-- dump date 20140620_034550 -- class Genbank::misc_feature -- table misc_feature_note -- id note 392021000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 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 ATP-binding cassette component of polysaccharide transport system; 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-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 392021000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 392021000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 392021000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 392021000017 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 392021000018 FAD binding pocket [chemical binding]; other site 392021000019 FAD binding motif [chemical binding]; other site 392021000020 phosphate binding motif [ion binding]; other site 392021000021 beta-alpha-beta structure motif; other site 392021000022 NAD binding pocket [chemical binding]; other site 392021000023 Iron coordination center [ion binding]; other site 392021000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 392021000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 392021000026 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 392021000027 active site 392021000028 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 392021000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 392021000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 392021000031 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 392021000032 trimer interface [polypeptide binding]; other site 392021000033 active site 392021000034 UDP-GlcNAc binding site [chemical binding]; other site 392021000035 lipid binding site [chemical binding]; lipid-binding site 392021000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 392021000037 active site 392021000038 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 392021000039 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 392021000040 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 392021000041 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 392021000042 FMN binding site [chemical binding]; other site 392021000043 active site 392021000044 catalytic residues [active] 392021000045 substrate binding site [chemical binding]; other site 392021000046 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 392021000047 NodB motif; other site 392021000048 putative active site [active] 392021000049 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 392021000050 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 392021000051 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 392021000052 intersubunit interface [polypeptide binding]; other site 392021000053 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 392021000054 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 392021000055 active site 392021000056 NTP binding site [chemical binding]; other site 392021000057 metal binding triad [ion binding]; metal-binding site 392021000058 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 392021000059 Competence protein; Region: Competence; pfam03772 392021000060 Autotransporter beta-domain; Region: Autotransporter; pfam03797 392021000061 AAA domain; Region: AAA_22; pfam13401 392021000062 Tetratricopeptide repeat; Region: TPR_12; pfam13424 392021000063 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 392021000064 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 392021000065 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 392021000066 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 392021000067 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 392021000068 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 392021000069 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 392021000070 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 392021000071 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 392021000072 Thioredoxin; Region: Thioredoxin_4; pfam13462 392021000073 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 392021000074 Methyltransferase domain; Region: Methyltransf_31; pfam13847 392021000075 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 392021000076 S-adenosylmethionine binding site [chemical binding]; other site 392021000077 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 392021000078 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 392021000079 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 392021000080 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021000081 Walker A/P-loop; other site 392021000082 ATP binding site [chemical binding]; other site 392021000083 Q-loop/lid; other site 392021000084 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021000085 ABC transporter signature motif; other site 392021000086 Walker B; other site 392021000087 D-loop; other site 392021000088 H-loop/switch region; other site 392021000089 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 392021000090 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 392021000091 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 392021000092 folate binding site [chemical binding]; other site 392021000093 NADP+ binding site [chemical binding]; other site 392021000094 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 392021000095 catalytic center binding site [active] 392021000096 ATP binding site [chemical binding]; other site 392021000097 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 392021000098 substrate binding pocket [chemical binding]; other site 392021000099 tetratricopeptide repeat protein; Provisional; Region: PRK11788 392021000100 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 392021000101 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 392021000102 Cu(I) binding site [ion binding]; other site 392021000103 Putative transcriptional regulator [Transcription]; Region: COG1678 392021000104 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 392021000105 Colicin V production protein; Region: Colicin_V; pfam02674 392021000106 Autotransporter beta-domain; Region: Autotransporter; smart00869 392021000107 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 392021000108 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 392021000109 Clp amino terminal domain; Region: Clp_N; pfam02861 392021000110 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 392021000111 Walker A motif; other site 392021000112 ATP binding site [chemical binding]; other site 392021000113 Walker B motif; other site 392021000114 arginine finger; other site 392021000115 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 392021000116 Walker A motif; other site 392021000117 ATP binding site [chemical binding]; other site 392021000118 Walker B motif; other site 392021000119 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 392021000120 UGMP family protein; Validated; Region: PRK09604 392021000121 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 392021000122 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 392021000123 Fatty acid desaturase; Region: FA_desaturase; pfam00487 392021000124 Di-iron ligands [ion binding]; other site 392021000125 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 392021000126 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cl17355 392021000127 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 392021000128 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 392021000129 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 392021000130 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 392021000131 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 392021000132 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 392021000133 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 392021000134 Ligand Binding Site [chemical binding]; other site 392021000135 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000136 FtsH Extracellular; Region: FtsH_ext; pfam06480 392021000137 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 392021000138 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 392021000139 Walker A motif; other site 392021000140 ATP binding site [chemical binding]; other site 392021000141 Walker B motif; other site 392021000142 arginine finger; other site 392021000143 Peptidase family M41; Region: Peptidase_M41; pfam01434 392021000144 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 392021000145 cofactor binding site; other site 392021000146 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 392021000147 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 392021000148 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 392021000149 Uncharacterized conserved protein [Function unknown]; Region: COG1565 392021000150 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000151 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 392021000152 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 392021000153 Mechanosensitive ion channel; Region: MS_channel; pfam00924 392021000154 membrane protein insertase; Provisional; Region: PRK01318 392021000155 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 392021000156 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 392021000157 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 392021000158 active site 392021000159 catalytic residues [active] 392021000160 metal binding site [ion binding]; metal-binding site 392021000161 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021000162 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 392021000163 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 392021000164 putative substrate translocation pore; other site 392021000165 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 392021000166 active site 392021000167 multimer interface [polypeptide binding]; other site 392021000168 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 392021000169 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 392021000170 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 392021000171 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 392021000172 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 392021000173 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 392021000174 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 392021000175 P-loop; other site 392021000176 Magnesium ion binding site [ion binding]; other site 392021000177 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 392021000178 Magnesium ion binding site [ion binding]; other site 392021000179 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 392021000180 ParB-like nuclease domain; Region: ParB; smart00470 392021000181 KorB domain; Region: KorB; pfam08535 392021000182 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 392021000183 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 392021000184 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 392021000185 ABC transporter; Region: ABC_tran_2; pfam12848 392021000186 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 392021000187 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 392021000188 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 392021000189 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 392021000190 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 392021000191 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 392021000192 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 392021000193 Zn2+ binding site [ion binding]; other site 392021000194 Mg2+ binding site [ion binding]; other site 392021000195 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 392021000196 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 392021000197 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 392021000198 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 392021000199 active site 392021000200 HIGH motif; other site 392021000201 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021000202 KMSK motif region; other site 392021000203 tRNA binding surface [nucleotide binding]; other site 392021000204 DALR anticodon binding domain; Region: DALR_1; smart00836 392021000205 anticodon binding site; other site 392021000206 Sporulation related domain; Region: SPOR; pfam05036 392021000207 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 392021000208 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 392021000209 CAP-like domain; other site 392021000210 active site 392021000211 primary dimer interface [polypeptide binding]; other site 392021000212 Gram-negative porin; Region: Porin_4; pfam13609 392021000213 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 392021000214 trimer interface [polypeptide binding]; other site 392021000215 active site 392021000216 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 392021000217 SecA binding site; other site 392021000218 Preprotein binding site; other site 392021000219 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 392021000220 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 392021000221 active site 392021000222 phosphorylation site [posttranslational modification] 392021000223 intermolecular recognition site; other site 392021000224 dimerization interface [polypeptide binding]; other site 392021000225 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 392021000226 DNA binding site [nucleotide binding] 392021000227 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 392021000228 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 392021000229 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 392021000230 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 392021000231 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 392021000232 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 392021000233 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 392021000234 EamA-like transporter family; Region: EamA; pfam00892 392021000235 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 392021000236 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 392021000237 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021000238 putative substrate translocation pore; other site 392021000239 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 392021000240 Autotransporter beta-domain; Region: Autotransporter; pfam03797 392021000241 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 392021000242 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 392021000243 active site 392021000244 HIGH motif; other site 392021000245 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 392021000246 KMSKS motif; other site 392021000247 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 392021000248 tRNA binding surface [nucleotide binding]; other site 392021000249 anticodon binding site; other site 392021000250 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 392021000251 rRNA interaction site [nucleotide binding]; other site 392021000252 S8 interaction site; other site 392021000253 putative laminin-1 binding site; other site 392021000254 elongation factor Ts; Provisional; Region: tsf; PRK09377 392021000255 UBA/TS-N domain; Region: UBA; pfam00627 392021000256 Elongation factor TS; Region: EF_TS; pfam00889 392021000257 Elongation factor TS; Region: EF_TS; pfam00889 392021000258 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 392021000259 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000260 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 392021000261 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 392021000262 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 392021000263 putative acyl-acceptor binding pocket; other site 392021000264 aspartate aminotransferase; Provisional; Region: PRK05764 392021000265 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 392021000266 pyridoxal 5'-phosphate binding site [chemical binding]; other site 392021000267 homodimer interface [polypeptide binding]; other site 392021000268 catalytic residue [active] 392021000269 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 392021000270 Tetratricopeptide repeat; Region: TPR_12; pfam13424 392021000271 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 392021000272 binding surface 392021000273 TPR motif; other site 392021000274 Methyltransferase domain; Region: Methyltransf_23; pfam13489 392021000275 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 392021000276 S-adenosylmethionine binding site [chemical binding]; other site 392021000277 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 392021000278 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 392021000279 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 392021000280 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 392021000281 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 392021000282 active site 392021000283 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000284 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 392021000285 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 392021000286 active site 392021000287 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 392021000288 dimer interface [polypeptide binding]; other site 392021000289 substrate binding site [chemical binding]; other site 392021000290 catalytic residues [active] 392021000291 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 392021000292 Permease; Region: Permease; pfam02405 392021000293 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 392021000294 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021000295 Walker A/P-loop; other site 392021000296 ATP binding site [chemical binding]; other site 392021000297 Q-loop/lid; other site 392021000298 ABC transporter signature motif; other site 392021000299 Walker B; other site 392021000300 D-loop; other site 392021000301 H-loop/switch region; other site 392021000302 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 392021000303 50S ribosomal protein L31; Provisional; Region: PRK01397 392021000304 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 392021000305 G1 box; other site 392021000306 GTP/Mg2+ binding site [chemical binding]; other site 392021000307 Switch I region; other site 392021000308 G2 box; other site 392021000309 G3 box; other site 392021000310 Switch II region; other site 392021000311 G4 box; other site 392021000312 G5 box; other site 392021000313 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 392021000314 nucleotide binding site [chemical binding]; other site 392021000315 substrate binding site [chemical binding]; other site 392021000316 type IV secretion system protein VirB3; Provisional; Region: PRK13899 392021000317 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 392021000318 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 392021000319 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021000320 Walker A/P-loop; other site 392021000321 ATP binding site [chemical binding]; other site 392021000322 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 392021000323 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 392021000324 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 392021000325 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 392021000326 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 392021000327 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 392021000328 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 392021000329 hypothetical protein; Provisional; Region: PRK13694 392021000330 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 392021000331 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 392021000332 Protein export membrane protein; Region: SecD_SecF; pfam02355 392021000333 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 392021000334 SLBB domain; Region: SLBB; pfam10531 392021000335 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 392021000336 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 392021000337 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 392021000338 Catalytic site [active] 392021000339 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 392021000340 ribonuclease III; Reviewed; Region: rnc; PRK00102 392021000341 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 392021000342 dimerization interface [polypeptide binding]; other site 392021000343 active site 392021000344 metal binding site [ion binding]; metal-binding site 392021000345 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 392021000346 dsRNA binding site [nucleotide binding]; other site 392021000347 GTPase Era; Provisional; Region: era; PRK15494 392021000348 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000349 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 392021000350 G1 box; other site 392021000351 GTP/Mg2+ binding site [chemical binding]; other site 392021000352 Switch I region; other site 392021000353 G2 box; other site 392021000354 Switch II region; other site 392021000355 G3 box; other site 392021000356 G4 box; other site 392021000357 G5 box; other site 392021000358 KH domain; Region: KH_2; pfam07650 392021000359 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 392021000360 active site 392021000361 putative DNA-binding cleft [nucleotide binding]; other site 392021000362 dimer interface [polypeptide binding]; other site 392021000363 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 392021000364 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 392021000365 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 392021000366 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 392021000367 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 392021000368 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 392021000369 AAA domain; Region: AAA_31; pfam13614 392021000370 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 392021000371 Walker A motif; other site 392021000372 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 392021000373 HflK protein; Region: hflK; TIGR01933 392021000374 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 392021000375 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 392021000376 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 392021000377 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 392021000378 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 392021000379 protein binding site [polypeptide binding]; other site 392021000380 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 392021000381 protein binding site [polypeptide binding]; other site 392021000382 hypothetical protein; Validated; Region: PRK01415 392021000383 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 392021000384 active site residue [active] 392021000385 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 392021000386 Iron-sulfur protein interface; other site 392021000387 proximal quinone binding site [chemical binding]; other site 392021000388 SdhD (CybS) interface [polypeptide binding]; other site 392021000389 proximal heme binding site [chemical binding]; other site 392021000390 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 392021000391 putative SdhC subunit interface [polypeptide binding]; other site 392021000392 putative proximal heme binding site [chemical binding]; other site 392021000393 putative Iron-sulfur protein interface [polypeptide binding]; other site 392021000394 putative proximal quinone binding site; other site 