binding site [chemical binding]; other site 392021000087 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 392021000088 catalytic center binding site [active] 392021000089 ATP binding site [chemical binding]; other site 392021000090 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 392021000091 substrate binding pocket [chemical binding]; other site 392021000092 tetratricopeptide repeat protein; Provisional; Region: PRK11788 392021000093 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 392021000094 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 392021000095 Cu(I) binding site [ion binding]; other site 392021000096 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 392021000097 Colicin V production protein; Region: Colicin_V; cl00567 392021000098 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021000099 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 392021000100 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 392021000101 Clp amino terminal domain; Region: Clp_N; pfam02861 392021000102 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 392021000103 Walker A motif; other site 392021000104 ATP binding site [chemical binding]; other site 392021000105 Walker B motif; other site 392021000106 arginine finger; other site 392021000107 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 392021000108 Walker A motif; other site 392021000109 ATP binding site [chemical binding]; other site 392021000110 Walker B motif; other site 392021000111 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 392021000112 UGMP family protein; Validated; Region: PRK09604 392021000113 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 392021000114 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 392021000115 Fatty acid desaturase; Region: FA_desaturase; pfam00487 392021000116 Di-iron ligands [ion binding]; other site 392021000117 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 392021000118 Helix-turn-helix domains; Region: HTH; cl00088 392021000119 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 392021000120 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 392021000121 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 392021000122 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 392021000123 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 392021000124 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 392021000125 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 392021000126 Ligand Binding Site [chemical binding]; other site 392021000127 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000128 FtsH Extracellular; Region: FtsH_ext; pfam06480 392021000129 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 392021000130 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 392021000131 Walker A motif; other site 392021000132 ATP binding site [chemical binding]; other site 392021000133 Walker B motif; other site 392021000134 arginine finger; other site 392021000135 Peptidase family M41; Region: Peptidase_M41; pfam01434 392021000136 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 392021000137 cofactor binding site; other site 392021000138 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 392021000139 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 392021000140 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 392021000141 Uncharacterized conserved protein [Function unknown]; Region: COG1565 392021000142 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 392021000143 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000144 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 392021000145 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 392021000146 Mechanosensitive ion channel; Region: MS_channel; pfam00924 392021000147 membrane protein insertase; Provisional; Region: PRK01318 392021000148 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 392021000149 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 392021000150 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 392021000151 active site 392021000152 catalytic residues [active] 392021000153 metal binding site [ion binding]; metal-binding site 392021000154 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021000155 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 392021000156 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 392021000157 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 392021000158 putative substrate translocation pore; other site 392021000159 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 392021000160 active site 392021000161 multimer interface [polypeptide binding]; other site 392021000162 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 392021000163 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021000164 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 392021000165 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 392021000166 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 392021000167 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 392021000168 P-loop; other site 392021000169 Magnesium ion binding site [ion binding]; other site 392021000170 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 392021000171 Magnesium ion binding site [ion binding]; other site 392021000172 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 392021000173 ParB-like nuclease domain; Region: ParBc; cl02129 392021000174 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 392021000175 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 392021000176 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 392021000177 ABC transporter; Region: ABC_tran_2; pfam12848 392021000178 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 392021000179 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 392021000180 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 392021000181 NeuB family; Region: NeuB; cl00496 392021000182 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 392021000183 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 392021000184 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 392021000185 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 392021000186 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 392021000187 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 392021000188 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 392021000189 active site 392021000190 HIGH motif; other site 392021000191 KMSK motif region; other site 392021000192 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 392021000193 tRNA binding surface [nucleotide binding]; other site 392021000194 anticodon binding site; other site 392021000195 Sporulation related domain; Region: SPOR; cl10051 392021000196 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 392021000197 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 392021000198 CAP-like domain; other site 392021000199 active site 392021000200 primary dimer interface [polypeptide binding]; other site 392021000201 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 392021000202 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 392021000203 trimer interface [polypeptide binding]; other site 392021000204 active site 392021000205 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 392021000206 SecA binding site; other site 392021000207 Preprotein binding site; other site 392021000208 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 392021000209 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 392021000210 active site 392021000211 phosphorylation site [posttranslational modification] 392021000212 intermolecular recognition site; other site 392021000213 dimerization interface [polypeptide binding]; other site 392021000214 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 392021000215 DNA binding site [nucleotide binding] 392021000216 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 392021000217 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 392021000218 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 392021000219 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 392021000220 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 392021000221 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 392021000222 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021000223 EamA-like transporter family; Region: EamA; cl01037 392021000224 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 392021000225 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 392021000226 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021000227 putative substrate translocation pore; other site 392021000228 Preprotein translocase SecG subunit; Region: SecG; cl09123 392021000229 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021000230 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 392021000231 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 392021000232 active site 392021000233 HIGH motif; other site 392021000234 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 392021000235 KMSKS motif; other site 392021000236 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 392021000237 tRNA binding surface [nucleotide binding]; other site 392021000238 anticodon binding site; other site 392021000239 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 392021000240 rRNA interaction site [nucleotide binding]; other site 392021000241 S8 interaction site; other site 392021000242 putative laminin-1 binding site; other site 392021000243 elongation factor Ts; Provisional; Region: tsf; PRK09377 392021000244 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 392021000245 Elongation factor TS; Region: EF_TS; pfam00889 392021000246 Elongation factor TS; Region: EF_TS; pfam00889 392021000247 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 392021000248 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000249 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 392021000250 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 392021000251 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 392021000252 putative acyl-acceptor binding pocket; other site 392021000253 aspartate aminotransferase; Provisional; Region: PRK05764 392021000254 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 392021000255 pyridoxal 5'-phosphate binding site [chemical binding]; other site 392021000256 homodimer interface [polypeptide binding]; other site 392021000257 catalytic residue [active] 392021000258 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 392021000259 Tetratricopeptide repeat; Region: TPR_16; pfam13432 392021000260 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021000261 VacJ like lipoprotein; Region: VacJ; cl01073 392021000262 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 392021000263 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 392021000264 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 392021000265 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 392021000266 active site 392021000267 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000268 alanine racemase; Reviewed; Region: alr; PRK00053 392021000269 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 392021000270 active site 392021000271 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 392021000272 dimer interface [polypeptide binding]; other site 392021000273 substrate binding site [chemical binding]; other site 392021000274 catalytic residues [active] 392021000275 Permease; Region: Permease; cl00510 392021000276 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 392021000277 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021000278 Walker A/P-loop; other site 392021000279 ATP binding site [chemical binding]; other site 392021000280 Q-loop/lid; other site 392021000281 ABC transporter signature motif; other site 392021000282 Walker B; other site 392021000283 D-loop; other site 392021000284 H-loop/switch region; other site 392021000285 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 392021000286 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 392021000287 Predicted GTPase [General function prediction only]; Region: COG0218 392021000288 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 392021000289 G1 box; other site 392021000290 GTP/Mg2+ binding site [chemical binding]; other site 392021000291 Switch I region; other site 392021000292 G2 box; other site 392021000293 G3 box; other site 392021000294 Switch II region; other site 392021000295 G4 box; other site 392021000296 G5 box; other site 392021000297 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 392021000298 nucleotide binding site [chemical binding]; other site 392021000299 substrate binding site [chemical binding]; other site 392021000300 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 392021000301 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 392021000302 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 392021000303 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021000304 Walker A motif; other site 392021000305 ATP binding site [chemical binding]; other site 392021000306 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 392021000307 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 392021000308 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 392021000309 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 392021000310 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 392021000311 aspartyl-tRNA synthetase; Provisional; Region: PTZ00401 392021000312 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 392021000313 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 392021000314 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 392021000315 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 392021000316 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 392021000317 Protein export membrane protein; Region: SecD_SecF; cl14618 392021000318 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 392021000319 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 392021000320 SLBB domain; Region: SLBB; pfam10531 392021000321 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 392021000322 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 392021000323 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 392021000324 Catalytic site [active] 392021000325 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 392021000326 ribonuclease III; Reviewed; Region: rnc; PRK00102 392021000327 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 392021000328 dimerization interface [polypeptide binding]; other site 392021000329 active site 392021000330 metal binding site [ion binding]; metal-binding site 392021000331 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 392021000332 dsRNA binding site [nucleotide binding]; other site 392021000333 GTPase Era; Provisional; Region: era; PRK15494 392021000334 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000335 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 392021000336 G1 box; other site 392021000337 GTP/Mg2+ binding site [chemical binding]; other site 392021000338 Switch I region; other site 392021000339 G2 box; other site 392021000340 Switch II region; other site 392021000341 G3 box; other site 392021000342 G4 box; other site 392021000343 G5 box; other site 392021000344 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 392021000345 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 392021000346 active site 392021000347 putative DNA-binding cleft [nucleotide binding]; other site 392021000348 dimer interface [polypeptide binding]; other site 392021000349 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 392021000350 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 392021000351 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 392021000352 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 392021000353 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 392021000354 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 392021000355 AAA domain; Region: AAA_31; pfam13614 392021000356 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 392021000357 Walker A motif; other site 392021000358 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 392021000359 HflK protein; Region: hflK; TIGR01933 392021000360 FtsH protease regulator HflC; Provisional; Region: PRK11029 392021000361 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 392021000362 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 392021000363 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 392021000364 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 392021000365 protein binding site [polypeptide binding]; other site 392021000366 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 392021000367 protein binding site [polypeptide binding]; other site 392021000368 hypothetical protein; Validated; Region: PRK01415 392021000369 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 392021000370 active site residue [active] 392021000371 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 392021000372 Iron-sulfur protein interface; other site 392021000373 proximal quinone binding site [chemical binding]; other site 392021000374 SdhD (CybS) interface [polypeptide binding]; other site 392021000375 proximal heme binding site [chemical binding]; other site 392021000376 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 392021000377 putative SdhC subunit interface [polypeptide binding]; other site 392021000378 putative proximal heme binding site [chemical binding]; other site 392021000379 putative Iron-sulfur protein interface [polypeptide binding]; other site 392021000380 putative proximal quinone binding site; other site 392021000381 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 392021000382 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021000383 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 392021000384 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 392021000385 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 392021000386 dimer interface [polypeptide binding]; other site 392021000387 conserved gate region; other site 392021000388 putative PBP binding loops; other site 392021000389 ABC-ATPase subunit interface; other site 392021000390 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 392021000391 S17 interaction site [polypeptide binding]; other site 392021000392 S8 interaction site; other site 392021000393 16S rRNA interaction site [nucleotide binding]; other site 392021000394 streptomycin interaction site [chemical binding]; other site 392021000395 23S rRNA interaction site [nucleotide binding]; other site 392021000396 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 392021000397 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 392021000398 elongation factor G; Reviewed; Region: PRK00007 392021000399 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 392021000400 G1 box; other site 392021000401 putative GEF interaction site [polypeptide binding]; other site 392021000402 GTP/Mg2+ binding site [chemical binding]; other site 392021000403 Switch I region; other site 392021000404 G2 box; other site 392021000405 G3 box; other site 392021000406 Switch II region; other site 392021000407 G4 box; other site 392021000408 G5 box; other site 392021000409 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 392021000410 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 392021000411 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 392021000412 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 392021000413 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 392021000414 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 392021000415 putative homodimer interface [polypeptide binding]; other site 392021000416 KOW motif; Region: KOW; cl00354 392021000417 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 392021000418 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 392021000419 23S rRNA interface [nucleotide binding]; other site 392021000420 putative thiostrepton binding site; other site 392021000421 L7/L12 interface [polypeptide binding]; other site 392021000422 L25 interface [polypeptide binding]; other site 392021000423 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 392021000424 mRNA/rRNA interface [nucleotide binding]; other site 392021000425 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 392021000426 23S rRNA interface [nucleotide binding]; other site 392021000427 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 392021000428 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 392021000429 core dimer interface [polypeptide binding]; other site 392021000430 peripheral dimer interface [polypeptide binding]; other site 392021000431 L10 interface [polypeptide binding]; other site 392021000432 L11 interface [polypeptide binding]; other site 392021000433 putative EF-Tu interaction site [polypeptide binding]; other site 392021000434 putative EF-G interaction site [polypeptide binding]; other site 392021000435 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 392021000436 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 392021000437 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 392021000438 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 392021000439 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 392021000440 RPB10 interaction site [polypeptide binding]; other site 392021000441 RPB11 interaction site [polypeptide binding]; other site 392021000442 RPB3 interaction site [polypeptide binding]; other site 392021000443 RPB12 interaction site [polypeptide binding]; other