-- dump date 20140620_033907 -- class Genbank::misc_feature -- table misc_feature_note -- id note 416276000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 416276000002 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 416276000003 Leucine-rich repeats; other site 416276000004 Substrate binding site [chemical binding]; other site 416276000005 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 416276000006 HD domain; Region: HD_4; pfam13328 416276000007 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 416276000008 synthetase active site [active] 416276000009 NTP binding site [chemical binding]; other site 416276000010 metal binding site [ion binding]; metal-binding site 416276000011 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 416276000012 catalytic residues [active] 416276000013 catalytic nucleophile [active] 416276000014 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 416276000015 Presynaptic Site I dimer interface [polypeptide binding]; other site 416276000016 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 416276000017 Synaptic Flat tetramer interface [polypeptide binding]; other site 416276000018 Synaptic Site I dimer interface [polypeptide binding]; other site 416276000019 DNA binding site [nucleotide binding] 416276000020 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 416276000021 DNA-binding interface [nucleotide binding]; DNA binding site 416276000022 putative transposase; Provisional; Region: PRK09857 416276000023 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 416276000024 ParA-like protein; Provisional; Region: PHA02518 416276000025 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 416276000026 P-loop; other site 416276000027 Magnesium ion binding site [ion binding]; other site 416276000028 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 416276000029 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 416276000030 catalytic residues [active] 416276000031 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 416276000032 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 416276000033 Walker A/P-loop; other site 416276000034 ATP binding site [chemical binding]; other site 416276000035 Q-loop/lid; other site 416276000036 ABC transporter signature motif; other site 416276000037 Walker B; other site 416276000038 D-loop; other site 416276000039 H-loop/switch region; other site 416276000040 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 416276000041 ABC-2 type transporter; Region: ABC2_membrane; cl17235 416276000042 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 416276000043 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 416276000044 FAD binding pocket [chemical binding]; other site 416276000045 FAD binding motif [chemical binding]; other site 416276000046 phosphate binding motif [ion binding]; other site 416276000047 beta-alpha-beta structure motif; other site 416276000048 NAD binding pocket [chemical binding]; other site 416276000049 Iron coordination center [ion binding]; other site 416276000050 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 416276000051 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 416276000052 active site 416276000053 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 416276000054 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 416276000055 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 416276000056 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 416276000057 trimer interface [polypeptide binding]; other site 416276000058 active site 416276000059 UDP-GlcNAc binding site [chemical binding]; other site 416276000060 lipid binding site [chemical binding]; lipid-binding site 416276000061 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 416276000062 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 416276000063 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 416276000064 intersubunit interface [polypeptide binding]; other site 416276000065 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 416276000066 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 416276000067 active site 416276000068 NTP binding site [chemical binding]; other site 416276000069 metal binding triad [ion binding]; metal-binding site 416276000070 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 416276000071 Autotransporter beta-domain; Region: Autotransporter; pfam03797 416276000072 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 416276000073 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 416276000074 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 416276000075 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 416276000076 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 416276000077 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 416276000078 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 416276000079 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 416276000080 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 416276000081 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 416276000082 catalytic residues [active] 416276000083 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 416276000084 Methyltransferase domain; Region: Methyltransf_31; pfam13847 416276000085 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 416276000086 S-adenosylmethionine binding site [chemical binding]; other site 416276000087 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 416276000088 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 416276000089 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 416276000090 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276000091 Walker A/P-loop; other site 416276000092 ATP binding site [chemical binding]; other site 416276000093 Q-loop/lid; other site 416276000094 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276000095 ABC transporter signature motif; other site 416276000096 Walker B; other site 416276000097 D-loop; other site 416276000098 H-loop/switch region; other site 416276000099 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 416276000100 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 416276000101 Cu(I) binding site [ion binding]; other site 416276000102 Putative transcriptional regulator [Transcription]; Region: COG1678 416276000103 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 416276000104 Colicin V production protein; Region: Colicin_V; pfam02674 416276000105 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 416276000106 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 416276000107 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 416276000108 Walker A motif; other site 416276000109 ATP binding site [chemical binding]; other site 416276000110 Walker B motif; other site 416276000111 arginine finger; other site 416276000112 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 416276000113 Walker A motif; other site 416276000114 ATP binding site [chemical binding]; other site 416276000115 Walker B motif; other site 416276000116 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 416276000117 UGMP family protein; Validated; Region: PRK09604 416276000118 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 416276000119 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 416276000120 Fatty acid desaturase; Region: FA_desaturase; pfam00487 416276000121 Di-iron ligands [ion binding]; other site 416276000122 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 416276000123 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 416276000124 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 416276000125 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 416276000126 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 416276000127 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 416276000128 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 416276000129 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 416276000130 Ligand Binding Site [chemical binding]; other site 416276000131 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276000132 FtsH Extracellular; Region: FtsH_ext; pfam06480 416276000133 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 416276000134 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 416276000135 Walker A motif; other site 416276000136 ATP binding site [chemical binding]; other site 416276000137 Walker B motif; other site 416276000138 arginine finger; other site 416276000139 Peptidase family M41; Region: Peptidase_M41; pfam01434 416276000140 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 416276000141 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 416276000142 Uncharacterized conserved protein [Function unknown]; Region: COG1565 416276000143 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276000144 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 416276000145 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 416276000146 Mechanosensitive ion channel; Region: MS_channel; pfam00924 416276000147 membrane protein insertase; Provisional; Region: PRK01318 416276000148 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 416276000149 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 416276000150 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 416276000151 S-adenosylmethionine binding site [chemical binding]; other site 416276000152 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 416276000153 active site 416276000154 catalytic residues [active] 416276000155 metal binding site [ion binding]; metal-binding site 416276000156 TLC ATP/ADP