392021000395 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 392021000396 L-aspartate oxidase; Provisional; Region: PRK06175 392021000397 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 392021000398 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 392021000399 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 392021000400 dimer interface [polypeptide binding]; other site 392021000401 conserved gate region; other site 392021000402 putative PBP binding loops; other site 392021000403 ABC-ATPase subunit interface; other site 392021000404 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 392021000405 S17 interaction site [polypeptide binding]; other site 392021000406 S8 interaction site; other site 392021000407 16S rRNA interaction site [nucleotide binding]; other site 392021000408 streptomycin interaction site [chemical binding]; other site 392021000409 23S rRNA interaction site [nucleotide binding]; other site 392021000410 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 392021000411 30S ribosomal protein S7; Validated; Region: PRK05302 392021000412 elongation factor G; Reviewed; Region: PRK00007 392021000413 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 392021000414 G1 box; other site 392021000415 putative GEF interaction site [polypeptide binding]; other site 392021000416 GTP/Mg2+ binding site [chemical binding]; other site 392021000417 Switch I region; other site 392021000418 G2 box; other site 392021000419 G3 box; other site 392021000420 Switch II region; other site 392021000421 G4 box; other site 392021000422 G5 box; other site 392021000423 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 392021000424 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 392021000425 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 392021000426 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 392021000427 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 392021000428 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 392021000429 putative homodimer interface [polypeptide binding]; other site 392021000430 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 392021000431 heterodimer interface [polypeptide binding]; other site 392021000432 homodimer interface [polypeptide binding]; other site 392021000433 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 392021000434 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 392021000435 23S rRNA interface [nucleotide binding]; other site 392021000436 putative thiostrepton binding site; other site 392021000437 L7/L12 interface [polypeptide binding]; other site 392021000438 L25 interface [polypeptide binding]; other site 392021000439 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 392021000440 mRNA/rRNA interface [nucleotide binding]; other site 392021000441 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 392021000442 23S rRNA interface [nucleotide binding]; other site 392021000443 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 392021000444 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 392021000445 core dimer interface [polypeptide binding]; other site 392021000446 peripheral dimer interface [polypeptide binding]; other site 392021000447 L10 interface [polypeptide binding]; other site 392021000448 L11 interface [polypeptide binding]; other site 392021000449 putative EF-Tu interaction site [polypeptide binding]; other site 392021000450 putative EF-G interaction site [polypeptide binding]; other site 392021000451 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 392021000452 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 392021000453 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 392021000454 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 392021000455 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 392021000456 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 392021000457 RPB3 interaction site [polypeptide binding]; other site 392021000458 RPB1 interaction site [polypeptide binding]; other site 392021000459 RPB11 interaction site [polypeptide binding]; other site 392021000460 RPB10 interaction site [polypeptide binding]; other site 392021000461 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 392021000462 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 392021000463 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 392021000464 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 392021000465 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 392021000466 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 392021000467 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 392021000468 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 392021000469 DNA binding site [nucleotide binding] 392021000470 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 392021000471 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000472 multifunctional aminopeptidase A; Provisional; Region: PRK00913 392021000473 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 392021000474 interface (dimer of trimers) [polypeptide binding]; other site 392021000475 Substrate-binding/catalytic site; other site 392021000476 Zn-binding sites [ion binding]; other site 392021000477 ATPase MipZ; Region: MipZ; pfam09140 392021000478 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 392021000479 P-loop; other site 392021000480 Magnesium ion binding site [ion binding]; other site 392021000481 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 392021000482 Magnesium ion binding site [ion binding]; other site 392021000483 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 392021000484 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 392021000485 dimer interface [polypeptide binding]; other site 392021000486 anticodon binding site; other site 392021000487 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 392021000488 homodimer interface [polypeptide binding]; other site 392021000489 motif 1; other site 392021000490 active site 392021000491 motif 2; other site 392021000492 GAD domain; Region: GAD; pfam02938 392021000493 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 392021000494 active site 392021000495 motif 3; other site 392021000496 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 392021000497 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 392021000498 dihydrodipicolinate reductase; Provisional; Region: PRK00048 392021000499 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 392021000500 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 392021000501 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 392021000502 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 392021000503 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 392021000504 substrate binding pocket [chemical binding]; other site 392021000505 membrane-bound complex binding site; other site 392021000506 hinge residues; other site 392021000507 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 392021000508 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 392021000509 GatB domain; Region: GatB_Yqey; smart00845 392021000510 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 392021000511 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 392021000512 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 392021000513 Uncharacterized conserved protein [Function unknown]; Region: COG4997 392021000514 ribosome recycling factor; Reviewed; Region: frr; PRK00083 392021000515 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 392021000516 hinge region; other site 392021000517 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 392021000518 putative nucleotide binding site [chemical binding]; other site 392021000519 uridine monophosphate binding site [chemical binding]; other site 392021000520 homohexameric interface [polypeptide binding]; other site 392021000521 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 392021000522 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 392021000523 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 392021000524 putative substrate translocation pore; other site 392021000525 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 392021000526 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 392021000527 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 392021000528 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 392021000529 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 392021000530 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 392021000531 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 392021000532 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 392021000533 Surface antigen; Region: Bac_surface_Ag; pfam01103 392021000534 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 392021000535 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 392021000536 active site 392021000537 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 392021000538 protein binding site [polypeptide binding]; other site 392021000539 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 392021000540 putative substrate binding region [chemical binding]; other site 392021000541 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 392021000542 putative RNA binding site [nucleotide binding]; other site 392021000543 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 392021000544 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 392021000545 S-adenosylmethionine binding site [chemical binding]; other site 392021000546 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 392021000547 putative coenzyme Q binding site [chemical binding]; other site 392021000548 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021000549 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 392021000550 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 392021000551 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 392021000552 RNA methyltransferase, RsmE family; Region: TIGR00046 392021000553 Uncharacterized conserved protein [Function unknown]; Region: COG2155 392021000554 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 392021000555 Protein export membrane protein; Region: SecD_SecF; cl14618 392021000556 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 392021000557 IHF dimer interface [polypeptide binding]; other site 392021000558 IHF - DNA interface [nucleotide binding]; other site 392021000559 DNA polymerase III subunit delta'; Validated; Region: PRK06581 392021000560 signal recognition particle protein; Provisional; Region: PRK10867 392021000561 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 392021000562 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 392021000563 P loop; other site 392021000564 GTP binding site [chemical binding]; other site 392021000565 Signal peptide binding domain; Region: SRP_SPB; pfam02978 392021000566 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 392021000567 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 392021000568 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 392021000569 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 392021000570 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 392021000571 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 392021000572 FeS/SAM binding site; other site 392021000573 HemN C-terminal domain; Region: HemN_C; pfam06969 392021000574 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 392021000575 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 392021000576 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 392021000577 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 392021000578 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 392021000579 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 392021000580 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 392021000581 active site 392021000582 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 392021000583 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 392021000584 E3 interaction surface; other site 392021000585 lipoyl attachment site [posttranslational modification]; other site 392021000586 e3 binding domain; Region: E3_binding; pfam02817 392021000587 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 392021000588 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 392021000589 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 392021000590 TPP-binding site [chemical binding]; other site 392021000591 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 392021000592 dimer interface [polypeptide binding]; other site 392021000593 PYR/PP interface [polypeptide binding]; other site 392021000594 TPP binding site [chemical binding]; other site 392021000595 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 392021000596 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 392021000597 active site 392021000598 Zn binding site [ion binding]; other site 392021000599 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 392021000600 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 392021000601 Walker A/P-loop; other site 392021000602 ATP binding site [chemical binding]; other site 392021000603 Q-loop/lid; other site 392021000604 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 392021000605 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 392021000606 ABC transporter signature motif; other site 392021000607 Walker B; other site 392021000608 D-loop; other site 392021000609 H-loop/switch region; other site 392021000610 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 392021000611 Tetratricopeptide repeat; Region: TPR_6; pfam13174 392021000612 ChaB; Region: ChaB; cl01887 392021000613 ChaB; Region: ChaB; cl01887 392021000614 chaperone protein DnaJ; Provisional; Region: PRK14300 392021000615 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 392021000616 HSP70 interaction site [polypeptide binding]; other site 392021000617 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 392021000618 substrate binding site [polypeptide binding]; other site 392021000619 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 392021000620 Zn binding sites [ion binding]; other site 392021000621 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 392021000622 dimer interface [polypeptide binding]; other site 392021000623 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 392021000624 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 392021000625 nucleotide binding site [chemical binding]; other site 392021000626 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 392021000627 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 392021000628 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 392021000629 Lipopolysaccharide-assembly; Region: LptE; cl01125 392021000630 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 392021000631 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 392021000632 diiron binding motif [ion binding]; other site 392021000633 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 392021000634 Subunit III/VIIa interface [polypeptide binding]; other site 392021000635 Phospholipid binding site [chemical binding]; other site 392021000636 Subunit I/III interface [polypeptide binding]; other site 392021000637 Subunit III/VIb interface [polypeptide binding]; other site 392021000638 Subunit III/VIa interface; other site 392021000639 Subunit III/Vb interface [polypeptide binding]; other site 392021000640 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 392021000641 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 392021000642 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 392021000643 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 392021000644 trimer interface [polypeptide binding]; other site 392021000645 active site 392021000646 substrate binding site [chemical binding]; other site 392021000647 CoA binding site [chemical binding]; other site 392021000648 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 392021000649 Ligand Binding Site [chemical binding]; other site 392021000650 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 392021000651 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 392021000652 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 392021000653 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 392021000654 catalytic loop [active] 392021000655 iron binding site [ion binding]; other site 392021000656 chaperone protein HscA; Provisional; Region: hscA; PRK01433 392021000657 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 392021000658 nucleotide binding site [chemical binding]; other site 392021000659 co-chaperone HscB; Provisional; Region: hscB; PRK01356 392021000660 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 392021000661 HSP70 interaction site [polypeptide binding]; other site 392021000662 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 392021000663 RNA/DNA hybrid binding site [nucleotide binding]; other site 392021000664 active site 392021000665 excinuclease ABC subunit B; Provisional; Region: PRK05298 392021000666 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 392021000667 ATP binding site [chemical binding]; other site 392021000668 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 392021000669 nucleotide binding region [chemical binding]; other site 392021000670 ATP-binding site [chemical binding]; other site 392021000671 Ultra-violet resistance protein B; Region: UvrB; pfam12344 392021000672 UvrB/uvrC motif; Region: UVR; pfam02151 392021000673 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 392021000674 GSH binding site [chemical binding]; other site 392021000675 catalytic residues [active] 392021000676 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 392021000677 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021000678 Walker A/P-loop; other site 392021000679 ATP binding site [chemical binding]; other site 392021000680 Q-loop/lid; other site 392021000681 Pleckstrin homology-like domain; Region: PH-like; cl17171 392021000682 DNA gyrase subunit A; Validated; Region: PRK05560 392021000683 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 392021000684 CAP-like domain; other site 392021000685 active site 392021000686 primary dimer interface [polypeptide binding]; other site 392021000687 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000688 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000689 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000690 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000691 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 392021000692 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 392021000693 active site 392021000694 catalytic residues [active] 392021000695 metal binding site [ion binding]; metal-binding site 392021000696 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 392021000697 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 392021000698 putative active site [active] 392021000699 substrate binding site [chemical binding]; other site 392021000700 putative cosubstrate binding site; other site 392021000701 catalytic site [active] 392021000702 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 392021000703 substrate binding site [chemical binding]; other site 392021000704 Protein of unknown function (DUF563); Region: DUF563; cl15705 392021000705 Predicted ATPase [General function prediction only]; Region: COG1485 392021000706 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 392021000707 Walker A motif; other site 392021000708 ATP binding site [chemical binding]; other site 392021000709 Walker B motif; other site 392021000710 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 392021000711 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 392021000712 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 392021000713 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 392021000714 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 392021000715 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 392021000716 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021000717 Walker A/P-loop; other site 392021000718 ATP binding site [chemical binding]; other site 392021000719 Q-loop/lid; other site 392021000720 ABC transporter signature motif; other site 392021000721 Walker B; other site 392021000722 D-loop; other site 392021000723 H-loop/switch region; other site 392021000724 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 392021000725 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 392021000726 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 392021000727 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 392021000728 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 392021000729 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 392021000730 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 392021000731 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 392021000732 putative metal binding site; other site 392021000733 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 392021000734 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 392021000735 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 392021000736 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 392021000737 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 392021000738 ATP binding site [chemical binding]; other site 392021000739 active site 392021000740 substrate binding site [chemical binding]; other site 392021000741 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 392021000742 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 392021000743 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 392021000744 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 392021000745 active site 392021000746 dimer interface [polypeptide binding]; other site 392021000747 motif 1; other site 392021000748 motif 2; other site 392021000749 motif 3; other site 392021000750 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 392021000751 anticodon binding site; other site 392021000752 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021000753 Walker A/P-loop; other site 392021000754 ATP binding site [chemical binding]; other site 392021000755 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 392021000756 V-type ATP synthase subunit I; Validated; Region: PRK05771 392021000757 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 392021000758 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 392021000759 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 392021000760 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 392021000761 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 392021000762 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 392021000763 ATP binding site [chemical binding]; other site 392021000764 Mg2+ binding site [ion binding]; other site 392021000765 G-X-G motif; other site 392021000766 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 392021000767 anchoring element; other site 392021000768 dimer interface [polypeptide binding]; other site 392021000769 ATP binding site [chemical binding]; other site 392021000770 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 392021000771 active site 392021000772 metal binding site [ion binding]; metal-binding site 392021000773 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 