site 392021000444 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 392021000445 RPB3 interaction site [polypeptide binding]; other site 392021000446 RPB1 interaction site [polypeptide binding]; other site 392021000447 RPB11 interaction site [polypeptide binding]; other site 392021000448 RPB10 interaction site [polypeptide binding]; other site 392021000449 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 392021000450 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 392021000451 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 392021000452 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 392021000453 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 392021000454 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 392021000455 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 392021000456 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 392021000457 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 392021000458 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 392021000459 DNA binding site [nucleotide binding] 392021000460 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 392021000461 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000462 multifunctional aminopeptidase A; Provisional; Region: PRK00913 392021000463 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 392021000464 interface (dimer of trimers) [polypeptide binding]; other site 392021000465 Substrate-binding/catalytic site; other site 392021000466 Zn-binding sites [ion binding]; other site 392021000467 ATPase MipZ; Region: MipZ; pfam09140 392021000468 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 392021000469 P-loop; other site 392021000470 Magnesium ion binding site [ion binding]; other site 392021000471 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 392021000472 Magnesium ion binding site [ion binding]; other site 392021000473 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 392021000474 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 392021000475 dimer interface [polypeptide binding]; other site 392021000476 anticodon binding site; other site 392021000477 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 392021000478 homodimer interface [polypeptide binding]; other site 392021000479 motif 1; other site 392021000480 active site 392021000481 motif 2; other site 392021000482 GAD domain; Region: GAD; pfam02938 392021000483 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 attaches...; Region: class_II_aaRS-like_core; cl00268 392021000484 active site 392021000485 motif 3; other site 392021000486 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 392021000487 dihydrodipicolinate reductase; Provisional; Region: PRK00048 392021000488 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021000489 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 392021000490 Flavin Reductases; Region: FlaRed; cl00801 392021000491 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 392021000492 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 392021000493 substrate binding pocket [chemical binding]; other site 392021000494 membrane-bound complex binding site; other site 392021000495 hinge residues; other site 392021000496 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 392021000497 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 392021000498 GatB domain; Region: GatB_Yqey; cl11497 392021000499 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 392021000500 Amidase; Region: Amidase; cl11426 392021000501 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 392021000502 Uncharacterized conserved protein [Function unknown]; Region: COG4997 392021000503 ribosome recycling factor; Reviewed; Region: frr; PRK00083 392021000504 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 392021000505 hinge region; other site 392021000506 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 392021000507 putative nucleotide binding site [chemical binding]; other site 392021000508 uridine monophosphate binding site [chemical binding]; other site 392021000509 homohexameric interface [polypeptide binding]; other site 392021000510 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 392021000511 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 392021000512 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 392021000513 putative substrate translocation pore; other site 392021000514 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 392021000515 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 392021000516 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 392021000517 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 392021000518 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 392021000519 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 392021000520 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 392021000521 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 392021000522 Surface antigen; Region: Bac_surface_Ag; cl03097 392021000523 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 392021000524 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 392021000525 active site 392021000526 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 392021000527 protein binding site [polypeptide binding]; other site 392021000528 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 392021000529 putative substrate binding region [chemical binding]; other site 392021000530 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 392021000531 putative RNA binding site [nucleotide binding]; other site 392021000532 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 392021000533 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 392021000534 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 392021000535 putative coenzyme Q binding site [chemical binding]; other site 392021000536 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000537 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 392021000538 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 392021000539 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 392021000540 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 392021000541 Domain of unknown function (DUF378); Region: DUF378; cl00943 392021000542 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 392021000543 Protein export membrane protein; Region: SecD_SecF; cl14618 392021000544 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 392021000545 IHF dimer interface [polypeptide binding]; other site 392021000546 IHF - DNA interface [nucleotide binding]; other site 392021000547 DNA polymerase III subunit delta'; Validated; Region: PRK06581 392021000548 signal recognition particle protein; Provisional; Region: PRK10867 392021000549 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 392021000550 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 392021000551 P loop; other site 392021000552 GTP binding site [chemical binding]; other site 392021000553 Signal peptide binding domain; Region: SRP_SPB; pfam02978 392021000554 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 392021000555 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 392021000556 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 392021000557 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 392021000558 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 392021000559 FeS/SAM binding site; other site 392021000560 HemN C-terminal domain; Region: HemN_C; pfam06969 392021000561 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 392021000562 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 392021000563 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021000564 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 392021000565 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 392021000566 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 392021000567 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 392021000568 active site 392021000569 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 392021000570 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 392021000571 E3 interaction surface; other site 392021000572 lipoyl attachment site [posttranslational modification]; other site 392021000573 e3 binding domain; Region: E3_binding; pfam02817 392021000574 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 392021000575 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 392021000576 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 392021000577 TPP-binding site [chemical binding]; other site 392021000578 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 392021000579 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 392021000580 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 392021000581 active site 392021000582 Zn binding site [ion binding]; other site 392021000583 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 392021000584 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 392021000585 Walker A/P-loop; other site 392021000586 ATP binding site [chemical binding]; other site 392021000587 Q-loop/lid; other site 392021000588 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 392021000589 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 392021000590 ABC transporter signature motif; other site 392021000591 Walker B; other site 392021000592 D-loop; other site 392021000593 H-loop/switch region; other site 392021000594 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 392021000595 Tetratricopeptide repeat; Region: TPR_6; pfam13174 392021000596 ChaB; Region: ChaB; cl01887 392021000597 ChaB; Region: ChaB; cl01887 392021000598 chaperone protein DnaJ; Provisional; Region: PRK14300 392021000599 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 392021000600 HSP70 interaction site [polypeptide binding]; other site 392021000601 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 392021000602 substrate binding site [polypeptide binding]; other site 392021000603 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 392021000604 Zn binding sites [ion binding]; other site 392021000605 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 392021000606 dimer interface [polypeptide binding]; other site 392021000607 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 392021000608 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 392021000609 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 392021000610 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 392021000611 Lipopolysaccharide-assembly; Region: LptE; cl01125 392021000612 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 392021000613 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 392021000614 diiron binding motif [ion binding]; other site 392021000615 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 392021000616 Subunit III/VIIa interface [polypeptide binding]; other site 392021000617 Phospholipid binding site [chemical binding]; other site 392021000618 Subunit I/III interface [polypeptide binding]; other site 392021000619 Subunit III/VIb interface [polypeptide binding]; other site 392021000620 Subunit III/VIa interface; other site 392021000621 Subunit III/Vb interface [polypeptide binding]; other site 392021000622 TrbC/VIRB2 family; Region: TrbC; cl01583 392021000623 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 392021000624 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 392021000625 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 392021000626 trimer interface [polypeptide binding]; other site 392021000627 active site 392021000628 substrate binding site [chemical binding]; other site 392021000629 CoA binding site [chemical binding]; other site 392021000630 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 392021000631 Ligand Binding Site [chemical binding]; other site 392021000632 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 392021000633 NMT1-like family; Region: NMT1_2; cl15260 392021000634 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 392021000635 catalytic loop [active] 392021000636 iron binding site [ion binding]; other site 392021000637 chaperone protein HscA; Provisional; Region: hscA; PRK01433 392021000638 co-chaperone HscB; Provisional; Region: hscB; PRK01356 392021000639 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 392021000640 HSP70 interaction site [polypeptide binding]; other site 392021000641 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 392021000642 RNA/DNA hybrid binding site [nucleotide binding]; other site 392021000643 active site 392021000644 excinuclease ABC subunit B; Provisional; Region: PRK05298 392021000645 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 392021000646 ATP binding site [chemical binding]; other site 392021000647 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 392021000648 nucleotide binding region [chemical binding]; other site 392021000649 ATP-binding site [chemical binding]; other site 392021000650 Ultra-violet resistance protein B; Region: UvrB; pfam12344 392021000651 UvrB/uvrC motif; Region: UVR; pfam02151 392021000652 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 392021000653 GSH binding site [chemical binding]; other site 392021000654 catalytic residues [active] 392021000655 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 392021000656 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021000657 Walker A/P-loop; other site 392021000658 ATP binding site [chemical binding]; other site 392021000659 Q-loop/lid; other site 392021000660 DNA gyrase subunit A; Validated; Region: PRK05560 392021000661 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 392021000662 CAP-like domain; other site 392021000663 active site 392021000664 primary dimer interface [polypeptide binding]; other site 392021000665 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000666 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000667 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000668 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000669 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000670 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 392021000671 active site 392021000672 catalytic residues [active] 392021000673 metal binding site [ion binding]; metal-binding site 392021000674 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 392021000675 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 392021000676 putative active site [active] 392021000677 substrate binding site [chemical binding]; other site 392021000678 putative cosubstrate binding site; other site 392021000679 catalytic site [active] 392021000680 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 392021000681 substrate binding site [chemical binding]; other site 392021000682 Protein of unknown function (DUF563); Region: DUF563; cl15705 392021000683 Predicted ATPase [General function prediction only]; Region: COG1485 392021000684 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 392021000685 Walker A motif; other site 392021000686 ATP binding site [chemical binding]; other site 392021000687 Walker B motif; other site 392021000688 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 392021000689 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 392021000690 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 392021000691 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 392021000692 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 392021000693 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 392021000694 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021000695 Walker A/P-loop; other site 392021000696 ATP binding site [chemical binding]; other site 392021000697 Q-loop/lid; other site 392021000698 ABC transporter signature motif; other site 392021000699 Walker B; other site 392021000700 D-loop; other site 392021000701 H-loop/switch region; other site 392021000702 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 392021000703 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 392021000704 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 392021000705 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 392021000706 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 392021000707 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 392021000708 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 392021000709 putative metal binding site; other site 392021000710 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 392021000711 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 392021000712 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 392021000713 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 392021000714 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 392021000715 ATP binding site [chemical binding]; other site 392021000716 active site 392021000717 substrate binding site [chemical binding]; other site 392021000718 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 392021000719 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 392021000720 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 392021000721 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 392021000722 active site 392021000723 dimer interface [polypeptide binding]; other site 392021000724 motif 1; other site 392021000725 motif 2; other site 392021000726 motif 3; other site 392021000727 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 392021000728 anticodon binding site; other site 392021000729 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021000730 Walker A/P-loop; other site 392021000731 ATP binding site [chemical binding]; other site 392021000732 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 392021000733 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated; Region: PRK04028 392021000734 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 392021000735 Protein of unknown function (DUF2497); Region: DUF2497; cl11534 392021000736 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 392021000737 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 392021000738 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 392021000739 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 392021000740 ATP binding site [chemical binding]; other site 392021000741 Mg2+ binding site [ion binding]; other site 392021000742 G-X-G motif; other site 392021000743 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 392021000744 anchoring element; other site 392021000745 dimer interface [polypeptide binding]; other site 392021000746 ATP binding site [chemical binding]; other site 392021000747 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 392021000748 active site 392021000749 metal binding site [ion binding]; metal-binding site 392021000750 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 392021000751 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 392021000752 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 392021000753 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 392021000754 protein binding site [polypeptide binding]; other site 392021000755 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 392021000756 Catalytic dyad [active] 392021000757 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 392021000758 dimer interface [polypeptide binding]; other site 392021000759 phosphorylation site [posttranslational modification] 392021000760 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 392021000761 ATP binding site [chemical binding]; other site 392021000762 Mg2+ binding site [ion binding]; other site 392021000763 G-X-G motif; other site 392021000764 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 392021000765 Tetratricopeptide repeat; Region: TPR_6; pfam13174 392021000766 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 392021000767 FOG: WD40-like repeat [Function unknown]; Region: COG1520 392021000768 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 392021000769 Trp docking motif [polypeptide binding]; other site 392021000770 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 392021000771 23S rRNA interface [nucleotide binding]; other site 392021000772 L3 interface [polypeptide binding]; other site 392021000773 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 392021000774 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cl00942 392021000775 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 392021000776 DCoH tetramer interaction site [polypeptide binding]; other site 392021000777 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 392021000778 putative active site [active] 392021000779 Ap4A binding site [chemical binding]; other site 392021000780 nudix motif; other site 392021000781 putative metal binding site [ion binding]; other site 392021000782 elongation factor P; Validated; Region: PRK00529 392021000783 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 392021000784 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 392021000785 RNA binding site [nucleotide binding]; other site 392021000786 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 392021000787 RNA binding site [nucleotide binding]; other site 392021000788 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1; Region: IMPase_like; cd01637 392021000789 active site 392021000790 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 392021000791 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 392021000792 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 392021000793 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 392021000794 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 392021000795 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 