-- dump date 20140620_033319 -- class Genbank::misc_feature -- table misc_feature_note -- id note 347255000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 347255000002 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 347255000003 catalytic residues [active] 347255000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 347255000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 347255000006 Walker A/P-loop; other site 347255000007 ATP binding site [chemical binding]; other site 347255000008 Q-loop/lid; other site 347255000009 ABC transporter signature motif; other site 347255000010 Walker B; other site 347255000011 D-loop; other site 347255000012 H-loop/switch region; other site 347255000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 347255000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 347255000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 347255000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 347255000017 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 347255000018 FAD binding pocket [chemical binding]; other site 347255000019 FAD binding motif [chemical binding]; other site 347255000020 phosphate binding motif [ion binding]; other site 347255000021 beta-alpha-beta structure motif; other site 347255000022 NAD binding pocket [chemical binding]; other site 347255000023 Iron coordination center [ion binding]; other site 347255000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 347255000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 347255000026 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 347255000027 active site 347255000028 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 347255000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 347255000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 347255000031 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 347255000032 trimer interface [polypeptide binding]; other site 347255000033 active site 347255000034 UDP-GlcNAc binding site [chemical binding]; other site 347255000035 lipid binding site [chemical binding]; lipid-binding site 347255000036 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 347255000037 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 347255000038 FMN binding site [chemical binding]; other site 347255000039 active site 347255000040 catalytic residues [active] 347255000041 substrate binding site [chemical binding]; other site 347255000042 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 347255000043 NodB motif; other site 347255000044 putative active site [active] 347255000045 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 347255000046 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 347255000047 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 347255000048 intersubunit interface [polypeptide binding]; other site 347255000049 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 347255000050 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 347255000051 active site 347255000052 NTP binding site [chemical binding]; other site 347255000053 metal binding triad [ion binding]; metal-binding site 347255000054 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 347255000055 Autotransporter beta-domain; Region: Autotransporter; pfam03797 347255000056 AAA domain; Region: AAA_22; pfam13401 347255000057 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 347255000058 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 347255000059 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 347255000060 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 347255000061 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 347255000062 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 347255000063 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 347255000064 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 347255000065 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 347255000066 DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a...; Region: DsbA_family; cd02972 347255000067 catalytic residues [active] 347255000068 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 347255000069 Methyltransferase domain; Region: Methyltransf_31; pfam13847 347255000070 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 347255000071 S-adenosylmethionine binding site [chemical binding]; other site 347255000072 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 347255000073 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 347255000074 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 347255000075 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255000076 Walker A/P-loop; other site 347255000077 ATP binding site [chemical binding]; other site 347255000078 Q-loop/lid; other site 347255000079 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255000080 ABC transporter signature motif; other site 347255000081 Walker B; other site 347255000082 D-loop; other site 347255000083 H-loop/switch region; other site 347255000084 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 347255000085 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 347255000086 folate binding site [chemical binding]; other site 347255000087 NADP+ binding site [chemical binding]; other site 347255000088 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 347255000089 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 347255000090 Cu(I) binding site [ion binding]; other site 347255000091 Putative transcriptional regulator [Transcription]; Region: COG1678 347255000092 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 347255000093 Colicin V production protein; Region: Colicin_V; pfam02674 347255000094 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 347255000095 acetoacetyl-CoA reductase; Provisional; Region: PRK12824 347255000096 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 347255000097 NAD(P) binding site [chemical binding]; other site 347255000098 active site 347255000099 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 347255000100 Clp amino terminal domain; Region: Clp_N; pfam02861 347255000101 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 347255000102 Walker A motif; other site 347255000103 ATP binding site [chemical binding]; other site 347255000104 Walker B motif; other site 347255000105 arginine finger; other site 347255000106 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 347255000107 Walker A motif; other site 347255000108 ATP binding site [chemical binding]; other site 347255000109 Walker B motif; other site 347255000110 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 347255000111 UGMP family protein; Validated; Region: PRK09604 347255000112 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 347255000113 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 347255000114 Fatty acid desaturase; Region: FA_desaturase; pfam00487 347255000115 Di-iron ligands [ion binding]; other site 347255000116 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 347255000117 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 347255000118 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 347255000119 DNA binding site [nucleotide binding] 347255000120 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 347255000121 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 347255000122 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 347255000123 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 347255000124 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 347255000125 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 347255000126 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 347255000127 Ligand Binding Site [chemical binding]; other site 347255000128 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255000129 FtsH Extracellular; Region: FtsH_ext; pfam06480 347255000130 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 347255000131 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 347255000132 Walker A motif; other site 347255000133 ATP binding site [chemical binding]; other site 347255000134 Walker B motif; other site 347255000135 arginine finger; other site 347255000136 Peptidase family M41; Region: Peptidase_M41; pfam01434 347255000137 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 347255000138 cofactor binding site; other site 347255000139 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 347255000140 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 347255000141 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3755 347255000142 Uncharacterized conserved protein [Function unknown]; Region: COG1565 347255000143 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255000144 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 347255000145 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 347255000146 Mechanosensitive ion channel; Region: MS_channel; pfam00924 347255000147 membrane protein insertase; Provisional; Region: PRK01318 347255000148 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 347255000149 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 347255000150 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 347255000151 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 347255000152 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 347255000153 active site 347255000154 catalytic residues [active] 347255000155 metal binding site [ion binding]; metal-binding site 347255000156 TLC ATP/ADP transporter; Region: TLC; pfam03219 347255000157 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 347255000158 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 347255000159 putative substrate translocation pore; other site 347255000160 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 347255000161 active site 347255000162 multimer interface [polypeptide binding]; other site 347255000163 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 347255000164 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 347255000165 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 347255000166 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 347255000167 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 347255000168 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 347255000169 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 347255000170 P-loop; other site 347255000171 Magnesium ion binding site [ion binding]; other site 347255000172 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 347255000173 Magnesium ion binding site [ion binding]; other site 347255000174 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 347255000175 ParB-like nuclease domain; Region: ParB; smart00470 347255000176 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 347255000177 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 347255000178 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 347255000179 ABC transporter; Region: ABC_tran_2; pfam12848 347255000180 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 347255000181 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 347255000182 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 347255000183 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 347255000184 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 347255000185 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 347255000186 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 347255000187 Zn2+ binding site [ion binding]; other site 347255000188 Mg2+ binding site [ion binding]; other site 347255000189 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 347255000190 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 347255000191 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 347255000192 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 347255000193 active site 347255000194 HIGH motif; other site 347255000195 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347255000196 KMSK motif region; other site 347255000197 tRNA binding surface [nucleotide binding]; other site 347255000198 DALR anticodon binding domain; Region: DALR_1; smart00836 347255000199 anticodon binding site; other site 347255000200 Sporulation related domain; Region: SPOR; pfam05036 347255000201 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 347255000202 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 347255000203 CAP-like domain; other site 347255000204 active site 347255000205 primary dimer interface [polypeptide binding]; other site 347255000206 Gram-negative porin; Region: Porin_4; pfam13609 347255000207 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 347255000208 trimer interface [polypeptide binding]; other site 347255000209 active site 347255000210 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 347255000211 SecA binding site; other site 347255000212 Preprotein binding site; other site 347255000213 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 347255000214 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 347255000215 active site 347255000216 phosphorylation site [posttranslational modification] 347255000217 intermolecular recognition site; other site 347255000218 dimerization interface [polypeptide binding]; other site 347255000219 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 347255000220 DNA binding site [nucleotide binding] 347255000221 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 347255000222 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 347255000223 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 347255000224 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3820 347255000225 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 347255000226 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 347255000227 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 347255000228 EamA-like transporter family; Region: EamA; pfam00892 347255000229 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 347255000230 EamA-like transporter family; Region: EamA; pfam00892 347255000231 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 347255000232 metabolite-proton symporter; Region: 2A0106; TIGR00883 347255000233 putative substrate translocation pore; other site 347255000234 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 347255000235 Mitochondrial inner membrane protein; Region: Mitofilin; pfam09731 347255000236 Protein of unknown function (DUF2869); Region: DUF2869; pfam11068 347255000237 Autotransporter beta-domain; Region: Autotransporter; pfam03797 347255000238 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 347255000239 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 347255000240 active site 347255000241 HIGH motif; other site 347255000242 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 347255000243 KMSKS motif; other site 347255000244 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 347255000245 tRNA binding surface [nucleotide binding]; other site 347255000246 anticodon binding site; other site 347255000247 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 347255000248 rRNA interaction site [nucleotide binding]; other site 347255000249 S8 interaction site; other site 347255000250 putative laminin-1 binding site; other site 347255000251 elongation factor Ts; Provisional; Region: tsf; PRK09377 347255000252 UBA/TS-N domain; Region: UBA; pfam00627 347255000253 Elongation factor TS; Region: EF_TS; pfam00889 347255000254 Elongation factor TS; Region: EF_TS; pfam00889 347255000255 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 347255000256 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255000257 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 347255000258 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 347255000259 putative acyl-acceptor binding pocket; other site 347255000260 aspartate aminotransferase; Provisional; Region: PRK05764 347255000261 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 347255000262 pyridoxal 5'-phosphate binding site [chemical binding]; other site 347255000263 homodimer interface [polypeptide binding]; other site 347255000264 catalytic residue [active] 347255000265 Tetratricopeptide repeat; Region: TPR_12; pfam13424 347255000266 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 347255000267 binding surface 347255000268 TPR motif; other site 347255000269 Methyltransferase domain; Region: Methyltransf_23; pfam13489 347255000270 Methyltransferase domain; Region: Methyltransf_18; pfam12847 347255000271 S-adenosylmethionine binding site [chemical binding]; other site 347255000272 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 347255000273 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 347255000274 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 347255000275 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 347255000276 active site 347255000277 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 347255000278 dimer interface [polypeptide binding]; other site 347255000279 substrate binding site [chemical binding]; other site 347255000280 catalytic residues [active] 347255000281 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 347255000282 Permease; Region: Permease; pfam02405 347255000283 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 347255000284 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255000285 Walker A/P-loop; other site 347255000286 ATP binding site [chemical binding]; other site 347255000287 Q-loop/lid; other site 347255000288 ABC transporter signature motif; other site 347255000289 Walker B; other site 347255000290 D-loop; other site 347255000291 H-loop/switch region; other site 347255000292 CheD chemotactic sensory transduction; Region: CheD; cl00810 347255000293 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 347255000294 50S ribosomal protein L31; Provisional; Region: PRK01397 347255000295 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 347255000296 G1 box; other site 347255000297 GTP/Mg2+ binding site [chemical binding]; other site 347255000298 Switch I region; other site 347255000299 G2 box; other site 347255000300 G3 box; other site 347255000301 Switch II region; other site 347255000302 G4 box; other site 347255000303 G5 box; other site 347255000304 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 347255000305 nucleotide binding site [chemical binding]; other site 347255000306 substrate binding site [chemical binding]; other site 347255000307 type IV secretion system protein VirB3; Provisional; Region: PRK13899 347255000308 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 347255000309 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 347255000310 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255000311 Walker A/P-loop; other site 347255000312 ATP binding site [chemical binding]; other site 347255000313 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 347255000314 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 347255000315 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 347255000316 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 347255000317 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 347255000318 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 347255000319 hypothetical protein; Provisional; Region: PRK13694 347255000320 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 347255000321 Protein export membrane protein; Region: SecD_SecF; pfam02355 347255000322 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 347255000323 SLBB domain; Region: SLBB; pfam10531 347255000324 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 347255000325 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 347255000326 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 347255000327 Catalytic site [active] 347255000328 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 347255000329 ribonuclease III; Reviewed; Region: rnc; PRK00102 347255000330 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 347255000331 dimerization interface [polypeptide binding]; other site 347255000332 active site 347255000333 metal binding site [ion binding]; metal-binding site 347255000334 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 347255000335 dsRNA binding site [nucleotide binding]; other site 347255000336 GTPase Era; Provisional; Region: era; PRK15494 347255000337 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255000338 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 347255000339 G1 box; other site 347255000340 GTP/Mg2+ binding site [chemical binding]; other site 347255000341 Switch I region; other site 347255000342 G2 box; other site 347255000343 Switch II region; other site 347255000344 G3 box; other site 347255000345 G4 box; other site 347255000346 G5 box; other site 347255000347 KH domain; Region: KH_2; pfam07650 347255000348 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 347255000349 active site 347255000350 putative DNA-binding cleft [nucleotide binding]; other site 347255000351 dimer interface [polypeptide binding]; other site 347255000352 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 347255000353 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 347255000354 nucleotidyltransferase substrate binding protein, HI0074 family; Region: HI0074; TIGR01987 347255000355 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 347255000356 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 347255000357 AAA domain; Region: AAA_31; pfam13614 347255000358 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 347255000359 Walker A motif; other site 347255000360 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 347255000361 HflK protein; Region: hflK; TIGR01933 347255000362 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 347255000363 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 347255000364 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 347255000365 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 347255000366 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 347255000367 protein binding site [polypeptide binding]; other site 347255000368 hypothetical protein; Validated; Region: PRK01415 347255000369 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 347255000370 active site residue [active] 347255000371 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 347255000372 Iron-sulfur protein interface; other site 347255000373 proximal quinone binding site [chemical binding]; other site 347255000374 SdhD (CybS) interface [polypeptide binding]; other site 347255000375 proximal heme binding site [chemical binding]; other site 347255000376 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 347255000377 putative SdhC subunit interface [polypeptide binding]; other site 347255000378 putative proximal heme binding site [chemical binding]; other site 347255000379 putative Iron-sulfur protein interface [polypeptide binding]; other site 347255000380 putative proximal quinone binding site; other site 347255000381 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 347255000382 L-aspartate oxidase; Provisional; Region: PRK06175 347255000383 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 347255000384 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 