392021000774 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 392021000775 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 392021000776 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 392021000777 protein binding site [polypeptide binding]; other site 392021000778 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 392021000779 Catalytic dyad [active] 392021000780 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 392021000781 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 392021000782 dimer interface [polypeptide binding]; other site 392021000783 phosphorylation site [posttranslational modification] 392021000784 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 392021000785 ATP binding site [chemical binding]; other site 392021000786 Mg2+ binding site [ion binding]; other site 392021000787 G-X-G motif; other site 392021000788 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 392021000789 Tetratricopeptide repeat; Region: TPR_6; pfam13174 392021000790 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 392021000791 FOG: WD40-like repeat [Function unknown]; Region: COG1520 392021000792 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 392021000793 Trp docking motif [polypeptide binding]; other site 392021000794 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 392021000795 23S rRNA interface [nucleotide binding]; other site 392021000796 L3 interface [polypeptide binding]; other site 392021000797 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 392021000798 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 392021000799 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 392021000800 DCoH tetramer interaction site [polypeptide binding]; other site 392021000801 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 392021000802 putative active site [active] 392021000803 Ap4A binding site [chemical binding]; other site 392021000804 nudix motif; other site 392021000805 putative metal binding site [ion binding]; other site 392021000806 elongation factor P; Validated; Region: PRK00529 392021000807 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 392021000808 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 392021000809 RNA binding site [nucleotide binding]; other site 392021000810 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 392021000811 RNA binding site [nucleotide binding]; other site 392021000812 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 392021000813 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 392021000814 active site 392021000815 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 392021000816 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 392021000817 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 392021000818 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 392021000819 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 392021000820 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 392021000821 HlyD family secretion protein; Region: HlyD_3; pfam13437 392021000822 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021000823 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 392021000824 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 392021000825 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 392021000826 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 392021000827 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 392021000828 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 392021000829 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 392021000830 FAD binding domain; Region: FAD_binding_4; pfam01565 392021000831 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 392021000832 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 392021000833 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 392021000834 ATP-grasp domain; Region: ATP-grasp_4; cl17255 392021000835 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 392021000836 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 392021000837 Cell division protein FtsQ; Region: FtsQ; pfam03799 392021000838 cell division protein FtsA; Region: ftsA; TIGR01174 392021000839 Cell division protein FtsA; Region: FtsA; smart00842 392021000840 Cell division protein FtsA; Region: FtsA; pfam14450 392021000841 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 392021000842 Cytochrome c2 [Energy production and conversion]; Region: COG3474 392021000843 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 392021000844 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 392021000845 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 392021000846 RNA binding site [nucleotide binding]; other site 392021000847 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 392021000848 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 392021000849 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 392021000850 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 392021000851 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 392021000852 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 392021000853 RNA binding surface [nucleotide binding]; other site 392021000854 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 392021000855 active site 392021000856 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 392021000857 putative catalytic site [active] 392021000858 putative phosphate binding site [ion binding]; other site 392021000859 active site 392021000860 metal binding site A [ion binding]; metal-binding site 392021000861 DNA binding site [nucleotide binding] 392021000862 putative AP binding site [nucleotide binding]; other site 392021000863 putative metal binding site B [ion binding]; other site 392021000864 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 392021000865 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 392021000866 tetramer interface [polypeptide binding]; other site 392021000867 TPP-binding site [chemical binding]; other site 392021000868 heterodimer interface [polypeptide binding]; other site 392021000869 phosphorylation loop region [posttranslational modification] 392021000870 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 392021000871 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 392021000872 alpha subunit interface [polypeptide binding]; other site 392021000873 TPP binding site [chemical binding]; other site 392021000874 heterodimer interface [polypeptide binding]; other site 392021000875 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 392021000876 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 392021000877 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 392021000878 G1 box; other site 392021000879 putative GEF interaction site [polypeptide binding]; other site 392021000880 GTP/Mg2+ binding site [chemical binding]; other site 392021000881 Switch I region; other site 392021000882 G2 box; other site 392021000883 G3 box; other site 392021000884 Switch II region; other site 392021000885 G4 box; other site 392021000886 G5 box; other site 392021000887 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 392021000888 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 392021000889 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 392021000890 isocitrate dehydrogenase; Validated; Region: PRK09222 392021000891 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 392021000892 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 392021000893 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 392021000894 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 392021000895 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 392021000896 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 392021000897 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 392021000898 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 392021000899 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 392021000900 [2Fe-2S] cluster binding site [ion binding]; other site 392021000901 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 392021000902 Qi binding site; other site 392021000903 cytochrome b; Provisional; Region: CYTB; MTH00191 392021000904 intrachain domain interface; other site 392021000905 interchain domain interface [polypeptide binding]; other site 392021000906 heme bH binding site [chemical binding]; other site 392021000907 heme bL binding site [chemical binding]; other site 392021000908 Qo binding site; other site 392021000909 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 392021000910 interchain domain interface [polypeptide binding]; other site 392021000911 intrachain domain interface; other site 392021000912 Qi binding site; other site 392021000913 Qo binding site; other site 392021000914 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 392021000915 catalytic site [active] 392021000916 metal binding site [ion binding]; metal-binding site 392021000917 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 392021000918 Cytochrome c; Region: Cytochrom_C; cl11414 392021000919 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 392021000920 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 392021000921 putative dimer interface [polypeptide binding]; other site 392021000922 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 392021000923 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 392021000924 PCRF domain; Region: PCRF; pfam03462 392021000925 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 392021000926 RF-1 domain; Region: RF-1; pfam00472 392021000927 GTP-binding protein LepA; Provisional; Region: PRK05433 392021000928 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 392021000929 G1 box; other site 392021000930 putative GEF interaction site [polypeptide binding]; other site 392021000931 GTP/Mg2+ binding site [chemical binding]; other site 392021000932 Switch I region; other site 392021000933 G2 box; other site 392021000934 G3 box; other site 392021000935 Switch II region; other site 392021000936 G4 box; other site 392021000937 G5 box; other site 392021000938 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 392021000939 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 392021000940 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 392021000941 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 392021000942 HD domain; Region: HD_4; pfam13328 392021000943 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021000944 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 392021000945 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 392021000946 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021000947 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 392021000948 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 392021000949 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 392021000950 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 392021000951 oligomeric interface; other site 392021000952 putative active site [active] 392021000953 homodimer interface [polypeptide binding]; other site 392021000954 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 392021000955 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 392021000956 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 392021000957 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 392021000958 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 392021000959 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 392021000960 VirB7 interaction site; other site 392021000961 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 392021000962 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 392021000963 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 392021000964 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 392021000965 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 392021000966 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 392021000967 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 392021000968 Walker A motif; other site 392021000969 hexamer interface [polypeptide binding]; other site 392021000970 ATP binding site [chemical binding]; other site 392021000971 Walker B motif; other site 392021000972 type IV secretion system component VirD4; Provisional; Region: PRK13897 392021000973 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 392021000974 Walker A motif; other site 392021000975 ATP binding site [chemical binding]; other site 392021000976 Walker B motif; other site 392021000977 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 392021000978 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 392021000979 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 392021000980 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 392021000981 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 392021000982 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 392021000983 active site 392021000984 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 392021000985 MutS domain I; Region: MutS_I; pfam01624 392021000986 MutS domain II; Region: MutS_II; pfam05188 392021000987 MutS domain III; Region: MutS_III; pfam05192 392021000988 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 392021000989 Walker A/P-loop; other site 392021000990 ATP binding site [chemical binding]; other site 392021000991 Q-loop/lid; other site 392021000992 ABC transporter signature motif; other site 392021000993 Walker B; other site 392021000994 D-loop; other site 392021000995 H-loop/switch region; other site 392021000996 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 392021000997 Peptidase family M23; Region: Peptidase_M23; pfam01551 392021000998 Protein of unknown function DUF45; Region: DUF45; pfam01863 392021000999 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 392021001000 translocation protein TolB; Provisional; Region: tolB; PRK05137 392021001001 TolB amino-terminal domain; Region: TolB_N; pfam04052 392021001002 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 392021001003 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 392021001004 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 392021001005 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 392021001006 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 392021001007 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 392021001008 DNA binding residues [nucleotide binding] 392021001009 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 392021001010 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 392021001011 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 392021001012 Ligand Binding Site [chemical binding]; other site 392021001013 amino acid transporter; Region: 2A0306; TIGR00909 392021001014 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 392021001015 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 392021001016 dimer interface [polypeptide binding]; other site 392021001017 motif 1; other site 392021001018 active site 392021001019 motif 2; other site 392021001020 motif 3; other site 392021001021 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 392021001022 anticodon binding site; other site 392021001023 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 392021001024 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 392021001025 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 392021001026 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 392021001027 TolQ protein; Region: tolQ; TIGR02796 392021001028 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 392021001029 TolR protein; Region: tolR; TIGR02801 392021001030 Gram-negative bacterial tonB protein; Region: TonB; cl10048 392021001031 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 392021001032 HD domain; Region: HD_4; pfam13328 392021001033 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 392021001034 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021001035 putative substrate translocation pore; other site 392021001036 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 392021001037 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 392021001038 HlyD family secretion protein; Region: HlyD_3; pfam13437 392021001039 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 392021001040 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 392021001041 Walker A/P-loop; other site 392021001042 ATP binding site [chemical binding]; other site 392021001043 Q-loop/lid; other site 392021001044 ABC transporter signature motif; other site 392021001045 Walker B; other site 392021001046 D-loop; other site 392021001047 H-loop/switch region; other site 392021001048 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 392021001049 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 392021001050 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 392021001051 nucleotide binding site/active site [active] 392021001052 HIT family signature motif; other site 392021001053 catalytic residue [active] 392021001054 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 392021001055 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 392021001056 active site 392021001057 HslU subunit interaction site [polypeptide binding]; other site 392021001058 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 392021001059 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 392021001060 Walker A motif; other site 392021001061 ATP binding site [chemical binding]; other site 392021001062 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 392021001063 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 392021001064 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021001065 Uncharacterized conserved protein [Function unknown]; Region: COG5464 392021001066 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021001067 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 392021001068 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 392021001069 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021001070 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 392021001071 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 392021001072 dimerization interface [polypeptide binding]; other site 392021001073 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...; Region: Frataxin; cd00503 392021001074 putative iron binding site [ion binding]; other site 392021001075 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 392021001076 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 392021001077 HIGH motif; other site 392021001078 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021001079 active site 392021001080 KMSKS motif; other site 392021001081 DNA topoisomerase I; Validated; Region: PRK06599 392021001082 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 392021001083 active site 392021001084 interdomain interaction site; other site 392021001085 putative metal-binding site [ion binding]; other site 392021001086 nucleotide binding site [chemical binding]; other site 392021001087 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 392021001088 domain I; other site 392021001089 DNA binding groove [nucleotide binding] 392021001090 phosphate binding site [ion binding]; other site 392021001091 domain II; other site 392021001092 domain III; other site 392021001093 nucleotide binding site [chemical binding]; other site 392021001094 catalytic site [active] 392021001095 domain IV; other site 392021001096 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 392021001097 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 392021001098 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 392021001099 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 392021001100 dimer interface [polypeptide binding]; other site 392021001101 decamer (pentamer of dimers) interface [polypeptide binding]; other site 392021001102 catalytic triad [active] 392021001103 peroxidatic and resolving cysteines [active] 392021001104 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 392021001105 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 392021001106 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 392021001107 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 392021001108 Sulfatase; Region: Sulfatase; pfam00884 392021001109 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 392021001110 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 392021001111 sequence-specific DNA binding site [nucleotide binding]; other site 392021001112 salt bridge; other site 392021001113 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 392021001114 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 392021001115 NADP binding site [chemical binding]; other site 392021001116 active site 392021001117 putative substrate binding site [chemical binding]; other site 392021001118 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 392021001119 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 392021001120 NAD(P) binding site [chemical binding]; other site 392021001121 homodimer interface [polypeptide binding]; other site 392021001122 substrate binding site [chemical binding]; other site 392021001123 active site 392021001124 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 392021001125 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 392021001126 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 392021001127 active site 392021001128 homodimer interface [polypeptide binding]; other site 392021001129 Methyltransferase domain; Region: Methyltransf_31; pfam13847 392021001130 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 392021001131 S-adenosylmethionine binding site [chemical binding]; other site 392021001132 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 392021001133 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 392021001134 active site 392021001135 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 392021001136 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 392021001137 active site 392021001138 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 392021001139 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 392021001140 HlyD family secretion protein; Region: HlyD_3; pfam13437 392021001141 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 392021001142 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 392021001143 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 392021001144 catalytic site [active] 392021001145 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 392021001146 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 392021001147 putative ADP-binding pocket [chemical binding]; other site 392021001148 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021001149 Walker A/P-loop; other site 392021001150 ATP binding site [chemical binding]; other site 392021001151 Q-loop/lid; other site 392021001152 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 392021001153 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 392021001154 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 392021001155 RNA binding surface [nucleotide binding]; other site 392021001156 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 392021001157 UbiA prenyltransferase family; Region: UbiA; pfam01040 392021001158 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 392021001159 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 