transporter; Region: TLC; pfam03219 416276000157 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 416276000158 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 416276000159 putative substrate translocation pore; other site 416276000160 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 416276000161 active site 416276000162 multimer interface [polypeptide binding]; other site 416276000163 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 416276000164 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 416276000165 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 416276000166 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 416276000167 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 416276000168 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 416276000169 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 416276000170 P-loop; other site 416276000171 Magnesium ion binding site [ion binding]; other site 416276000172 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 416276000173 Magnesium ion binding site [ion binding]; other site 416276000174 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 416276000175 ParB-like nuclease domain; Region: ParB; smart00470 416276000176 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 416276000177 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 416276000178 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 416276000179 ABC transporter; Region: ABC_tran_2; pfam12848 416276000180 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 416276000181 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 416276000182 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 416276000183 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 416276000184 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 416276000185 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 416276000186 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 416276000187 Zn2+ binding site [ion binding]; other site 416276000188 Mg2+ binding site [ion binding]; other site 416276000189 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 416276000190 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 416276000191 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 416276000192 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 416276000193 active site 416276000194 HIGH motif; other site 416276000195 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 416276000196 KMSK motif region; other site 416276000197 tRNA binding surface [nucleotide binding]; other site 416276000198 DALR anticodon binding domain; Region: DALR_1; smart00836 416276000199 anticodon binding site; other site 416276000200 Sporulation related domain; Region: SPOR; pfam05036 416276000201 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 416276000202 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 416276000203 CAP-like domain; other site 416276000204 active site 416276000205 primary dimer interface [polypeptide binding]; other site 416276000206 Gram-negative porin; Region: Porin_4; pfam13609 416276000207 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 416276000208 trimer interface [polypeptide binding]; other site 416276000209 active site 416276000210 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 416276000211 SecA binding site; other site 416276000212 Preprotein binding site; other site 416276000213 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 416276000214 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 416276000215 active site 416276000216 phosphorylation site [posttranslational modification] 416276000217 intermolecular recognition site; other site 416276000218 dimerization interface [polypeptide binding]; other site 416276000219 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 416276000220 DNA binding site [nucleotide binding] 416276000221 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 416276000222 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 416276000223 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 416276000224 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 416276000225 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 416276000226 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 416276000227 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 416276000228 EamA-like transporter family; Region: EamA; pfam00892 416276000229 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 416276000230 EamA-like transporter family; Region: EamA; pfam00892 416276000231 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 416276000232 metabolite-proton symporter; Region: 2A0106; TIGR00883 416276000233 putative substrate translocation pore; other site 416276000234 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 416276000235 Autotransporter beta-domain; Region: Autotransporter; pfam03797 416276000236 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 416276000237 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 416276000238 active site 416276000239 HIGH motif; other site 416276000240 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 416276000241 KMSKS motif; other site 416276000242 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 416276000243 tRNA binding surface [nucleotide binding]; other site 416276000244 anticodon binding site; other site 416276000245 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 416276000246 rRNA interaction site [nucleotide binding]; other site 416276000247 S8 interaction site; other site 416276000248 putative laminin-1 binding site; other site 416276000249 elongation factor Ts; Provisional; Region: tsf; PRK09377 416276000250 UBA/TS-N domain; Region: UBA; pfam00627 416276000251 Elongation factor TS; Region: EF_TS; pfam00889 416276000252 Elongation factor TS; Region: EF_TS; pfam00889 416276000253 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 416276000254 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276000255 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 416276000256 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 416276000257 putative acyl-acceptor binding pocket; other site 416276000258 aspartate aminotransferase; Provisional; Region: PRK05764 416276000259 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 416276000260 pyridoxal 5'-phosphate binding site [chemical binding]; other site 416276000261 homodimer interface [polypeptide binding]; other site 416276000262 catalytic residue [active] 416276000263 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 416276000264 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 416276000265 TPR repeat; Region: TPR_11; pfam13414 416276000266 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 416276000267 binding surface 416276000268 TPR motif; other site 416276000269 Methyltransferase domain; Region: Methyltransf_23; pfam13489 416276000270 Methyltransferase domain; Region: Methyltransf_18; pfam12847 416276000271 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 416276000272 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 416276000273 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 416276000274 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 416276000275 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 416276000276 active site 416276000277 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276000278 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 416276000279 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 416276000280 active site 416276000281 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 416276000282 dimer interface [polypeptide binding]; other site 416276000283 substrate binding site [chemical binding]; other site 416276000284 catalytic residues [active] 416276000285 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 416276000286 Permease; Region: Permease; pfam02405 416276000287 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 416276000288 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276000289 Walker A/P-loop; other site 416276000290 ATP binding site [chemical binding]; other site 416276000291 Q-loop/lid; other site 416276000292 ABC transporter signature motif; other site 416276000293 Walker B; other site 416276000294 D-loop; other site 416276000295 H-loop/switch region; other site 416276000296 CheD chemotactic sensory transduction; Region: CheD; cl00810 416276000297 Tetratricopeptide repeat; Region: TPR_12; pfam13424 416276000298 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 416276000299 50S ribosomal protein L31; Provisional; Region: PRK01397 416276000300 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 416276000301 G1 box; other site 416276000302 GTP/Mg2+ binding site [chemical binding]; other site 416276000303 Switch I region; other site 416276000304 G2 box; other site 416276000305 G3 box; other site 416276000306 Switch II region; other site 416276000307 G4 box; other site 416276000308 G5 box; other site 416276000309 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 416276000310 nucleotide binding site [chemical binding]; other site 416276000311 substrate binding site [chemical binding]; other site 416276000312 type IV secretion system protein VirB3; Provisional; Region: PRK13899 416276000313 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 416276000314 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 416276000315 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276000316 Walker A/P-loop; other site 416276000317 ATP binding site [chemical binding]; other site 416276000318 