392021000796 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 392021000797 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021000798 BolA-like protein; Region: BolA; cl00386 392021000799 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 392021000800 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 392021000801 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 392021000802 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 392021000803 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 392021000804 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 392021000805 FAD binding domain; Region: FAD_binding_4; pfam01565 392021000806 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 392021000807 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 392021000808 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 392021000809 ATP-grasp domain; Region: ATP-grasp_4; cl03087 392021000810 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 392021000811 Cell division protein FtsQ; Region: FtsQ; pfam03799 392021000812 cell division protein FtsA; Region: ftsA; TIGR01174 392021000813 Cell division protein FtsA; Region: FtsA; cl11496 392021000814 Cell division protein FtsA; Region: FtsA; cl11496 392021000815 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 392021000816 Cytochrome c; Region: Cytochrom_C; cl11414 392021000817 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 392021000818 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 392021000819 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 392021000820 RNA binding site [nucleotide binding]; other site 392021000821 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 392021000822 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 392021000823 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 392021000824 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 392021000825 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 392021000826 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 392021000827 RNA binding surface [nucleotide binding]; other site 392021000828 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 392021000829 active site 392021000830 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 392021000831 putative phosphate binding site [ion binding]; other site 392021000832 putative catalytic site [active] 392021000833 active site 392021000834 metal binding site A [ion binding]; metal-binding site 392021000835 DNA binding site [nucleotide binding] 392021000836 putative AP binding site [nucleotide binding]; other site 392021000837 putative metal binding site B [ion binding]; other site 392021000838 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 392021000839 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 392021000840 tetramer interface [polypeptide binding]; other site 392021000841 TPP-binding site [chemical binding]; other site 392021000842 heterodimer interface [polypeptide binding]; other site 392021000843 phosphorylation loop region [posttranslational modification] 392021000844 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 392021000845 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 392021000846 alpha subunit interface [polypeptide binding]; other site 392021000847 TPP binding site [chemical binding]; other site 392021000848 heterodimer interface [polypeptide binding]; other site 392021000849 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 392021000850 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 392021000851 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 392021000852 G1 box; other site 392021000853 putative GEF interaction site [polypeptide binding]; other site 392021000854 GTP/Mg2+ binding site [chemical binding]; other site 392021000855 Switch I region; other site 392021000856 G2 box; other site 392021000857 G3 box; other site 392021000858 Switch II region; other site 392021000859 G4 box; other site 392021000860 G5 box; other site 392021000861 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 392021000862 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 392021000863 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 392021000864 isocitrate dehydrogenase; Validated; Region: PRK09222 392021000865 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 392021000866 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 392021000867 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 392021000868 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 392021000869 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 392021000870 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 392021000871 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 392021000872 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 392021000873 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 392021000874 [2Fe-2S] cluster binding site [ion binding]; other site 392021000875 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 392021000876 Qi binding site; other site 392021000877 cytochrome b; Provisional; Region: CYTB; MTH00191 392021000878 intrachain domain interface; other site 392021000879 interchain domain interface [polypeptide binding]; other site 392021000880 heme bH binding site [chemical binding]; other site 392021000881 heme bL binding site [chemical binding]; other site 392021000882 Qo binding site; other site 392021000883 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 392021000884 interchain domain interface [polypeptide binding]; other site 392021000885 intrachain domain interface; other site 392021000886 Qi binding site; other site 392021000887 Qo binding site; other site 392021000888 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 392021000889 catalytic site [active] 392021000890 metal binding site [ion binding]; metal-binding site 392021000891 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 392021000892 Cytochrome c; Region: Cytochrom_C; cl11414 392021000893 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 392021000894 putative dimer interface [polypeptide binding]; other site 392021000895 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 392021000896 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 392021000897 RF-1 domain; Region: RF-1; cl02875 392021000898 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 392021000899 RF-1 domain; Region: RF-1; cl02875 392021000900 GTP-binding protein LepA; Provisional; Region: PRK05433 392021000901 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 392021000902 G1 box; other site 392021000903 putative GEF interaction site [polypeptide binding]; other site 392021000904 GTP/Mg2+ binding site [chemical binding]; other site 392021000905 Switch I region; other site 392021000906 G2 box; other site 392021000907 G3 box; other site 392021000908 Switch II region; other site 392021000909 G4 box; other site 392021000910 G5 box; other site 392021000911 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 392021000912 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 392021000913 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 392021000914 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 392021000915 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021000916 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 392021000917 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 392021000918 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021000919 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 392021000920 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 392021000921 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 392021000922 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 392021000923 oligomeric interface; other site 392021000924 putative active site [active] 392021000925 homodimer interface [polypeptide binding]; other site 392021000926 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 392021000927 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 392021000928 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 392021000929 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 392021000930 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 392021000931 VirB7 interaction site; other site 392021000932 VirB8 protein; Region: VirB8; cl01500 392021000933 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 392021000934 VirB8 protein; Region: VirB8; cl01500 392021000935 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 392021000936 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 392021000937 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 392021000938 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 392021000939 Walker A motif; other site 392021000940 hexamer interface [polypeptide binding]; other site 392021000941 ATP binding site [chemical binding]; other site 392021000942 Walker B motif; other site 392021000943 type IV secretion system component VirD4; Provisional; Region: PRK13897 392021000944 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 392021000945 Walker A motif; other site 392021000946 ATP binding site [chemical binding]; other site 392021000947 Walker B motif; other site 392021000948 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 392021000949 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 392021000950 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 392021000951 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 392021000952 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 392021000953 active site 392021000954 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 392021000955 MutS domain I; Region: MutS_I; pfam01624 392021000956 MutS domain II; Region: MutS_II; pfam05188 392021000957 MutS family domain IV; Region: MutS_IV; pfam05190 392021000958 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 392021000959 Walker A/P-loop; other site 392021000960 ATP binding site [chemical binding]; other site 392021000961 Q-loop/lid; other site 392021000962 ABC transporter signature motif; other site 392021000963 Walker B; other site 392021000964 D-loop; other site 392021000965 H-loop/switch region; other site 392021000966 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 392021000967 Peptidase family M23; Region: Peptidase_M23; pfam01551 392021000968 Protein of unknown function DUF45; Region: DUF45; cl00636 392021000969 Thymidylate synthase complementing protein; Region: Thy1; cl03630 392021000970 translocation protein TolB; Provisional; Region: tolB; PRK05137 392021000971 TolB amino-terminal domain; Region: TolB_N; cl00639 392021000972 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 392021000973 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 392021000974 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 392021000975 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 392021000976 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 392021000977 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 392021000978 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 392021000979 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 392021000980 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 392021000981 Ligand Binding Site [chemical binding]; other site 392021000982 amino acid transporter; Region: 2A0306; TIGR00909 392021000983 Spore germination protein; Region: Spore_permease; cl15802 392021000984 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 392021000985 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 392021000986 dimer interface [polypeptide binding]; other site 392021000987 motif 1; other site 392021000988 active site 392021000989 motif 2; other site 392021000990 motif 3; other site 392021000991 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 392021000992 anticodon binding site; other site 392021000993 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 392021000994 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 392021000995 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 392021000996 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 392021000997 Gram-negative bacterial tonB protein; Region: TonB; cl10048 392021000998 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 392021000999 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 392021001000 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021001001 putative substrate translocation pore; other site 392021001002 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 392021001003 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 392021001004 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 392021001005 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 392021001006 This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export...; Region: ABCC_Protease_Secretion; cd03246 392021001007 Walker A/P-loop; other site 392021001008 ATP binding site [chemical binding]; other site 392021001009 Q-loop/lid; other site 392021001010 ABC transporter signature motif; other site 392021001011 Walker B; other site 392021001012 D-loop; other site 392021001013 H-loop/switch region; other site 392021001014 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 392021001015 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001016 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 392021001017 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 392021001018 nucleotide binding site/active site [active] 392021001019 HIT family signature motif; other site 392021001020 catalytic residue [active] 392021001021 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 392021001022 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 392021001023 active site 392021001024 HslU subunit interaction site [polypeptide binding]; other site 392021001025 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 392021001026 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 392021001027 Walker A motif; other site 392021001028 ATP binding site [chemical binding]; other site 392021001029 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021001030 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 392021001031 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021001032 Uncharacterized conserved protein [Function unknown]; Region: COG5464 392021001033 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021001034 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 392021001035 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 392021001036 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021001037 YceG-like family; Region: YceG; pfam02618 392021001038 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 392021001039 dimerization interface [polypeptide binding]; other site 392021001040 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 392021001041 putative iron binding site [ion binding]; other site 392021001042 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 392021001043 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 392021001044 HIGH motif; other site 392021001045 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021001046 active site 392021001047 KMSKS motif; other site 392021001048 DNA topoisomerase I; Validated; Region: PRK06599 392021001049 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 392021001050 active site 392021001051 interdomain interaction site; other site 392021001052 putative metal-binding site [ion binding]; other site 392021001053 nucleotide binding site [chemical binding]; other site 392021001054 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 392021001055 domain I; other site 392021001056 DNA binding groove [nucleotide binding] 392021001057 phosphate binding site [ion binding]; other site 392021001058 domain II; other site 392021001059 domain III; other site 392021001060 nucleotide binding site [chemical binding]; other site 392021001061 catalytic site [active] 392021001062 domain IV; other site 392021001063 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 392021001064 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]; Region: COG1754 392021001065 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 392021001066 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 392021001067 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 392021001068 dimer interface [polypeptide binding]; other site 392021001069 decamer (pentamer of dimers) interface [polypeptide binding]; other site 392021001070 catalytic triad [active] 392021001071 peroxidatic and resolving cysteines [active] 392021001072 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 392021001073 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 392021001074 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 392021001075 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 392021001076 Sulfatase; Region: Sulfatase; cl10460 392021001077 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 392021001078 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 392021001079 sequence-specific DNA binding site [nucleotide binding]; other site 392021001080 salt bridge; other site 392021001081 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 392021001082 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 392021001083 NADP binding site [chemical binding]; other site 392021001084 active site 392021001085 putative substrate binding site [chemical binding]; other site 392021001086 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 392021001087 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 392021001088 NAD(P) binding site [chemical binding]; other site 392021001089 homodimer interface [polypeptide binding]; other site 392021001090 substrate binding site [chemical binding]; other site 392021001091 active site 392021001092 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 392021001093 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 392021001094 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 392021001095 active site 392021001096 homodimer interface [polypeptide binding]; other site 392021001097 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 392021001098 S-adenosylmethionine binding site [chemical binding]; other site 392021001099 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 392021001100 active site 392021001101 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 392021001102 active site 392021001103 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 392021001104 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 392021001105 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 392021001106 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 392021001107 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 392021001108 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 392021001109 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 392021001110 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 392021001111 putative ADP-binding pocket [chemical binding]; other site 392021001112 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021001113 Walker A/P-loop; other site 392021001114 ATP binding site [chemical binding]; other site 392021001115 Q-loop/lid; other site 392021001116 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 392021001117 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 392021001118 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 392021001119 RNA binding surface [nucleotide binding]; other site 392021001120 UbiA prenyltransferase family; Region: UbiA; cl00337 392021001121 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 392021001122 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 392021001123 TPR repeat; Region: TPR_11; pfam13414 392021001124 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 392021001125 TPR motif; other site 392021001126 binding surface 392021001127 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 392021001128 AsmA-like C-terminal region; Region: AsmA_2; cl15864 392021001129 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 392021001130 RimM N-terminal domain; Region: RimM; pfam01782 392021001131 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 392021001132 AsmA-like C-terminal region; Region: AsmA_2; cl15864 392021001133 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 392021001134 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 392021001135 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 392021001136 active site 392021001137 DNA binding site [nucleotide binding] 392021001138 YCII-related domain; Region: YCII; cl00999 392021001139 Haemolytic domain; Region: Haemolytic; cl00506 392021001140 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 392021001141 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 392021001142 putative dimer interface [polypeptide binding]; other site 392021001143 [2Fe-2S] cluster binding site [ion binding]; other site 392021001144 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 392021001145 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 392021001146 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 392021001147 NADH dehydrogenase subunit B; Provisional; Region: PRK14816 392021001148 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 392021001149 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 392021001150 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 392021001151 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; cl01970 392021001152 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 392021001153 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 392021001154 DNA binding site [nucleotide binding] 392021001155 Int/Topo IB