347255000385 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 347255000386 dimer interface [polypeptide binding]; other site 347255000387 conserved gate region; other site 347255000388 putative PBP binding loops; other site 347255000389 ABC-ATPase subunit interface; other site 347255000390 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 347255000391 S17 interaction site [polypeptide binding]; other site 347255000392 S8 interaction site; other site 347255000393 16S rRNA interaction site [nucleotide binding]; other site 347255000394 streptomycin interaction site [chemical binding]; other site 347255000395 23S rRNA interaction site [nucleotide binding]; other site 347255000396 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 347255000397 30S ribosomal protein S7; Validated; Region: PRK05302 347255000398 elongation factor G; Reviewed; Region: PRK00007 347255000399 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 347255000400 G1 box; other site 347255000401 putative GEF interaction site [polypeptide binding]; other site 347255000402 GTP/Mg2+ binding site [chemical binding]; other site 347255000403 Switch I region; other site 347255000404 G2 box; other site 347255000405 G3 box; other site 347255000406 Switch II region; other site 347255000407 G4 box; other site 347255000408 G5 box; other site 347255000409 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 347255000410 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 347255000411 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 347255000412 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 347255000413 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 347255000414 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 347255000415 putative homodimer interface [polypeptide binding]; other site 347255000416 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 347255000417 heterodimer interface [polypeptide binding]; other site 347255000418 homodimer interface [polypeptide binding]; other site 347255000419 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 347255000420 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 347255000421 23S rRNA interface [nucleotide binding]; other site 347255000422 putative thiostrepton binding site; other site 347255000423 L7/L12 interface [polypeptide binding]; other site 347255000424 L25 interface [polypeptide binding]; other site 347255000425 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 347255000426 mRNA/rRNA interface [nucleotide binding]; other site 347255000427 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 347255000428 23S rRNA interface [nucleotide binding]; other site 347255000429 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 347255000430 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 347255000431 core dimer interface [polypeptide binding]; other site 347255000432 peripheral dimer interface [polypeptide binding]; other site 347255000433 L10 interface [polypeptide binding]; other site 347255000434 L11 interface [polypeptide binding]; other site 347255000435 putative EF-Tu interaction site [polypeptide binding]; other site 347255000436 putative EF-G interaction site [polypeptide binding]; other site 347255000437 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 347255000438 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 347255000439 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 347255000440 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 347255000441 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 347255000442 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 347255000443 RPB3 interaction site [polypeptide binding]; other site 347255000444 RPB1 interaction site [polypeptide binding]; other site 347255000445 RPB11 interaction site [polypeptide binding]; other site 347255000446 RPB10 interaction site [polypeptide binding]; other site 347255000447 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 347255000448 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 347255000449 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 347255000450 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 347255000451 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 347255000452 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 347255000453 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 347255000454 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 347255000455 DNA binding site [nucleotide binding] 347255000456 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 347255000457 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255000458 multifunctional aminopeptidase A; Provisional; Region: PRK00913 347255000459 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 347255000460 interface (dimer of trimers) [polypeptide binding]; other site 347255000461 Substrate-binding/catalytic site; other site 347255000462 Zn-binding sites [ion binding]; other site 347255000463 ATPase MipZ; Region: MipZ; pfam09140 347255000464 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 347255000465 P-loop; other site 347255000466 Magnesium ion binding site [ion binding]; other site 347255000467 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 347255000468 Magnesium ion binding site [ion binding]; other site 347255000469 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 347255000470 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 347255000471 dimer interface [polypeptide binding]; other site 347255000472 anticodon binding site; other site 347255000473 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 347255000474 homodimer interface [polypeptide binding]; other site 347255000475 motif 1; other site 347255000476 active site 347255000477 motif 2; other site 347255000478 GAD domain; Region: GAD; pfam02938 347255000479 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 347255000480 active site 347255000481 motif 3; other site 347255000482 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 347255000483 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 347255000484 dihydrodipicolinate reductase; Provisional; Region: PRK00048 347255000485 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 347255000486 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 347255000487 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 347255000488 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 347255000489 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 347255000490 substrate binding pocket [chemical binding]; other site 347255000491 membrane-bound complex binding site; other site 347255000492 hinge residues; other site 347255000493 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 347255000494 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 347255000495 GatB domain; Region: GatB_Yqey; smart00845 347255000496 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 347255000497 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 347255000498 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 347255000499 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 347255000500 ribosome recycling factor; Reviewed; Region: frr; PRK00083 347255000501 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 347255000502 hinge region; other site 347255000503 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 347255000504 putative nucleotide binding site [chemical binding]; other site 347255000505 uridine monophosphate binding site [chemical binding]; other site 347255000506 homohexameric interface [polypeptide binding]; other site 347255000507 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 347255000508 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 347255000509 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 347255000510 putative substrate translocation pore; other site 347255000511 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 347255000512 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 347255000513 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 347255000514 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 347255000515 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 347255000516 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 347255000517 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 347255000518 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 347255000519 Surface antigen; Region: Bac_surface_Ag; pfam01103 347255000520 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 347255000521 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 347255000522 active site 347255000523 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 347255000524 protein binding site [polypeptide binding]; other site 347255000525 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 347255000526 putative substrate binding region [chemical binding]; other site 347255000527 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 347255000528 putative RNA binding site [nucleotide binding]; other site 347255000529 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 347255000530 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 347255000531 S-adenosylmethionine binding site [chemical binding]; other site 347255000532 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 347255000533 putative coenzyme Q binding site [chemical binding]; other site 347255000534 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255000535 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 347255000536 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 347255000537 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 347255000538 RNA methyltransferase, RsmE family; Region: TIGR00046 347255000539 Uncharacterized conserved protein [Function unknown]; Region: COG2155 347255000540 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 347255000541 Protein export membrane protein; Region: SecD_SecF; cl14618 347255000542 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 347255000543 IHF dimer interface [polypeptide binding]; other site 347255000544 IHF - DNA interface [nucleotide binding]; other site 347255000545 DNA polymerase III subunit delta'; Validated; Region: PRK06581 347255000546 signal recognition particle protein; Provisional; Region: PRK10867 347255000547 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 347255000548 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 347255000549 P loop; other site 347255000550 GTP binding site [chemical binding]; other site 347255000551 Signal peptide binding domain; Region: SRP_SPB; pfam02978 347255000552 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 347255000553 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 347255000554 FeS/SAM binding site; other site 347255000555 HemN C-terminal domain; Region: HemN_C; pfam06969 347255000556 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 347255000557 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 347255000558 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 347255000559 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 347255000560 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 347255000561 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 347255000562 active site 347255000563 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 347255000564 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 347255000565 E3 interaction surface; other site 347255000566 lipoyl attachment site [posttranslational modification]; other site 347255000567 e3 binding domain; Region: E3_binding; pfam02817 347255000568 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 347255000569 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 347255000570 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 347255000571 TPP-binding site [chemical binding]; other site 347255000572 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 347255000573 dimer interface [polypeptide binding]; other site 347255000574 PYR/PP interface [polypeptide binding]; other site 347255000575 TPP binding site [chemical binding]; other site 347255000576 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 347255000577 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 347255000578 active site 347255000579 Zn binding site [ion binding]; other site 347255000580 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 347255000581 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 347255000582 Walker A/P-loop; other site 347255000583 ATP binding site [chemical binding]; other site 347255000584 Q-loop/lid; other site 347255000585 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 347255000586 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 347255000587 ABC transporter signature motif; other site 347255000588 Walker B; other site 347255000589 D-loop; other site 347255000590 H-loop/switch region; other site 347255000591 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 347255000592 Tetratricopeptide repeat; Region: TPR_6; pfam13174 347255000593 ChaB; Region: ChaB; cl01887 347255000594 chaperone protein DnaJ; Provisional; Region: PRK14300 347255000595 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 347255000596 HSP70 interaction site [polypeptide binding]; other site 347255000597 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 347255000598 substrate binding site [polypeptide binding]; other site 347255000599 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 347255000600 Zn binding sites [ion binding]; other site 347255000601 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 347255000602 dimer interface [polypeptide binding]; other site 347255000603 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 347255000604 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 347255000605 nucleotide binding site [chemical binding]; other site 347255000606 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 347255000607 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 347255000608 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 347255000609 Lipopolysaccharide-assembly; Region: LptE; cl01125 347255000610 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 347255000611 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 347255000612 diiron binding motif [ion binding]; other site 347255000613 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 347255000614 Subunit III/VIIa interface [polypeptide binding]; other site 347255000615 Phospholipid binding site [chemical binding]; other site 347255000616 Subunit I/III interface [polypeptide binding]; other site 347255000617 Subunit III/VIb interface [polypeptide binding]; other site 347255000618 Subunit III/VIa interface; other site 347255000619 Subunit III/Vb interface [polypeptide binding]; other site 347255000620 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 347255000621 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 347255000622 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 347255000623 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 347255000624 trimer interface [polypeptide binding]; other site 347255000625 active site 347255000626 substrate binding site [chemical binding]; other site 347255000627 CoA binding site [chemical binding]; other site 347255000628 Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]; Region: PbpC; COG4953 347255000629 Transglycosylase; Region: Transgly; pfam00912 347255000630 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 347255000631 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 347255000632 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 347255000633 Ligand Binding Site [chemical binding]; other site 347255000634 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 347255000635 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 347255000636 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 347255000637 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 347255000638 catalytic loop [active] 347255000639 iron binding site [ion binding]; other site 347255000640 chaperone protein HscA; Provisional; Region: hscA; PRK01433 347255000641 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 347255000642 nucleotide binding site [chemical binding]; other site 347255000643 co-chaperone HscB; Provisional; Region: hscB; PRK01356 347255000644 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 347255000645 HSP70 interaction site [polypeptide binding]; other site 347255000646 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 347255000647 RNA/DNA hybrid binding site [nucleotide binding]; other site 347255000648 active site 347255000649 excinuclease ABC subunit B; Provisional; Region: PRK05298 347255000650 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 347255000651 ATP binding site [chemical binding]; other site 347255000652 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 347255000653 nucleotide binding region [chemical binding]; other site 347255000654 ATP-binding site [chemical binding]; other site 347255000655 Ultra-violet resistance protein B; Region: UvrB; pfam12344 347255000656 UvrB/uvrC motif; Region: UVR; pfam02151 347255000657 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 347255000658 GSH binding site [chemical binding]; other site 347255000659 catalytic residues [active] 347255000660 DNA gyrase subunit A; Validated; Region: PRK05560 347255000661 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 347255000662 CAP-like domain; other site 347255000663 active site 347255000664 primary dimer interface [polypeptide binding]; other site 347255000665 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347255000666 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347255000667 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347255000668 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347255000669 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347255000670 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 347255000671 active site 347255000672 catalytic residues [active] 347255000673 metal binding site [ion binding]; metal-binding site 347255000674 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 347255000675 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 347255000676 putative active site [active] 347255000677 substrate binding site [chemical binding]; other site 347255000678 putative cosubstrate binding site; other site 347255000679 catalytic site [active] 347255000680 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 347255000681 substrate binding site [chemical binding]; other site 347255000682 Predicted ATPase [General function prediction only]; Region: COG1485 347255000683 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 347255000684 Walker A motif; other site 347255000685 ATP binding site [chemical binding]; other site 347255000686 Walker B motif; other site 347255000687 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 347255000688 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 347255000689 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 347255000690 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 347255000691 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255000692 Walker A/P-loop; other site 347255000693 ATP binding site [chemical binding]; other site 347255000694 Q-loop/lid; other site 347255000695 ABC transporter signature motif; other site 347255000696 Walker B; other site 347255000697 D-loop; other site 347255000698 H-loop/switch region; other site 347255000699 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 347255000700 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 347255000701 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 347255000702 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 347255000703 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 347255000704 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 347255000705 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 347255000706 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 347255000707 putative metal binding site; other site 347255000708 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 347255000709 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 347255000710 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 347255000711 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 347255000712 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 347255000713 ATP binding site [chemical binding]; other site 347255000714 active site 347255000715 substrate binding site [chemical binding]; other site 347255000716 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 347255000717 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 347255000718 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 347255000719 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 347255000720 active site 347255000721 dimer interface [polypeptide binding]; other site 347255000722 motif 1; other site 347255000723 motif 2; other site 347255000724 motif 3; other site 347255000725 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 347255000726 anticodon binding site; other site 347255000727 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 347255000728 V-type ATP synthase subunit I; Validated; Region: PRK05771 347255000729 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 347255000730 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 347255000731 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 347255000732 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 347255000733 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 347255000734 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 347255000735 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 347255000736 ATP binding site [chemical binding]; other site 347255000737 Mg2+ binding site [ion binding]; other site 347255000738 G-X-G motif; other site 347255000739 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 347255000740 anchoring element; other site 347255000741 dimer interface [polypeptide binding]; other site 347255000742 ATP binding site [chemical binding]; other site 347255000743 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 347255000744 active site 347255000745 metal binding site [ion binding]; metal-binding site 347255000746 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 347255000747 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 347255000748 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 347255000749 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 347255000750 protein binding site [polypeptide binding]; other site 347255000751 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 347255000752 Catalytic dyad [active] 347255000753 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 347255000754 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 347255000755 dimer interface [polypeptide binding]; other site 347255000756 phosphorylation site [posttranslational modification] 347255000757 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 347255000758 ATP binding site [chemical binding]; other site 347255000759 Mg2+ binding site [ion binding]; other site 347255000760 G-X-G