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 416276000319 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 416276000320 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 416276000321 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 416276000322 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 416276000323 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 416276000324 hypothetical protein; Provisional; Region: PRK13694 416276000325 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 416276000326 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 416276000327 Protein export membrane protein; Region: SecD_SecF; pfam02355 416276000328 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 416276000329 SLBB domain; Region: SLBB; pfam10531 416276000330 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 416276000331 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 416276000332 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 416276000333 Catalytic site [active] 416276000334 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 416276000335 ribonuclease III; Reviewed; Region: rnc; PRK00102 416276000336 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 416276000337 dimerization interface [polypeptide binding]; other site 416276000338 active site 416276000339 metal binding site [ion binding]; metal-binding site 416276000340 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 416276000341 dsRNA binding site [nucleotide binding]; other site 416276000342 GTPase Era; Provisional; Region: era; PRK15494 416276000343 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276000344 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 416276000345 G1 box; other site 416276000346 GTP/Mg2+ binding site [chemical binding]; other site 416276000347 Switch I region; other site 416276000348 G2 box; other site 416276000349 Switch II region; other site 416276000350 G3 box; other site 416276000351 G4 box; other site 416276000352 G5 box; other site 416276000353 KH domain; Region: KH_2; pfam07650 416276000354 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 416276000355 active site 416276000356 putative DNA-binding cleft [nucleotide binding]; other site 416276000357 dimer interface [polypeptide binding]; other site 416276000358 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 416276000359 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 416276000360 nucleotidyltransferase substrate binding protein, HI0074 family; Region: HI0074; TIGR01987 416276000361 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 416276000362 active site 416276000363 NTP binding site [chemical binding]; other site 416276000364 metal binding triad [ion binding]; metal-binding site 416276000365 antibiotic binding site [chemical binding]; other site 416276000366 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 416276000367 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 416276000368 AAA domain; Region: AAA_31; pfam13614 416276000369 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 416276000370 Walker A motif; other site 416276000371 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 416276000372 HflK protein; Region: hflK; TIGR01933 416276000373 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 416276000374 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 416276000375 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 416276000376 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 416276000377 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 416276000378 protein binding site [polypeptide binding]; other site 416276000379 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 416276000380 protein binding site [polypeptide binding]; other site 416276000381 hypothetical protein; Validated; Region: PRK01415 416276000382 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 416276000383 active site residue [active] 416276000384 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 416276000385 Iron-sulfur protein interface; other site 416276000386 proximal quinone binding site [chemical binding]; other site 416276000387 SdhD (CybS) interface [polypeptide binding]; other site 416276000388 proximal heme binding site [chemical binding]; other site 416276000389 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 416276000390 putative SdhC subunit interface [polypeptide binding]; other site 416276000391 putative proximal heme binding site [chemical binding]; other site 416276000392 putative Iron-sulfur protein interface [polypeptide binding]; other site 416276000393 putative proximal quinone binding site; other site 416276000394 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 416276000395 L-aspartate oxidase; Provisional; Region: PRK06175 416276000396 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 416276000397 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 416276000398 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 416276000399 dimer interface [polypeptide binding]; other site 416276000400 conserved gate region; other site 416276000401 putative PBP binding loops; other site 416276000402 ABC-ATPase subunit interface; other site 416276000403 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 416276000404 S17 interaction site [polypeptide binding]; other site 416276000405 S8 interaction site; other site 416276000406 16S rRNA interaction site [nucleotide binding]; other site 416276000407 streptomycin interaction site [chemical binding]; other site 416276000408 23S rRNA interaction site [nucleotide binding]; other site 416276000409 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 416276000410 30S ribosomal protein S7; Validated; Region: PRK05302 416276000411 elongation factor G; Reviewed; Region: PRK00007 416276000412 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 416276000413 G1 box; other site 416276000414 putative GEF interaction site [polypeptide binding]; other site 416276000415 GTP/Mg2+ binding site [chemical binding]; other site 416276000416 Switch I region; other site 416276000417 G2 box; other site 416276000418 G3 box; other site 416276000419 Switch II region; other site 416276000420 G4 box; other site 416276000421 G5 box; other site 416276000422 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 416276000423 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 416276000424 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 416276000425 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276000426 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 416276000427 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 416276000428 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 416276000429 putative homodimer interface [polypeptide binding]; other site 416276000430 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 416276000431 heterodimer interface [polypeptide binding]; other site 416276000432 homodimer interface [polypeptide binding]; other site 416276000433 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 416276000434 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 416276000435 23S rRNA interface [nucleotide binding]; other site 416276000436 putative thiostrepton binding site; other site 416276000437 L7/L12 interface [polypeptide binding]; other site 416276000438 L25 interface [polypeptide binding]; other site 416276000439 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 416276000440 mRNA/rRNA interface [nucleotide binding]; other site 416276000441 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 416276000442 23S rRNA interface [nucleotide binding]; other site 416276000443 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 416276000444 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 416276000445 core dimer interface [polypeptide binding]; other site 416276000446 peripheral dimer interface [polypeptide binding]; other site 416276000447 L10 interface [polypeptide binding]; other site 416276000448 L11 interface [polypeptide binding]; other site 416276000449 putative EF-Tu interaction site [polypeptide binding]; other site 416276000450 putative EF-G interaction site [polypeptide binding]; other site 416276000451 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 416276000452 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 416276000453 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 416276000454 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 416276000455 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 416276000456 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 416276000457 RPB3 interaction site [polypeptide binding]; other site 416276000458 RPB1 interaction site [polypeptide binding]; other site 416276000459 RPB11 interaction site [polypeptide binding]; other site 416276000460 RPB10 interaction site [polypeptide binding]; other site 416276000461 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 416276000462 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 416276000463 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 416276000464 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 416276000465 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 416276000466 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 416276000467 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 416276000468 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 416276000469 DNA binding site [nucleotide binding] 416276000470 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 416276000471 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276000472 