signature motif; other site 392021001156 active site 392021001157 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 392021001158 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 392021001159 NAD binding site [chemical binding]; other site 392021001160 homotetramer interface [polypeptide binding]; other site 392021001161 homodimer interface [polypeptide binding]; other site 392021001162 substrate binding site [chemical binding]; other site 392021001163 active site 392021001164 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 392021001165 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 392021001166 putative active site [active] 392021001167 catalytic triad [active] 392021001168 putative dimer interface [polypeptide binding]; other site 392021001169 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 392021001170 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 392021001171 amidase catalytic site [active] 392021001172 Zn binding residues [ion binding]; other site 392021001173 substrate binding site [chemical binding]; other site 392021001174 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 392021001175 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 392021001176 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 392021001177 TM-ABC transporter signature motif; other site 392021001178 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 392021001179 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 392021001180 Walker A/P-loop; other site 392021001181 ATP binding site [chemical binding]; other site 392021001182 Q-loop/lid; other site 392021001183 ABC transporter signature motif; other site 392021001184 Walker B; other site 392021001185 D-loop; other site 392021001186 H-loop/switch region; other site 392021001187 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 392021001188 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 392021001189 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 392021001190 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 392021001191 active site 392021001192 HIGH motif; other site 392021001193 KMSKS motif; other site 392021001194 Membrane transport protein; Region: Mem_trans; cl09117 392021001195 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 392021001196 Malic enzyme, N-terminal domain; Region: malic; pfam00390 392021001197 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 392021001198 putative NAD(P) binding site [chemical binding]; other site 392021001199 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 392021001200 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 392021001201 putative active site [active] 392021001202 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 392021001203 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021001204 malate dehydrogenase; Reviewed; Region: PRK06223 392021001205 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 392021001206 NAD(P) binding site [chemical binding]; other site 392021001207 dimer interface [polypeptide binding]; other site 392021001208 tetramer (dimer of dimers) interface [polypeptide binding]; other site 392021001209 substrate binding site [chemical binding]; other site 392021001210 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 392021001211 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 392021001212 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021001213 CTP synthetase; Validated; Region: pyrG; PRK05380 392021001214 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 392021001215 Catalytic site [active] 392021001216 active site 392021001217 UTP binding site [chemical binding]; other site 392021001218 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 392021001219 active site 392021001220 putative oxyanion hole; other site 392021001221 catalytic triad [active] 392021001222 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 392021001223 Ligand binding site; other site 392021001224 oligomer interface; other site 392021001225 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 392021001226 GTP cyclohydrolase I; Provisional; Region: PLN03044 392021001227 active site 392021001228 prolyl-tRNA synthetase; Provisional; Region: PRK12325 392021001229 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_prok; cd00779 392021001230 dimer interface [polypeptide binding]; other site 392021001231 motif 1; other site 392021001232 active site 392021001233 motif 2; other site 392021001234 motif 3; other site 392021001235 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 392021001236 anticodon binding site; other site 392021001237 Fic family protein [Function unknown]; Region: COG3177 392021001238 Fic/DOC family; Region: Fic; cl00960 392021001239 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 392021001240 RuvA N terminal domain; Region: RuvA_N; pfam01330 392021001241 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 392021001242 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 392021001243 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 392021001244 Walker A motif; other site 392021001245 ATP binding site [chemical binding]; other site 392021001246 Walker B motif; other site 392021001247 arginine finger; other site 392021001248 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 392021001249 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 392021001250 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 392021001251 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 392021001252 Walker A/P-loop; other site 392021001253 ATP binding site [chemical binding]; other site 392021001254 Q-loop/lid; other site 392021001255 ABC transporter signature motif; other site 392021001256 Walker B; other site 392021001257 D-loop; other site 392021001258 H-loop/switch region; other site 392021001259 muropeptide transporter; Validated; Region: ampG; PRK11010 392021001260 muropeptide transporter; Reviewed; Region: ampG; PRK11902 392021001261 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 392021001262 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 392021001263 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001264 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 392021001265 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 392021001266 BON domain; Region: BON; cl02771 392021001267 BON domain; Region: BON; cl02771 392021001268 Intracellular septation protein A; Region: IspA; cl01098 392021001269 Iron permease FTR1 family; Region: FTR1; cl00475 392021001270 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 392021001271 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 392021001272 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 392021001273 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 392021001274 active site 392021001275 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 392021001276 catalytic residues [active] 392021001277 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 392021001278 tandem repeat interface [polypeptide binding]; other site 392021001279 oligomer interface [polypeptide binding]; other site 392021001280 active site residues [active] 392021001281 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 392021001282 trimer interface [polypeptide binding]; other site 392021001283 active site 392021001284 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 392021001285 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 392021001286 N-acetyl-D-glucosamine binding site [chemical binding]; other site 392021001287 catalytic residue [active] 392021001288 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 392021001289 dimer interface [polypeptide binding]; other site 392021001290 catalytic triad [active] 392021001291 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 392021001292 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 392021001293 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 392021001294 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 392021001295 catalytic triad [active] 392021001296 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 392021001297 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 392021001298 Subunit I/III interface [polypeptide binding]; other site 392021001299 D-pathway; other site 392021001300 Subunit I/VIIc interface [polypeptide binding]; other site 392021001301 Subunit I/IV interface [polypeptide binding]; other site 392021001302 Subunit I/II interface [polypeptide binding]; other site 392021001303 Low-spin heme (heme a) binding site [chemical binding]; other site 392021001304 Subunit I/VIIa interface [polypeptide binding]; other site 392021001305 Subunit I/VIa interface [polypeptide binding]; other site 392021001306 Dimer interface; other site 392021001307 Putative water exit pathway; other site 392021001308 Binuclear center (heme a3/CuB) [ion binding]; other site 392021001309 K-pathway; other site 392021001310 Subunit I/Vb interface [polypeptide binding]; other site 392021001311 Putative proton exit pathway; other site 392021001312 Subunit I/VIb interface; other site 392021001313 Subunit I/VIc interface [polypeptide binding]; other site 392021001314 Electron transfer pathway; other site 392021001315 Subunit I/VIIIb interface [polypeptide binding]; other site 392021001316 Subunit I/VIIb interface [polypeptide binding]; other site 392021001317 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 392021001318 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 392021001319 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001320 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 392021001321 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 392021001322 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 392021001323 putative peptidase; Provisional; Region: PRK11649 392021001324 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 392021001325 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 392021001326 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 392021001327 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 392021001328 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021001329 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 392021001330 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 392021001331 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 392021001332 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 392021001333 active site 392021001334 homodimer interface [polypeptide binding]; other site 392021001335 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 392021001336 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 392021001337 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 392021001338 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 392021001339 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 392021001340 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 392021001341 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021001342 diaminopimelate epimerase; Region: DapF; TIGR00652 392021001343 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 392021001344 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 392021001345 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 392021001346 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 392021001347 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 392021001348 FeS/SAM binding site; other site 392021001349 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 392021001350 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 392021001351 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 392021001352 dimer interface [polypeptide binding]; other site 392021001353 motif 1; other site 392021001354 active site 392021001355 motif 2; other site 392021001356 motif 3; other site 392021001357 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 392021001358 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 392021001359 putative tRNA-binding site [nucleotide binding]; other site 392021001360 B3/4 domain; Region: B3_4; cl11458 392021001361 tRNA synthetase B5 domain; Region: B5; cl08394 392021001362 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an...; Region: PheRS_beta_core; cd00769 392021001363 dimer interface [polypeptide binding]; other site 392021001364 motif 1; other site 392021001365 motif 3; other site 392021001366 motif 2; other site 392021001367 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 392021001368 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 392021001369 DNA polymerase III subunit beta; Validated; Region: PRK05643 392021001370 putative DNA binding surface [nucleotide binding]; other site 392021001371 dimer interface [polypeptide binding]; other site 392021001372 beta-clamp/clamp loader binding surface; other site 392021001373 beta-clamp/translesion DNA polymerase binding surface; other site 392021001374 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 392021001375 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 392021001376 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 392021001377 HIGH motif; other site 392021001378 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 392021001379 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021001380 active site 392021001381 KMSKS motif; other site 392021001382 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 392021001383 tRNA binding surface [nucleotide binding]; other site 392021001384 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 392021001385 putative active site [active] 392021001386 catalytic site [active] 392021001387 putative substrate binding site [chemical binding]; other site 392021001388 Septum formation initiator; Region: DivIC; cl11433 392021001389 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 392021001390 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 392021001391 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 392021001392 catalytic residue [active] 392021001393 putative FPP diphosphate binding site; other site 392021001394 putative FPP binding hydrophobic cleft; other site 392021001395 dimer interface [polypeptide binding]; other site 392021001396 putative IPP diphosphate binding site; other site 392021001397 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021001398 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 392021001399 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 392021001400 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 392021001401 ATP binding site [chemical binding]; other site 392021001402 Mg2+ binding site [ion binding]; other site 392021001403 G-X-G motif; other site 392021001404 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 392021001405 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 392021001406 active site 392021001407 phosphorylation site [posttranslational modification] 392021001408 intermolecular recognition site; other site 392021001409 dimerization interface [polypeptide binding]; other site 392021001410 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 392021001411 DNA binding site [nucleotide binding] 392021001412 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 392021001413 homodimer interface [polypeptide binding]; other site 392021001414 substrate-cofactor binding pocket; other site 392021001415 catalytic residue [active] 392021001416 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 392021001417 dihydrodipicolinate synthase; Region: dapA; TIGR00674 392021001418 dimer interface [polypeptide binding]; other site 392021001419 active site 392021001420 catalytic residue [active] 392021001421 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 392021001422 SmpB-tmRNA interface; other site 392021001423 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 392021001424 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 392021001425 catalytic residues [active] 392021001426 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 392021001427 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001428 CoA-ligase; Region: Ligase_CoA; cl02894 392021001429 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 392021001430 ATP-grasp domain; Region: ATP-grasp_4; cl03087 392021001431 CoA-ligase; Region: Ligase_CoA; cl02894 392021001432 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 392021001433 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 392021001434 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 392021001435 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 392021001436 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 392021001437 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 392021001438 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 392021001439 substrate binding pocket [chemical binding]; other site 392021001440 catalytic triad [active] 392021001441 Tim44-like domain; Region: Tim44; cl09208 392021001442 OpgC protein; Region: OpgC_C; cl00792 392021001443 Ribosome-binding factor A; Region: RBFA; cl00542 392021001444 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 392021001445 RDD family; Region: RDD; cl00746 392021001446 recombination protein RecR; Reviewed; Region: recR; PRK00076 392021001447 RecR protein; Region: RecR; pfam02132 392021001448 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 392021001449 putative active site [active] 392021001450 putative metal-binding site [ion binding]; other site 392021001451 tetramer interface [polypeptide binding]; other site 392021001452 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 392021001453 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 392021001454 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 392021001455 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 392021001456 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 392021001457 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001458 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 392021001459 Membrane transport protein; Region: Mem_trans; cl09117 392021001460 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 392021001461 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 392021001462 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 392021001463 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 392021001464 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 392021001465 tetramerization interface [polypeptide binding]; other site 392021001466 NAD(P) binding site [chemical binding]; other site 392021001467 catalytic residues [active] 392021001468 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 392021001469 active site 392021001470 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 392021001471 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021001472 Family description; Region: UvrD_C_2; cl15862 392021001473 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 392021001474 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 392021001475 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 392021001476 tetramer interface [polypeptide binding]; other site 392021001477 pyridoxal 5'-phosphate binding site [chemical binding]; other site 392021001478 catalytic residue [active] 392021001479 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 392021001480 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 392021001481 Walker A motif; other site 392021001482 ATP binding site [chemical binding]; other site 392021001483 Walker B motif; other site 392021001484 arginine finger; other site 392021001485 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 392021001486 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 392021001487 30S subunit binding site; other site 392021001488 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 392021001489 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 392021001490 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 392021001491 homodimer interface [polypeptide binding]; other site 392021001492 NADP binding site [chemical binding]; other site 392021001493 substrate binding site [chemical binding]; other site 392021001494 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 392021001495 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001496 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 392021001497 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 392021001498 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 392021001499 Spore Coat Protein U domain; Region: SCPU; cl02253 392021001500 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 392021001501 Class I ribonucleotide reductase; Region: RNR_I; cd01679 392021001502 active site 392021001503 dimer interface [polypeptide binding]; other site 392021001504 catalytic residues [active] 392021001505 effector binding site; other site 392021001506 R2 peptide binding site; other site 392021001507 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 392021001508 dimer interface [polypeptide binding]; other site 392021001509 putative radical transfer pathway; other site 392021001510 diiron center [ion binding]; other site 392021001511 tyrosyl radical; other site 392021001512 similar to hypothetical protein 392021001513 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021001514 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 392021001515 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 392021001516 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 392021001517 active site 392021001518 substrate binding site [chemical binding]; other site 392021001519 metal binding site [ion binding]; metal-binding site 392021001520 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 392021001521 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 