392021001160 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 392021001161 TPR repeat; Region: TPR_11; pfam13414 392021001162 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 392021001163 TPR motif; other site 392021001164 binding surface 392021001165 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 392021001166 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 392021001167 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 392021001168 RimM N-terminal domain; Region: RimM; pfam01782 392021001169 PRC-barrel domain; Region: PRC; pfam05239 392021001170 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 392021001171 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 392021001172 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 392021001173 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 392021001174 active site 392021001175 DNA binding site [nucleotide binding] 392021001176 YCII-related domain; Region: YCII; cl00999 392021001177 hypothetical protein; Provisional; Region: PRK14388 392021001178 NADH dehydrogenase subunit E; Validated; Region: PRK07539 392021001179 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 392021001180 putative dimer interface [polypeptide binding]; other site 392021001181 [2Fe-2S] cluster binding site [ion binding]; other site 392021001182 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 392021001183 NADH dehydrogenase subunit D; Validated; Region: PRK06075 392021001184 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 392021001185 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 392021001186 NADH dehydrogenase subunit B; Validated; Region: PRK06411 392021001187 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 392021001188 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 392021001189 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 392021001190 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 392021001191 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 392021001192 active site 392021001193 DNA binding site [nucleotide binding] 392021001194 Int/Topo IB signature motif; other site 392021001195 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 392021001196 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 392021001197 NAD binding site [chemical binding]; other site 392021001198 homotetramer interface [polypeptide binding]; other site 392021001199 homodimer interface [polypeptide binding]; other site 392021001200 substrate binding site [chemical binding]; other site 392021001201 active site 392021001202 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 392021001203 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 392021001204 putative active site [active] 392021001205 catalytic triad [active] 392021001206 putative dimer interface [polypeptide binding]; other site 392021001207 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 392021001208 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 392021001209 amidase catalytic site [active] 392021001210 Zn binding residues [ion binding]; other site 392021001211 substrate binding site [chemical binding]; other site 392021001212 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 392021001213 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 392021001214 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 392021001215 TM-ABC transporter signature motif; other site 392021001216 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 392021001217 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021001218 Walker A/P-loop; other site 392021001219 ATP binding site [chemical binding]; other site 392021001220 Q-loop/lid; other site 392021001221 ABC transporter signature motif; other site 392021001222 Walker B; other site 392021001223 D-loop; other site 392021001224 H-loop/switch region; other site 392021001225 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 392021001226 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 392021001227 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 392021001228 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 392021001229 active site 392021001230 HIGH motif; other site 392021001231 KMSKS motif; other site 392021001232 Predicted permeases [General function prediction only]; Region: COG0679 392021001233 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 392021001234 Malic enzyme, N-terminal domain; Region: malic; pfam00390 392021001235 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 392021001236 putative NAD(P) binding site [chemical binding]; other site 392021001237 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 392021001238 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 392021001239 putative active site [active] 392021001240 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 392021001241 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021001242 malate dehydrogenase; Reviewed; Region: PRK06223 392021001243 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 392021001244 NAD(P) binding site [chemical binding]; other site 392021001245 dimer interface [polypeptide binding]; other site 392021001246 tetramer (dimer of dimers) interface [polypeptide binding]; other site 392021001247 substrate binding site [chemical binding]; other site 392021001248 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 392021001249 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021001250 CTP synthetase; Validated; Region: pyrG; PRK05380 392021001251 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 392021001252 Catalytic site [active] 392021001253 active site 392021001254 UTP binding site [chemical binding]; other site 392021001255 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 392021001256 active site 392021001257 putative oxyanion hole; other site 392021001258 catalytic triad [active] 392021001259 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 392021001260 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 392021001261 Ligand binding site; other site 392021001262 oligomer interface; other site 392021001263 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 392021001264 GTP cyclohydrolase I; Provisional; Region: PLN03044 392021001265 active site 392021001266 prolyl-tRNA synthetase; Provisional; Region: PRK12325 392021001267 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 392021001268 dimer interface [polypeptide binding]; other site 392021001269 motif 1; other site 392021001270 active site 392021001271 motif 2; other site 392021001272 motif 3; other site 392021001273 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 392021001274 anticodon binding site; other site 392021001275 Fic family protein [Function unknown]; Region: COG3177 392021001276 Fic/DOC family; Region: Fic; pfam02661 392021001277 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 392021001278 RuvA N terminal domain; Region: RuvA_N; pfam01330 392021001279 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 392021001280 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 392021001281 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 392021001282 Walker A motif; other site 392021001283 ATP binding site [chemical binding]; other site 392021001284 Walker B motif; other site 392021001285 arginine finger; other site 392021001286 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 392021001287 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 392021001288 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 392021001289 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021001290 Walker A/P-loop; other site 392021001291 ATP binding site [chemical binding]; other site 392021001292 Q-loop/lid; other site 392021001293 ABC transporter signature motif; other site 392021001294 Walker B; other site 392021001295 D-loop; other site 392021001296 H-loop/switch region; other site 392021001297 muropeptide transporter; Validated; Region: ampG; cl17669 392021001298 muropeptide transporter; Reviewed; Region: ampG; PRK11902 392021001299 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 392021001300 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 392021001301 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001302 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 392021001303 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 392021001304 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 392021001305 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 392021001306 BON domain; Region: BON; pfam04972 392021001307 BON domain; Region: BON; pfam04972 392021001308 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 392021001309 Iron permease FTR1 family; Region: FTR1; cl00475 392021001310 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 392021001311 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 392021001312 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 392021001313 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 392021001314 active site 392021001315 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 392021001316 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 392021001317 catalytic residues [active] 392021001318 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 392021001319 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 392021001320 tandem repeat interface [polypeptide binding]; other site 392021001321 oligomer interface [polypeptide binding]; other site 392021001322 active site residues [active] 392021001323 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 392021001324 trimer interface [polypeptide binding]; other site 392021001325 active site 392021001326 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 392021001327 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 392021001328 N-acetyl-D-glucosamine binding site [chemical binding]; other site 392021001329 catalytic residue [active] 392021001330 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 392021001331 dimer interface [polypeptide binding]; other site 392021001332 catalytic triad [active] 392021001333 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 392021001334 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 392021001335 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 392021001336 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 392021001337 catalytic triad [active] 392021001338 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 392021001339 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 392021001340 Subunit I/III interface [polypeptide binding]; other site 392021001341 D-pathway; other site 392021001342 Subunit I/VIIc interface [polypeptide binding]; other site 392021001343 Subunit I/IV interface [polypeptide binding]; other site 392021001344 Subunit I/II interface [polypeptide binding]; other site 392021001345 Low-spin heme (heme a) binding site [chemical binding]; other site 392021001346 Subunit I/VIIa interface [polypeptide binding]; other site 392021001347 Subunit I/VIa interface [polypeptide binding]; other site 392021001348 Dimer interface; other site 392021001349 Putative water exit pathway; other site 392021001350 Binuclear center (heme a3/CuB) [ion binding]; other site 392021001351 K-pathway; other site 392021001352 Subunit I/Vb interface [polypeptide binding]; other site 392021001353 Putative proton exit pathway; other site 392021001354 Subunit I/VIb interface; other site 392021001355 Subunit I/VIc interface [polypeptide binding]; other site 392021001356 Electron transfer pathway; other site 392021001357 Subunit I/VIIIb interface [polypeptide binding]; other site 392021001358 Subunit I/VIIb interface [polypeptide binding]; other site 392021001359 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 392021001360 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 392021001361 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001362 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 392021001363 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 392021001364 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 392021001365 putative peptidase; Provisional; Region: PRK11649 392021001366 Peptidase family M23; Region: Peptidase_M23; pfam01551 392021001367 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 392021001368 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 392021001369 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 392021001370 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 392021001371 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 392021001372 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021001373 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 392021001374 cell division protein FtsW; Region: ftsW; TIGR02614 392021001375 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 392021001376 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 392021001377 active site 392021001378 homodimer interface [polypeptide binding]; other site 392021001379 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 392021001380 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 392021001381 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 392021001382 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 392021001383 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 392021001384 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 392021001385 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 392021001386 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021001387 diaminopimelate epimerase; Region: DapF; TIGR00652 392021001388 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 392021001389 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 392021001390 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 392021001391 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 392021001392 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 392021001393 FeS/SAM binding site; other site 392021001394 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 392021001395 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 392021001396 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 392021001397 dimer interface [polypeptide binding]; other site 392021001398 motif 1; other site 392021001399 active site 392021001400 motif 2; other site 392021001401 motif 3; other site 392021001402 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 392021001403 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 392021001404 putative tRNA-binding site [nucleotide binding]; other site 392021001405 B3/4 domain; Region: B3_4; pfam03483 392021001406 tRNA synthetase B5 domain; Region: B5; smart00874 392021001407 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 392021001408 dimer interface [polypeptide binding]; other site 392021001409 motif 1; other site 392021001410 motif 3; other site 392021001411 motif 2; other site 392021001412 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 392021001413 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 392021001414 DNA polymerase III subunit beta; Validated; Region: PRK05643 392021001415 putative DNA binding surface [nucleotide binding]; other site 392021001416 dimer interface [polypeptide binding]; other site 392021001417 beta-clamp/clamp loader binding surface; other site 392021001418 beta-clamp/translesion DNA polymerase binding surface; other site 392021001419 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 392021001420 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 392021001421 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 392021001422 HIGH motif; other site 392021001423 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 392021001424 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021001425 active site 392021001426 KMSKS motif; other site 392021001427 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 392021001428 tRNA binding surface [nucleotide binding]; other site 392021001429 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 392021001430 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 392021001431 catalytic site [active] 392021001432 putative active site [active] 392021001433 putative substrate binding site [chemical binding]; other site 392021001434 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 392021001435 Septum formation initiator; Region: DivIC; pfam04977 392021001436 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 392021001437 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 392021001438 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 392021001439 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 392021001440 catalytic residue [active] 392021001441 putative FPP diphosphate binding site; other site 392021001442 putative FPP binding hydrophobic cleft; other site 392021001443 dimer interface [polypeptide binding]; other site 392021001444 putative IPP diphosphate binding site; other site 392021001445 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021001446 HAMP domain; Region: HAMP; pfam00672 392021001447 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 392021001448 dimer interface [polypeptide binding]; other site 392021001449 phosphorylation site [posttranslational modification] 392021001450 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 392021001451 ATP binding site [chemical binding]; other site 392021001452 Mg2+ binding site [ion binding]; other site 392021001453 G-X-G motif; other site 392021001454 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 392021001455 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 392021001456 active site 392021001457 phosphorylation site [posttranslational modification] 392021001458 intermolecular recognition site; other site 392021001459 dimerization interface [polypeptide binding]; other site 392021001460 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 392021001461 DNA binding site [nucleotide binding] 392021001462 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 392021001463 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 392021001464 homodimer interface [polypeptide binding]; other site 392021001465 substrate-cofactor binding pocket; other site 392021001466 catalytic residue [active] 392021001467 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 392021001468 dihydrodipicolinate synthase; Region: dapA; TIGR00674 392021001469 dimer interface [polypeptide binding]; other site 392021001470 active site 392021001471 catalytic residue [active] 392021001472 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 392021001473 SmpB-tmRNA interface; other site 392021001474 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 392021001475 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 392021001476 catalytic residues [active] 392021001477 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 392021001478 CoA binding domain; Region: CoA_binding; pfam02629 392021001479 CoA-ligase; Region: Ligase_CoA; pfam00549 392021001480 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 392021001481 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 392021001482 CoA-ligase; Region: Ligase_CoA; pfam00549 392021001483 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 392021001484 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 392021001485 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 392021001486 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 392021001487 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 392021001488 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 392021001489 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 392021001490 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 392021001491 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 392021001492 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 392021001493 Predicted membrane protein [Function unknown]; Region: COG1238 392021001494 Predicted membrane protein/domain [Function unknown]; Region: COG1714 392021001495 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 392021001496 RecR protein; Region: RecR; pfam02132 392021001497 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 392021001498 putative active site [active] 392021001499 putative metal-binding site [ion binding]; other site 392021001500 tetramer interface [polypeptide binding]; other site 392021001501 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 392021001502 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 392021001503 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 392021001504 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 392021001505 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 392021001506 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 392021001507 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 392021001508 Predicted permeases [General function prediction only]; Region: COG0679 392021001509 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 392021001510 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 392021001511 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 392021001512 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 392021001513 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 392021001514 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 392021001515 tetramerization interface [polypeptide binding]; other site 392021001516 NAD(P) binding site [chemical binding]; other site 392021001517 catalytic residues [active] 392021001518 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 392021001519 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 392021001520 active site 392021001521 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 392021001522 Part of AAA domain; Region: AAA_19; pfam13245 392021001523 Family description; Region: UvrD_C_2; pfam13538 392021001524 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 392021001525 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 392021001526 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 392021001527 tetramer interface [polypeptide binding]; other site 392021001528 pyridoxal 5'-phosphate binding site [chemical binding]; other site 392021001529 catalytic residue [active] 392021001530 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 392021001531 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 392021001532 Walker A motif; other site 392021001533 ATP binding site [chemical binding]; other site 392021001534 Walker B motif; other site 392021001535 arginine finger; other site 392021001536 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 392021001537 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 392021001538 30S subunit binding site; other site 392021001539 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 392021001540 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 392021001541 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 392021001542 homodimer interface [polypeptide binding]; other site 392021001543 NADP binding site [chemical binding]; other site 392021001544 substrate binding site [chemical binding]; other site 392021001545 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 392021001546 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 392021001547 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 392021001548 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 392021001549 