multifunctional aminopeptidase A; Provisional; Region: PRK00913 416276000473 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 416276000474 interface (dimer of trimers) [polypeptide binding]; other site 416276000475 Substrate-binding/catalytic site; other site 416276000476 Zn-binding sites [ion binding]; other site 416276000477 ATPase MipZ; Region: MipZ; pfam09140 416276000478 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 416276000479 P-loop; other site 416276000480 Magnesium ion binding site [ion binding]; other site 416276000481 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 416276000482 Magnesium ion binding site [ion binding]; other site 416276000483 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 416276000484 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 416276000485 dimer interface [polypeptide binding]; other site 416276000486 anticodon binding site; other site 416276000487 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 416276000488 homodimer interface [polypeptide binding]; other site 416276000489 motif 1; other site 416276000490 active site 416276000491 motif 2; other site 416276000492 GAD domain; Region: GAD; pfam02938 416276000493 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 416276000494 active site 416276000495 motif 3; other site 416276000496 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 416276000497 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 416276000498 dihydrodipicolinate reductase; Provisional; Region: PRK00048 416276000499 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 416276000500 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 416276000501 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 416276000502 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 416276000503 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 416276000504 substrate binding pocket [chemical binding]; other site 416276000505 membrane-bound complex binding site; other site 416276000506 hinge residues; other site 416276000507 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 416276000508 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 416276000509 GatB domain; Region: GatB_Yqey; smart00845 416276000510 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 416276000511 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 416276000512 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 416276000513 ribosome recycling factor; Reviewed; Region: frr; PRK00083 416276000514 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 416276000515 hinge region; other site 416276000516 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 416276000517 putative nucleotide binding site [chemical binding]; other site 416276000518 uridine monophosphate binding site [chemical binding]; other site 416276000519 homohexameric interface [polypeptide binding]; other site 416276000520 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 416276000521 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 416276000522 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 416276000523 putative substrate translocation pore; other site 416276000524 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 416276000525 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 416276000526 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 416276000527 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 416276000528 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 416276000529 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 416276000530 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 416276000531 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 416276000532 Surface antigen; Region: Bac_surface_Ag; pfam01103 416276000533 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 416276000534 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 416276000535 active site 416276000536 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 416276000537 protein binding site [polypeptide binding]; other site 416276000538 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 416276000539 putative substrate binding region [chemical binding]; other site 416276000540 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 416276000541 putative RNA binding site [nucleotide binding]; other site 416276000542 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 416276000543 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 416276000544 S-adenosylmethionine binding site [chemical binding]; other site 416276000545 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 416276000546 putative coenzyme Q binding site [chemical binding]; other site 416276000547 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276000548 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 416276000549 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 416276000550 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 416276000551 RNA methyltransferase, RsmE family; Region: TIGR00046 416276000552 Uncharacterized conserved protein [Function unknown]; Region: COG2155 416276000553 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 416276000554 Protein export membrane protein; Region: SecD_SecF; cl14618 416276000555 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 416276000556 IHF dimer interface [polypeptide binding]; other site 416276000557 IHF - DNA interface [nucleotide binding]; other site 416276000558 DNA polymerase III subunit delta'; Validated; Region: PRK06581 416276000559 signal recognition particle protein; Provisional; Region: PRK10867 416276000560 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 416276000561 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 416276000562 P loop; other site 416276000563 GTP binding site [chemical binding]; other site 416276000564 Signal peptide binding domain; Region: SRP_SPB; pfam02978 416276000565 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 416276000566 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 416276000567 FeS/SAM binding site; other site 416276000568 HemN C-terminal domain; Region: HemN_C; pfam06969 416276000569 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 416276000570 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 416276000571 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 416276000572 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 416276000573 active site 416276000574 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 416276000575 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 416276000576 E3 interaction surface; other site 416276000577 lipoyl attachment site [posttranslational modification]; other site 416276000578 e3 binding domain; Region: E3_binding; pfam02817 416276000579 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 416276000580 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 416276000581 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 416276000582 TPP-binding site [chemical binding]; other site 416276000583 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 416276000584 dimer interface [polypeptide binding]; other site 416276000585 PYR/PP interface [polypeptide binding]; other site 416276000586 TPP binding site [chemical binding]; other site 416276000587 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 416276000588 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 416276000589 Walker A/P-loop; other site 416276000590 ATP binding site [chemical binding]; other site 416276000591 Q-loop/lid; other site 416276000592 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 416276000593 ABC transporter signature motif; other site 416276000594 Walker B; other site 416276000595 D-loop; other site 416276000596 H-loop/switch region; other site 416276000597 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 416276000598 Tetratricopeptide repeat; Region: TPR_6; pfam13174 416276000599 chaperone protein DnaJ; Provisional; Region: PRK14300 416276000600 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 416276000601 HSP70 interaction site [polypeptide binding]; other site 416276000602 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 416276000603 substrate binding site [polypeptide binding]; other site 416276000604 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 416276000605 Zn binding sites [ion binding]; other site 416276000606 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 416276000607 dimer interface [polypeptide binding]; other site 416276000608 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 416276000609 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 416276000610 nucleotide binding site [chemical binding]; other site 416276000611 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 416276000612 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 416276000613 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 416276000614 Lipopolysaccharide-assembly; Region: LptE; cl01125 416276000615 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 416276000616 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 416276000617 diiron binding motif [ion binding]; other site 416276000618 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 416276000619 Subunit III/VIIa interface [polypeptide binding]; other site 416276000620 Phospholipid binding site [chemical binding]; other site 416276000621 Subunit I/III interface [polypeptide binding]; other site 416276000622 Subunit III/VIb interface [polypeptide binding]; other site 416276000623 Subunit III/VIa interface; other site 