392021001522 Walker A/P-loop; other site 392021001523 ATP binding site [chemical binding]; other site 392021001524 Q-loop/lid; other site 392021001525 ABC transporter signature motif; other site 392021001526 Walker B; other site 392021001527 D-loop; other site 392021001528 H-loop/switch region; other site 392021001529 OstA-like protein; Region: OstA; cl00844 392021001530 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 392021001531 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 392021001532 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 392021001533 putative active site [active] 392021001534 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 392021001535 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 392021001536 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 392021001537 RNase E interface [polypeptide binding]; other site 392021001538 trimer interface [polypeptide binding]; other site 392021001539 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 392021001540 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 392021001541 RNase E interface [polypeptide binding]; other site 392021001542 trimer interface [polypeptide binding]; other site 392021001543 active site 392021001544 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 392021001545 putative nucleic acid binding region [nucleotide binding]; other site 392021001546 G-X-X-G motif; other site 392021001547 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 392021001548 RNA binding site [nucleotide binding]; other site 392021001549 domain interface; other site 392021001550 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 392021001551 16S/18S rRNA binding site [nucleotide binding]; other site 392021001552 S13e-L30e interaction site [polypeptide binding]; other site 392021001553 25S rRNA binding site [nucleotide binding]; other site 392021001554 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 392021001555 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 392021001556 RNA binding site [nucleotide binding]; other site 392021001557 active site 392021001558 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001559 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 392021001560 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021001561 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 392021001562 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 392021001563 non-specific DNA binding site [nucleotide binding]; other site 392021001564 salt bridge; other site 392021001565 sequence-specific DNA binding site [nucleotide binding]; other site 392021001566 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 392021001567 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 392021001568 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 392021001569 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 392021001570 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; cl00234 392021001571 catalytic residues [active] 392021001572 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 392021001573 putative active site [active] 392021001574 homotetrameric interface [polypeptide binding]; other site 392021001575 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 392021001576 intersubunit interface [polypeptide binding]; other site 392021001577 active site 392021001578 Zn2+ binding site [ion binding]; other site 392021001579 pyruvate phosphate dikinase; Provisional; Region: PRK09279 392021001580 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 392021001581 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 392021001582 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 392021001583 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 392021001584 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 392021001585 GSH binding site (G-site) [chemical binding]; other site 392021001586 C-terminal domain interface [polypeptide binding]; other site 392021001587 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 392021001588 N-terminal domain interface [polypeptide binding]; other site 392021001589 dimer interface [polypeptide binding]; other site 392021001590 substrate binding pocket (H-site) [chemical binding]; other site 392021001591 Uncharacterized conserved protein [Function unknown]; Region: COG4285 392021001592 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 392021001593 conserved cys residue [active] 392021001594 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 392021001595 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 392021001596 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 392021001597 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 392021001598 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 392021001599 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 392021001600 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 392021001601 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 392021001602 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 392021001603 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 392021001604 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 392021001605 Predicted membrane protein (DUF2335); Region: DUF2335; cl02210 392021001606 translation initiation factor IF-3; Region: infC; TIGR00168 392021001607 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 392021001608 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 392021001609 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 392021001610 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 392021001611 E3 interaction surface; other site 392021001612 lipoyl attachment site [posttranslational modification]; other site 392021001613 e3 binding domain; Region: E3_binding; pfam02817 392021001614 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 392021001615 peptide chain release factor 1; Validated; Region: prfA; PRK00591 392021001616 RF-1 domain; Region: RF-1; cl02875 392021001617 RF-1 domain; Region: RF-1; cl02875 392021001618 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 392021001619 DHH family; Region: DHH; pfam01368 392021001620 DHHA1 domain; Region: DHHA1; pfam02272 392021001621 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 392021001622 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 392021001623 S-adenosylmethionine binding site [chemical binding]; other site 392021001624 transcription termination factor Rho; Provisional; Region: rho; PRK09376 392021001625 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 392021001626 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 392021001627 RNA binding site [nucleotide binding]; other site 392021001628 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 392021001629 multimer interface [polypeptide binding]; other site 392021001630 Walker A motif; other site 392021001631 ATP binding site [chemical binding]; other site 392021001632 Walker B motif; other site 392021001633 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 392021001634 tandem repeat interface [polypeptide binding]; other site 392021001635 oligomer interface [polypeptide binding]; other site 392021001636 active site residues [active] 392021001637 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 392021001638 IHF - DNA interface [nucleotide binding]; other site 392021001639 IHF dimer interface [polypeptide binding]; other site 392021001640 Protein of unknown function (DUF328); Region: DUF328; cl01143 392021001641 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 392021001642 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 392021001643 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 392021001644 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 392021001645 active site 392021001646 HIGH motif; other site 392021001647 dimer interface [polypeptide binding]; other site 392021001648 KMSKS motif; other site 392021001649 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 392021001650 putative acyl-acceptor binding pocket; other site 392021001651 Protein required for attachment to host cells; Region: Host_attach; cl02398 392021001652 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 392021001653 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 392021001654 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 392021001655 HemY protein N-terminus; Region: HemY_N; pfam07219 392021001656 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 392021001657 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 392021001658 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 392021001659 active site 392021001660 LysE type translocator; Region: LysE; cl00565 392021001661 muropeptide transporter; Validated; Region: ampG; PRK11010 392021001662 AmpG-related permease; Region: 2A0125; TIGR00901 392021001663 muropeptide transporter; Validated; Region: ampG; PRK11010 392021001664 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 392021001665 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 392021001666 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021001667 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 392021001668 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 392021001669 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 392021001670 substrate binding pocket [chemical binding]; other site 392021001671 chain length determination region; other site 392021001672 substrate-Mg2+ binding site; other site 392021001673 catalytic residues [active] 392021001674 aspartate-rich region 1; other site 392021001675 active site lid residues [active] 392021001676 aspartate-rich region 2; other site 392021001677 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 392021001678 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 392021001679 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 392021001680 active site 392021001681 Spore germination protein; Region: Spore_permease; cl15802 392021001682 arginine:agmatin antiporter; Provisional; Region: PRK10644 392021001683 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 392021001684 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 392021001685 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 392021001686 trimerization site [polypeptide binding]; other site 392021001687 active site 392021001688 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 392021001689 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 392021001690 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 392021001691 catalytic residue [active] 392021001692 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 392021001693 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 392021001694 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 392021001695 catalytic residue [active] 392021001696 Predicted transcriptional regulator [Transcription]; Region: COG1959 392021001697 Helix-turn-helix domains; Region: HTH; cl00088 392021001698 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 392021001699 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 392021001700 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 392021001701 Coenzyme A binding pocket [chemical binding]; other site 392021001702 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 392021001703 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 392021001704 homotetramer interface [polypeptide binding]; other site 392021001705 FMN binding site [chemical binding]; other site 392021001706 homodimer contacts [polypeptide binding]; other site 392021001707 putative active site [active] 392021001708 putative substrate binding site [chemical binding]; other site 392021001709 Clp protease; Region: CLP_protease; pfam00574 392021001710 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 392021001711 oligomer interface [polypeptide binding]; other site 392021001712 active site residues [active] 392021001713 cytidylate kinase; Provisional; Region: cmk; PRK00023 392021001714 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 392021001715 CMP-binding site; other site 392021001716 The sites determining sugar specificity; other site 392021001717 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 392021001718 non-specific DNA binding site [nucleotide binding]; other site 392021001719 salt bridge; other site 392021001720 sequence-specific DNA binding site [nucleotide binding]; other site 392021001721 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 392021001722 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 392021001723 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 392021001724 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 392021001725 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 392021001726 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 392021001727 domain interfaces; other site 392021001728 active site 392021001729 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 392021001730 dimer interface [polypeptide binding]; other site 392021001731 catalytic triad [active] 392021001732 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 392021001733 G-X-G motif; other site 392021001734 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 392021001735 dimer interface [polypeptide binding]; other site 392021001736 phosphorylation site [posttranslational modification] 392021001737 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 392021001738 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 392021001739 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 392021001740 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 392021001741 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 392021001742 Uncharacterized ACR, YagE family COG1723; Region: DUF155; cl00751 392021001743 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 392021001744 putative active site [active] 392021001745 catalytic site [active] 392021001746 putative substrate binding site [chemical binding]; other site 392021001747 HRDC domain; Region: HRDC; cl02578 392021001748 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 392021001749 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 392021001750 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001751 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 392021001752 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 392021001753 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 392021001754 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001755 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001756 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 392021001757 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 392021001758 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 392021001759 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 392021001760 N-acetyl-D-glucosamine binding site [chemical binding]; other site 392021001761 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 392021001762 Transcriptional regulator; Region: Transcrip_reg; cl00361 392021001763 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 392021001764 Substrate binding site; other site 392021001765 Mg++ binding site; other site 392021001766 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 392021001767 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 392021001768 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021001769 AAA domain; Region: AAA_18; pfam13238 392021001770 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 392021001771 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 392021001772 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 392021001773 dimer interface [polypeptide binding]; other site 392021001774 allosteric magnesium binding site [ion binding]; other site 392021001775 active site 392021001776 aspartate-rich active site metal binding site; other site 392021001777 Schiff base residues; other site 392021001778 primosome assembly protein PriA; Validated; Region: PRK05580 392021001779 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 392021001780 ATP binding site [chemical binding]; other site 392021001781 putative Mg++ binding site [ion binding]; other site 392021001782 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021001783 aromatic acid decarboxylase; Validated; Region: PRK05920 392021001784 Flavoprotein; Region: Flavoprotein; cl08021 392021001785 replicative DNA helicase; Provisional; Region: PRK09165 392021001786 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 392021001787 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 392021001788 Walker A motif; other site 392021001789 ATP binding site [chemical binding]; other site 392021001790 Walker B motif; other site 392021001791 DNA binding loops [nucleotide binding] 392021001792 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 392021001793 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 392021001794 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 392021001795 RNA binding surface [nucleotide binding]; other site 392021001796 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 392021001797 active site 392021001798 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 392021001799 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001800 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 392021001801 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001802 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001803 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001804 DNA repair protein RadA; Provisional; Region: PRK11823 392021001805 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 392021001806 Walker A motif/ATP binding site; other site 392021001807 ATP binding site [chemical binding]; other site 392021001808 Walker B motif; other site 392021001809 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 392021001810 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 392021001811 Recombination protein O N terminal; Region: RecO_N; cl15812 392021001812 Recombination protein O C terminal; Region: RecO_C; pfam02565 392021001813 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 392021001814 translation initiation factor IF-2; Validated; Region: infB; PRK05306 392021001815 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 392021001816 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 392021001817 G1 box; other site 392021001818 putative GEF interaction site [polypeptide binding]; other site 392021001819 GTP/Mg2+ binding site [chemical binding]; other site 392021001820 Switch I region; other site 392021001821 G2 box; other site 392021001822 G3 box; other site 392021001823 Switch II region; other site 392021001824 G4 box; other site 392021001825 G5 box; other site 392021001826 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 392021001827 Translation-initiation factor 2; Region: IF-2; pfam11987 392021001828 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 392021001829 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 392021001830 NusA N-terminal domain; Region: NusA_N; pfam08529 392021001831 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 392021001832 RNA binding site [nucleotide binding]; other site 392021001833 homodimer interface [polypeptide binding]; other site 392021001834 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 392021001835 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 392021001836 G-X-X-G motif; other site 392021001837 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 392021001838 ribosome maturation protein RimP; Reviewed; Region: PRK00092 392021001839 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 392021001840 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 392021001841 Sm1 motif; other site 392021001842 D3 - B interaction site; other site 392021001843 D1 - D2 interaction site; other site 392021001844 Hfq - Hfq interaction site; other site 392021001845 RNA binding pocket [nucleotide binding]; other site 392021001846 Sm2 motif; other site 392021001847 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 392021001848 NAD binding pocket [chemical binding]; other site 392021001849 Helix-turn-helix domains; Region: HTH; cl00088 392021001850 Rrf2 family protein; Region: rrf2_super; TIGR00738 392021001851 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 392021001852 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 392021001853 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 392021001854 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 392021001855 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 392021001856 active site 392021001857 HIGH motif; other site 392021001858 dimer interface [polypeptide binding]; other site 392021001859 KMSKS motif; other site 392021001860 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 392021001861 RNA binding surface [nucleotide binding]; other site 392021001862 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 392021001863 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 392021001864 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 392021001865 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001866 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 392021001867 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021001868 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 392021001869 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 392021001870 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 392021001871 active site 392021001872 phosphorylation site [posttranslational modification] 392021001873 intermolecular recognition site; other site 392021001874 dimerization interface [polypeptide binding]; other site 392021001875 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 392021001876 Walker A motif; other site 392021001877 ATP binding site [chemical binding]; other site 392021001878 Walker B motif; other site 392021001879 arginine finger; other site 392021001880 Helix-turn-helix domains; Region: HTH; cl00088 392021001881 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001882 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 392021001883 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 392021001884 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001885 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 392021001886 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001887 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 392021001888 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 392021001889 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 392021001890 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 392021001891 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 392021001892 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 392021001893 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 392021001894 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 392021001895 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 392021001896 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 392021001897 S-adenosylmethionine binding site [chemical binding]; other site 392021001898 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 392021001899 MraZ protein; Region: MraZ; pfam02381 392021001900 similar to hypothetical protein 392021001901 Sodium:solute symporter family; Region: SSF; cl00456 392021001902 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 392021001903 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 392021001904 GIY-YIG motif/motif A; other site 392021001905 active site 392021001906 catalytic site [active] 392021001907 putative DNA binding site [nucleotide binding]; other site 392021001908 metal binding site [ion binding]; metal-binding site 392021001909 UvrB/uvrC motif; Region: UVR; pfam02151 392021001910 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 392021001911 Protein of unknown function (DUF461); Region: DUF461; cl01071 392021001912 A new structural DNA glycosylase; Region: AlkD_like; cd06561 392021001913 active site 392021001914 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 392021001915 active site 392021001916 DNA binding site [nucleotide binding] 392021001917 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 392021001918 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 392021001919 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 392021001920 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 392021001921 DNA binding site [nucleotide binding] 392021001922 active site 392021001923 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 392021001924 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 392021001925 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021001926 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 392021001927 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 392021001928 nucleotide binding region [chemical binding]; other site 392021001929 ATP-binding site [chemical binding]; other site 392021001930 SEC-C motif; Region: SEC-C; pfam02810 392021001931 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 392021001932 PPIC-type PPIASE domain; Region: Rotamase; cl08278 392021001933 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 392021001934 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 392021001935 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 392021001936 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 392021001937 hinge; other site 392021001938 active site 392021001939 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 392021001940 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 392021001941 ATP binding site [chemical binding]; other site 392021001942 Mg2+ binding site [ion binding]; other site 392021001943 G-X-G motif; other site 392021001944 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 392021001945 anchoring element; other site 392021001946 dimer interface [polypeptide binding]; other site 392021001947 ATP binding site [chemical binding]; other site 392021001948 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 392021001949 active site 392021001950 putative metal-binding site [ion binding]; other site 392021001951 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 392021001952 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 392021001953 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 392021001954 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 392021001955 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 392021001956 MgtE intracellular N domain; Region: MgtE_N; cl15244 392021001957 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 392021001958 Divalent cation transporter; Region: MgtE; cl00786 392021001959 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 392021001960 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 392021001961 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 392021001962 Preprotein translocase subunit; Region: YajC; cl00806 392021001963 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 392021001964 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 392021001965 Protein export membrane protein; Region: SecD_SecF; cl14618 392021001966 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 392021001967 Cu(I) binding site [ion binding]; other site 392021001968 CcmE; Region: CcmE; cl00994 392021001969 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 392021001970 dimer interface [polypeptide binding]; other site 392021001971 substrate binding site [chemical binding]; other site 392021001972 metal binding sites [ion binding]; metal-binding site 392021001973 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001974 MviN-like protein; Region: MVIN; pfam03023 392021001975 TraX protein; Region: TraX; cl05434 392021001976 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 392021001977 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 392021001978 ssDNA binding site; other site 392021001979 generic binding surface II; other site 392021001980 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 392021001981 ATP binding site [chemical binding]; other site 392021001982 putative Mg++ binding site [ion binding]; other site 392021001983 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 392021001984 nucleotide binding region [chemical binding]; other site 392021001985 ATP-binding site [chemical binding]; other site 392021001986 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 392021001987 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 392021001988 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 392021001989 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 392021001990 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 392021001991 Mg++ binding site [ion binding]; other site 392021001992 putative catalytic motif [active] 392021001993 putative substrate binding site [chemical binding]; other site 392021001994 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 392021001995 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 392021001996 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 392021001997 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 392021001998 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 392021001999 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 392021002000 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 392021002001 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 392021002002 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 392021002003 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 392021002004 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 392021002005 ATP binding site [chemical binding]; other site 392021002006 putative Mg++ binding site [ion binding]; other site 392021002007 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 392021002008 nucleotide binding region [chemical binding]; other site 392021002009 ATP-binding site [chemical binding]; other site 392021002010 TRCF domain; Region: TRCF; cl04088 392021002011 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 392021002012 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 392021002013 active site residue [active] 392021002014 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 392021002015 DnaA N-terminal domain; Region: DnaA_N; pfam11638 392021002016 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 392021002017 Walker A motif; other site 392021002018 ATP binding site [chemical binding]; other site 392021002019 Walker B motif; other site 392021002020 arginine finger; other site 392021002021 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 392021002022 DnaA box-binding interface [nucleotide binding]; other site 392021002023 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 392021002024 active site 392021002025 nucleophile elbow; other site 392021002026 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 392021002027 HEPN domain; Region: HEPN; cl00824 392021002028 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 392021002029 metal binding triad [ion binding]; metal-binding site 392021002030 GTP-binding protein YchF; Reviewed; Region: PRK09601 392021002031 YchF GTPase; Region: YchF; cd01900 392021002032 G1 box; other site 392021002033 GTP/Mg2+ binding site [chemical binding]; other site 392021002034 Switch I region; other site 392021002035 G2 box; other site 392021002036 Switch II region; other site 392021002037 G3 box; other site 392021002038 G4 box; other site 392021002039 G5 box; other site 392021002040 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 392021002041 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 392021002042 putative active site [active] 392021002043 catalytic residue [active] 392021002044 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 392021002045 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 392021002046 5S rRNA interface [nucleotide binding]; other site 392021002047 CTC domain interface [polypeptide binding]; other site 392021002048 L16 interface [polypeptide binding]; other site 392021002049 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 392021002050 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 392021002051 FeS/SAM binding site; other site 392021002052 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 392021002053 ribosomal protein L20; Region: rpl20; CHL00068 392021002054 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 392021002055 23S rRNA binding site [nucleotide binding]; other site 392021002056 L21 binding site [polypeptide binding]; other site 392021002057 L13 binding site [polypeptide binding]; other site 392021002058 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 392021002059 Ribonuclease P; Region: Ribonuclease_P; cl00457 392021002060 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 392021002061 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 392021002062 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 392021002063 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 392021002064 active site 392021002065 ATP binding site [chemical binding]; other site 392021002066 substrate binding site [chemical binding]; other site 392021002067 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 392021002068 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 392021002069 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 392021002070 dimerization interface [polypeptide binding]; other site 392021002071 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 392021002072 dimer interface [polypeptide binding]; other site 392021002073 phosphorylation site [posttranslational modification] 392021002074 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 392021002075 ATP binding site [chemical binding]; other site 392021002076 Mg2+ binding site [ion binding]; other site 392021002077 G-X-G motif; other site 392021002078 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 392021002079 Uncharacterized conserved protein [Function unknown]; Region: COG5590 392021002080 Helix-turn-helix domains; Region: HTH; cl00088 392021002081 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 392021002082 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 392021002083 HIGH motif; other site 392021002084 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 392021002085 active site 392021002086 KMSKS motif; other site 392021002087 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 392021002088 tRNA binding surface [nucleotide binding]; other site 392021002089 anticodon binding site; other site 392021002090 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 392021002091 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 392021002092 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 392021002093 ATP-grasp domain; Region: ATP-grasp_4; cl03087 392021002094 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 392021002095 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 392021002096 carboxyltransferase (CT) interaction site; other site 392021002097 biotinylation site [posttranslational modification]; other site 392021002098 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 392021002099 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 392021002100 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 392021002101 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 392021002102 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 392021002103 putative substrate translocation pore; other site 392021002104 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 392021002105 putative acyl-acceptor binding pocket; other site 392021002106 AMP-binding enzyme; Region: AMP-binding; cl15778 392021002107 TfoX N-terminal domain; Region: TfoX_N; cl01167 392021002108 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 392021002109 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002110 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 392021002111 S-adenosylmethionine binding site [chemical binding]; other site 392021002112 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 392021002113 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 392021002114 HIGH motif; other site 392021002115 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 392021002116 active site 392021002117 KMSKS motif; other site 392021002118 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002119 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 392021002120 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 392021002121 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 392021002122 ring oligomerisation interface [polypeptide binding]; other site 392021002123 ATP/Mg binding site [chemical binding]; other site 392021002124 stacking interactions; other site 392021002125 hinge regions; other site 392021002126 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 392021002127 oligomerisation interface [polypeptide binding]; other site 392021002128 mobile loop; other site 392021002129 roof hairpin; other site 392021002130 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 392021002131 ribonuclease PH; Reviewed; Region: rph; PRK00173 392021002132 Ribonuclease PH; Region: RNase_PH_bact; cd11362 392021002133 hexamer interface [polypeptide binding]; other site 392021002134 active site 392021002135 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 392021002136 dimer interface [polypeptide binding]; other site 392021002137 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 392021002138 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 392021002139 Domain of unknown function DUF20; Region: UPF0118; pfam01594 392021002140 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002141 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 392021002142 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 392021002143 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 392021002144 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 392021002145 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 392021002146 alphaNTD - beta interaction site [polypeptide binding]; other site 392021002147 alphaNTD homodimer interface [polypeptide binding]; other site 392021002148 alphaNTD - beta' interaction site [polypeptide binding]; other site 392021002149 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 392021002150 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 392021002151 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 392021002152 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 392021002153 adenylate kinase; Reviewed; Region: adk; PRK00279 392021002154 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 392021002155 AMP-binding site [chemical binding]; other site 392021002156 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 392021002157 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 392021002158 SecY translocase; Region: SecY; pfam00344 392021002159 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 392021002160 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 392021002161 23S rRNA binding site [nucleotide binding]; other site 392021002162 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 392021002163 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 392021002164 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 392021002165 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 392021002166 5S rRNA interface [nucleotide binding]; other site 392021002167 23S rRNA interface [nucleotide binding]; other site 392021002168 L5 interface [polypeptide binding]; other site 392021002169 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 392021002170 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 392021002171 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 392021002172 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 392021002173 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 392021002174 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 392021002175 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 392021002176 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 392021002177 KOW motif; Region: KOW; cl00354 392021002178 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 392021002179 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 392021002180 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 392021002181 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cl09943 392021002182 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 392021002183 23S rRNA interface [nucleotide binding]; other site 392021002184 5S rRNA interface [nucleotide binding]; other site 392021002185 putative antibiotic binding site [chemical binding]; other site 392021002186 L25 interface [polypeptide binding]; other site 392021002187 L27 interface [polypeptide binding]; other site 392021002188 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 392021002189 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 392021002190 G-X-X-G motif; other site 392021002191 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 392021002192 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 392021002193 putative translocon binding site; other site 392021002194 protein-rRNA interface [nucleotide binding]; other site 392021002195 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 392021002196 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 392021002197 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 392021002198 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 392021002199 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 392021002200 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 392021002201 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 392021002202 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 392021002203 elongation factor Tu; Reviewed; Region: PRK00049 392021002204 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 392021002205 G1 box; other site 392021002206 GEF interaction site [polypeptide binding]; other site 392021002207 GTP/Mg2+ binding site [chemical binding]; other site 392021002208 Switch I region; other site 392021002209 G2 box; other site 392021002210 G3 box; other site 392021002211 Switch II region; other site 392021002212 G4 box; other site 392021002213 G5 box; other site 392021002214 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 392021002215 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 392021002216 Antibiotic Binding Site [chemical binding]; other site 392021002217 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 392021002218 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 392021002219 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 392021002220 fumarate hydratase; Reviewed; Region: fumC; PRK00485 392021002221 Class II fumarases; Region: Fumarase_classII; cd01362 392021002222 active site 392021002223 tetramer interface [polypeptide binding]; other site 392021002224 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 392021002225 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 392021002226 putative active site [active] 392021002227 homotetrameric interface [polypeptide binding]; other site 392021002228 cell division protein FtsZ; Validated; Region: PRK09330 392021002229 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 392021002230 