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 392021001550 Spore Coat Protein U domain; Region: SCPU; pfam05229 392021001551 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 392021001552 Class I ribonucleotide reductase; Region: RNR_I; cd01679 392021001553 active site 392021001554 dimer interface [polypeptide binding]; other site 392021001555 catalytic residues [active] 392021001556 effector binding site; other site 392021001557 R2 peptide binding site; other site 392021001558 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 392021001559 dimer interface [polypeptide binding]; other site 392021001560 putative radical transfer pathway; other site 392021001561 diiron center [ion binding]; other site 392021001562 tyrosyl radical; other site 392021001563 similar to hypothetical protein 392021001564 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 392021001565 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 392021001566 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 392021001567 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 392021001568 active site 392021001569 substrate binding site [chemical binding]; other site 392021001570 metal binding site [ion binding]; metal-binding site 392021001571 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 392021001572 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021001573 Walker A/P-loop; other site 392021001574 ATP binding site [chemical binding]; other site 392021001575 Q-loop/lid; other site 392021001576 ABC transporter signature motif; other site 392021001577 Walker B; other site 392021001578 D-loop; other site 392021001579 H-loop/switch region; other site 392021001580 OstA-like protein; Region: OstA; pfam03968 392021001581 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 392021001582 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 392021001583 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 392021001584 putative active site [active] 392021001585 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 392021001586 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 392021001587 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 392021001588 RNase E interface [polypeptide binding]; other site 392021001589 trimer interface [polypeptide binding]; other site 392021001590 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 392021001591 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 392021001592 RNase E interface [polypeptide binding]; other site 392021001593 trimer interface [polypeptide binding]; other site 392021001594 active site 392021001595 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 392021001596 putative nucleic acid binding region [nucleotide binding]; other site 392021001597 G-X-X-G motif; other site 392021001598 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 392021001599 RNA binding site [nucleotide binding]; other site 392021001600 domain interface; other site 392021001601 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 392021001602 16S/18S rRNA binding site [nucleotide binding]; other site 392021001603 S13e-L30e interaction site [polypeptide binding]; other site 392021001604 25S rRNA binding site [nucleotide binding]; other site 392021001605 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 392021001606 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 392021001607 RNA binding site [nucleotide binding]; other site 392021001608 active site 392021001609 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001610 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021001611 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 392021001612 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 392021001613 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 392021001614 non-specific DNA binding site [nucleotide binding]; other site 392021001615 salt bridge; other site 392021001616 sequence-specific DNA binding site [nucleotide binding]; other site 392021001617 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 392021001618 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 392021001619 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 392021001620 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 392021001621 uncharacterized protein, YfiH family; Region: TIGR00726 392021001622 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 392021001623 catalytic residues [active] 392021001624 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 392021001625 putative active site [active] 392021001626 homotetrameric interface [polypeptide binding]; other site 392021001627 hypothetical protein; Provisional; Region: PRK06661 392021001628 intersubunit interface [polypeptide binding]; other site 392021001629 active site 392021001630 Zn2+ binding site [ion binding]; other site 392021001631 pyruvate phosphate dikinase; Provisional; Region: PRK09279 392021001632 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 392021001633 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 392021001634 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 392021001635 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 392021001636 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 392021001637 GSH binding site (G-site) [chemical binding]; other site 392021001638 C-terminal domain interface [polypeptide binding]; other site 392021001639 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 392021001640 N-terminal domain interface [polypeptide binding]; other site 392021001641 dimer interface [polypeptide binding]; other site 392021001642 substrate binding pocket (H-site) [chemical binding]; other site 392021001643 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 392021001644 conserved cys residue [active] 392021001645 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 392021001646 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 392021001647 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 392021001648 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 392021001649 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 392021001650 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 392021001651 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 392021001652 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 392021001653 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 392021001654 Uncharacterized conserved protein [Function unknown]; Region: COG5448 392021001655 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 392021001656 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 392021001657 Predicted membrane protein [Function unknown]; Region: COG5346 392021001658 translation initiation factor IF-3; Region: infC; TIGR00168 392021001659 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 392021001660 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 392021001661 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 392021001662 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 392021001663 E3 interaction surface; other site 392021001664 lipoyl attachment site [posttranslational modification]; other site 392021001665 e3 binding domain; Region: E3_binding; pfam02817 392021001666 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 392021001667 peptide chain release factor 1; Validated; Region: prfA; PRK00591 392021001668 This domain is found in peptide chain release factors; Region: PCRF; smart00937 392021001669 RF-1 domain; Region: RF-1; pfam00472 392021001670 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 392021001671 DHH family; Region: DHH; pfam01368 392021001672 DHHA1 domain; Region: DHHA1; pfam02272 392021001673 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 392021001674 S-adenosylmethionine binding site [chemical binding]; other site 392021001675 Methyltransferase domain; Region: Methyltransf_31; pfam13847 392021001676 transcription termination factor Rho; Provisional; Region: rho; PRK09376 392021001677 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 392021001678 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 392021001679 RNA binding site [nucleotide binding]; other site 392021001680 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 392021001681 multimer interface [polypeptide binding]; other site 392021001682 Walker A motif; other site 392021001683 ATP binding site [chemical binding]; other site 392021001684 Walker B motif; other site 392021001685 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 392021001686 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 392021001687 tandem repeat interface [polypeptide binding]; other site 392021001688 oligomer interface [polypeptide binding]; other site 392021001689 active site residues [active] 392021001690 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 392021001691 IHF - DNA interface [nucleotide binding]; other site 392021001692 IHF dimer interface [polypeptide binding]; other site 392021001693 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 392021001694 hypothetical protein; Region: PHA00670 392021001695 hypothetical protein; Region: PHA00670 392021001696 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 392021001697 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 392021001698 active site 392021001699 HIGH motif; other site 392021001700 dimer interface [polypeptide binding]; other site 392021001701 KMSKS motif; other site 392021001702 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 392021001703 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 392021001704 putative acyl-acceptor binding pocket; other site 392021001705 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 392021001706 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 392021001707 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 392021001708 HemY protein N-terminus; Region: HemY_N; pfam07219 392021001709 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 392021001710 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 392021001711 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 392021001712 active site 392021001713 Lysine efflux permease [General function prediction only]; Region: COG1279 392021001714 muropeptide transporter; Reviewed; Region: ampG; PRK11902 392021001715 AmpG-like permease; Region: 2A0125; TIGR00901 392021001716 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 392021001717 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 392021001718 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 392021001719 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021001720 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 392021001721 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 392021001722 substrate binding pocket [chemical binding]; other site 392021001723 chain length determination region; other site 392021001724 substrate-Mg2+ binding site; other site 392021001725 catalytic residues [active] 392021001726 aspartate-rich region 1; other site 392021001727 active site lid residues [active] 392021001728 aspartate-rich region 2; other site 392021001729 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 392021001730 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 392021001731 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 392021001732 active site 392021001733 arginine:agmatin antiporter; Provisional; Region: PRK10644 392021001734 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 392021001735 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 392021001736 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 392021001737 trimerization site [polypeptide binding]; other site 392021001738 active site 392021001739 cysteine desulfurase; Provisional; Region: PRK14012 392021001740 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 392021001741 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 392021001742 catalytic residue [active] 392021001743 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 392021001744 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 392021001745 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 392021001746 catalytic residue [active] 392021001747 Predicted transcriptional regulator [Transcription]; Region: COG1959 392021001748 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 392021001749 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 392021001750 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 392021001751 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 392021001752 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 392021001753 Coenzyme A binding pocket [chemical binding]; other site 392021001754 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 392021001755 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 392021001756 homotetramer interface [polypeptide binding]; other site 392021001757 FMN binding site [chemical binding]; other site 392021001758 homodimer contacts [polypeptide binding]; other site 392021001759 putative active site [active] 392021001760 putative substrate binding site [chemical binding]; other site 392021001761 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 392021001762 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 392021001763 oligomer interface [polypeptide binding]; other site 392021001764 active site residues [active] 392021001765 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 392021001766 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 392021001767 CMP-binding site; other site 392021001768 The sites determining sugar specificity; other site 392021001769 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 392021001770 non-specific DNA binding site [nucleotide binding]; other site 392021001771 salt bridge; other site 392021001772 sequence-specific DNA binding site [nucleotide binding]; other site 392021001773 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 392021001774 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 392021001775 hypothetical protein; Region: PHA00670 392021001776 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 392021001777 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 392021001778 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 392021001779 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 392021001780 domain interfaces; other site 392021001781 active site 392021001782 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 392021001783 dimer interface [polypeptide binding]; other site 392021001784 catalytic triad [active] 392021001785 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 392021001786 G-X-G motif; other site 392021001787 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 392021001788 dimer interface [polypeptide binding]; other site 392021001789 phosphorylation site [posttranslational modification] 392021001790 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 392021001791 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 392021001792 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 392021001793 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 392021001794 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 392021001795 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 392021001796 Uncharacterized conserved protein [Function unknown]; Region: COG1723 392021001797 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 392021001798 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 392021001799 catalytic site [active] 392021001800 putative active site [active] 392021001801 putative substrate binding site [chemical binding]; other site 392021001802 Helicase and RNase D C-terminal; Region: HRDC; smart00341 392021001803 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 392021001804 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 392021001805 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 392021001806 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 392021001807 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 392021001808 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 392021001809 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 392021001810 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 392021001811 S-adenosylmethionine binding site [chemical binding]; other site 392021001812 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 392021001813 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 392021001814 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 392021001815 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 392021001816 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 392021001817 N-acetyl-D-glucosamine binding site [chemical binding]; other site 392021001818 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 392021001819 hypothetical protein; Validated; Region: PRK00110 392021001820 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 392021001821 Substrate binding site; other site 392021001822 Mg++ binding site; other site 392021001823 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 392021001824 active site 392021001825 homodimer interface [polypeptide binding]; other site 392021001826 putative chemical substrate binding site [chemical binding]; other site 392021001827 metal binding site [ion binding]; metal-binding site 392021001828 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 392021001829 Coenzyme A binding pocket [chemical binding]; other site 392021001830 AAA domain; Region: AAA_17; pfam13207 392021001831 AAA domain; Region: AAA_18; pfam13238 392021001832 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 392021001833 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 392021001834 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 392021001835 dimer interface [polypeptide binding]; other site 392021001836 allosteric magnesium binding site [ion binding]; other site 392021001837 active site 392021001838 aspartate-rich active site metal binding site; other site 392021001839 Schiff base residues; other site 392021001840 primosome assembly protein PriA; Validated; Region: PRK05580 392021001841 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 392021001842 ATP binding site [chemical binding]; other site 392021001843 putative Mg++ binding site [ion binding]; other site 392021001844 helicase superfamily c-terminal domain; Region: HELICc; smart00490 392021001845 aromatic acid decarboxylase; Validated; Region: PRK05920 392021001846 Flavoprotein; Region: Flavoprotein; pfam02441 392021001847 SacI restriction endonuclease; Region: RE_SacI; pfam09566 392021001848 replicative DNA helicase; Provisional; Region: PRK09165 392021001849 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 392021001850 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 392021001851 Walker A motif; other site 392021001852 ATP binding site [chemical binding]; other site 392021001853 Walker B motif; other site 392021001854 DNA binding loops [nucleotide binding] 392021001855 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 392021001856 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 392021001857 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 392021001858 RNA binding surface [nucleotide binding]; other site 392021001859 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 392021001860 active site 392021001861 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 392021001862 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001863 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 392021001864 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001865 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 392021001866 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 392021001867 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 392021001868 S-adenosylmethionine binding site [chemical binding]; other site 392021001869 DNA repair protein RadA; Provisional; Region: PRK11823 392021001870 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 392021001871 Walker A motif/ATP binding site; other site 392021001872 ATP binding site [chemical binding]; other site 392021001873 Walker B motif; other site 392021001874 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 392021001875 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 392021001876 Recombination protein O N terminal; Region: RecO_N; pfam11967 392021001877 Recombination protein O C terminal; Region: RecO_C; pfam02565 392021001878 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 392021001879 Glycoprotease family; Region: Peptidase_M22; pfam00814 392021001880 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 392021001881 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 392021001882 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 392021001883 G1 box; other site 392021001884 putative GEF interaction site [polypeptide binding]; other site 392021001885 GTP/Mg2+ binding site [chemical binding]; other site 392021001886 Switch I region; other site 392021001887 G2 box; other site 392021001888 G3 box; other site 392021001889 Switch II region; other site 392021001890 G4 box; other site 392021001891 G5 box; other site 392021001892 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 392021001893 Translation-initiation factor 2; Region: IF-2; pfam11987 392021001894 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 392021001895 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 392021001896 NusA N-terminal domain; Region: NusA_N; pfam08529 392021001897 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 392021001898 RNA binding site [nucleotide binding]; other site 392021001899 homodimer interface [polypeptide binding]; other site 392021001900 NusA-like KH domain; Region: KH_5; pfam13184 392021001901 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 392021001902 G-X-X-G motif; other site 392021001903 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 392021001904 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 392021001905 Sm and related proteins; Region: Sm_like; cl00259 392021001906 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 392021001907 putative oligomer interface [polypeptide binding]; other site 392021001908 putative RNA binding site [nucleotide binding]; other site 392021001909 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 392021001910 NAD binding pocket [chemical binding]; other site 392021001911 Predicted transcriptional regulator [Transcription]; Region: COG1959 392021001912 Transcriptional regulator; Region: Rrf2; cl17282 392021001913 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 392021001914 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 392021001915 RNA binding surface [nucleotide binding]; other site 392021001916 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 392021001917 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 392021001918 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 392021001919 active site 392021001920 HIGH motif; other site 392021001921 dimer interface [polypeptide binding]; other site 392021001922 KMSKS motif; other site 392021001923 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 392021001924 RNA binding surface [nucleotide binding]; other site 392021001925 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 392021001926 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 392021001927 