416276000624 Subunit III/Vb interface [polypeptide binding]; other site 416276000625 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 416276000626 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 416276000627 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 416276000628 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 416276000629 trimer interface [polypeptide binding]; other site 416276000630 active site 416276000631 substrate binding site [chemical binding]; other site 416276000632 CoA binding site [chemical binding]; other site 416276000633 Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]; Region: PbpC; COG4953 416276000634 Transglycosylase; Region: Transgly; pfam00912 416276000635 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 416276000636 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 416276000637 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 416276000638 Ligand Binding Site [chemical binding]; other site 416276000639 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 416276000640 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 416276000641 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 416276000642 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 416276000643 catalytic loop [active] 416276000644 iron binding site [ion binding]; other site 416276000645 chaperone protein HscA; Provisional; Region: hscA; PRK01433 416276000646 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 416276000647 nucleotide binding site [chemical binding]; other site 416276000648 co-chaperone HscB; Provisional; Region: hscB; PRK01356 416276000649 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 416276000650 HSP70 interaction site [polypeptide binding]; other site 416276000651 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 416276000652 RNA/DNA hybrid binding site [nucleotide binding]; other site 416276000653 active site 416276000654 excinuclease ABC subunit B; Provisional; Region: PRK05298 416276000655 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 416276000656 ATP binding site [chemical binding]; other site 416276000657 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 416276000658 nucleotide binding region [chemical binding]; other site 416276000659 ATP-binding site [chemical binding]; other site 416276000660 Ultra-violet resistance protein B; Region: UvrB; pfam12344 416276000661 UvrB/uvrC motif; Region: UVR; pfam02151 416276000662 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 416276000663 GSH binding site [chemical binding]; other site 416276000664 catalytic residues [active] 416276000665 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 416276000666 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 416276000667 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 416276000668 Walker A/P-loop; other site 416276000669 ATP binding site [chemical binding]; other site 416276000670 Q-loop/lid; other site 416276000671 ABC transporter signature motif; other site 416276000672 Walker B; other site 416276000673 D-loop; other site 416276000674 H-loop/switch region; other site 416276000675 DNA gyrase subunit A; Validated; Region: PRK05560 416276000676 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 416276000677 CAP-like domain; other site 416276000678 active site 416276000679 primary dimer interface [polypeptide binding]; other site 416276000680 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 416276000681 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 416276000682 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 416276000683 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 416276000684 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 416276000685 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 416276000686 active site 416276000687 catalytic residues [active] 416276000688 metal binding site [ion binding]; metal-binding site 416276000689 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 416276000690 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 416276000691 putative active site [active] 416276000692 substrate binding site [chemical binding]; other site 416276000693 putative cosubstrate binding site; other site 416276000694 catalytic site [active] 416276000695 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 416276000696 substrate binding site [chemical binding]; other site 416276000697 Predicted ATPase [General function prediction only]; Region: COG1485 416276000698 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 416276000699 Walker A motif; other site 416276000700 ATP binding site [chemical binding]; other site 416276000701 Walker B motif; other site 416276000702 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 416276000703 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 416276000704 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276000705 Walker A/P-loop; other site 416276000706 ATP binding site [chemical binding]; other site 416276000707 Q-loop/lid; other site 416276000708 ABC transporter signature motif; other site 416276000709 Walker B; other site 416276000710 D-loop; other site 416276000711 H-loop/switch region; other site 416276000712 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 416276000713 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 416276000714 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 416276000715 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 416276000716 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 416276000717 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 416276000718 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 416276000719 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 416276000720 putative metal binding site; other site 416276000721 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 416276000722 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 416276000723 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 416276000724 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 416276000725 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 416276000726 ATP binding site [chemical binding]; other site 416276000727 active site 416276000728 substrate binding site [chemical binding]; other site 416276000729 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 416276000730 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 416276000731 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 416276000732 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 416276000733 active site 416276000734 dimer interface [polypeptide binding]; other site 416276000735 motif 1; other site 416276000736 motif 2; other site 416276000737 motif 3; other site 416276000738 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 416276000739 anticodon binding site; other site 416276000740 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276000741 Walker A/P-loop; other site 416276000742 ATP binding site [chemical binding]; other site 416276000743 ABC transporter; Region: ABC_tran; pfam00005 416276000744 Q-loop/lid; other site 416276000745 ABC transporter signature motif; other site 416276000746 Walker B; other site 416276000747 D-loop; other site 416276000748 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 416276000749 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 416276000750 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 416276000751 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 416276000752 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 416276000753 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 416276000754 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 416276000755 ATP binding site [chemical binding]; other site 416276000756 Mg2+ binding site [ion binding]; other site 416276000757 G-X-G motif; other site 416276000758 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 416276000759 anchoring element; other site 416276000760 dimer interface [polypeptide binding]; other site 416276000761 ATP binding site [chemical binding]; other site 416276000762 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 416276000763 active site 416276000764 metal binding site [ion binding]; metal-binding site 416276000765 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 416276000766 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 416276000767 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 416276000768 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 416276000769 protein binding site [polypeptide binding]; other site 416276000770 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 416276000771 Catalytic dyad [active] 416276000772 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 416276000773 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 416276000774 dimer interface [polypeptide binding]; other site 416276000775 phosphorylation site [posttranslational modification] 416276000776 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 416276000777 ATP binding site [chemical binding]; other site 416276000778 Mg2+ binding site [ion binding]; other site 416276000779 G-X-G motif; other site 416276000780 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 416276000781 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 416276000782 FOG: WD40-like repeat [Function unknown]; Region: COG1520 416276000783 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 416276000784 Trp docking motif [polypeptide binding]; other site 416276000785 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 416276000786 23S rRNA interface [nucleotide binding]; other site 416276000787 L3 interface [polypeptide binding]; other site 416276000788 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 416276000789 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276000790 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 416276000791 aromatic arch; other site 416276000792 DCoH dimer interaction site [polypeptide binding]; other site 416276000793 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 416276000794 DCoH tetramer interaction site [polypeptide binding]; other site 416276000795 substrate binding site [chemical binding]; other site 416276000796 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 416276000797 putative active site [active] 416276000798 Ap4A binding site [chemical binding]; other site 416276000799 nudix motif; other site 416276000800 putative metal binding site [ion binding]; other site 416276000801 response regulator PleD; Reviewed; Region: pleD; PRK09581 416276000802 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 416276000803 active site 416276000804 phosphorylation site [posttranslational modification] 416276000805 intermolecular recognition site; other site 416276000806 dimerization interface [polypeptide binding]; other site 416276000807 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 416276000808 active site 416276000809 phosphorylation site [posttranslational modification] 416276000810 intermolecular recognition site; other site 416276000811 dimerization interface [polypeptide binding]; other site 416276000812 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 416276000813 metal binding site [ion binding]; metal-binding site 416276000814 active site 416276000815 I-site; other site 416276000816 elongation factor P; Validated; Region: PRK00529 416276000817 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 416276000818 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 416276000819 RNA binding site [nucleotide binding]; other site 416276000820 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 416276000821 RNA binding site [nucleotide binding]; other site 416276000822 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 416276000823 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 416276000824 active site 416276000825 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 416276000826 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 416276000827 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 416276000828 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 416276000829 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 416276000830 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 416276000831 HlyD family secretion protein; Region: HlyD_3; pfam13437 416276000832 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 416276000833 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 416276000834 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 416276000835 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 416276000836 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 416276000837 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 416276000838 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 416276000839 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 416276000840 FAD binding domain; Region: FAD_binding_4; pfam01565 416276000841 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 416276000842 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 416276000843 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 416276000844 ATP-grasp domain; Region: ATP-grasp_4; cl17255 416276000845 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 416276000846 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 416276000847 Cell division protein FtsQ; Region: FtsQ; pfam03799 416276000848 cell division protein FtsA; Region: ftsA; TIGR01174 416276000849 Cell division protein FtsA; Region: FtsA; smart00842 416276000850 Cell division protein FtsA; Region: FtsA; pfam14450 416276000851 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 416276000852 Cytochrome c2 [Energy production and conversion]; Region: COG3474 416276000853 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 416276000854 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 416276000855 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 416276000856 RNA binding site [nucleotide binding]; other site 416276000857 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 416276000858 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 416276000859 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 416276000860 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 416276000861 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 416276000862 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 416276000863 RNA binding surface [nucleotide binding]; other site 416276000864 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 416276000865 active site 416276000866 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 416276000867 Beta-lactamase; Region: Beta-lactamase; pfam00144 416276000868 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 416276000869 putative catalytic site [active] 416276000870 putative phosphate binding site [ion binding]; other site 416276000871 active site 416276000872 metal binding site A [ion binding]; metal-binding site 416276000873 DNA binding site [nucleotide binding] 416276000874 putative AP binding site [nucleotide binding]; other site 416276000875 putative metal binding site B [ion binding]; other site 416276000876 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 416276000877 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 416276000878 tetramer interface [polypeptide binding]; other site 416276000879 TPP-binding site [chemical binding]; other site 416276000880 heterodimer interface [polypeptide binding]; other site 416276000881 phosphorylation loop region [posttranslational modification] 416276000882 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 416276000883 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 416276000884 alpha subunit interface [polypeptide binding]; other site 416276000885 TPP binding site [chemical binding]; other site 416276000886 heterodimer interface [polypeptide binding]; other site 416276000887 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 416276000888 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 416276000889 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 416276000890 G1 box; other site 416276000891 putative GEF interaction site [polypeptide binding]; other site 416276000892 GTP/Mg2+ binding site [chemical binding]; other site 416276000893 Switch I region; other site 416276000894 G2 box; other site 416276000895 G3 box; other site 416276000896 Switch II region; other site 416276000897 G4 box; other site 416276000898 G5 box; other site 416276000899 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 416276000900 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 416276000901 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 416276000902 isocitrate dehydrogenase; Validated; Region: PRK09222 416276000903 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 416276000904 monovalent cation/proton antiporter, MnhG/PhaG subunit; Region: CPA3_mnhG_phaG; TIGR01300 416276000905 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 416276000906 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 416276000907 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 416276000908 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 416276000909 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 416276000910 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 416276000911 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 416276000912 [2Fe-2S] cluster binding site [ion binding]; other site 416276000913 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 416276000914 Qi binding site; other site 416276000915 cytochrome b; Provisional; Region: CYTB; MTH00191 416276000916 intrachain domain interface; other site 416276000917 interchain domain interface [polypeptide binding]; other site 416276000918 heme bH binding site [chemical binding]; other site 416276000919 heme bL binding site [chemical binding]; other site 416276000920 Qo binding site; other site 416276000921 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 416276000922 interchain domain interface [polypeptide binding]; other site 416276000923 intrachain domain interface; other site 416276000924 Qi binding site; other site 416276000925 Qo binding site; other site 416276000926 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 416276000927 GIY-YIG motif/motif A; other site 416276000928 putative active site [active] 416276000929 putative metal binding site [ion binding]; other site 416276000930 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 416276000931 Cytochrome c; Region: Cytochrom_C; cl11414 416276000932 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 416276000933 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 416276000934 putative dimer interface [polypeptide binding]; other site 416276000935 peptide chain release factor 2; Validated; Region: prfB; PRK00578 416276000936 PCRF domain; Region: PCRF; pfam03462 416276000937 RF-1 domain; Region: RF-1; pfam00472 416276000938 GTP-binding protein LepA; Provisional; Region: PRK05433 416276000939 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 416276000940 G1 box; other site 416276000941 putative GEF interaction site [polypeptide