motif; other site 347255000761 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 347255000762 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 347255000763 FOG: WD40-like repeat [Function unknown]; Region: COG1520 347255000764 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 347255000765 Trp docking motif [polypeptide binding]; other site 347255000766 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 347255000767 23S rRNA interface [nucleotide binding]; other site 347255000768 L3 interface [polypeptide binding]; other site 347255000769 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 347255000770 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 347255000771 putative active site [active] 347255000772 Ap4A binding site [chemical binding]; other site 347255000773 nudix motif; other site 347255000774 putative metal binding site [ion binding]; other site 347255000775 response regulator PleD; Reviewed; Region: pleD; PRK09581 347255000776 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 347255000777 active site 347255000778 phosphorylation site [posttranslational modification] 347255000779 intermolecular recognition site; other site 347255000780 dimerization interface [polypeptide binding]; other site 347255000781 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 347255000782 active site 347255000783 phosphorylation site [posttranslational modification] 347255000784 intermolecular recognition site; other site 347255000785 dimerization interface [polypeptide binding]; other site 347255000786 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 347255000787 metal binding site [ion binding]; metal-binding site 347255000788 active site 347255000789 I-site; other site 347255000790 elongation factor P; Validated; Region: PRK00529 347255000791 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 347255000792 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 347255000793 RNA binding site [nucleotide binding]; other site 347255000794 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 347255000795 RNA binding site [nucleotide binding]; other site 347255000796 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 347255000797 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 347255000798 active site 347255000799 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 347255000800 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 347255000801 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 347255000802 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 347255000803 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 347255000804 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 347255000805 HlyD family secretion protein; Region: HlyD_3; pfam13437 347255000806 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 347255000807 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 347255000808 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 347255000809 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 347255000810 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 347255000811 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 347255000812 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 347255000813 FAD binding domain; Region: FAD_binding_4; pfam01565 347255000814 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 347255000815 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 347255000816 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 347255000817 ATP-grasp domain; Region: ATP-grasp_4; cl17255 347255000818 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 347255000819 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 347255000820 Cell division protein FtsQ; Region: FtsQ; pfam03799 347255000821 cell division protein FtsA; Region: ftsA; TIGR01174 347255000822 Cell division protein FtsA; Region: FtsA; smart00842 347255000823 Cell division protein FtsA; Region: FtsA; pfam14450 347255000824 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 347255000825 Cytochrome c2 [Energy production and conversion]; Region: COG3474 347255000826 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 347255000827 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 347255000828 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 347255000829 RNA binding site [nucleotide binding]; other site 347255000830 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 347255000831 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 347255000832 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 347255000833 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 347255000834 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 347255000835 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 347255000836 RNA binding surface [nucleotide binding]; other site 347255000837 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 347255000838 active site 347255000839 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 347255000840 Beta-lactamase; Region: Beta-lactamase; pfam00144 347255000841 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 347255000842 putative catalytic site [active] 347255000843 putative phosphate binding site [ion binding]; other site 347255000844 active site 347255000845 metal binding site A [ion binding]; metal-binding site 347255000846 DNA binding site [nucleotide binding] 347255000847 putative AP binding site [nucleotide binding]; other site 347255000848 putative metal binding site B [ion binding]; other site 347255000849 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 347255000850 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 347255000851 tetramer interface [polypeptide binding]; other site 347255000852 TPP-binding site [chemical binding]; other site 347255000853 heterodimer interface [polypeptide binding]; other site 347255000854 phosphorylation loop region [posttranslational modification] 347255000855 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 347255000856 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 347255000857 alpha subunit interface [polypeptide binding]; other site 347255000858 TPP binding site [chemical binding]; other site 347255000859 heterodimer interface [polypeptide binding]; other site 347255000860 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 347255000861 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 347255000862 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 347255000863 G1 box; other site 347255000864 putative GEF interaction site [polypeptide binding]; other site 347255000865 GTP/Mg2+ binding site [chemical binding]; other site 347255000866 Switch I region; other site 347255000867 G2 box; other site 347255000868 G3 box; other site 347255000869 Switch II region; other site 347255000870 G4 box; other site 347255000871 G5 box; other site 347255000872 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 347255000873 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 347255000874 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 347255000875 isocitrate dehydrogenase; Validated; Region: PRK09222 347255000876 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 347255000877 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 347255000878 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 347255000879 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 347255000880 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 347255000881 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 347255000882 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 347255000883 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 347255000884 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 347255000885 [2Fe-2S] cluster binding site [ion binding]; other site 347255000886 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 347255000887 Qi binding site; other site 347255000888 cytochrome b; Provisional; Region: CYTB; MTH00191 347255000889 intrachain domain interface; other site 347255000890 interchain domain interface [polypeptide binding]; other site 347255000891 heme bH binding site [chemical binding]; other site 347255000892 heme bL binding site [chemical binding]; other site 347255000893 Qo binding site; other site 347255000894 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 347255000895 interchain domain interface [polypeptide binding]; other site 347255000896 intrachain domain interface; other site 347255000897 Qi binding site; other site 347255000898 Qo binding site; other site 347255000899 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 347255000900 Cytochrome c; Region: Cytochrom_C; cl11414 347255000901 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 347255000902 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 347255000903 putative dimer interface [polypeptide binding]; other site 347255000904 peptide chain release factor 2; Validated; Region: prfB; PRK00578 347255000905 PCRF domain; Region: PCRF; pfam03462 347255000906 RF-1 domain; Region: RF-1; pfam00472 347255000907 GTP-binding protein LepA; Provisional; Region: PRK05433 347255000908 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 347255000909 G1 box; other site 347255000910 putative GEF interaction site [polypeptide binding]; other site 347255000911 GTP/Mg2+ binding site [chemical binding]; other site 347255000912 Switch I region; other site 347255000913 G2 box; other site 347255000914 G3 box; other site 347255000915 Switch II region; other site 347255000916 G4 box; other site 347255000917 G5 box; other site 347255000918 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 347255000919 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 347255000920 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 347255000921 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 347255000922 HD domain; Region: HD_4; pfam13328 347255000923 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 347255000924 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 347255000925 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 347255000926 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 347255000927 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 347255000928 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 347255000929 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 347255000930 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 347255000931 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 347255000932 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 347255000933 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 347255000934 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 347255000935 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 347255000936 VirB7 interaction site; other site 347255000937 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 347255000938 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 347255000939 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 347255000940 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 347255000941 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 347255000942 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 347255000943 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 347255000944 Walker A motif; other site 347255000945 hexamer interface [polypeptide binding]; other site 347255000946 ATP binding site [chemical binding]; other site 347255000947 Walker B motif; other site 347255000948 type IV secretion system component VirD4; Provisional; Region: PRK13897 347255000949 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 347255000950 Walker A motif; other site 347255000951 ATP binding site [chemical binding]; other site 347255000952 Walker B motif; other site 347255000953 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 347255000954 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 347255000955 Phage-related protein [Function unknown]; Region: COG4695; cl01923 347255000956 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 347255000957 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 347255000958 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 347255000959 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 347255000960 active site 347255000961 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 347255000962 MutS domain I; Region: MutS_I; pfam01624 347255000963 MutS domain II; Region: MutS_II; pfam05188 347255000964 MutS domain III; Region: MutS_III; pfam05192 347255000965 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 347255000966 Walker A/P-loop; other site 347255000967 ATP binding site [chemical binding]; other site 347255000968 Q-loop/lid; other site 347255000969 ABC transporter signature motif; other site 347255000970 Walker B; other site 347255000971 D-loop; other site 347255000972 H-loop/switch region; other site 347255000973 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 347255000974 Peptidase family M23; Region: Peptidase_M23; pfam01551 347255000975 Protein of unknown function DUF45; Region: DUF45; pfam01863 347255000976 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 347255000977 translocation protein TolB; Provisional; Region: tolB; PRK05137 347255000978 TolB amino-terminal domain; Region: TolB_N; pfam04052 347255000979 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 347255000980 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 347255000981 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 347255000982 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 347255000983 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 347255000984 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 347255000985 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 347255000986 DNA binding residues [nucleotide binding] 347255000987 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 347255000988 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 347255000989 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 347255000990 Ligand Binding Site [chemical binding]; other site 347255000991 amino acid transporter; Region: 2A0306; TIGR00909 347255000992 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 347255000993 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 347255000994 dimer interface [polypeptide binding]; other site 347255000995 motif 1; other site 347255000996 active site 347255000997 motif 2; other site 347255000998 motif 3; other site 347255000999 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 347255001000 anticodon binding site; other site 347255001001 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 347255001002 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255001003 Walker A/P-loop; other site 347255001004 ATP binding site [chemical binding]; other site 347255001005 Q-loop/lid; other site 347255001006 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 347255001007 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 347255001008 TolQ protein; Region: tolQ; TIGR02796 347255001009 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 347255001010 TolR protein; Region: tolR; TIGR02801 347255001011 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 347255001012 HD domain; Region: HD_4; pfam13328 347255001013 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 347255001014 metabolite-proton symporter; Region: 2A0106; TIGR00883 347255001015 putative substrate translocation pore; other site 347255001016 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 347255001017 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 347255001018 HlyD family secretion protein; Region: HlyD_3; pfam13437 347255001019 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 347255001020 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 347255001021 Walker A/P-loop; other site 347255001022 ATP binding site [chemical binding]; other site 347255001023 Q-loop/lid; other site 347255001024 ABC transporter signature motif; other site 347255001025 Walker B; other site 347255001026 D-loop; other site 347255001027 H-loop/switch region; other site 347255001028 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 347255001029 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 347255001030 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 347255001031 nucleotide binding site/active site [active] 347255001032 HIT family signature motif; other site 347255001033 catalytic residue [active] 347255001034 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 347255001035 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 347255001036 active site 347255001037 HslU subunit interaction site [polypeptide binding]; other site 347255001038 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 347255001039 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 347255001040 Walker A motif; other site 347255001041 ATP binding site [chemical binding]; other site 347255001042 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 347255001043 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 347255001044 Uncharacterized conserved protein [Function unknown]; Region: COG5464 347255001045 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 347255001046 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 347255001047 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 347255001048 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 347255001049 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 347255001050 dimerization interface [polypeptide binding]; other site 347255001051 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 347255001052 putative iron binding site [ion binding]; other site 347255001053 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 347255001054 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 347255001055 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 347255001056 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 347255001057 HIGH motif; other site 347255001058 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347255001059 active site 347255001060 KMSKS motif; other site 347255001061 DNA topoisomerase I; Validated; Region: PRK06599 347255001062 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 347255001063 active site 347255001064 interdomain interaction site; other site 347255001065 putative metal-binding site [ion binding]; other site 347255001066 nucleotide binding site [chemical binding]; other site 347255001067 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 347255001068 domain I; other site 347255001069 DNA binding groove [nucleotide binding] 347255001070 phosphate binding site [ion binding]; other site 347255001071 domain II; other site 347255001072 domain III; other site 347255001073 nucleotide binding site [chemical binding]; other site 347255001074 catalytic site [active] 347255001075 domain IV; other site 347255001076 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 347255001077 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 347255001078 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 347255001079 dimer interface [polypeptide binding]; other site 347255001080 decamer (pentamer of dimers) interface [polypeptide binding]; other site 347255001081 catalytic triad [active] 347255001082 peroxidatic and resolving cysteines [active] 347255001083 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 347255001084 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 347255001085 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 347255001086 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 347255001087 Sulfatase; Region: Sulfatase; pfam00884 347255001088 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 347255001089 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 347255001090 sequence-specific DNA binding site [nucleotide binding]; other site 347255001091 salt bridge; other site 347255001092 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 347255001093 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 347255001094 NADP binding site [chemical binding]; other site 347255001095 active site 347255001096 putative substrate binding site [chemical binding]; other site 347255001097 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 347255001098 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 347255001099 NAD(P) binding site [chemical binding]; other site 347255001100 homodimer interface [polypeptide binding]; other site 347255001101 substrate binding site [chemical binding]; other site 347255001102 active site 347255001103 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 347255001104 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 347255001105 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 347255001106 active site 347255001107 homodimer interface [polypeptide binding]; other site 347255001108 Methyltransferase domain; Region: Methyltransf_31; pfam13847 347255001109 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 347255001110 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 347255001111 active site 347255001112 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 347255001113 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 347255001114 active site 347255001115 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 347255001116 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 347255001117 HlyD family secretion protein; Region: HlyD_3; pfam13437 347255001118 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 347255001119 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 347255001120 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 347255001121 catalytic site [active] 347255001122 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 347255001123 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 347255001124 putative ADP-binding pocket [chemical binding]; other site 347255001125 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 347255001126 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 347255001127 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 347255001128 RNA binding surface [nucleotide binding]; other site 347255001129 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 347255001130 UbiA prenyltransferase family; Region: UbiA; pfam01040 347255001131 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 347255001132 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 347255001133 TPR motif; other site 347255001134 binding surface 347255001135 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 347255001136 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 347255001137 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 347255001138 RimM N-terminal domain; Region: RimM; pfam01782 347255001139 PRC-barrel domain; Region: PRC; pfam05239 347255001140 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 347255001141 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 347255001142 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 347255001143 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 347255001144 active site 347255001145 DNA binding site [nucleotide binding] 347255001146 hypothetical protein; Provisional; Region: PRK14388 347255001147 NADH