nucleotide binding site [chemical binding]; other site 392021002231 SulA interaction site; other site 392021002232 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 392021002233 secondary substrate binding site; other site 392021002234 primary substrate binding site; other site 392021002235 inhibition loop; other site 392021002236 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; cl07364 392021002237 NifU-like domain; Region: NifU; cl00484 392021002238 muropeptide transporter; Validated; Region: ampG; PRK11010 392021002239 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 392021002240 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 392021002241 ATP binding site [chemical binding]; other site 392021002242 Mg++ binding site [ion binding]; other site 392021002243 motif III; other site 392021002244 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 392021002245 nucleotide binding region [chemical binding]; other site 392021002246 ATP-binding site [chemical binding]; other site 392021002247 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 392021002248 DNA-binding site [nucleotide binding]; DNA binding site 392021002249 RNA-binding motif; other site 392021002250 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 392021002251 S-adenosylmethionine binding site [chemical binding]; other site 392021002252 SurA N-terminal domain; Region: SurA_N_3; cl07813 392021002253 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 392021002254 Organic solvent tolerance protein; Region: OstA_C; pfam04453 392021002255 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 392021002256 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 392021002257 generic binding surface II; other site 392021002258 generic binding surface I; other site 392021002259 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 392021002260 putative phosphate binding site [ion binding]; other site 392021002261 putative catalytic site [active] 392021002262 active site 392021002263 metal binding site A [ion binding]; metal-binding site 392021002264 DNA binding site [nucleotide binding] 392021002265 putative AP binding site [nucleotide binding]; other site 392021002266 putative metal binding site B [ion binding]; other site 392021002267 PQ loop repeat; Region: PQ-loop; cl12056 392021002268 GTP-binding protein Der; Reviewed; Region: PRK00093 392021002269 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 392021002270 G1 box; other site 392021002271 GTP/Mg2+ binding site [chemical binding]; other site 392021002272 Switch I region; other site 392021002273 G2 box; other site 392021002274 Switch II region; other site 392021002275 G3 box; other site 392021002276 G4 box; other site 392021002277 G5 box; other site 392021002278 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 392021002279 G1 box; other site 392021002280 GTP/Mg2+ binding site [chemical binding]; other site 392021002281 Switch I region; other site 392021002282 G2 box; other site 392021002283 G3 box; other site 392021002284 Switch II region; other site 392021002285 G4 box; other site 392021002286 G5 box; other site 392021002287 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002288 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 392021002289 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 392021002290 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: APH_ChoK_like; cd05120 392021002291 active site 392021002292 ATP binding site [chemical binding]; other site 392021002293 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 392021002294 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 392021002295 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 392021002296 S-adenosylmethionine binding site [chemical binding]; other site 392021002297 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 392021002298 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 392021002299 DNA binding site [nucleotide binding] 392021002300 catalytic residue [active] 392021002301 H2TH interface [polypeptide binding]; other site 392021002302 putative catalytic residues [active] 392021002303 turnover-facilitating residue; other site 392021002304 intercalation triad [nucleotide binding]; other site 392021002305 8OG recognition residue [nucleotide binding]; other site 392021002306 putative reading head residues; other site 392021002307 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 392021002308 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 392021002309 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002310 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 392021002311 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 392021002312 active site 392021002313 Protein of unknown function (DUF511); Region: DUF511; cl01114 392021002314 Protein of unknown function (DUF511); Region: DUF511; cl01114 392021002315 Protein of unknown function (DUF511); Region: DUF511; cl01114 392021002316 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 392021002317 active site 392021002318 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 392021002319 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 392021002320 HIGH motif; other site 392021002321 active site 392021002322 KMSKS motif; other site 392021002323 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 392021002324 tRNA binding surface [nucleotide binding]; other site 392021002325 anticodon binding site; other site 392021002326 thymidylate kinase; Validated; Region: tmk; PRK00698 392021002327 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 392021002328 TMP-binding site; other site 392021002329 ATP-binding site [chemical binding]; other site 392021002330 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021002331 UbiA prenyltransferase family; Region: UbiA; cl00337 392021002332 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 392021002333 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021002334 active site 392021002335 HIGH motif; other site 392021002336 nucleotide binding site [chemical binding]; other site 392021002337 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 392021002338 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021002339 active site 392021002340 KMSKS motif; other site 392021002341 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 392021002342 tRNA binding surface [nucleotide binding]; other site 392021002343 anticodon binding site; other site 392021002344 LicD family; Region: LicD; cl01378 392021002345 LicD family; Region: LicD; cl01378 392021002346 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002347 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 392021002348 RmuC family; Region: RmuC; pfam02646 392021002349 DoxX-like family; Region: DoxX_3; pfam13781 392021002350 Predicted integral membrane protein (DUF2269); Region: DUF2269; cl02335 392021002351 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 392021002352 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 392021002353 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 392021002354 Walker A motif; other site 392021002355 ATP binding site [chemical binding]; other site 392021002356 Walker B motif; other site 392021002357 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 392021002358 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 392021002359 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 392021002360 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 392021002361 Ligand Binding Site [chemical binding]; other site 392021002362 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 392021002363 HicB family; Region: HicB; pfam05534 392021002364 YcfA-like protein; Region: YcfA; cl00752 392021002365 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 392021002366 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 392021002367 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002368 Walker A/P-loop; other site 392021002369 ATP binding site [chemical binding]; other site 392021002370 Q-loop/lid; other site 392021002371 ABC transporter signature motif; other site 392021002372 Walker B; other site 392021002373 D-loop; other site 392021002374 H-loop/switch region; other site 392021002375 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 392021002376 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 392021002377 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 392021002378 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 392021002379 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 392021002380 FtsX-like permease family; Region: FtsX; cl15850 392021002381 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 392021002382 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 392021002383 Walker A/P-loop; other site 392021002384 ATP binding site [chemical binding]; other site 392021002385 Q-loop/lid; other site 392021002386 ABC transporter signature motif; other site 392021002387 Walker B; other site 392021002388 D-loop; other site 392021002389 H-loop/switch region; other site 392021002390 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 392021002391 Domain of unknown function DUF21; Region: DUF21; pfam01595 392021002392 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 392021002393 Transporter associated domain; Region: CorC_HlyC; cl08393 392021002394 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 392021002395 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 392021002396 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 392021002397 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021002398 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 392021002399 synthetase active site [active] 392021002400 NTP binding site [chemical binding]; other site 392021002401 metal binding site [ion binding]; metal-binding site 392021002402 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 392021002403 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 392021002404 DNA binding residues [nucleotide binding] 392021002405 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 392021002406 IHF dimer interface [polypeptide binding]; other site 392021002407 IHF - DNA interface [nucleotide binding]; other site 392021002408 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 392021002409 catalytic triad [active] 392021002410 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 392021002411 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 392021002412 putative acyl-acceptor binding pocket; other site 392021002413 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 392021002414 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 392021002415 Peptidase family M23; Region: Peptidase_M23; pfam01551 392021002416 Protein of unknown function (DUF519); Region: DUF519; pfam04378 392021002417 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 392021002418 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 392021002419 nucleotide binding pocket [chemical binding]; other site 392021002420 K-X-D-G motif; other site 392021002421 catalytic site [active] 392021002422 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 392021002423 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 392021002424 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 392021002425 Dimer interface [polypeptide binding]; other site 392021002426 BRCT sequence motif; other site 392021002427 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 392021002428 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 392021002429 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 392021002430 mce related protein; Region: MCE; pfam02470 392021002431 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 392021002432 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 392021002433 RNA/DNA hybrid binding site [nucleotide binding]; other site 392021002434 active site 392021002435 Stringent starvation protein B; Region: SspB; cl01120 392021002436 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 392021002437 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 392021002438 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 392021002439 CoA-binding site [chemical binding]; other site 392021002440 ATP-binding [chemical binding]; other site 392021002441 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 392021002442 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 392021002443 active site 392021002444 substrate binding site [chemical binding]; other site 392021002445 catalytic site [active] 392021002446 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 392021002447 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 392021002448 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002449 Acyl transferase domain; Region: Acyl_transf_1; cl08282 392021002450 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 392021002451 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 392021002452 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 392021002453 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021002454 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 392021002455 nudix motif; other site 392021002456 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 392021002457 Transporter associated domain; Region: CorC_HlyC; cl08393 392021002458 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 392021002459 lipoyl synthase; Provisional; Region: PRK05481 392021002460 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 392021002461 FeS/SAM binding site; other site 392021002462 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 392021002463 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 392021002464 dimer interface [polypeptide binding]; other site 392021002465 glycine-pyridoxal phosphate binding site [chemical binding]; other site 392021002466 active site 392021002467 folate binding site [chemical binding]; other site 392021002468 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 392021002469 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 392021002470 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 392021002471 putative GSH binding site [chemical binding]; other site 392021002472 catalytic residues [active] 392021002473 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 392021002474 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 392021002475 minor groove reading motif; other site 392021002476 helix-hairpin-helix signature motif; other site 392021002477 substrate binding pocket [chemical binding]; other site 392021002478 active site 392021002479 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 392021002480 Entericidin EcnA/B family; Region: Entericidin; cl02322 392021002481 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021002482 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021002483 Predicted methyltransferases [General function prediction only]; Region: COG0313 392021002484 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 392021002485 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 392021002486 putative ligand binding site [chemical binding]; other site 392021002487 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 392021002488 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 392021002489 tetramer interfaces [polypeptide binding]; other site 392021002490 binuclear metal-binding site [ion binding]; other site 392021002491 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 392021002492 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 392021002493 aspartate kinase; Reviewed; Region: PRK06635 392021002494 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 392021002495 putative nucleotide binding site [chemical binding]; other site 392021002496 putative catalytic residues [active] 392021002497 putative Mg ion binding site [ion binding]; other site 392021002498 putative aspartate binding site [chemical binding]; other site 392021002499 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 392021002500 putative allosteric regulatory residue; other site 392021002501 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 392021002502 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021002503 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 392021002504 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 392021002505 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021002506 putative substrate translocation pore; other site 392021002507 Cell division protein ZapA; Region: ZapA; cl01146 392021002508 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 392021002509 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002510 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 392021002511 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 392021002512 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021002513 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 392021002514 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 392021002515 trmE is a tRNA modification GTPase; Region: trmE; cd04164 392021002516 G1 box; other site 392021002517 GTP/Mg2+ binding site [chemical binding]; other site 392021002518 Switch I region; other site 392021002519 G2 box; other site 392021002520 Switch II region; other site 392021002521 G3 box; other site 392021002522 G4 box; other site 392021002523 G5 box; other site 392021002524 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 392021002525 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 392021002526 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 392021002527 protein RecA; Region: tigrfam_recA; TIGR02012 392021002528 hexamer interface [polypeptide binding]; other site 392021002529 Walker A motif; other site 392021002530 ATP binding site [chemical binding]; other site 392021002531 Walker B motif; other site 392021002532 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 392021002533 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021002534 NAD(P) binding site [chemical binding]; other site 392021002535 active site 392021002536 Phosphopantetheine attachment site; Region: PP-binding; cl09936 392021002537 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 392021002538 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 392021002539 dimer interface [polypeptide binding]; other site 392021002540 active site 392021002541 ABC transporter ATPase component; Reviewed; Region: PRK11147 392021002542 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 392021002543 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 392021002544 endonuclease subunit; Provisional; Region: 46; PHA02562 392021002545 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002546 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 392021002547 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002548 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 392021002549 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 392021002550 catalytic site [active] 392021002551 G-X2-G-X-G-K; other site 392021002552 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 392021002553 rod shape-determining protein MreC; Provisional; Region: PRK13922 392021002554 rod shape-determining protein MreC; Region: MreC; pfam04085 392021002555 rod shape-determining protein MreB; Provisional; Region: PRK13927 392021002556 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 392021002557 ATP binding site [chemical binding]; other site 392021002558 profilin binding site; other site 392021002559 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 392021002560 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 392021002561 putative outer membrane lipoprotein; Provisional; Region: PRK09967 392021002562 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 392021002563 ligand binding site [chemical binding]; other site 392021002564 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002565 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 392021002566 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 392021002567 dimer interface [polypeptide binding]; other site 392021002568 active site 392021002569 CoA binding pocket [chemical binding]; other site 392021002570 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 392021002571 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 392021002572 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 392021002573 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 392021002574 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 392021002575 P loop; other site 392021002576 GTP binding site [chemical binding]; other site 392021002577 DNA polymerase I; Provisional; Region: PRK05755 392021002578 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 392021002579 active site 392021002580 metal binding site 1 [ion binding]; metal-binding site 392021002581 putative 5' ssDNA interaction site; other site 392021002582 metal binding site 3; metal-binding site 392021002583 metal binding site 2 [ion binding]; metal-binding site 392021002584 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 392021002585 putative DNA binding site [nucleotide binding]; other site 392021002586 putative metal binding site [ion binding]; other site 392021002587 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 392021002588 active site 392021002589 substrate binding site [chemical binding]; other site 392021002590 catalytic site [active] 392021002591 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 392021002592 active site 392021002593 DNA binding site [nucleotide binding] 392021002594 catalytic site [active] 392021002595 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 392021002596 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 