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 392021001928 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021001929 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 392021001930 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 392021001931 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 392021001932 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 392021001933 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 392021001934 active site 392021001935 phosphorylation site [posttranslational modification] 392021001936 intermolecular recognition site; other site 392021001937 dimerization interface [polypeptide binding]; other site 392021001938 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 392021001939 Walker A motif; other site 392021001940 ATP binding site [chemical binding]; other site 392021001941 Walker B motif; other site 392021001942 arginine finger; other site 392021001943 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 392021001944 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 392021001945 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 392021001946 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 392021001947 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 392021001948 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 392021001949 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 392021001950 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 392021001951 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 392021001952 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 392021001953 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 392021001954 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 392021001955 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 392021001956 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 392021001957 S-adenosylmethionine binding site [chemical binding]; other site 392021001958 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 392021001959 MraZ protein; Region: MraZ; pfam02381 392021001960 similar to hypothetical protein 392021001961 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 392021001962 Na binding site [ion binding]; other site 392021001963 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 392021001964 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 392021001965 GIY-YIG motif/motif A; other site 392021001966 active site 392021001967 catalytic site [active] 392021001968 putative DNA binding site [nucleotide binding]; other site 392021001969 metal binding site [ion binding]; metal-binding site 392021001970 UvrB/uvrC motif; Region: UVR; pfam02151 392021001971 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 392021001972 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 392021001973 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 392021001974 A new structural DNA glycosylase; Region: AlkD_like; cd06561 392021001975 active site 392021001976 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 392021001977 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 392021001978 active site 392021001979 DNA binding site [nucleotide binding] 392021001980 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 392021001981 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 392021001982 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 392021001983 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 392021001984 DNA binding site [nucleotide binding] 392021001985 active site 392021001986 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 392021001987 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 392021001988 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 392021001989 DEAD/DEAH box helicase; Region: DEAD; pfam00270 392021001990 ATP binding site [chemical binding]; other site 392021001991 putative Mg++ binding site [ion binding]; other site 392021001992 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 392021001993 SEC-C motif; Region: SEC-C; pfam02810 392021001994 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 392021001995 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 392021001996 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 392021001997 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 392021001998 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 392021001999 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 392021002000 hinge; other site 392021002001 active site 392021002002 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 392021002003 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 392021002004 ATP binding site [chemical binding]; other site 392021002005 Mg2+ binding site [ion binding]; other site 392021002006 G-X-G motif; other site 392021002007 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 392021002008 anchoring element; other site 392021002009 dimer interface [polypeptide binding]; other site 392021002010 ATP binding site [chemical binding]; other site 392021002011 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 392021002012 active site 392021002013 putative metal-binding site [ion binding]; other site 392021002014 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 392021002015 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 392021002016 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 392021002017 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 392021002018 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 392021002019 MgtE intracellular N domain; Region: MgtE_N; pfam03448 392021002020 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 392021002021 Divalent cation transporter; Region: MgtE; pfam01769 392021002022 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 392021002023 HD domain; Region: HD_4; pfam13328 392021002024 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 392021002025 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 392021002026 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 392021002027 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 392021002028 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 392021002029 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 392021002030 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 392021002031 Cu(I) binding site [ion binding]; other site 392021002032 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 392021002033 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 392021002034 dimer interface [polypeptide binding]; other site 392021002035 substrate binding site [chemical binding]; other site 392021002036 metal binding sites [ion binding]; metal-binding site 392021002037 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002038 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 392021002039 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 392021002040 TraX protein; Region: TraX; pfam05857 392021002041 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 392021002042 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 392021002043 ssDNA binding site; other site 392021002044 generic binding surface II; other site 392021002045 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 392021002046 ATP binding site [chemical binding]; other site 392021002047 putative Mg++ binding site [ion binding]; other site 392021002048 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 392021002049 nucleotide binding region [chemical binding]; other site 392021002050 ATP-binding site [chemical binding]; other site 392021002051 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 392021002052 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 392021002053 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 392021002054 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 392021002055 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 392021002056 Mg++ binding site [ion binding]; other site 392021002057 putative catalytic motif [active] 392021002058 putative substrate binding site [chemical binding]; other site 392021002059 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 392021002060 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 392021002061 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 392021002062 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 392021002063 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 392021002064 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 392021002065 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 392021002066 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 392021002067 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 392021002068 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 392021002069 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 392021002070 ATP binding site [chemical binding]; other site 392021002071 putative Mg++ binding site [ion binding]; other site 392021002072 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 392021002073 nucleotide binding region [chemical binding]; other site 392021002074 ATP-binding site [chemical binding]; other site 392021002075 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 392021002076 Uncharacterized conserved protein [Function unknown]; Region: COG2938 392021002077 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 392021002078 active site residue [active] 392021002079 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 392021002080 DnaA N-terminal domain; Region: DnaA_N; pfam11638 392021002081 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 392021002082 Walker A motif; other site 392021002083 ATP binding site [chemical binding]; other site 392021002084 Walker B motif; other site 392021002085 arginine finger; other site 392021002086 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 392021002087 DnaA box-binding interface [nucleotide binding]; other site 392021002088 Patatin [General function prediction only]; Region: COG3621 392021002089 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 392021002090 active site 392021002091 nucleophile elbow; other site 392021002092 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 392021002093 HEPN domain; Region: HEPN; cl00824 392021002094 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 392021002095 metal binding triad [ion binding]; metal-binding site 392021002096 GTP-binding protein YchF; Reviewed; Region: PRK09601 392021002097 YchF GTPase; Region: YchF; cd01900 392021002098 G1 box; other site 392021002099 GTP/Mg2+ binding site [chemical binding]; other site 392021002100 Switch I region; other site 392021002101 G2 box; other site 392021002102 Switch II region; other site 392021002103 G3 box; other site 392021002104 G4 box; other site 392021002105 G5 box; other site 392021002106 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 392021002107 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 392021002108 putative active site [active] 392021002109 catalytic residue [active] 392021002110 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 392021002111 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 392021002112 5S rRNA interface [nucleotide binding]; other site 392021002113 CTC domain interface [polypeptide binding]; other site 392021002114 L16 interface [polypeptide binding]; other site 392021002115 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 392021002116 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 392021002117 FeS/SAM binding site; other site 392021002118 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 392021002119 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 392021002120 23S rRNA binding site [nucleotide binding]; other site 392021002121 L21 binding site [polypeptide binding]; other site 392021002122 L13 binding site [polypeptide binding]; other site 392021002123 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 392021002124 ribonuclease P; Reviewed; Region: rnpA; PRK01492 392021002125 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 392021002126 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 392021002127 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 392021002128 Cl binding site [ion binding]; other site 392021002129 oligomer interface [polypeptide binding]; other site 392021002130 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; cl17270 392021002131 Phosphotransferase enzyme family; Region: APH; pfam01636 392021002132 active site 392021002133 ATP binding site [chemical binding]; other site 392021002134 substrate binding site [chemical binding]; other site 392021002135 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; cl17270 392021002136 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 392021002137 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 392021002138 dimerization interface [polypeptide binding]; other site 392021002139 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 392021002140 dimer interface [polypeptide binding]; other site 392021002141 phosphorylation site [posttranslational modification] 392021002142 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 392021002143 ATP binding site [chemical binding]; other site 392021002144 Mg2+ binding site [ion binding]; other site 392021002145 G-X-G motif; other site 392021002146 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 392021002147 Uncharacterized conserved protein [Function unknown]; Region: COG5590 392021002148 COQ9; Region: COQ9; pfam08511 392021002149 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 392021002150 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 392021002151 HIGH motif; other site 392021002152 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 392021002153 active site 392021002154 KMSKS motif; other site 392021002155 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 392021002156 tRNA binding surface [nucleotide binding]; other site 392021002157 anticodon binding site; other site 392021002158 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 392021002159 TPR motif; other site 392021002160 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 392021002161 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 392021002162 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 392021002163 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 392021002164 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 392021002165 carboxyltransferase (CT) interaction site; other site 392021002166 biotinylation site [posttranslational modification]; other site 392021002167 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 392021002168 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 392021002169 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 392021002170 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 392021002171 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 392021002172 putative substrate translocation pore; other site 392021002173 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 392021002174 putative acyl-acceptor binding pocket; other site 392021002175 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 392021002176 acyl-activating enzyme (AAE) consensus motif; other site 392021002177 putative AMP binding site [chemical binding]; other site 392021002178 TfoX N-terminal domain; Region: TfoX_N; pfam04993 392021002179 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 392021002180 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002181 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 392021002182 S-adenosylmethionine binding site [chemical binding]; other site 392021002183 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 392021002184 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 392021002185 HIGH motif; other site 392021002186 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 392021002187 active site 392021002188 KMSKS motif; other site 392021002189 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002190 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 392021002191 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 392021002192 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 392021002193 ring oligomerisation interface [polypeptide binding]; other site 392021002194 ATP/Mg binding site [chemical binding]; other site 392021002195 stacking interactions; other site 392021002196 hinge regions; other site 392021002197 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 392021002198 oligomerisation interface [polypeptide binding]; other site 392021002199 mobile loop; other site 392021002200 roof hairpin; other site 392021002201 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 392021002202 ribonuclease PH; Reviewed; Region: rph; PRK00173 392021002203 Ribonuclease PH; Region: RNase_PH_bact; cd11362 392021002204 hexamer interface [polypeptide binding]; other site 392021002205 active site 392021002206 GrpE; Region: GrpE; pfam01025 392021002207 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 392021002208 dimer interface [polypeptide binding]; other site 392021002209 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 392021002210 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 392021002211 Domain of unknown function DUF20; Region: UPF0118; pfam01594 392021002212 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 392021002213 hypothetical protein; Validated; Region: PRK06620 392021002214 HD domain; Region: HD_4; pfam13328 392021002215 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 392021002216 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 392021002217 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 392021002218 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 392021002219 alphaNTD - beta interaction site [polypeptide binding]; other site 392021002220 alphaNTD homodimer interface [polypeptide binding]; other site 392021002221 alphaNTD - beta' interaction site [polypeptide binding]; other site 392021002222 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 392021002223 30S ribosomal protein S11; Validated; Region: PRK05309 392021002224 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 392021002225 30S ribosomal protein S13; Region: bact_S13; TIGR03631 392021002226 adenylate kinase; Reviewed; Region: adk; PRK00279 392021002227 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 392021002228 AMP-binding site [chemical binding]; other site 392021002229 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 392021002230 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 392021002231 SecY translocase; Region: SecY; pfam00344 392021002232 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 392021002233 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 392021002234 23S rRNA binding site [nucleotide binding]; other site 392021002235 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 392021002236 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 392021002237 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 392021002238 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 392021002239 5S rRNA interface [nucleotide binding]; other site 392021002240 23S rRNA interface [nucleotide binding]; other site 392021002241 L5 interface [polypeptide binding]; other site 392021002242 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 392021002243 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 392021002244 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 392021002245 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 392021002246 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 392021002247 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 392021002248 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 392021002249 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 392021002250 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 392021002251 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 392021002252 RNA binding site [nucleotide binding]; other site 392021002253 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 392021002254 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 392021002255 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 392021002256 L23 interface [polypeptide binding]; other site 392021002257 trigger factor interaction site; other site 392021002258 23S rRNA interface [nucleotide binding]; other site 392021002259 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 392021002260 23S rRNA interface [nucleotide binding]; other site 392021002261 5S rRNA interface [nucleotide binding]; other site 392021002262 putative antibiotic binding site [chemical binding]; other site 392021002263 L25 interface [polypeptide binding]; other site 392021002264 L27 interface [polypeptide binding]; other site 392021002265 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 392021002266 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 392021002267 G-X-X-G motif; other site 392021002268 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 392021002269 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 392021002270 putative translocon binding site; other site 392021002271 protein-rRNA interface [nucleotide binding]; other site 392021002272 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 392021002273 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 392021002274 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 392021002275 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 392021002276 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 392021002277 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 392021002278 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 392021002279 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 392021002280 elongation factor Tu; Reviewed; Region: PRK00049 392021002281 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 392021002282 G1 box; other site 392021002283 GEF interaction site [polypeptide binding]; other site 392021002284 GTP/Mg2+ binding site [chemical binding]; other site 392021002285 Switch I region; other site 392021002286 G2 box; other site 392021002287 G3 box; other site 392021002288 Switch II region; other site 392021002289 G4 box; other site 392021002290 G5 box; other site 392021002291 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 392021002292 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 392021002293 Antibiotic Binding Site [chemical binding]; other site 392021002294 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 392021002295 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 392021002296 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 392021002297 fumarate hydratase; Reviewed; Region: fumC; PRK00485 392021002298 Class II fumarases; Region: Fumarase_classII; cd01362 392021002299 active site 392021002300 tetramer interface [polypeptide binding]; other site 392021002301 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 392021002302 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 392021002303 putative active site [active] 392021002304 homotetrameric interface [polypeptide binding]; other site 392021002305 cell division protein FtsZ; Validated; Region: PRK09330 392021002306 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 392021002307 nucleotide binding site [chemical binding]; other site 392021002308 SulA interaction site; other site 392021002309 