dehydrogenase subunit E; Validated; Region: PRK07539 347255001148 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 347255001149 putative dimer interface [polypeptide binding]; other site 347255001150 [2Fe-2S] cluster binding site [ion binding]; other site 347255001151 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 347255001152 NADH dehydrogenase subunit D; Validated; Region: PRK06075 347255001153 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 347255001154 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 347255001155 NADH dehydrogenase subunit B; Validated; Region: PRK06411 347255001156 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 347255001157 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 347255001158 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 347255001159 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 347255001160 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 347255001161 active site 347255001162 DNA binding site [nucleotide binding] 347255001163 Int/Topo IB signature motif; other site 347255001164 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 347255001165 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 347255001166 homotetramer interface [polypeptide binding]; other site 347255001167 NAD binding site [chemical binding]; other site 347255001168 homodimer interface [polypeptide binding]; other site 347255001169 substrate binding site [chemical binding]; other site 347255001170 active site 347255001171 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 347255001172 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 347255001173 putative active site [active] 347255001174 catalytic triad [active] 347255001175 putative dimer interface [polypeptide binding]; other site 347255001176 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 347255001177 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 347255001178 amidase catalytic site [active] 347255001179 Zn binding residues [ion binding]; other site 347255001180 substrate binding site [chemical binding]; other site 347255001181 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 347255001182 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 347255001183 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 347255001184 TM-ABC transporter signature motif; other site 347255001185 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 347255001186 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 347255001187 Walker A/P-loop; other site 347255001188 ATP binding site [chemical binding]; other site 347255001189 Q-loop/lid; other site 347255001190 ABC transporter signature motif; other site 347255001191 Walker B; other site 347255001192 D-loop; other site 347255001193 H-loop/switch region; other site 347255001194 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 347255001195 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 347255001196 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 347255001197 active site 347255001198 HIGH motif; other site 347255001199 KMSKS motif; other site 347255001200 Predicted permeases [General function prediction only]; Region: COG0679 347255001201 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 347255001202 Malic enzyme, N-terminal domain; Region: malic; pfam00390 347255001203 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 347255001204 putative NAD(P) binding site [chemical binding]; other site 347255001205 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 347255001206 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 347255001207 putative active site [active] 347255001208 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 347255001209 metabolite-proton symporter; Region: 2A0106; TIGR00883 347255001210 malate dehydrogenase; Reviewed; Region: PRK06223 347255001211 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 347255001212 NAD(P) binding site [chemical binding]; other site 347255001213 dimer interface [polypeptide binding]; other site 347255001214 tetramer (dimer of dimers) interface [polypeptide binding]; other site 347255001215 substrate binding site [chemical binding]; other site 347255001216 TLC ATP/ADP transporter; Region: TLC; pfam03219 347255001217 CTP synthetase; Validated; Region: pyrG; PRK05380 347255001218 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 347255001219 Catalytic site [active] 347255001220 active site 347255001221 UTP binding site [chemical binding]; other site 347255001222 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 347255001223 active site 347255001224 putative oxyanion hole; other site 347255001225 catalytic triad [active] 347255001226 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 347255001227 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 347255001228 Ligand binding site; other site 347255001229 oligomer interface; other site 347255001230 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 347255001231 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_19; cd04678 347255001232 nudix motif; other site 347255001233 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 347255001234 GTP cyclohydrolase I; Provisional; Region: PLN03044 347255001235 active site 347255001236 prolyl-tRNA synthetase; Provisional; Region: PRK12325 347255001237 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 347255001238 dimer interface [polypeptide binding]; other site 347255001239 motif 1; other site 347255001240 active site 347255001241 motif 2; other site 347255001242 motif 3; other site 347255001243 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 347255001244 anticodon binding site; other site 347255001245 Fic family protein [Function unknown]; Region: COG3177 347255001246 Fic/DOC family; Region: Fic; pfam02661 347255001247 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 347255001248 RuvA N terminal domain; Region: RuvA_N; pfam01330 347255001249 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 347255001250 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 347255001251 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 347255001252 Walker A motif; other site 347255001253 ATP binding site [chemical binding]; other site 347255001254 Walker B motif; other site 347255001255 arginine finger; other site 347255001256 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 347255001257 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 347255001258 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 347255001259 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255001260 Walker A/P-loop; other site 347255001261 ATP binding site [chemical binding]; other site 347255001262 Q-loop/lid; other site 347255001263 ABC transporter signature motif; other site 347255001264 Walker B; other site 347255001265 D-loop; other site 347255001266 H-loop/switch region; other site 347255001267 muropeptide transporter; Reviewed; Region: ampG; PRK11902 347255001268 muropeptide transporter; Validated; Region: ampG; cl17669 347255001269 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 347255001270 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 347255001271 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255001272 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 347255001273 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 347255001274 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 347255001275 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 347255001276 BON domain; Region: BON; pfam04972 347255001277 BON domain; Region: BON; pfam04972 347255001278 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 347255001279 Iron permease FTR1 family; Region: FTR1; cl00475 347255001280 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 347255001281 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 347255001282 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 347255001283 Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion...; Region: 3,4-PCD; cd03459 347255001284 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 347255001285 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 347255001286 catalytic residues [active] 347255001287 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 347255001288 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 347255001289 tandem repeat interface [polypeptide binding]; other site 347255001290 oligomer interface [polypeptide binding]; other site 347255001291 active site residues [active] 347255001292 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 347255001293 trimer interface [polypeptide binding]; other site 347255001294 active site 347255001295 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 347255001296 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 347255001297 N-acetyl-D-glucosamine binding site [chemical binding]; other site 347255001298 catalytic residue [active] 347255001299 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 347255001300 dimer interface [polypeptide binding]; other site 347255001301 catalytic triad [active] 347255001302 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 347255001303 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 347255001304 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 347255001305 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 347255001306 catalytic triad [active] 347255001307 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 347255001308 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 347255001309 Subunit I/III interface [polypeptide binding]; other site 347255001310 D-pathway; other site 347255001311 Subunit I/VIIc interface [polypeptide binding]; other site 347255001312 Subunit I/IV interface [polypeptide binding]; other site 347255001313 Subunit I/II interface [polypeptide binding]; other site 347255001314 Low-spin heme (heme a) binding site [chemical binding]; other site 347255001315 Subunit I/VIIa interface [polypeptide binding]; other site 347255001316 Subunit I/VIa interface [polypeptide binding]; other site 347255001317 Dimer interface; other site 347255001318 Putative water exit pathway; other site 347255001319 Binuclear center (heme a3/CuB) [ion binding]; other site 347255001320 K-pathway; other site 347255001321 Subunit I/Vb interface [polypeptide binding]; other site 347255001322 Putative proton exit pathway; other site 347255001323 Subunit I/VIb interface; other site 347255001324 Subunit I/VIc interface [polypeptide binding]; other site 347255001325 Electron transfer pathway; other site 347255001326 Subunit I/VIIIb interface [polypeptide binding]; other site 347255001327 Subunit I/VIIb interface [polypeptide binding]; other site 347255001328 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 347255001329 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 347255001330 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255001331 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 347255001332 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 347255001333 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 347255001334 Cytidylyltransferase [Cell envelope biogenesis, outer membrane / Lipid metabolism]; Region: TagD; COG0615 347255001335 active site 347255001336 HIGH motif; other site 347255001337 nucleotide binding site [chemical binding]; other site 347255001338 putative peptidase; Provisional; Region: PRK11649 347255001339 Peptidase family M23; Region: Peptidase_M23; pfam01551 347255001340 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 347255001341 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 347255001342 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 347255001343 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 347255001344 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 347255001345 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 347255001346 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 347255001347 cell division protein FtsW; Region: ftsW; TIGR02614 347255001348 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 347255001349 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 347255001350 active site 347255001351 homodimer interface [polypeptide binding]; other site 347255001352 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 347255001353 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 347255001354 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 347255001355 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 347255001356 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 347255001357 diaminopimelate epimerase; Region: DapF; TIGR00652 347255001358 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 347255001359 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 347255001360 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 347255001361 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 347255001362 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 347255001363 FeS/SAM binding site; other site 347255001364 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 347255001365 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 347255001366 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 347255001367 dimer interface [polypeptide binding]; other site 347255001368 motif 1; other site 347255001369 active site 347255001370 motif 2; other site 347255001371 motif 3; other site 347255001372 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 347255001373 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 347255001374 putative tRNA-binding site [nucleotide binding]; other site 347255001375 B3/4 domain; Region: B3_4; pfam03483 347255001376 tRNA synthetase B5 domain; Region: B5; smart00874 347255001377 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 347255001378 dimer interface [polypeptide binding]; other site 347255001379 motif 1; other site 347255001380 motif 3; other site 347255001381 motif 2; other site 347255001382 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 347255001383 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 347255001384 DNA polymerase III subunit beta; Validated; Region: PRK05643 347255001385 putative DNA binding surface [nucleotide binding]; other site 347255001386 dimer interface [polypeptide binding]; other site 347255001387 beta-clamp/clamp loader binding surface; other site 347255001388 beta-clamp/translesion DNA polymerase binding surface; other site 347255001389 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 347255001390 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 347255001391 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 347255001392 HIGH motif; other site 347255001393 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 347255001394 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347255001395 active site 347255001396 KMSKS motif; other site 347255001397 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 347255001398 tRNA binding surface [nucleotide binding]; other site 347255001399 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 347255001400 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 347255001401 catalytic site [active] 347255001402 putative active site [active] 347255001403 putative substrate binding site [chemical binding]; other site 347255001404 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 347255001405 Septum formation initiator; Region: DivIC; pfam04977 347255001406 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 347255001407 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 347255001408 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 347255001409 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 347255001410 catalytic residue [active] 347255001411 putative FPP diphosphate binding site; other site 347255001412 putative FPP binding hydrophobic cleft; other site 347255001413 dimer interface [polypeptide binding]; other site 347255001414 putative IPP diphosphate binding site; other site 347255001415 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 347255001416 HAMP domain; Region: HAMP; pfam00672 347255001417 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 347255001418 dimer interface [polypeptide binding]; other site 347255001419 phosphorylation site [posttranslational modification] 347255001420 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 347255001421 ATP binding site [chemical binding]; other site 347255001422 Mg2+ binding site [ion binding]; other site 347255001423 G-X-G motif; other site 347255001424 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 347255001425 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 347255001426 active site 347255001427 phosphorylation site [posttranslational modification] 347255001428 intermolecular recognition site; other site 347255001429 dimerization interface [polypeptide binding]; other site 347255001430 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 347255001431 DNA binding site [nucleotide binding] 347255001432 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 347255001433 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 347255001434 homodimer interface [polypeptide binding]; other site 347255001435 substrate-cofactor binding pocket; other site 347255001436 catalytic residue [active] 347255001437 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 347255001438 dihydrodipicolinate synthase; Region: dapA; TIGR00674 347255001439 dimer interface [polypeptide binding]; other site 347255001440 active site 347255001441 catalytic residue [active] 347255001442 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 347255001443 SmpB-tmRNA interface; other site 347255001444 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 347255001445 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 347255001446 catalytic residues [active] 347255001447 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 347255001448 CoA binding domain; Region: CoA_binding; pfam02629 347255001449 CoA-ligase; Region: Ligase_CoA; pfam00549 347255001450 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 347255001451 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 347255001452 CoA-ligase; Region: Ligase_CoA; pfam00549 347255001453 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 347255001454 putative active site [active] 347255001455 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 347255001456 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 347255001457 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 347255001458 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 347255001459 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 347255001460 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 347255001461 Predicted membrane protein [Function unknown]; Region: COG1238 347255001462 Predicted membrane protein/domain [Function unknown]; Region: COG1714 347255001463 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 347255001464 RecR protein; Region: RecR; pfam02132 347255001465 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 347255001466 putative active site [active] 347255001467 putative metal-binding site [ion binding]; other site 347255001468 tetramer interface [polypeptide binding]; other site 347255001469 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 347255001470 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 347255001471 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 347255001472 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 347255001473 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 347255001474 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 347255001475 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 347255001476 Predicted permeases [General function prediction only]; Region: COG0679 347255001477 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 347255001478 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 347255001479 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 347255001480 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 347255001481 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 347255001482 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 347255001483 tetramerization interface [polypeptide binding]; other site 347255001484 NAD(P) binding site [chemical binding]; other site 347255001485 catalytic residues [active] 347255001486 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 347255001487 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 347255001488 active site 347255001489 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 347255001490 Part of AAA domain; Region: AAA_19; pfam13245 347255001491 Family description; Region: UvrD_C_2; pfam13538 347255001492 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 347255001493 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 347255001494 tetramer interface [polypeptide binding]; other site 347255001495 pyridoxal 5'-phosphate binding site [chemical binding]; other site 347255001496 catalytic residue [active] 347255001497 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 347255001498 Found in ATP-dependent protease La (LON); Region: LON; smart00464 347255001499 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 347255001500 Walker A motif; other site 347255001501 ATP binding site [chemical binding]; other site 347255001502 Walker B motif; other site 347255001503 arginine finger; other site 347255001504 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 347255001505 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 347255001506 30S subunit binding site; other site 347255001507 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 347255001508 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 347255001509 trimer interface [polypeptide binding]; other site 347255001510 putative metal binding site [ion binding]; other site 347255001511 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 347255001512 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 347255001513 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 347255001514 homodimer interface [polypeptide binding]; other site 347255001515 NADP binding site [chemical binding]; other site 347255001516 substrate binding site [chemical binding]; other site 347255001517 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 347255001518 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 347255001519 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 347255001520 Spore Coat Protein U domain; Region: SCPU; pfam05229 347255001521 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 347255001522 Class I ribonucleotide reductase; Region: RNR_I; cd01679 347255001523 active site 347255001524 dimer interface [polypeptide binding]; other site 347255001525 catalytic residues [active] 347255001526 effector binding site; other site 347255001527 R2 peptide binding site; other site 347255001528 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 347255001529 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 347255001530 dimer interface [polypeptide binding]; other site 347255001531 putative radical transfer pathway; other site 347255001532 diiron center [ion binding]; other site 347255001533 