392021002597 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 392021002598 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 392021002599 generic binding surface I; other site 392021002600 generic binding surface II; other site 392021002601 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 392021002602 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 392021002603 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021002604 Protein of unknown function; Region: DUF3971; pfam13116 392021002605 AsmA-like C-terminal region; Region: AsmA_2; cl15864 392021002606 AmpG-related permease; Region: 2A0125; TIGR00901 392021002607 muropeptide transporter; Validated; Region: ampG; PRK11010 392021002608 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 392021002609 seryl-tRNA synthetase; Provisional; Region: PRK05431 392021002610 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 392021002611 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound...; Region: SerRS_core; cd00770 392021002612 dimer interface [polypeptide binding]; other site 392021002613 active site 392021002614 motif 1; other site 392021002615 motif 2; other site 392021002616 motif 3; other site 392021002617 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 392021002618 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 392021002619 Integral membrane protein TerC family; Region: TerC; cl10468 392021002620 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021002621 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 392021002622 S-adenosylmethionine binding site [chemical binding]; other site 392021002623 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 392021002624 Predicted transcriptional regulator [Transcription]; Region: COG2944 392021002625 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 392021002626 salt bridge; other site 392021002627 non-specific DNA binding site [nucleotide binding]; other site 392021002628 sequence-specific DNA binding site [nucleotide binding]; other site 392021002629 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 392021002630 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 392021002631 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 392021002632 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 392021002633 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 392021002634 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 392021002635 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 392021002636 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 392021002637 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 392021002638 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002639 Walker A/P-loop; other site 392021002640 ATP binding site [chemical binding]; other site 392021002641 Q-loop/lid; other site 392021002642 ABC transporter signature motif; other site 392021002643 Walker B; other site 392021002644 D-loop; other site 392021002645 H-loop/switch region; other site 392021002646 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 392021002647 4Fe-4S binding domain; Region: Fer4; cl02805 392021002648 4Fe-4S binding domain; Region: Fer4; cl02805 392021002649 NADH dehydrogenase; Region: NADHdh; cl00469 392021002650 NADH dehydrogenase subunit G; Validated; Region: PRK09130 392021002651 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 392021002652 catalytic loop [active] 392021002653 iron binding site [ion binding]; other site 392021002654 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 392021002655 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 392021002656 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 392021002657 Predicted membrane protein [Function unknown]; Region: COG3671 392021002658 aconitate hydratase; Validated; Region: PRK09277 392021002659 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 392021002660 substrate binding site [chemical binding]; other site 392021002661 ligand binding site [chemical binding]; other site 392021002662 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 392021002663 substrate binding site [chemical binding]; other site 392021002664 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 392021002665 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 392021002666 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 392021002667 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 392021002668 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 392021002669 alpha subunit interaction interface [polypeptide binding]; other site 392021002670 Walker A motif; other site 392021002671 ATP binding site [chemical binding]; other site 392021002672 Walker B motif; other site 392021002673 inhibitor binding site; inhibition site 392021002674 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 392021002675 ATP synthase; Region: ATP-synt; cl00365 392021002676 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 392021002677 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 392021002678 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 392021002679 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 392021002680 beta subunit interaction interface [polypeptide binding]; other site 392021002681 Walker A motif; other site 392021002682 ATP binding site [chemical binding]; other site 392021002683 Walker B motif; other site 392021002684 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 392021002685 Plant ATP synthase F0; Region: YMF19; cl07975 392021002686 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 392021002687 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 392021002688 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021002689 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 392021002690 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 392021002691 Ferritin-like domain; Region: Ferritin; pfam00210 392021002692 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 392021002693 dimerization interface [polypeptide binding]; other site 392021002694 DPS ferroxidase diiron center [ion binding]; other site 392021002695 ion pore; other site 392021002696 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 392021002697 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 392021002698 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 392021002699 Transglycosylase; Region: Transgly; cl07896 392021002700 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 392021002701 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 392021002702 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 392021002703 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 392021002704 TRAM domain; Region: TRAM; cl01282 392021002705 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021002706 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021002707 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002708 Bacterial SH3 domain; Region: SH3_3; cl02551 392021002709 Bacterial SH3 domain; Region: SH3_3; cl02551 392021002710 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 392021002711 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 392021002712 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021002713 Oligomerisation domain; Region: Oligomerisation; cl00519 392021002714 BolA-like protein; Region: BolA; cl00386 392021002715 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 392021002716 rRNA binding site [nucleotide binding]; other site 392021002717 predicted 30S ribosome binding site; other site 392021002718 Maf-like protein; Region: Maf; pfam02545 392021002719 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 392021002720 active site 392021002721 dimer interface [polypeptide binding]; other site 392021002722 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 392021002723 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 392021002724 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 392021002725 DNA binding site [nucleotide binding] 392021002726 Int/Topo IB signature motif; other site 392021002727 active site 392021002728 Phasin protein; Region: Phasin_2; cl11491 392021002729 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 392021002730 PLD-like domain; Region: PLDc_2; pfam13091 392021002731 putative active site [active] 392021002732 catalytic site [active] 392021002733 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 392021002734 periplasmic folding chaperone; Provisional; Region: PRK10788 392021002735 PPIC-type PPIASE domain; Region: Rotamase; cl08278 392021002736 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 392021002737 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021002738 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 392021002739 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002740 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 392021002741 OpgC protein; Region: OpgC_C; cl00792 392021002742 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 392021002743 active site 392021002744 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 392021002745 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 392021002746 MPN+ (JAMM) motif; other site 392021002747 Zinc-binding site [ion binding]; other site 392021002748 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 392021002749 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 392021002750 Mg++ binding site [ion binding]; other site 392021002751 putative catalytic motif [active] 392021002752 putative substrate binding site [chemical binding]; other site 392021002753 Protein of unknown function (DUF721); Region: DUF721; cl02324 392021002754 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021002755 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 392021002756 Ferredoxin [Energy production and conversion]; Region: COG1146 392021002757 4Fe-4S binding domain; Region: Fer4; cl02805 392021002758 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 392021002759 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 392021002760 nucleoside/Zn binding site; other site 392021002761 dimer interface [polypeptide binding]; other site 392021002762 catalytic motif [active] 392021002763 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 392021002764 Cation efflux family; Region: Cation_efflux; cl00316 392021002765 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 392021002766 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 392021002767 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 392021002768 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 392021002769 Arenavirus nucleocapsid protein; Region: Arena_nucleocap; pfam00843 392021002770 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 392021002771 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 392021002772 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 392021002773 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 392021002774 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 392021002775 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 392021002776 dimer interface [polypeptide binding]; other site 392021002777 ssDNA binding site [nucleotide binding]; other site 392021002778 tetramer (dimer of dimers) interface [polypeptide binding]; other site 392021002779 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 392021002780 heat shock protein 90; Provisional; Region: PRK05218 392021002781 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 392021002782 ATP binding site [chemical binding]; other site 392021002783 Mg2+ binding site [ion binding]; other site 392021002784 G-X-G motif; other site 392021002785 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 392021002786 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 392021002787 substrate-cofactor binding pocket; other site 392021002788 pyridoxal 5'-phosphate binding site [chemical binding]; other site 392021002789 catalytic residue [active] 392021002790 trigger factor; Provisional; Region: tig; PRK01490 392021002791 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 392021002792 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 392021002793 GTPase CgtA; Reviewed; Region: obgE; PRK12299 392021002794 GTP1/OBG; Region: GTP1_OBG; pfam01018 392021002795 Obg GTPase; Region: Obg; cd01898 392021002796 G1 box; other site 392021002797 GTP/Mg2+ binding site [chemical binding]; other site 392021002798 Switch I region; other site 392021002799 G2 box; other site 392021002800 G3 box; other site 392021002801 Switch II region; other site 392021002802 G4 box; other site 392021002803 G5 box; other site 392021002804 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 392021002805 dimer interface [polypeptide binding]; other site 392021002806 Citrate synthase; Region: Citrate_synt; pfam00285 392021002807 active site 392021002808 citrylCoA binding site [chemical binding]; other site 392021002809 NADH binding [chemical binding]; other site 392021002810 cationic pore residues; other site 392021002811 oxalacetate/citrate binding site [chemical binding]; other site 392021002812 coenzyme A binding site [chemical binding]; other site 392021002813 catalytic triad [active] 392021002814 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 392021002815 Fe-S cluster binding site [ion binding]; other site 392021002816 active site 392021002817 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 392021002818 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 392021002819 RNA binding surface [nucleotide binding]; other site 392021002820 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 392021002821 active site 392021002822 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 392021002823 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 392021002824 S-adenosylmethionine binding site [chemical binding]; other site 392021002825 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 392021002826 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 392021002827 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 392021002828 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 392021002829 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 392021002830 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 attaches...; Region: class_II_aaRS-like_core; cl00268 392021002831 motif 1; other site 392021002832 dimer interface [polypeptide binding]; other site 392021002833 active site 392021002834 motif 2; other site 392021002835 motif 3; other site 392021002836 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 392021002837 oligomeric interface; other site 392021002838 putative active site [active] 392021002839 homodimer interface [polypeptide binding]; other site 392021002840 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 392021002841 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 392021002842 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 392021002843 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 392021002844 motif 1; other site 392021002845 active site 392021002846 motif 2; other site 392021002847 motif 3; other site 392021002848 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 392021002849 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 392021002850 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 392021002851 dimerization interface 3.5A [polypeptide binding]; other site 392021002852 active site 392021002853 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 392021002854 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 392021002855 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 392021002856 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 392021002857 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 392021002858 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 392021002859 DNA binding residues [nucleotide binding] 392021002860 DNA primase, catalytic core; Region: dnaG; TIGR01391 392021002861 CHC2 zinc finger; Region: zf-CHC2; cl15369 392021002862 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 392021002863 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 392021002864 active site 392021002865 metal binding site [ion binding]; metal-binding site 392021002866 interdomain interaction site; other site 392021002867 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 392021002868 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 392021002869 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 392021002870 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 392021002871 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 392021002872 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 392021002873 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 392021002874 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021002875 NAD(P) binding site [chemical binding]; other site 392021002876 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 392021002877 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 392021002878 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 392021002879 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 392021002880 Walker A motif; other site 392021002881 ATP binding site [chemical binding]; other site 392021002882 Walker B motif; other site 392021002883 arginine finger; other site 392021002884 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 392021002885 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 392021002886 Predicted aspartyl protease [General function prediction only]; Region: COG3577 392021002887 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 392021002888 catalytic motif [active] 392021002889 Catalytic residue [active] 392021002890 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 392021002891 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 392021002892 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 392021002893 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 392021002894 Walker A/P-loop; other site 392021002895 ATP binding site [chemical binding]; other site 392021002896 Q-loop/lid; other site 392021002897 ABC transporter signature motif; other site 392021002898 Walker B; other site 392021002899 D-loop; other site 392021002900 H-loop/switch region; other site 392021002901 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 392021002902 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 392021002903 active site 392021002904 RelB antitoxin; Region: RelB; cl01171 392021002905 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 392021002906 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 392021002907 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 392021002908 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 392021002909 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 392021002910 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 392021002911 metal binding site [ion binding]; metal-binding site 392021002912 dimer interface [polypeptide binding]; other site 392021002913 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 392021002914 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 392021002915 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 392021002916 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 392021002917 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cl00630 392021002918 putative active site [active] 392021002919 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 392021002920 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 392021002921 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 392021002922 amidase catalytic site [active] 392021002923 Zn binding residues [ion binding]; other site 392021002924 substrate binding site [chemical binding]; other site 392021002925 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 392021002926 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 392021002927 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 392021002928 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 392021002929 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 392021002930 ATP binding site [chemical binding]; other site 392021002931 Mg2+ binding site [ion binding]; other site 392021002932 G-X-G motif; other site 392021002933 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 392021002934 ATP binding site [chemical binding]; other site 392021002935 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 392021002936 Zinc-finger domain; Region: zf-CHCC; cl01821 392021002937 Tetratricopeptide repeat; Region: TPR_12; pfam13424 392021002938 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 392021002939 TPR motif; other site 392021002940 TPR repeat; Region: TPR_11; pfam13414 392021002941 binding surface 392021002942 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 392021002943 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021002944 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 392021002945 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 392021002946 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 392021002947 ferrochelatase; Reviewed; Region: hemH; PRK00035 392021002948 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 392021002949 C-terminal domain interface [polypeptide binding]; other site 392021002950 active site 392021002951 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 392021002952 active site 392021002953 N-terminal domain interface [polypeptide binding]; other site 392021002954 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 392021002955 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 392021002956 substrate binding site [chemical binding]; other site 392021002957 active site