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 392021002310 secondary substrate binding site; other site 392021002311 primary substrate binding site; other site 392021002312 inhibition loop; other site 392021002313 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 392021002314 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 392021002315 muropeptide transporter; Validated; Region: ampG; cl17669 392021002316 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 392021002317 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 392021002318 ATP binding site [chemical binding]; other site 392021002319 Mg++ binding site [ion binding]; other site 392021002320 motif III; other site 392021002321 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 392021002322 nucleotide binding region [chemical binding]; other site 392021002323 ATP-binding site [chemical binding]; other site 392021002324 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...; Region: CSP_CDS; cd04458 392021002325 DNA-binding site [nucleotide binding]; DNA binding site 392021002326 RNA-binding motif; other site 392021002327 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 392021002328 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 392021002329 S-adenosylmethionine binding site [chemical binding]; other site 392021002330 SurA N-terminal domain; Region: SurA_N_3; cl07813 392021002331 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 392021002332 Organic solvent tolerance protein; Region: OstA_C; pfam04453 392021002333 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 392021002334 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 392021002335 generic binding surface II; other site 392021002336 generic binding surface I; other site 392021002337 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 392021002338 putative catalytic site [active] 392021002339 putative phosphate binding site [ion binding]; other site 392021002340 active site 392021002341 metal binding site A [ion binding]; metal-binding site 392021002342 DNA binding site [nucleotide binding] 392021002343 putative AP binding site [nucleotide binding]; other site 392021002344 putative metal binding site B [ion binding]; other site 392021002345 Uncharacterized conserved protein [Function unknown]; Region: COG4095 392021002346 GTP-binding protein Der; Reviewed; Region: PRK00093 392021002347 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 392021002348 G1 box; other site 392021002349 GTP/Mg2+ binding site [chemical binding]; other site 392021002350 Switch I region; other site 392021002351 G2 box; other site 392021002352 Switch II region; other site 392021002353 G3 box; other site 392021002354 G4 box; other site 392021002355 G5 box; other site 392021002356 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 392021002357 G1 box; other site 392021002358 GTP/Mg2+ binding site [chemical binding]; other site 392021002359 Switch I region; other site 392021002360 G2 box; other site 392021002361 G3 box; other site 392021002362 Switch II region; other site 392021002363 G4 box; other site 392021002364 G5 box; other site 392021002365 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 392021002366 AAA domain; Region: AAA_14; pfam13173 392021002367 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 392021002368 ABC1 family; Region: ABC1; pfam03109 392021002369 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 392021002370 active site 392021002371 ATP binding site [chemical binding]; other site 392021002372 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 392021002373 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 392021002374 S-adenosylmethionine binding site [chemical binding]; other site 392021002375 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 392021002376 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 392021002377 DNA binding site [nucleotide binding] 392021002378 catalytic residue [active] 392021002379 H2TH interface [polypeptide binding]; other site 392021002380 putative catalytic residues [active] 392021002381 turnover-facilitating residue; other site 392021002382 intercalation triad [nucleotide binding]; other site 392021002383 8OG recognition residue [nucleotide binding]; other site 392021002384 putative reading head residues; other site 392021002385 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 392021002386 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 392021002387 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002388 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 392021002389 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 392021002390 active site 392021002391 Protein of unknown function (DUF511); Region: DUF511; cl01114 392021002392 Protein of unknown function (DUF511); Region: DUF511; cl01114 392021002393 Protein of unknown function (DUF511); Region: DUF511; cl01114 392021002394 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 392021002395 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 392021002396 active site 392021002397 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 392021002398 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 392021002399 HIGH motif; other site 392021002400 active site 392021002401 KMSKS motif; other site 392021002402 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 392021002403 tRNA binding surface [nucleotide binding]; other site 392021002404 anticodon binding site; other site 392021002405 thymidylate kinase; Validated; Region: tmk; PRK00698 392021002406 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 392021002407 TMP-binding site; other site 392021002408 ATP-binding site [chemical binding]; other site 392021002409 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021002410 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 392021002411 UbiA prenyltransferase family; Region: UbiA; pfam01040 392021002412 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 392021002413 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021002414 active site 392021002415 HIGH motif; other site 392021002416 nucleotide binding site [chemical binding]; other site 392021002417 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 392021002418 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 392021002419 active site 392021002420 KMSKS motif; other site 392021002421 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 392021002422 tRNA binding surface [nucleotide binding]; other site 392021002423 anticodon binding site; other site 392021002424 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 392021002425 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 392021002426 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 392021002427 AAA domain; Region: AAA_14; pfam13173 392021002428 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 392021002429 RmuC family; Region: RmuC; pfam02646 392021002430 DoxX-like family; Region: DoxX_3; pfam13781 392021002431 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 392021002432 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 392021002433 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 392021002434 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 392021002435 Walker A motif; other site 392021002436 ATP binding site [chemical binding]; other site 392021002437 Walker B motif; other site 392021002438 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 392021002439 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 392021002440 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 392021002441 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 392021002442 Ligand Binding Site [chemical binding]; other site 392021002443 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 392021002444 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 392021002445 HicB family; Region: HicB; pfam05534 392021002446 YcfA-like protein; Region: YcfA; cl00752 392021002447 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 392021002448 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 392021002449 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021002450 Walker A/P-loop; other site 392021002451 ATP binding site [chemical binding]; other site 392021002452 Q-loop/lid; other site 392021002453 ABC transporter signature motif; other site 392021002454 Walker B; other site 392021002455 D-loop; other site 392021002456 H-loop/switch region; other site 392021002457 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 392021002458 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 392021002459 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 392021002460 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 392021002461 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 392021002462 FtsX-like permease family; Region: FtsX; pfam02687 392021002463 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 392021002464 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 392021002465 Walker A/P-loop; other site 392021002466 ATP binding site [chemical binding]; other site 392021002467 Q-loop/lid; other site 392021002468 ABC transporter signature motif; other site 392021002469 Walker B; other site 392021002470 D-loop; other site 392021002471 H-loop/switch region; other site 392021002472 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 392021002473 Domain of unknown function DUF21; Region: DUF21; pfam01595 392021002474 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 392021002475 Transporter associated domain; Region: CorC_HlyC; smart01091 392021002476 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 392021002477 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 392021002478 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 392021002479 Autotransporter beta-domain; Region: Autotransporter; smart00869 392021002480 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 392021002481 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 392021002482 synthetase active site [active] 392021002483 NTP binding site [chemical binding]; other site 392021002484 metal binding site [ion binding]; metal-binding site 392021002485 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 392021002486 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 392021002487 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 392021002488 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 392021002489 DNA binding residues [nucleotide binding] 392021002490 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 392021002491 IHF dimer interface [polypeptide binding]; other site 392021002492 IHF - DNA interface [nucleotide binding]; other site 392021002493 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 392021002494 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 392021002495 catalytic triad [active] 392021002496 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 392021002497 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 392021002498 putative acyl-acceptor binding pocket; other site 392021002499 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 392021002500 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 392021002501 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 392021002502 Peptidase family M23; Region: Peptidase_M23; pfam01551 392021002503 Protein of unknown function (DUF519); Region: DUF519; pfam04378 392021002504 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 392021002505 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 392021002506 nucleotide binding pocket [chemical binding]; other site 392021002507 K-X-D-G motif; other site 392021002508 catalytic site [active] 392021002509 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 392021002510 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 392021002511 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 392021002512 Dimer interface [polypeptide binding]; other site 392021002513 BRCT sequence motif; other site 392021002514 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 392021002515 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 392021002516 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 392021002517 HD domain; Region: HD_4; pfam13328 392021002518 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 392021002519 mce related protein; Region: MCE; pfam02470 392021002520 hypothetical protein; Provisional; Region: PRK06630 392021002521 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 392021002522 RNA/DNA hybrid binding site [nucleotide binding]; other site 392021002523 active site 392021002524 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 392021002525 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 392021002526 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 392021002527 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 392021002528 CoA-binding site [chemical binding]; other site 392021002529 ATP-binding [chemical binding]; other site 392021002530 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 392021002531 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 392021002532 active site 392021002533 catalytic site [active] 392021002534 substrate binding site [chemical binding]; other site 392021002535 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 392021002536 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 392021002537 Part of AAA domain; Region: AAA_19; pfam13245 392021002538 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 392021002539 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 392021002540 Family description; Region: UvrD_C_2; pfam13538 392021002541 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 392021002542 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 392021002543 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 392021002544 TLC ATP/ADP transporter; Region: TLC; pfam03219 392021002545 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 392021002546 nudix motif; other site 392021002547 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 392021002548 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 392021002549 Transporter associated domain; Region: CorC_HlyC; smart01091 392021002550 metal-binding heat shock protein; Provisional; Region: PRK00016 392021002551 lipoyl synthase; Provisional; Region: PRK05481 392021002552 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 392021002553 FeS/SAM binding site; other site 392021002554 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 392021002555 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 392021002556 dimer interface [polypeptide binding]; other site 392021002557 active site 392021002558 glycine-pyridoxal phosphate binding site [chemical binding]; other site 392021002559 folate binding site [chemical binding]; other site 392021002560 Predicted esterase [General function prediction only]; Region: COG0400 392021002561 putative hydrolase; Provisional; Region: PRK11460 392021002562 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 392021002563 putative GSH binding site [chemical binding]; other site 392021002564 catalytic residues [active] 392021002565 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 392021002566 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 392021002567 minor groove reading motif; other site 392021002568 helix-hairpin-helix signature motif; other site 392021002569 substrate binding pocket [chemical binding]; other site 392021002570 active site 392021002571 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 392021002572 Predicted small secreted protein [Function unknown]; Region: COG5510 392021002573 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021002574 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021002575 Predicted methyltransferases [General function prediction only]; Region: COG0313 392021002576 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 392021002577 putative SAM binding site [chemical binding]; other site 392021002578 putative homodimer interface [polypeptide binding]; other site 392021002579 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 392021002580 putative ligand binding site [chemical binding]; other site 392021002581 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 392021002582 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 392021002583 tetramer interfaces [polypeptide binding]; other site 392021002584 binuclear metal-binding site [ion binding]; other site 392021002585 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 392021002586 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 392021002587 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 392021002588 aspartate kinase; Reviewed; Region: PRK06635 392021002589 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 392021002590 putative nucleotide binding site [chemical binding]; other site 392021002591 putative catalytic residues [active] 392021002592 putative Mg ion binding site [ion binding]; other site 392021002593 putative aspartate binding site [chemical binding]; other site 392021002594 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 392021002595 putative allosteric regulatory residue; other site 392021002596 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 392021002597 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 392021002598 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 392021002599 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 392021002600 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 392021002601 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 392021002602 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021002603 putative substrate translocation pore; other site 392021002604 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 392021002605 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002606 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 392021002607 Helix-turn-helix domain; Region: HTH_25; pfam13413 392021002608 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 392021002609 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 392021002610 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 392021002611 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 392021002612 trmE is a tRNA modification GTPase; Region: trmE; cd04164 392021002613 G1 box; other site 392021002614 GTP/Mg2+ binding site [chemical binding]; other site 392021002615 Switch I region; other site 392021002616 G2 box; other site 392021002617 Switch II region; other site 392021002618 G3 box; other site 392021002619 G4 box; other site 392021002620 G5 box; other site 392021002621 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 392021002622 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 392021002623 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 392021002624 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 392021002625 hexamer interface [polypeptide binding]; other site 392021002626 Walker A motif; other site 392021002627 ATP binding site [chemical binding]; other site 392021002628 Walker B motif; other site 392021002629 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 392021002630 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 392021002631 NAD(P) binding site [chemical binding]; other site 392021002632 active site 392021002633 acyl carrier protein; Provisional; Region: acpP; PRK00982 392021002634 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 392021002635 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 392021002636 dimer interface [polypeptide binding]; other site 392021002637 active site 392021002638 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 392021002639 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 392021002640 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 392021002641 endonuclease subunit; Provisional; Region: 46; PHA02562 392021002642 AAA domain; Region: AAA_14; pfam13173 392021002643 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 392021002644 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002645 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 392021002646 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 392021002647 catalytic site [active] 392021002648 G-X2-G-X-G-K; other site 392021002649 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 392021002650 sequence-specific DNA binding site [nucleotide binding]; other site 392021002651 salt bridge; other site 392021002652 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 392021002653 rod shape-determining protein MreC; Region: MreC; pfam04085 392021002654 rod shape-determining protein MreB; Provisional; Region: PRK13927 392021002655 MreB and similar proteins; Region: MreB_like; cd10225 392021002656 nucleotide binding site [chemical binding]; other site 392021002657 Mg binding site [ion binding]; other site 392021002658 putative protofilament interaction site [polypeptide binding]; other site 392021002659 RodZ interaction site [polypeptide binding]; other site 392021002660 Predicted permeases [General function prediction only]; Region: COG0795 392021002661 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 392021002662 putative outer membrane lipoprotein; Provisional; Region: PRK09967 392021002663 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 392021002664 ligand binding site [chemical binding]; other site 392021002665 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002666 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 392021002667 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 392021002668 dimer interface [polypeptide binding]; other site 392021002669 active site 392021002670 CoA binding pocket [chemical binding]; other site 392021002671 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 392021002672 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 392021002673 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 392021002674 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 392021002675 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 392021002676 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 392021002677 P loop; other site 392021002678 GTP binding site [chemical binding]; other site 392021002679 DNA polymerase I; Provisional; Region: PRK05755 392021002680 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 392021002681 active site 392021002682 metal binding site 1 [ion binding]; metal-binding site 392021002683 putative 5' ssDNA interaction site; other site 392021002684 metal binding site 3; metal-binding site 392021002685 metal binding site 2 [ion binding]; metal-binding site 392021002686 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 392021002687 putative DNA binding site [nucleotide binding]; other site 392021002688 putative metal binding site [ion binding]; other site 392021002689 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 392021002690 active site 392021002691 substrate binding site [chemical binding]; other site 392021002692 catalytic site [active] 392021002693 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 392021002694 active site 392021002695 DNA binding site [nucleotide binding] 392021002696 catalytic site [active] 392021002697 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 392021002698 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 392021002699 