tyrosyl radical; other site 347255001534 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 347255001535 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 347255001536 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 347255001537 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 347255001538 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 347255001539 active site 347255001540 substrate binding site [chemical binding]; other site 347255001541 metal binding site [ion binding]; metal-binding site 347255001542 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 347255001543 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255001544 Walker A/P-loop; other site 347255001545 ATP binding site [chemical binding]; other site 347255001546 Q-loop/lid; other site 347255001547 ABC transporter signature motif; other site 347255001548 Walker B; other site 347255001549 D-loop; other site 347255001550 H-loop/switch region; other site 347255001551 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255001552 OstA-like protein; Region: OstA; pfam03968 347255001553 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 347255001554 KpsF/GutQ family protein; Region: kpsF; TIGR00393 347255001555 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 347255001556 putative active site [active] 347255001557 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 347255001558 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 347255001559 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 347255001560 oligomer interface [polypeptide binding]; other site 347255001561 RNA binding site [nucleotide binding]; other site 347255001562 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 347255001563 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 347255001564 RNase E interface [polypeptide binding]; other site 347255001565 trimer interface [polypeptide binding]; other site 347255001566 active site 347255001567 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 347255001568 putative nucleic acid binding region [nucleotide binding]; other site 347255001569 G-X-X-G motif; other site 347255001570 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 347255001571 RNA binding site [nucleotide binding]; other site 347255001572 domain interface; other site 347255001573 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 347255001574 16S/18S rRNA binding site [nucleotide binding]; other site 347255001575 S13e-L30e interaction site [polypeptide binding]; other site 347255001576 25S rRNA binding site [nucleotide binding]; other site 347255001577 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 347255001578 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 347255001579 RNA binding site [nucleotide binding]; other site 347255001580 active site 347255001581 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255001582 TLC ATP/ADP transporter; Region: TLC; pfam03219 347255001583 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 347255001584 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 347255001585 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 347255001586 non-specific DNA binding site [nucleotide binding]; other site 347255001587 salt bridge; other site 347255001588 sequence-specific DNA binding site [nucleotide binding]; other site 347255001589 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 347255001590 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 347255001591 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 347255001592 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 347255001593 uncharacterized protein, YfiH family; Region: TIGR00726 347255001594 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 347255001595 active site 347255001596 catalytic residues [active] 347255001597 metal binding site [ion binding]; metal-binding site 347255001598 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 347255001599 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 347255001600 putative active site [active] 347255001601 homotetrameric interface [polypeptide binding]; other site 347255001602 metal binding site [ion binding]; metal-binding site 347255001603 hypothetical protein; Provisional; Region: PRK06661 347255001604 intersubunit interface [polypeptide binding]; other site 347255001605 active site 347255001606 Zn2+ binding site [ion binding]; other site 347255001607 pyruvate phosphate dikinase; Provisional; Region: PRK09279 347255001608 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 347255001609 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 347255001610 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 347255001611 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 347255001612 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 347255001613 GSH binding site (G-site) [chemical binding]; other site 347255001614 C-terminal domain interface [polypeptide binding]; other site 347255001615 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 347255001616 N-terminal domain interface [polypeptide binding]; other site 347255001617 dimer interface [polypeptide binding]; other site 347255001618 substrate binding pocket (H-site) [chemical binding]; other site 347255001619 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 347255001620 conserved cys residue [active] 347255001621 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 347255001622 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 347255001623 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 347255001624 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 347255001625 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 347255001626 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 347255001627 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 347255001628 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 347255001629 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 347255001630 Uncharacterized conserved protein [Function unknown]; Region: COG5448 347255001631 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 347255001632 Uncharacterized conserved protein [Function unknown]; Region: COG5449 347255001633 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 347255001634 Predicted membrane protein [Function unknown]; Region: COG5346 347255001635 translation initiation factor IF-3; Region: infC; TIGR00168 347255001636 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 347255001637 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 347255001638 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 347255001639 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 347255001640 E3 interaction surface; other site 347255001641 lipoyl attachment site [posttranslational modification]; other site 347255001642 e3 binding domain; Region: E3_binding; pfam02817 347255001643 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 347255001644 peptide chain release factor 1; Validated; Region: prfA; PRK00591 347255001645 This domain is found in peptide chain release factors; Region: PCRF; smart00937 347255001646 RF-1 domain; Region: RF-1; pfam00472 347255001647 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 347255001648 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 347255001649 DHH family; Region: DHH; pfam01368 347255001650 DHHA1 domain; Region: DHHA1; pfam02272 347255001651 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 347255001652 S-adenosylmethionine binding site [chemical binding]; other site 347255001653 Methyltransferase domain; Region: Methyltransf_31; pfam13847 347255001654 transcription termination factor Rho; Provisional; Region: rho; PRK09376 347255001655 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 347255001656 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 347255001657 RNA binding site [nucleotide binding]; other site 347255001658 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 347255001659 multimer interface [polypeptide binding]; other site 347255001660 Walker A motif; other site 347255001661 ATP binding site [chemical binding]; other site 347255001662 Walker B motif; other site 347255001663 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 347255001664 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 347255001665 tandem repeat interface [polypeptide binding]; other site 347255001666 oligomer interface [polypeptide binding]; other site 347255001667 active site residues [active] 347255001668 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 347255001669 IHF - DNA interface [nucleotide binding]; other site 347255001670 IHF dimer interface [polypeptide binding]; other site 347255001671 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 347255001672 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 347255001673 Walker B motif; other site 347255001674 Uncharacterized conserved protein [Function unknown]; Region: COG5464 347255001675 HD domain; Region: HD_4; pfam13328 347255001676 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 347255001677 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 347255001678 DnaA N-terminal domain; Region: DnaA_N; pfam11638 347255001679 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 347255001680 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 347255001681 CMP-binding site; other site 347255001682 The sites determining sugar specificity; other site 347255001683 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 347255001684 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 347255001685 RNA binding site [nucleotide binding]; other site 347255001686 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 347255001687 RNA binding site [nucleotide binding]; other site 347255001688 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 347255001689 RNA binding site [nucleotide binding]; other site 347255001690 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 347255001691 RNA binding site [nucleotide binding]; other site 347255001692 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 347255001693 RNA binding site [nucleotide binding]; other site 347255001694 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 347255001695 RNA binding site [nucleotide binding]; other site 347255001696 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 347255001697 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 347255001698 oligomer interface [polypeptide binding]; other site 347255001699 active site residues [active] 347255001700 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 347255001701 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 347255001702 homotetramer interface [polypeptide binding]; other site 347255001703 FMN binding site [chemical binding]; other site 347255001704 homodimer contacts [polypeptide binding]; other site 347255001705 putative active site [active] 347255001706 putative substrate binding site [chemical binding]; other site 347255001707 potential frameshift: common BLAST hit: gi|157827377|ref|YP_001496441.1| acetyltransferase 347255001708 Predicted acetyltransferase [General function prediction only]; Region: COG5628 347255001709 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 347255001710 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 347255001711 Coenzyme A binding pocket [chemical binding]; other site 347255001712 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 347255001713 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 347255001714 Predicted transcriptional regulator [Transcription]; Region: COG1959 347255001715 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 347255001716 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 347255001717 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 347255001718 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 347255001719 catalytic residue [active] 347255001720 cysteine desulfurase; Provisional; Region: PRK14012 347255001721 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 347255001722 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 347255001723 catalytic residue [active] 347255001724 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 347255001725 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 347255001726 trimerization site [polypeptide binding]; other site 347255001727 active site 347255001728 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 347255001729 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 347255001730 arginine:agmatin antiporter; Provisional; Region: PRK10644 347255001731 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 347255001732 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 347255001733 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 347255001734 active site 347255001735 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 347255001736 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 347255001737 substrate binding pocket [chemical binding]; other site 347255001738 chain length determination region; other site 347255001739 substrate-Mg2+ binding site; other site 347255001740 catalytic residues [active] 347255001741 aspartate-rich region 1; other site 347255001742 active site lid residues [active] 347255001743 aspartate-rich region 2; other site 347255001744 TLC ATP/ADP transporter; Region: TLC; pfam03219 347255001745 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 347255001746 muropeptide transporter; Reviewed; Region: ampG; PRK11902 347255001747 AmpG-like permease; Region: 2A0125; TIGR00901 347255001748 Lysine efflux permease [General function prediction only]; Region: COG1279 347255001749 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 347255001750 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 347255001751 active site 347255001752 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 347255001753 HemY protein N-terminus; Region: HemY_N; pfam07219 347255001754 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 347255001755 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 347255001756 RelB antitoxin; Region: RelB; cl01171 347255001757 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 347255001758 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 347255001759 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 347255001760 putative acyl-acceptor binding pocket; other site 347255001761 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 347255001762 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 347255001763 active site 347255001764 HIGH motif; other site 347255001765 dimer interface [polypeptide binding]; other site 347255001766 KMSKS motif; other site 347255001767 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 347255001768 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 347255001769 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 347255001770 domain interfaces; other site 347255001771 active site 347255001772 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 347255001773 dimer interface [polypeptide binding]; other site 347255001774 catalytic triad [active] 347255001775 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 347255001776 Na binding site [ion binding]; other site 347255001777 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 347255001778 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 347255001779 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 347255001780 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 347255001781 Uncharacterized conserved protein [Function unknown]; Region: COG1723 347255001782 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 347255001783 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 347255001784 catalytic site [active] 347255001785 putative active site [active] 347255001786 putative substrate binding site [chemical binding]; other site 347255001787 Helicase and RNase D C-terminal; Region: HRDC; smart00341 347255001788 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 347255001789 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 347255001790 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 347255001791 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 347255001792 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 347255001793 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 347255001794 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 347255001795 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 347255001796 S-adenosylmethionine binding site [chemical binding]; other site 347255001797 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 347255001798 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 347255001799 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 347255001800 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 347255001801 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 347255001802 N-acetyl-D-glucosamine binding site [chemical binding]; other site 347255001803 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 347255001804 hypothetical protein; Validated; Region: PRK00110 347255001805 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 347255001806 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 347255001807 Substrate binding site; other site 347255001808 Mg++ binding site; other site 347255001809 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 347255001810 homodimer interface [polypeptide binding]; other site 347255001811 active site 347255001812 putative chemical substrate binding site [chemical binding]; other site 347255001813 metal binding site [ion binding]; metal-binding site 347255001814 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 347255001815 Coenzyme A binding pocket [chemical binding]; other site 347255001816 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 347255001817 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 347255001818 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 347255001819 dimer interface [polypeptide binding]; other site 347255001820 allosteric magnesium binding site [ion binding]; other site 347255001821 active site 347255001822 aspartate-rich active site metal binding site; other site 347255001823 Schiff base residues; other site 347255001824 primosome assembly protein PriA; Validated; Region: PRK05580 347255001825 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 347255001826 ATP binding site [chemical binding]; other site 347255001827 putative Mg++ binding site [ion binding]; other site 347255001828 helicase superfamily c-terminal domain; Region: HELICc; smart00490 347255001829 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 347255001830 Flavoprotein; Region: Flavoprotein; pfam02441 347255001831 replicative DNA helicase; Provisional; Region: PRK09165 347255001832 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 347255001833 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 347255001834 Walker A motif; other site 347255001835 ATP binding site [chemical binding]; other site 347255001836 Walker B motif; other site 347255001837 DNA binding loops [nucleotide binding] 347255001838 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 347255001839 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 347255001840 RNA binding surface [nucleotide binding]; other site 347255001841 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 347255001842 active site 347255001843 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 347255001844 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 347255001845 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 347255001846 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 347255001847 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 347255001848 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 347255001849 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 347255001850 S-adenosylmethionine binding site [chemical binding]; other site 347255001851 DNA repair protein RadA; Provisional; Region: PRK11823 347255001852 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 347255001853 Walker A motif/ATP binding site; other site 347255001854 ATP binding site [chemical binding]; other site 347255001855 Walker B motif; other site 347255001856 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 347255001857 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 347255001858 Recombination protein O N terminal; Region: RecO_N; pfam11967 347255001859 Recombination protein O C terminal; Region: RecO_C; pfam02565 347255001860 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 347255001861 Glycoprotease family; Region: Peptidase_M22; pfam00814 347255001862 translation initiation factor IF-2; Validated; Region: infB; PRK05306 347255001863 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 347255001864 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 347255001865 G1 box; other site 347255001866 putative GEF interaction site [polypeptide binding]; other site 347255001867 GTP/Mg2+ binding site [chemical binding]; other site 347255001868 Switch I region; other site 347255001869 G2 box; other site 347255001870 G3 box; other site 347255001871 Switch II region; other site 347255001872 G4 box; other site 347255001873 G5 box; other site 347255001874 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 347255001875 Translation-initiation factor 2; Region: IF-2; pfam11987 347255001876 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 347255001877 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 347255001878 NusA N-terminal domain; Region: NusA_N; pfam08529 347255001879 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 347255001880 RNA binding site [nucleotide binding]; other site 347255001881 homodimer interface [polypeptide binding]; other site 347255001882 NusA-like KH domain; Region: KH_5; pfam13184 347255001883 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 347255001884 G-X-X-G motif; other site 347255001885 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 347255001886 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 347255001887 Sm and related proteins; Region: Sm_like; cl00259 347255001888 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 347255001889 putative oligomer interface [polypeptide binding]; other site 347255001890 putative RNA binding site [nucleotide binding]; other site 347255001891 Predicted transcriptional regulator [Transcription]; Region: COG1959 347255001892 Transcriptional regulator; Region: Rrf2; cl17282 347255001893 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 347255001894 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 347255001895 RNA binding surface [nucleotide binding]; other site 347255001896 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 347255001897 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 347255001898 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 347255001899 active site 347255001900 HIGH motif; other site 347255001901 dimer interface [polypeptide binding]; other site 347255001902 KMSKS motif; other site 347255001903 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 347255001904 RNA binding surface [nucleotide binding]; other site 347255001905 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 347255001906 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 347255001907 Substrate binding site [chemical binding]; other site 347255001908 metabolite-proton symporter; Region: 2A0106; TIGR00883 347255001909 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 347255001910 MG2 domain; Region: A2M_N; pfam01835 347255001911 Alpha-2-macroglobulin family; Region: A2M; pfam00207 347255001912 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 347255001913 surface patch; other site 347255001914 thioester region; other site 347255001915 specificity defining residues; other site 347255001916 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 347255001917 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 347255001918 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255001919 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 347255001920 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 347255001921 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 347255001922 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 347255001923 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 347255001924 active site 347255001925 phosphorylation site [posttranslational modification] 347255001926 intermolecular recognition site; other site 347255001927 dimerization interface [polypeptide binding]; other site 347255001928 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 347255001929 Walker A motif; other site 347255001930 ATP binding site [chemical binding]; other site 347255001931 Walker B motif; other site 347255001932 arginine finger; other site 347255001933 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 347255001934 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 347255001935 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 347255001936 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 347255001937 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 347255001938 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 347255001939 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 347255001940 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 347255001941 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 347255001942 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 347255001943 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 347255001944 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 347255001945 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 347255001946 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 347255001947 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 347255001948 S-adenosylmethionine binding site [chemical binding]; other site 347255001949 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 347255001950 MraZ protein; Region: MraZ; pfam02381 347255001951 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 347255001952 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 347255001953 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 347255001954 Na binding site [ion binding]; other site 347255001955 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 347255001956 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 347255001957 GIY-YIG motif/motif A; other site 347255001958 active site 347255001959 catalytic site [active] 347255001960 putative DNA binding site [nucleotide binding]; other site 347255001961 metal binding site [ion binding]; metal-binding site 347255001962 UvrB/uvrC motif; Region: UVR; pfam02151 347255001963 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 347255001964 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 347255001965 A new structural DNA glycosylase; Region: AlkD_like; cd06561 347255001966 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 347255001967 active site 347255001968 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 347255001969 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 347255001970 DNA binding site [nucleotide binding] 347255001971 active site 347255001972 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 347255001973 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 347255001974 DEAD/DEAH box helicase; Region: DEAD; pfam00270 347255001975 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 347255001976 SEC-C motif; Region: SEC-C; pfam02810 347255001977 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 347255001978 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 347255001979 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 347255001980 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 347255001981 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 347255001982 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 347255001983 hinge; other site 347255001984 active site 347255001985 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 347255001986 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 347255001987 ATP binding site [chemical binding]; other site 347255001988 Mg2+ binding site [ion binding]; other site 347255001989 G-X-G motif; other site 347255001990 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 347255001991 anchoring element; other site 347255001992 dimer interface [polypeptide binding]; other site 347255001993 ATP binding site [chemical binding]; other site 347255001994 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 347255001995 active site 347255001996 putative metal-binding site [ion binding]; other site 347255001997 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 347255001998 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 347255001999 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 347255002000 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 347255002001 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 347255002002 MgtE intracellular N domain; Region: MgtE_N; pfam03448 347255002003 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 347255002004 Divalent cation transporter; Region: MgtE; pfam01769 347255002005 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 347255002006 HD domain; Region: HD_4; pfam13328 347255002007 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 347255002008 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 347255002009 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 347255002010 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 347255002011 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 347255002012 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 347255002013 Cu(I) binding site [ion binding]; other site 347255002014 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 347255002015 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 347255002016 dimer interface [polypeptide binding]; other site 347255002017 substrate binding site [chemical binding]; other site 347255002018 metal binding sites [ion binding]; metal-binding site 347255002019 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255002020 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 347255002021 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 347255002022 TraX protein; Region: TraX; pfam05857 347255002023 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 347255002024 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 347255002025 ssDNA binding site; other site 347255002026 generic binding surface II; other site 347255002027 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 347255002028 ATP binding site [chemical binding]; other site 347255002029 putative Mg++ binding site [ion binding]; other site 347255002030 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 347255002031 nucleotide binding region [chemical binding]; other site 347255002032 ATP-binding site [chemical binding]; other site 347255002033 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 347255002034 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 347255002035 V-type ATP synthase subunit I; Validated; Region: PRK05771 347255002036 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 347255002037 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 347255002038 Mg++ binding site [ion binding]; other site 347255002039 putative catalytic motif [active] 347255002040 putative substrate binding site [chemical binding]; other site 347255002041 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 347255002042 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 347255002043 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 347255002044 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 347255002045 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 347255002046 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 347255002047 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 347255002048 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 347255002049 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 347255002050 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 347255002051 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 347255002052 ATP binding site [chemical binding]; other site 347255002053 putative Mg++ binding site [ion binding]; other site 347255002054 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 347255002055 nucleotide binding region [chemical binding]; other site 347255002056 ATP-binding site [chemical binding]; other site 347255002057 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 347255002058 Uncharacterized conserved protein [Function unknown]; Region: COG2938 347255002059 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 347255002060 active site residue [active] 347255002061 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 347255002062 DnaA N-terminal domain; Region: DnaA_N; pfam11638 347255002063 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 347255002064 Walker A motif; other site 347255002065 ATP binding site [chemical binding]; other site 347255002066 Walker B motif; other site 347255002067 arginine finger; other site 347255002068 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 347255002069 DnaA box-binding interface [nucleotide binding]; other site 347255002070 Patatin [General function prediction only]; Region: COG3621 347255002071 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 347255002072 active site 347255002073 nucleophile elbow; other site 347255002074 GTP-binding protein YchF; Reviewed; Region: PRK09601 347255002075 YchF GTPase; Region: YchF; cd01900 347255002076 G1 box; other site 347255002077 GTP/Mg2+ binding site [chemical binding]; other site 347255002078 Switch I region; other site 347255002079 G2 box; other site 347255002080 Switch II region; other site 347255002081 G3 box; other site 347255002082 G4 box; other site 347255002083 G5 box; other site 347255002084 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 347255002085 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 347255002086 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 347255002087 putative active site [active] 347255002088 catalytic residue [active] 347255002089 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 347255002090 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 347255002091 5S rRNA interface [nucleotide binding]; other site 347255002092 CTC domain interface [polypeptide binding]; other site 347255002093 L16 interface [polypeptide binding]; other site 347255002094 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 347255002095 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 347255002096 FeS/SAM binding site; other site 347255002097 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 347255002098 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 347255002099 23S rRNA binding site [nucleotide binding]; other site 347255002100 L21 binding site [polypeptide binding]; other site 347255002101 L13 binding site [polypeptide binding]; other site 347255002102 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 347255002103 ribonuclease P; Reviewed; Region: rnpA; PRK01492 347255002104 Protein of unknown function (DUF416); Region: DUF416; cl01166 347255002105 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 347255002106 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 347255002107 Cl binding site [ion binding]; other site 347255002108 oligomer interface [polypeptide binding]; other site 347255002109 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 347255002110 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 347255002111 dimerization interface [polypeptide binding]; other site 347255002112 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 347255002113 dimer interface [polypeptide binding]; other site 347255002114 phosphorylation site [posttranslational modification] 347255002115 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 347255002116 ATP binding site [chemical binding]; other site 347255002117 Mg2+ binding site [ion binding]; other site 347255002118 G-X-G motif; other site 347255002119 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 347255002120 Uncharacterized conserved protein [Function unknown]; Region: COG5590 347255002121 COQ9; Region: COQ9; pfam08511 347255002122 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 347255002123 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 347255002124 HIGH motif; other site 347255002125 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 347255002126 active site 347255002127 KMSKS motif; other site 347255002128 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 347255002129 tRNA binding surface [nucleotide binding]; other site 347255002130 anticodon binding site; other site 347255002131 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 347255002132 TPR motif; other site 347255002133 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 347255002134 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 347255002135 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 347255002136 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 347255002137 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 347255002138 carboxyltransferase (CT) interaction site; other site 347255002139 biotinylation site [posttranslational modification]; other site 347255002140 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 347255002141 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 347255002142 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 347255002143 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 347255002144 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 347255002145 putative substrate translocation pore; other site 347255002146 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 347255002147 putative acyl-acceptor binding pocket; other site 347255002148 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 347255002149 acyl-activating enzyme (AAE) consensus motif; other site 347255002150 putative AMP binding site [chemical binding]; other site 347255002151 Regulator of competence-specific genes [Transcription]; Region: TfoX; COG3070 347255002152 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 347255002153 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 347255002154 ABC-ATPase subunit interface; other site 347255002155 dimer interface [polypeptide binding]; other site 347255002156 putative PBP binding regions; other site 347255002157 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 347255002158 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255002159 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 347255002160 S-adenosylmethionine binding site [chemical binding]; other site 347255002161 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 347255002162 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 347255002163 HIGH motif; other site 347255002164 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 347255002165 active site 347255002166 KMSKS motif; other site 347255002167 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255002168 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 347255002169 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 347255002170 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 347255002171 ring oligomerisation interface [polypeptide binding]; other site 347255002172 ATP/Mg binding site [chemical binding]; other site 347255002173 stacking interactions; other site 347255002174 hinge regions; other site 347255002175 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 347255002176 oligomerisation interface [polypeptide binding]; other site 347255002177 mobile loop; other site 347255002178 roof hairpin; other site 347255002179 ribonuclease PH; Reviewed; Region: rph; PRK00173 347255002180 Ribonuclease PH; Region: RNase_PH_bact; cd11362 347255002181 hexamer interface [polypeptide binding]; other site 347255002182 active site 347255002183 GrpE; Region: GrpE; pfam01025 347255002184 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 347255002185 dimer interface [polypeptide binding]; other site 347255002186 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 347255002187 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 347255002188 Domain of unknown function DUF20; Region: UPF0118; pfam01594 347255002189 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 347255002190 hypothetical protein; Validated; Region: PRK06620 347255002191 metabolite-proton symporter; Region: 2A0106; TIGR00883 347255002192 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 347255002193 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 347255002194 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 347255002195 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 347255002196 alphaNTD - beta interaction site [polypeptide binding]; other site 347255002197 alphaNTD homodimer interface [polypeptide binding]; other site 347255002198 alphaNTD - beta' interaction site [polypeptide binding]; other site 347255002199 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 347255002200 30S ribosomal protein S11; Validated; Region: PRK05309 347255002201 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 347255002202 30S ribosomal protein S13; Region: bact_S13; TIGR03631 347255002203 adenylate kinase; Reviewed; Region: adk; PRK00279 347255002204 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 347255002205 AMP-binding site [chemical binding]; other site 347255002206 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 347255002207 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 347255002208 SecY translocase; Region: SecY; pfam00344 347255002209 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 347255002210 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 347255002211 23S rRNA binding site [nucleotide binding]; other site 347255002212 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 347255002213 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 347255002214 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 347255002215 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 347255002216 5S rRNA interface [nucleotide binding]; other site 347255002217 23S rRNA interface [nucleotide binding]; other site 347255002218 L5 interface [polypeptide binding]; other site 347255002219 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 347255002220 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 347255002221 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 347255002222 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 347255002223 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 347255002224 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 347255002225 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 347255002226 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 347255002227 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 347255002228 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 347255002229 RNA binding site [nucleotide binding]; other site 347255002230 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 347255002231 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 347255002232 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 347255002233 L23 interface [polypeptide binding]; other site 347255002234 trigger factor interaction site; other site 347255002235 23S rRNA interface [nucleotide binding]; other site 347255002236 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 347255002237 23S rRNA interface [nucleotide binding]; other site 347255002238 5S rRNA interface [nucleotide binding]; other site 347255002239 putative antibiotic binding site [chemical binding]; other site 347255002240 L25 interface [polypeptide binding]; other site 347255002241 L27 interface [polypeptide binding]; other site 347255002242 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 347255002243 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 347255002244 G-X-X-G motif; other site 347255002245 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 347255002246 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 347255002247 putative translocon binding site; other site 347255002248 protein-rRNA interface [nucleotide binding]; other site 347255002249 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 347255002250 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 347255002251 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 347255002252 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 347255002253 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 347255002254 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 347255002255 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 347255002256 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 347255002257 elongation factor Tu; Reviewed; Region: PRK00049 347255002258 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 347255002259 G1 box; other site 347255002260 GEF interaction site [polypeptide binding]; other site 347255002261 GTP/Mg2+ binding site [chemical binding]; other site 347255002262 Switch I region; other site 347255002263 G2 box; other site 347255002264 G3 box; other site 347255002265 Switch II region; other site 347255002266 G4 box; other site 347255002267 G5 box; other site 347255002268 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 347255002269 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 347255002270 Antibiotic Binding Site [chemical binding]; other site 347255002271 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 347255002272 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 347255002273 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 347255002274 fumarate hydratase; Reviewed; Region: fumC; PRK00485 347255002275 Class II fumarases; Region: Fumarase_classII; cd01362 347255002276 active site 347255002277 tetramer interface [polypeptide binding]; other site 347255002278 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 347255002279 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 347255002280 putative active site [active] 347255002281 homotetrameric interface [polypeptide binding]; other site 347255002282 cell division protein FtsZ; Validated; Region: PRK09330 347255002283 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 