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 392021002700 putative active site [active] 392021002701 putative PHP Thumb interface [polypeptide binding]; other site 392021002702 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 392021002703 generic binding surface I; other site 392021002704 generic binding surface II; other site 392021002705 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 392021002706 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 392021002707 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 392021002708 Protein of unknown function; Region: DUF3971; pfam13116 392021002709 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 392021002710 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 392021002711 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 392021002712 putative substrate translocation pore; other site 392021002713 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 392021002714 seryl-tRNA synthetase; Provisional; Region: PRK05431 392021002715 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 392021002716 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 392021002717 dimer interface [polypeptide binding]; other site 392021002718 active site 392021002719 motif 1; other site 392021002720 motif 2; other site 392021002721 motif 3; other site 392021002722 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 392021002723 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 392021002724 Integral membrane protein TerC family; Region: TerC; cl10468 392021002725 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 392021002726 Methyltransferase domain; Region: Methyltransf_31; pfam13847 392021002727 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 392021002728 S-adenosylmethionine binding site [chemical binding]; other site 392021002729 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 392021002730 Predicted transcriptional regulator [Transcription]; Region: COG2944 392021002731 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 392021002732 salt bridge; other site 392021002733 non-specific DNA binding site [nucleotide binding]; other site 392021002734 sequence-specific DNA binding site [nucleotide binding]; other site 392021002735 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 392021002736 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 392021002737 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 392021002738 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 392021002739 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 392021002740 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 392021002741 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 392021002742 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 392021002743 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 392021002744 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021002745 Walker A/P-loop; other site 392021002746 ATP binding site [chemical binding]; other site 392021002747 Q-loop/lid; other site 392021002748 ABC transporter signature motif; other site 392021002749 Walker B; other site 392021002750 D-loop; other site 392021002751 H-loop/switch region; other site 392021002752 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 392021002753 4Fe-4S binding domain; Region: Fer4; cl02805 392021002754 4Fe-4S binding domain; Region: Fer4; pfam00037 392021002755 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 392021002756 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 392021002757 NADH dehydrogenase subunit G; Validated; Region: PRK09130 392021002758 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 392021002759 catalytic loop [active] 392021002760 iron binding site [ion binding]; other site 392021002761 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 392021002762 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 392021002763 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 392021002764 Predicted membrane protein [Function unknown]; Region: COG3671 392021002765 aconitate hydratase; Validated; Region: PRK09277 392021002766 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 392021002767 substrate binding site [chemical binding]; other site 392021002768 ligand binding site [chemical binding]; other site 392021002769 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 392021002770 substrate binding site [chemical binding]; other site 392021002771 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 392021002772 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 392021002773 gamma subunit interface [polypeptide binding]; other site 392021002774 epsilon subunit interface [polypeptide binding]; other site 392021002775 LBP interface [polypeptide binding]; other site 392021002776 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 392021002777 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 392021002778 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 392021002779 alpha subunit interaction interface [polypeptide binding]; other site 392021002780 Walker A motif; other site 392021002781 ATP binding site [chemical binding]; other site 392021002782 Walker B motif; other site 392021002783 inhibitor binding site; inhibition site 392021002784 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 392021002785 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 392021002786 core domain interface [polypeptide binding]; other site 392021002787 delta subunit interface [polypeptide binding]; other site 392021002788 epsilon subunit interface [polypeptide binding]; other site 392021002789 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 392021002790 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 392021002791 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 392021002792 beta subunit interaction interface [polypeptide binding]; other site 392021002793 Walker A motif; other site 392021002794 ATP binding site [chemical binding]; other site 392021002795 Walker B motif; other site 392021002796 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 392021002797 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 392021002798 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 392021002799 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 392021002800 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 392021002801 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 392021002802 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 392021002803 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 392021002804 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 392021002805 dimerization interface [polypeptide binding]; other site 392021002806 DPS ferroxidase diiron center [ion binding]; other site 392021002807 ion pore; other site 392021002808 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 392021002809 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 392021002810 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 392021002811 Transglycosylase; Region: Transgly; pfam00912 392021002812 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 392021002813 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 392021002814 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 392021002815 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 392021002816 FeS/SAM binding site; other site 392021002817 TRAM domain; Region: TRAM; pfam01938 392021002818 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021002819 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 392021002820 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 392021002821 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 392021002822 Bacterial SH3 domain; Region: SH3_4; pfam06347 392021002823 Bacterial SH3 domain; Region: SH3_4; pfam06347 392021002824 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 392021002825 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 392021002826 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 392021002827 TrkA-N domain; Region: TrkA_N; pfam02254 392021002828 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 392021002829 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 392021002830 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 392021002831 rRNA binding site [nucleotide binding]; other site 392021002832 predicted 30S ribosome binding site; other site 392021002833 Maf-like protein; Region: Maf; pfam02545 392021002834 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 392021002835 active site 392021002836 dimer interface [polypeptide binding]; other site 392021002837 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 392021002838 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 392021002839 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 392021002840 active site 392021002841 DNA binding site [nucleotide binding] 392021002842 Int/Topo IB signature motif; other site 392021002843 Phasin protein; Region: Phasin_2; cl11491 392021002844 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 392021002845 PLD-like domain; Region: PLDc_2; pfam13091 392021002846 putative active site [active] 392021002847 catalytic site [active] 392021002848 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 392021002849 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 392021002850 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 392021002851 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 392021002852 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 392021002853 Autotransporter beta-domain; Region: Autotransporter; pfam03797 392021002854 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 392021002855 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 392021002856 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 392021002857 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 392021002858 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 392021002859 active site 392021002860 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 392021002861 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 392021002862 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 392021002863 MPN+ (JAMM) motif; other site 392021002864 Zinc-binding site [ion binding]; other site 392021002865 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 392021002866 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 392021002867 Mg++ binding site [ion binding]; other site 392021002868 putative catalytic motif [active] 392021002869 putative substrate binding site [chemical binding]; other site 392021002870 Protein of unknown function (DUF721); Region: DUF721; pfam05258 392021002871 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 392021002872 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 392021002873 Ferredoxin [Energy production and conversion]; Region: COG1146 392021002874 4Fe-4S binding domain; Region: Fer4; cl02805 392021002875 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 392021002876 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 392021002877 nucleoside/Zn binding site; other site 392021002878 dimer interface [polypeptide binding]; other site 392021002879 catalytic motif [active] 392021002880 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 392021002881 Cation efflux family; Region: Cation_efflux; cl00316 392021002882 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 392021002883 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 392021002884 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 392021002885 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 392021002886 Arenavirus nucleocapsid protein; Region: Arena_nucleocap; pfam00843 392021002887 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 392021002888 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 392021002889 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 392021002890 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 392021002891 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 392021002892 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 392021002893 dimer interface [polypeptide binding]; other site 392021002894 ssDNA binding site [nucleotide binding]; other site 392021002895 tetramer (dimer of dimers) interface [polypeptide binding]; other site 392021002896 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 392021002897 hypothetical protein; Reviewed; Region: PRK01530 392021002898 heat shock protein 90; Provisional; Region: PRK05218 392021002899 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 392021002900 ATP binding site [chemical binding]; other site 392021002901 Mg2+ binding site [ion binding]; other site 392021002902 G-X-G motif; other site 392021002903 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 392021002904 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 392021002905 substrate-cofactor binding pocket; other site 392021002906 pyridoxal 5'-phosphate binding site [chemical binding]; other site 392021002907 catalytic residue [active] 392021002908 trigger factor; Provisional; Region: tig; PRK01490 392021002909 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 392021002910 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 392021002911 GTPase CgtA; Reviewed; Region: obgE; PRK12299 392021002912 GTP1/OBG; Region: GTP1_OBG; pfam01018 392021002913 Obg GTPase; Region: Obg; cd01898 392021002914 G1 box; other site 392021002915 GTP/Mg2+ binding site [chemical binding]; other site 392021002916 Switch I region; other site 392021002917 G2 box; other site 392021002918 G3 box; other site 392021002919 Switch II region; other site 392021002920 G4 box; other site 392021002921 G5 box; other site 392021002922 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 392021002923 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 392021002924 dimer interface [polypeptide binding]; other site 392021002925 active site 392021002926 citrylCoA binding site [chemical binding]; other site 392021002927 NADH binding [chemical binding]; other site 392021002928 cationic pore residues; other site 392021002929 oxalacetate/citrate binding site [chemical binding]; other site 392021002930 coenzyme A binding site [chemical binding]; other site 392021002931 catalytic triad [active] 392021002932 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 392021002933 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 392021002934 Fe-S cluster binding site [ion binding]; other site 392021002935 active site 392021002936 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 392021002937 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 392021002938 RNA binding surface [nucleotide binding]; other site 392021002939 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 392021002940 active site 392021002941 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 392021002942 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 392021002943 S-adenosylmethionine binding site [chemical binding]; other site 392021002944 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 392021002945 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 392021002946 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 392021002947 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 392021002948 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 392021002949 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 392021002950 motif 1; other site 392021002951 dimer interface [polypeptide binding]; other site 392021002952 active site 392021002953 motif 2; other site 392021002954 motif 3; other site 392021002955 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 392021002956 oligomeric interface; other site 392021002957 putative active site [active] 392021002958 homodimer interface [polypeptide binding]; other site 392021002959 prevent-host-death family protein; Region: phd_fam; TIGR01552 392021002960 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 392021002961 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 392021002962 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 392021002963 motif 1; other site 392021002964 active site 392021002965 motif 2; other site 392021002966 motif 3; other site 392021002967 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 392021002968 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 392021002969 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 392021002970 dimerization interface 3.5A [polypeptide binding]; other site 392021002971 active site 392021002972 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 392021002973 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 392021002974 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 392021002975 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 392021002976 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 392021002977 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 392021002978 DNA binding residues [nucleotide binding] 392021002979 DNA primase, catalytic core; Region: dnaG; TIGR01391 392021002980 CHC2 zinc finger; Region: zf-CHC2; pfam01807 392021002981 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 392021002982 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 392021002983 active site 392021002984 metal binding site [ion binding]; metal-binding site 392021002985 interdomain interaction site; other site 392021002986 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 392021002987 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 392021002988 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 392021002989 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 392021002990 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 392021002991 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 392021002992 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 392021002993 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 392021002994 ligand binding site [chemical binding]; other site 392021002995 homodimer interface [polypeptide binding]; other site 392021002996 NAD(P) binding site [chemical binding]; other site 392021002997 trimer interface B [polypeptide binding]; other site 392021002998 trimer interface A [polypeptide binding]; other site 392021002999 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 392021003000 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 392021003001 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 392021003002 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 392021003003 Walker A motif; other site 392021003004 ATP binding site [chemical binding]; other site 392021003005 Walker B motif; other site 392021003006 arginine finger; other site 392021003007 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 392021003008 hypothetical protein; Validated; Region: PRK00153 392021003009 Predicted aspartyl protease [General function prediction only]; Region: COG3577 392021003010 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 392021003011 catalytic motif [active] 392021003012 Catalytic residue [active] 392021003013 Beta-lactamase; Region: Beta-lactamase; cl17358 392021003014 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 392021003015 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 392021003016 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 392021003017 Walker A/P-loop; other site 392021003018 ATP binding site [chemical binding]; other site 392021003019 Q-loop/lid; other site 392021003020 ABC transporter signature motif; other site 392021003021 Walker B; other site 392021003022 D-loop; other site 392021003023 H-loop/switch region; other site 392021003024 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 392021003025 putative hydrolase; Provisional; Region: PRK02113 392021003026 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 392021003027 active site 392021003028 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 392021003029 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 392021003030 Predicted permeases [General function prediction only]; Region: COG0795 392021003031 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 392021003032 DNA polymerase III subunit chi; Provisional; Region: PRK06646 392021003033 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 392021003034 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 392021003035 metal binding site [ion binding]; metal-binding site 392021003036 dimer interface [polypeptide binding]; other site 392021003037 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 392021003038 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 392021003039 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 392021003040 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 392021003041 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 392021003042 Uncharacterized conserved protein [Function unknown]; Region: COG1434 392021003043 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 392021003044 putative active site [active] 392021003045 lipoate-protein ligase B; Provisional; Region: PRK14347 392021003046 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 392021003047 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 392021003048 amidase catalytic site [active] 392021003049 Zn binding residues [ion binding]; other site 392021003050 substrate binding site [chemical binding]; other site 392021003051 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 392021003052 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 392021003053 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 392021003054 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 392021003055 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 392021003056 ATP binding site [chemical binding]; other site 392021003057 Mg2+ binding site [ion binding]; other site 392021003058 G-X-G motif; other site 392021003059 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 392021003060 ATP binding site [chemical binding]; other site 392021003061 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 392021003062 Zinc-finger domain; Region: zf-CHCC; cl01821 392021003063 Tetratricopeptide repeat; Region: TPR_12; pfam13424 392021003064 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 392021003065 TPR motif; other site 392021003066 TPR repeat; Region: TPR_11; pfam13414 392021003067 binding surface 392021003068 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 392021003069 metabolite-proton symporter; Region: 2A0106; TIGR00883 392021003070 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 392021003071 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 392021003072 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 392021003073 TIGR00701 family protein; Region: TIGR00701 392021003074 ferrochelatase; Reviewed; Region: hemH; PRK00035 392021003075 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 392021003076 C-terminal domain interface [polypeptide binding]; other site 392021003077 active site 392021003078 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 392021003079 active site 392021003080 N-terminal domain interface [polypeptide binding]; other site 392021003081 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 392021003082 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 392021003083 substrate binding site [chemical binding]; other site 392021003084 active site