347255002284 nucleotide binding site [chemical binding]; other site 347255002285 SulA interaction site; other site 347255002286 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 347255002287 primary substrate binding site; other site 347255002288 inhibition loop; other site 347255002289 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 347255002290 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 347255002291 muropeptide transporter; Validated; Region: ampG; cl17669 347255002292 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 347255002293 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 347255002294 ATP binding site [chemical binding]; other site 347255002295 Mg++ binding site [ion binding]; other site 347255002296 motif III; other site 347255002297 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 347255002298 nucleotide binding region [chemical binding]; other site 347255002299 ATP-binding site [chemical binding]; other site 347255002300 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 347255002301 DNA-binding site [nucleotide binding]; DNA binding site 347255002302 RNA-binding motif; other site 347255002303 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 347255002304 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 347255002305 S-adenosylmethionine binding site [chemical binding]; other site 347255002306 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 347255002307 SurA N-terminal domain; Region: SurA_N_3; cl07813 347255002308 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 347255002309 Organic solvent tolerance protein; Region: OstA_C; pfam04453 347255002310 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 347255002311 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 347255002312 generic binding surface II; other site 347255002313 generic binding surface I; other site 347255002314 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 347255002315 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 347255002316 putative catalytic site [active] 347255002317 putative phosphate binding site [ion binding]; other site 347255002318 active site 347255002319 metal binding site A [ion binding]; metal-binding site 347255002320 DNA binding site [nucleotide binding] 347255002321 putative AP binding site [nucleotide binding]; other site 347255002322 putative metal binding site B [ion binding]; other site 347255002323 Uncharacterized conserved protein [Function unknown]; Region: COG4095 347255002324 GTP-binding protein Der; Reviewed; Region: PRK00093 347255002325 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 347255002326 G1 box; other site 347255002327 GTP/Mg2+ binding site [chemical binding]; other site 347255002328 Switch I region; other site 347255002329 G2 box; other site 347255002330 Switch II region; other site 347255002331 G3 box; other site 347255002332 G4 box; other site 347255002333 G5 box; other site 347255002334 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 347255002335 G1 box; other site 347255002336 GTP/Mg2+ binding site [chemical binding]; other site 347255002337 Switch I region; other site 347255002338 G2 box; other site 347255002339 G3 box; other site 347255002340 Switch II region; other site 347255002341 G4 box; other site 347255002342 G5 box; other site 347255002343 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 347255002344 AAA domain; Region: AAA_14; pfam13173 347255002345 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 347255002346 ABC1 family; Region: ABC1; pfam03109 347255002347 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 347255002348 active site 347255002349 ATP binding site [chemical binding]; other site 347255002350 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 347255002351 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 347255002352 S-adenosylmethionine binding site [chemical binding]; other site 347255002353 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 347255002354 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 347255002355 DNA binding site [nucleotide binding] 347255002356 catalytic residue [active] 347255002357 H2TH interface [polypeptide binding]; other site 347255002358 putative catalytic residues [active] 347255002359 turnover-facilitating residue; other site 347255002360 intercalation triad [nucleotide binding]; other site 347255002361 8OG recognition residue [nucleotide binding]; other site 347255002362 putative reading head residues; other site 347255002363 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 347255002364 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 347255002365 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 347255002366 active site 347255002367 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 347255002368 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 347255002369 active site 347255002370 HIGH motif; other site 347255002371 KMSKS motif; other site 347255002372 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 347255002373 tRNA binding surface [nucleotide binding]; other site 347255002374 anticodon binding site; other site 347255002375 thymidylate kinase; Validated; Region: tmk; PRK00698 347255002376 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 347255002377 TMP-binding site; other site 347255002378 ATP-binding site [chemical binding]; other site 347255002379 metabolite-proton symporter; Region: 2A0106; TIGR00883 347255002380 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 347255002381 UbiA prenyltransferase family; Region: UbiA; pfam01040 347255002382 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 347255002383 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347255002384 active site 347255002385 HIGH motif; other site 347255002386 nucleotide binding site [chemical binding]; other site 347255002387 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 347255002388 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347255002389 active site 347255002390 KMSKS motif; other site 347255002391 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 347255002392 tRNA binding surface [nucleotide binding]; other site 347255002393 anticodon binding site; other site 347255002394 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 347255002395 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 347255002396 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 347255002397 RmuC family; Region: RmuC; pfam02646 347255002398 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cl01298 347255002399 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 347255002400 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 347255002401 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 347255002402 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 347255002403 Walker A motif; other site 347255002404 ATP binding site [chemical binding]; other site 347255002405 Walker B motif; other site 347255002406 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 347255002407 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 347255002408 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 347255002409 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 347255002410 Ligand Binding Site [chemical binding]; other site 347255002411 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 347255002412 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 347255002413 HicB family; Region: HicB; pfam05534 347255002414 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 347255002415 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 347255002416 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255002417 Walker A/P-loop; other site 347255002418 ATP binding site [chemical binding]; other site 347255002419 Q-loop/lid; other site 347255002420 ABC transporter signature motif; other site 347255002421 Walker B; other site 347255002422 D-loop; other site 347255002423 H-loop/switch region; other site 347255002424 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 347255002425 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 347255002426 putative substrate translocation pore; other site 347255002427 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 347255002428 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 347255002429 FtsX-like permease family; Region: FtsX; pfam02687 347255002430 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 347255002431 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 347255002432 Walker A/P-loop; other site 347255002433 ATP binding site [chemical binding]; other site 347255002434 Q-loop/lid; other site 347255002435 ABC transporter signature motif; other site 347255002436 Walker B; other site 347255002437 D-loop; other site 347255002438 H-loop/switch region; other site 347255002439 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 347255002440 Domain of unknown function DUF21; Region: DUF21; pfam01595 347255002441 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 347255002442 Transporter associated domain; Region: CorC_HlyC; smart01091 347255002443 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 347255002444 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 347255002445 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 347255002446 Autotransporter beta-domain; Region: Autotransporter; smart00869 347255002447 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 347255002448 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 347255002449 synthetase active site [active] 347255002450 NTP binding site [chemical binding]; other site 347255002451 metal binding site [ion binding]; metal-binding site 347255002452 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 347255002453 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 347255002454 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 347255002455 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 347255002456 DNA binding residues [nucleotide binding] 347255002457 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 347255002458 IHF dimer interface [polypeptide binding]; other site 347255002459 IHF - DNA interface [nucleotide binding]; other site 347255002460 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 347255002461 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 347255002462 catalytic triad [active] 347255002463 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 347255002464 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 347255002465 putative acyl-acceptor binding pocket; other site 347255002466 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 347255002467 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 347255002468 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 347255002469 Peptidase family M23; Region: Peptidase_M23; pfam01551 347255002470 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 347255002471 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 347255002472 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 347255002473 nucleotide binding pocket [chemical binding]; other site 347255002474 K-X-D-G motif; other site 347255002475 catalytic site [active] 347255002476 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 347255002477 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 347255002478 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 347255002479 Dimer interface [polypeptide binding]; other site 347255002480 BRCT sequence motif; other site 347255002481 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 347255002482 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 347255002483 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 347255002484 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 347255002485 mce related protein; Region: MCE; pfam02470 347255002486 hypothetical protein; Provisional; Region: PRK06630 347255002487 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 347255002488 RNA/DNA hybrid binding site [nucleotide binding]; other site 347255002489 active site 347255002490 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 347255002491 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 347255002492 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 347255002493 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 347255002494 CoA-binding site [chemical binding]; other site 347255002495 ATP-binding [chemical binding]; other site 347255002496 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 347255002497 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 347255002498 active site 347255002499 catalytic site [active] 347255002500 substrate binding site [chemical binding]; other site 347255002501 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 347255002502 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 347255002503 Part of AAA domain; Region: AAA_19; pfam13245 347255002504 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 347255002505 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 347255002506 Family description; Region: UvrD_C_2; pfam13538 347255002507 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 347255002508 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 347255002509 acetyl-CoA acetyltransferase; Provisional; Region: PRK06633 347255002510 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 347255002511 dimer interface [polypeptide binding]; other site 347255002512 active site 347255002513 TLC ATP/ADP transporter; Region: TLC; pfam03219 347255002514 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 347255002515 nudix motif; other site 347255002516 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 347255002517 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 347255002518 Transporter associated domain; Region: CorC_HlyC; smart01091 347255002519 metal-binding heat shock protein; Provisional; Region: PRK00016 347255002520 PemK-like protein; Region: PemK; cl00995 347255002521 lipoyl synthase; Provisional; Region: PRK05481 347255002522 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 347255002523 FeS/SAM binding site; other site 347255002524 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 347255002525 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 347255002526 dimer interface [polypeptide binding]; other site 347255002527 active site 347255002528 glycine-pyridoxal phosphate binding site [chemical binding]; other site 347255002529 folate binding site [chemical binding]; other site 347255002530 Predicted esterase [General function prediction only]; Region: COG0400 347255002531 putative hydrolase; Provisional; Region: PRK11460 347255002532 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 347255002533 putative GSH binding site [chemical binding]; other site 347255002534 catalytic residues [active] 347255002535 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 347255002536 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 347255002537 minor groove reading motif; other site 347255002538 helix-hairpin-helix signature motif; other site 347255002539 substrate binding pocket [chemical binding]; other site 347255002540 active site 347255002541 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 347255002542 Predicted small secreted protein [Function unknown]; Region: COG5510 347255002543 Predicted methyltransferases [General function prediction only]; Region: COG0313 347255002544 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 347255002545 putative SAM binding site [chemical binding]; other site 347255002546 putative homodimer interface [polypeptide binding]; other site 347255002547 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 347255002548 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 347255002549 putative ligand binding site [chemical binding]; other site 347255002550 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 347255002551 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 347255002552 tetramer interfaces [polypeptide binding]; other site 347255002553 binuclear metal-binding site [ion binding]; other site 347255002554 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 347255002555 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 347255002556 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 347255002557 aspartate kinase; Reviewed; Region: PRK06635 347255002558 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 347255002559 putative nucleotide binding site [chemical binding]; other site 347255002560 putative catalytic residues [active] 347255002561 putative Mg ion binding site [ion binding]; other site 347255002562 putative aspartate binding site [chemical binding]; other site 347255002563 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 347255002564 putative allosteric regulatory residue; other site 347255002565 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 347255002566 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 347255002567 metabolite-proton symporter; Region: 2A0106; TIGR00883 347255002568 putative substrate translocation pore; other site 347255002569 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 347255002570 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255002571 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 347255002572 Helix-turn-helix domain; Region: HTH_25; pfam13413 347255002573 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 347255002574 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 347255002575 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 347255002576 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 347255002577 trmE is a tRNA modification GTPase; Region: trmE; cd04164 347255002578 G1 box; other site 347255002579 GTP/Mg2+ binding site [chemical binding]; other site 347255002580 Switch I region; other site 347255002581 G2 box; other site 347255002582 Switch II region; other site 347255002583 G3 box; other site 347255002584 G4 box; other site 347255002585 G5 box; other site 347255002586 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 347255002587 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 347255002588 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 347255002589 hexamer interface [polypeptide binding]; other site 347255002590 Walker A motif; other site 347255002591 ATP binding site [chemical binding]; other site 347255002592 Walker B motif; other site 347255002593 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 347255002594 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 347255002595 NAD(P) binding site [chemical binding]; other site 347255002596 active site 347255002597 acyl carrier protein; Provisional; Region: acpP; PRK00982 347255002598 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 347255002599 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 347255002600 dimer interface [polypeptide binding]; other site 347255002601 active site 347255002602 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 347255002603 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 347255002604 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 347255002605 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255002606 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 347255002607 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 347255002608 catalytic site [active] 347255002609 G-X2-G-X-G-K; other site 347255002610 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 347255002611 sequence-specific DNA binding site [nucleotide binding]; other site 347255002612 salt bridge; other site 347255002613 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 347255002614 rod shape-determining protein MreC; Region: MreC; pfam04085 347255002615 rod shape-determining protein MreB; Provisional; Region: PRK13927 347255002616 MreB and similar proteins; Region: MreB_like; cd10225 347255002617 nucleotide binding site [chemical binding]; other site 347255002618 Mg binding site [ion binding]; other site 347255002619 putative protofilament interaction site [polypeptide binding]; other site 347255002620 RodZ interaction site [polypeptide binding]; other site 347255002621 Predicted permeases [General function prediction only]; Region: COG0795 347255002622 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 347255002623 putative outer membrane lipoprotein; Provisional; Region: PRK09967 347255002624 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 347255002625 ligand binding site [chemical binding]; other site 347255002626 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 347255002627 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 347255002628 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 347255002629 dimer interface [polypeptide binding]; other site 347255002630 active site 347255002631 CoA binding pocket [chemical binding]; other site 347255002632 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 347255002633 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 347255002634 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 347255002635 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 347255002636 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 347255002637 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 347255002638 P loop; other site 347255002639 GTP binding site [chemical binding]; other site 347255002640 DNA polymerase I; Provisional; Region: PRK05755 347255002641 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 347255002642 active site 347255002643 metal binding site 1 [ion binding]; metal-binding site 347255002644 putative 5' ssDNA interaction site; other site 347255002645 metal binding site 3; metal-binding site 347255002646 metal binding site 2 [ion binding]; metal-binding site 347255002647 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 347255002648 putative DNA binding site [nucleotide binding]; other site 347255002649 putative metal binding site [ion binding]; other site 347255002650 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 347255002651 active site 347255002652 substrate binding site [chemical binding]; other site 347255002653 catalytic site [active] 347255002654 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 347255002655 active site 347255002656 DNA binding site [nucleotide binding] 347255002657 catalytic site [active] 347255002658 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 347255002659 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 347255002660 putative active site [active] 347255002661 putative PHP Thumb interface [polypeptide binding]; other site 347255002662 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 347255002663 generic binding surface I; other site 347255002664 generic binding surface II; other site 347255002665 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 347255002666 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 347255002667 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 347255002668 Protein of unknown function; Region: DUF3971; pfam13116 347255002669 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 347255002670 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 347255002671 putative substrate translocation pore; other site 347255002672 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 347255002673 seryl-tRNA synthetase; Provisional; Region: PRK05431 347255002674 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 347255002675 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 347255002676 dimer interface [polypeptide binding]; other site 347255002677 active site 347255002678 motif 1; other site 347255002679 motif 2; other site 347255002680 motif 3; other site 347255002681 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 347255002682 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 347255002683 Integral membrane protein TerC family; Region: TerC; cl10468 347255002684 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 347255002685 Methyltransferase domain; Region: Methyltransf_31; pfam13847 347255002686 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 347255002687 S-adenosylmethionine binding site [chemical binding]; other site 347255002688 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 347255002689 Predicted transcriptional regulator [Transcription]; Region: COG2944 347255002690 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 347255002691 salt bridge; other site 347255002692 non-specific DNA binding site [nucleotide binding]; other site 347255002693 sequence-specific DNA binding site [nucleotide binding]; other site 347255002694 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 347255002695 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 347255002696 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 347255002697 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 347255002698 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 347255002699 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 347255002700 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 347255002701 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 347255002702 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 347255002703 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255002704 Walker A/P-loop; other site 347255002705 ATP binding site [chemical binding]; other site 347255002706 Q-loop/lid; other site 347255002707 ABC transporter signature motif; other site 347255002708 Walker B; other site 347255002709 D-loop; other site 347255002710 H-loop/switch region; other site 347255002711 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 347255002712 4Fe-4S binding domain; Region: Fer4; cl02805 347255002713 4Fe-4S binding domain; Region: Fer4; pfam00037 347255002714 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 347255002715 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 347255002716 NADH dehydrogenase subunit G; Validated; Region: PRK09130 347255002717 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 347255002718 catalytic loop [active] 347255002719 iron binding site [ion binding]; other site 347255002720 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 347255002721 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 347255002722 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 347255002723 Predicted membrane protein [Function unknown]; Region: COG3671 347255002724 aconitate hydratase; Validated; Region: PRK09277 347255002725 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 347255002726 substrate binding site [chemical binding]; other site 347255002727 ligand binding site [chemical binding]; other site 347255002728 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 347255002729 substrate binding site [chemical binding]; other site 347255002730 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 347255002731 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 347255002732 gamma subunit interface [polypeptide binding]; other site 347255002733 epsilon subunit interface [polypeptide binding]; other site 347255002734 LBP interface [polypeptide binding]; other site 347255002735 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 347255002736 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 347255002737 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 347255002738 alpha subunit interaction interface [polypeptide binding]; other site 347255002739 Walker A motif; other site 347255002740 ATP binding site [chemical binding]; other site 347255002741 Walker B motif; other site 347255002742 inhibitor binding site; inhibition site 347255002743 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 347255002744 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 347255002745 core domain interface [polypeptide binding]; other site 347255002746 delta subunit interface [polypeptide binding]; other site 347255002747 epsilon subunit interface [polypeptide binding]; other site 347255002748 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 347255002749 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 347255002750 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 347255002751 beta subunit interaction interface [polypeptide binding]; other site 347255002752 Walker A motif; other site 347255002753 ATP binding site [chemical binding]; other site 347255002754 Walker B motif; other site 347255002755 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 347255002756 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 347255002757 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 347255002758 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 347255002759 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 347255002760 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 347255002761 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 347255002762 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 347255002763 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 347255002764 dimerization interface [polypeptide binding]; other site 347255002765 DPS ferroxidase diiron center [ion binding]; other site 347255002766 ion pore; other site 347255002767 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 347255002768 Transglycosylase; Region: Transgly; pfam00912 347255002769 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 347255002770 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 347255002771 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 347255002772 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 347255002773 FeS/SAM binding site; other site 347255002774 TRAM domain; Region: TRAM; pfam01938 347255002775 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 347255002776 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 347255002777 Bacterial SH3 domain; Region: SH3_4; pfam06347 347255002778 Bacterial SH3 domain; Region: SH3_4; pfam06347 347255002779 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 347255002780 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 347255002781 TrkA-N domain; Region: TrkA_N; pfam02254 347255002782 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 347255002783 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 347255002784 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 347255002785 rRNA binding site [nucleotide binding]; other site 347255002786 predicted 30S ribosome binding site; other site 347255002787 Maf-like protein; Region: Maf; pfam02545 347255002788 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 347255002789 active site 347255002790 dimer interface [polypeptide binding]; other site 347255002791 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 347255002792 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 347255002793 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 347255002794 active site 347255002795 DNA binding site [nucleotide binding] 347255002796 Int/Topo IB signature motif; other site 347255002797 Phasin protein; Region: Phasin_2; pfam09361 347255002798 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 347255002799 PLD-like domain; Region: PLDc_2; pfam13091 347255002800 putative active site [active] 347255002801 catalytic site [active] 347255002802 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 347255002803 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 347255002804 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 347255002805 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 347255002806 Autotransporter beta-domain; Region: Autotransporter; pfam03797 347255002807 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 347255002808 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 347255002809 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 347255002810 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 347255002811 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 347255002812 active site 347255002813 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 347255002814 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 347255002815 Mg++ binding site [ion binding]; other site 347255002816 putative catalytic motif [active] 347255002817 putative substrate binding site [chemical binding]; other site 347255002818 Protein of unknown function (DUF721); Region: DUF721; pfam05258 347255002819 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 347255002820 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 347255002821 Ferredoxin [Energy production and conversion]; Region: COG1146 347255002822 4Fe-4S binding domain; Region: Fer4; cl02805 347255002823 heme exporter protein CcmC; Region: ccmC; TIGR01191 347255002824 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 347255002825 nucleoside/Zn binding site; other site 347255002826 dimer interface [polypeptide binding]; other site 347255002827 catalytic motif [active] 347255002828 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 347255002829 Cation efflux family; Region: Cation_efflux; cl00316 347255002830 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 347255002831 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 347255002832 substrate binding site [chemical binding]; other site 347255002833 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 347255002834 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 347255002835 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 347255002836 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 347255002837 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 347255002838 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 347255002839 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 347255002840 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 347255002841 dimer interface [polypeptide binding]; other site 347255002842 ssDNA binding site [nucleotide binding]; other site 347255002843 tetramer (dimer of dimers) interface [polypeptide binding]; other site 347255002844 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 347255002845 Phage-related lysozyme (muraminidase) [General function prediction only]; Region: COG3772 347255002846 hypothetical protein; Reviewed; Region: PRK01530 347255002847 heat shock protein 90; Provisional; Region: PRK05218 347255002848 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 347255002849 ATP binding site [chemical binding]; other site 347255002850 Mg2+ binding site [ion binding]; other site 347255002851 G-X-G motif; other site 347255002852 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 347255002853 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 347255002854 substrate-cofactor binding pocket; other site 347255002855 pyridoxal 5'-phosphate binding site [chemical binding]; other site 347255002856 catalytic residue [active] 347255002857 trigger factor; Provisional; Region: tig; PRK01490 347255002858 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 347255002859 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 347255002860 GTPase CgtA; Reviewed; Region: obgE; PRK12299 347255002861 GTP1/OBG; Region: GTP1_OBG; pfam01018 347255002862 Obg GTPase; Region: Obg; cd01898 347255002863 G1 box; other site 347255002864 GTP/Mg2+ binding site [chemical binding]; other site 347255002865 Switch I region; other site 347255002866 G2 box; other site 347255002867 G3 box; other site 347255002868 Switch II region; other site 347255002869 G4 box; other site 347255002870 G5 box; other site 347255002871 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 347255002872 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 347255002873 dimer interface [polypeptide binding]; other site 347255002874 active site 347255002875 citrylCoA binding site [chemical binding]; other site 347255002876 NADH binding [chemical binding]; other site 347255002877 cationic pore residues; other site 347255002878 oxalacetate/citrate binding site [chemical binding]; other site 347255002879 coenzyme A binding site [chemical binding]; other site 347255002880 catalytic triad [active] 347255002881 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 347255002882 Fe-S cluster binding site [ion binding]; other site 347255002883 active site 347255002884 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 347255002885 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 347255002886 RNA binding surface [nucleotide binding]; other site 347255002887 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 347255002888 active site 347255002889 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 347255002890 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 347255002891 S-adenosylmethionine binding site [chemical binding]; other site 347255002892 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 347255002893 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 347255002894 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 347255002895 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 347255002896 DALR anticodon binding domain; Region: DALR_1; pfam05746 347255002897 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 347255002898 motif 1; other site 347255002899 dimer interface [polypeptide binding]; other site 347255002900 active site 347255002901 motif 2; other site 347255002902 motif 3; other site 347255002903 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 347255002904 oligomeric interface; other site 347255002905 putative active site [active] 347255002906 homodimer interface [polypeptide binding]; other site 347255002907 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 347255002908 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 347255002909 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 347255002910 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 347255002911 motif 1; other site 347255002912 active site 347255002913 motif 2; other site 347255002914 motif 3; other site 347255002915 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 347255002916 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 347255002917 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 347255002918 dimerization interface 3.5A [polypeptide binding]; other site 347255002919 active site 347255002920 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 347255002921 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 347255002922 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 347255002923 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 347255002924 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 347255002925 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 347255002926 DNA binding residues [nucleotide binding] 347255002927 DNA primase, catalytic core; Region: dnaG; TIGR01391 347255002928 CHC2 zinc finger; Region: zf-CHC2; pfam01807 347255002929 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 347255002930 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 347255002931 active site 347255002932 metal binding site [ion binding]; metal-binding site 347255002933 interdomain interaction site; other site 347255002934 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 347255002935 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 347255002936 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 347255002937 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 347255002938 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 347255002939 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 347255002940 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 347255002941 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 347255002942 ligand binding site [chemical binding]; other site 347255002943 homodimer interface [polypeptide binding]; other site 347255002944 NAD(P) binding site [chemical binding]; other site 347255002945 trimer interface B [polypeptide binding]; other site 347255002946 trimer interface A [polypeptide binding]; other site 347255002947 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 347255002948 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 347255002949 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 347255002950 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 347255002951 Walker A motif; other site 347255002952 ATP binding site [chemical binding]; other site 347255002953 Walker B motif; other site 347255002954 arginine finger; other site 347255002955 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 347255002956 hypothetical protein; Validated; Region: PRK00153 347255002957 Predicted aspartyl protease [General function prediction only]; Region: COG3577 347255002958 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 347255002959 catalytic motif [active] 347255002960 Catalytic residue [active] 347255002961 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 347255002962 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 347255002963 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 347255002964 Walker A/P-loop; other site 347255002965 ATP binding site [chemical binding]; other site 347255002966 Q-loop/lid; other site 347255002967 ABC transporter signature motif; other site 347255002968 Walker B; other site 347255002969 D-loop; other site 347255002970 H-loop/switch region; other site 347255002971 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 347255002972 putative hydrolase; Provisional; Region: PRK02113 347255002973 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 347255002974 active site 347255002975 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 347255002976 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 347255002977 Predicted permeases [General function prediction only]; Region: COG0795 347255002978 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 347255002979 DNA polymerase III subunit chi; Provisional; Region: PRK06646 347255002980 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 347255002981 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 347255002982 metal binding site [ion binding]; metal-binding site 347255002983 dimer interface [polypeptide binding]; other site 347255002984 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 347255002985 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347255002986 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 347255002987 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 347255002988 Uncharacterized conserved protein [Function unknown]; Region: COG1434 347255002989 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 347255002990 putative active site [active] 347255002991 lipoate-protein ligase B; Provisional; Region: PRK14347 347255002992 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 347255002993 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 347255002994 amidase catalytic site [active] 347255002995 Zn binding residues [ion binding]; other site 347255002996 substrate binding site [chemical binding]; other site 347255002997 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 347255002998 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 347255002999 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 347255003000 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 347255003001 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 347255003002 ATP binding site [chemical binding]; other site 347255003003 Mg2+ binding site [ion binding]; other site 347255003004 G-X-G motif; other site 347255003005 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 347255003006 ATP binding site [chemical binding]; other site 347255003007 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 347255003008 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 347255003009 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 347255003010 metabolite-proton symporter; Region: 2A0106; TIGR00883 347255003011 putative substrate translocation pore; other site 347255003012 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 347255003013 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 347255003014 TIGR00701 family protein; Region: TIGR00701 347255003015 ferrochelatase; Reviewed; Region: hemH; PRK00035 347255003016 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 347255003017 C-terminal domain interface [polypeptide binding]; other site 347255003018 active site 347255003019 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 347255003020 active site 347255003021 N-terminal domain interface [polypeptide binding]; other site 347255003022 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 347255003023 substrate binding site [chemical binding]; other site 347255003024 active site 347255003025 DnaA N-terminal domain; Region: DnaA_N; pfam11638 347255003026 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 347255003027 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 347255003028 catalytic residues [active] 347255003029 catalytic nucleophile [active] 347255003030 Presynaptic Site I dimer interface [polypeptide binding]; other site 347255003031 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 347255003032 Synaptic Flat tetramer interface [polypeptide binding]; other site 347255003033 Synaptic Site I dimer interface [polypeptide binding]; other site 347255003034 DNA binding site [nucleotide binding] 347255003035 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 347255003036 DNA-binding interface [nucleotide binding]; DNA binding site 347255003037 putative transposase; Provisional; Region: PRK09857 347255003038 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 347255003039 putative transposase; Provisional; Region: PRK09857 347255003040 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 347255003041 Autotransporter beta-domain; Region: Autotransporter; pfam03797 347255003042 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 347255003043 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 347255003044 sequence-specific DNA binding site [nucleotide binding]; other site 347255003045 salt bridge; other site 347255003046 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 347255003047 non-specific DNA binding site [nucleotide binding]; other site 347255003048 salt bridge; other site 347255003049 sequence-specific DNA binding site [nucleotide binding]; other site 347255003050 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 347255003051 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 347255003052 P-loop; other site 347255003053 Magnesium ion binding site [ion binding]; other site