binding]; other site 416276000942 GTP/Mg2+ binding site [chemical binding]; other site 416276000943 Switch I region; other site 416276000944 G2 box; other site 416276000945 G3 box; other site 416276000946 Switch II region; other site 416276000947 G4 box; other site 416276000948 G5 box; other site 416276000949 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 416276000950 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 416276000951 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 416276000952 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 416276000953 hydrophobic ligand binding site; other site 416276000954 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 416276000955 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 416276000956 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 416276000957 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 416276000958 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 416276000959 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 416276000960 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 416276000961 oligomeric interface; other site 416276000962 homodimer interface [polypeptide binding]; other site 416276000963 putative active site [active] 416276000964 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 416276000965 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 416276000966 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 416276000967 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 416276000968 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 416276000969 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 416276000970 VirB7 interaction site; other site 416276000971 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 416276000972 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 416276000973 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 416276000974 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 416276000975 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 416276000976 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 416276000977 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 416276000978 Walker A motif; other site 416276000979 hexamer interface [polypeptide binding]; other site 416276000980 ATP binding site [chemical binding]; other site 416276000981 Walker B motif; other site 416276000982 type IV secretion system component VirD4; Provisional; Region: PRK13897 416276000983 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 416276000984 Walker A motif; other site 416276000985 ATP binding site [chemical binding]; other site 416276000986 Walker B motif; other site 416276000987 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 416276000988 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 416276000989 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 416276000990 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 416276000991 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 416276000992 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 416276000993 active site 416276000994 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 416276000995 MutS domain I; Region: MutS_I; pfam01624 416276000996 MutS domain II; Region: MutS_II; pfam05188 416276000997 MutS domain III; Region: MutS_III; pfam05192 416276000998 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 416276000999 Walker A/P-loop; other site 416276001000 ATP binding site [chemical binding]; other site 416276001001 Q-loop/lid; other site 416276001002 ABC transporter signature motif; other site 416276001003 Walker B; other site 416276001004 D-loop; other site 416276001005 H-loop/switch region; other site 416276001006 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 416276001007 Peptidase family M23; Region: Peptidase_M23; pfam01551 416276001008 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 416276001009 TolB amino-terminal domain; Region: TolB_N; pfam04052 416276001010 translocation protein TolB; Provisional; Region: tolB; PRK05137 416276001011 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 416276001012 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 416276001013 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 416276001014 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 416276001015 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 416276001016 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 416276001017 DNA binding residues [nucleotide binding] 416276001018 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 416276001019 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 416276001020 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 416276001021 Ligand Binding Site [chemical binding]; other site 416276001022 amino acid transporter; Region: 2A0306; TIGR00909 416276001023 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 416276001024 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 416276001025 dimer interface [polypeptide binding]; other site 416276001026 motif 1; other site 416276001027 active site 416276001028 motif 2; other site 416276001029 motif 3; other site 416276001030 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 416276001031 anticodon binding site; other site 416276001032 TolQ protein; Region: tolQ; TIGR02796 416276001033 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 416276001034 TolR protein; Region: tolR; TIGR02801 416276001035 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 416276001036 HD domain; Region: HD_4; pfam13328 416276001037 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 416276001038 metabolite-proton symporter; Region: 2A0106; TIGR00883 416276001039 putative substrate translocation pore; other site 416276001040 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 416276001041 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 416276001042 HlyD family secretion protein; Region: HlyD_3; pfam13437 416276001043 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 416276001044 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 416276001045 Walker A/P-loop; other site 416276001046 ATP binding site [chemical binding]; other site 416276001047 Q-loop/lid; other site 416276001048 ABC transporter signature motif; other site 416276001049 Walker B; other site 416276001050 D-loop; other site 416276001051 H-loop/switch region; other site 416276001052 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 416276001053 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 416276001054 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 416276001055 nucleotide binding site/active site [active] 416276001056 HIT family signature motif; other site 416276001057 catalytic residue [active] 416276001058 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 416276001059 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 416276001060 active site 416276001061 HslU subunit interaction site [polypeptide binding]; other site 416276001062 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 416276001063 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 416276001064 Walker A motif; other site 416276001065 ATP binding site [chemical binding]; other site 416276001066 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 416276001067 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 416276001068 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276001069 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 416276001070 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 416276001071 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 416276001072 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 416276001073 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 416276001074 dimerization interface [polypeptide binding]; other site 416276001075 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 416276001076 putative iron binding site [ion binding]; other site 416276001077 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 416276001078 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276001079 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 416276001080 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 416276001081 HIGH motif; other site 416276001082 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 416276001083 active site 416276001084 KMSKS motif; other site 416276001085 DNA topoisomerase I; Validated; Region: PRK06599 416276001086 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 416276001087 active site 416276001088 interdomain interaction site; other site 416276001089 putative metal-binding site [ion binding]; other site 416276001090 nucleotide binding site [chemical binding]; other site 416276001091 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 416276001092 domain I; other site 416276001093 DNA binding groove [nucleotide binding] 416276001094 phosphate binding site [ion binding]; other site 416276001095 domain II; other site 416276001096 domain III; other site 416276001097 nucleotide binding site [chemical binding]; other site 416276001098 catalytic site [active] 416276001099 domain IV; other site 416276001100 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 416276001101 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 416276001102 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 416276001103 dimer interface [polypeptide binding]; other site 416276001104 decamer (pentamer of dimers) interface [polypeptide binding]; other site 416276001105 catalytic triad [active] 416276001106 peroxidatic and resolving cysteines [active] 416276001107 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 416276001108 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 416276001109 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 416276001110 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 416276001111 Sulfatase; Region: Sulfatase; pfam00884 416276001112 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 416276001113 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 416276001114 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 416276001115 non-specific DNA binding site [nucleotide binding]; other site 416276001116 salt bridge; other site 416276001117 sequence-specific DNA binding site [nucleotide binding]; other site 416276001118 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 416276001119 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 416276001120 NADP binding site [chemical binding]; other site 416276001121 active site 416276001122 putative substrate binding site [chemical binding]; other site 416276001123 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 416276001124 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 416276001125 NAD(P) binding site [chemical binding]; other site 416276001126 homodimer interface [polypeptide binding]; other site 416276001127 substrate binding site [chemical binding]; other site 416276001128 active site 416276001129 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 416276001130 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 416276001131 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 416276001132 active site 416276001133 homodimer interface [polypeptide binding]; other site 416276001134 Methyltransferase domain; Region: Methyltransf_31; pfam13847 416276001135 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 416276001136 S-adenosylmethionine binding site [chemical binding]; other site 416276001137 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 416276001138 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 416276001139 active site 416276001140 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 416276001141 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 416276001142 active site 416276001143 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 416276001144 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 416276001145 HlyD family secretion protein; Region: HlyD_3; pfam13437 416276001146 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 416276001147 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 416276001148 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 416276001149 catalytic site [active] 416276001150 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 416276001151 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 416276001152 putative ADP-binding pocket [chemical binding]; other site 416276001153 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 416276001154 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 416276001155 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 416276001156 RNA binding surface [nucleotide binding]; other site 416276001157 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 416276001158 UbiA prenyltransferase family; Region: UbiA; pfam01040 416276001159 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 416276001160 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 416276001161 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 416276001162 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 416276001163 RimM N-terminal domain; Region: RimM; pfam01782 416276001164 PRC-barrel domain; Region: PRC; pfam05239 416276001165 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 416276001166 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 416276001167 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 416276001168 active site 416276001169 DNA binding site [nucleotide binding] 416276001170 hypothetical protein; Provisional; Region: PRK14388 416276001171 NADH dehydrogenase subunit E; Validated; Region: PRK07539 416276001172 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 416276001173 putative dimer interface [polypeptide binding]; other site 416276001174 [2Fe-2S] cluster binding site [ion binding]; other site 416276001175 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 416276001176 NADH dehydrogenase subunit D; Validated; Region: PRK06075 416276001177 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 416276001178 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 416276001179 NADH dehydrogenase subunit B; Validated; Region: PRK06411 416276001180 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 416276001181 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 416276001182 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 416276001183 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 416276001184 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 416276001185 active site 416276001186 DNA binding site [nucleotide binding] 416276001187 Int/Topo IB signature motif; other site 416276001188 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 416276001189 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 416276001190 NAD binding site [chemical binding]; other site 416276001191 homotetramer interface [polypeptide binding]; other site 416276001192 homodimer interface [polypeptide binding]; other site 416276001193 substrate binding site [chemical binding]; other site 416276001194 active site 416276001195 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 416276001196 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 416276001197 putative active site [active] 416276001198 catalytic triad [active] 416276001199 putative dimer interface [polypeptide binding]; other site 416276001200 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 416276001201 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 416276001202 amidase catalytic site [active] 416276001203 Zn binding residues [ion binding]; other site 416276001204 substrate binding site [chemical binding]; other site 416276001205 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 416276001206 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 416276001207 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 416276001208 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 416276001209 active site 416276001210 HIGH motif; other site 416276001211 KMSKS motif; other site 416276001212 Predicted permeases [General function prediction only]; Region: COG0679 416276001213 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 416276001214 Malic enzyme, N-terminal domain; Region: malic; pfam00390 416276001215 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 416276001216 putative NAD(P) binding site [chemical binding]; other site 416276001217 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 416276001218 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 416276001219 putative active site [active] 416276001220 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 416276001221 metabolite-proton symporter; Region: 2A0106; TIGR00883 416276001222 malate dehydrogenase; Reviewed; Region: PRK06223 416276001223 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 416276001224 NAD(P) binding site [chemical binding]; other site 416276001225 dimer interface [polypeptide binding]; other site 416276001226 tetramer (dimer of dimers) interface [polypeptide binding]; other site 416276001227 substrate binding site [chemical binding]; other site 416276001228 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276001229 Helix-turn-helix domain; Region: HTH_28; pfam13518 416276001230 Winged helix-turn helix; Region: HTH_29; pfam13551 416276001231 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 416276001232 Integrase core domain; Region: rve; pfam00665 416276001233 Integrase core domain; Region: rve_3; pfam13683 416276001234 TLC ATP/ADP transporter; Region: TLC; pfam03219 416276001235 CTP synthetase; Validated; Region: pyrG; PRK05380 416276001236 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 416276001237 Catalytic site [active] 416276001238 active site 416276001239 UTP binding site [chemical binding]; other site 416276001240 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 416276001241 active site 416276001242 putative oxyanion hole; other site 416276001243 catalytic triad [active] 416276001244 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 416276001245 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 416276001246 Ligand binding site; other site 416276001247 oligomer interface; other site 416276001248 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 416276001249 nudix motif; other site 416276001250 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 416276001251 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 416276001252 GTP cyclohydrolase I; Provisional; Region: PLN03044 416276001253 active site 416276001254 prolyl-tRNA synthetase; Provisional; Region: PRK12325 416276001255 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 416276001256 dimer interface [polypeptide binding]; other site 416276001257 motif 1; other site 416276001258 active site 416276001259 motif 2; other site 416276001260 motif 3; other site 416276001261 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 416276001262 anticodon binding site; other site 416276001263 Fic family protein [Function unknown]; Region: COG3177 416276001264 Fic/DOC family; Region: Fic; pfam02661 416276001265 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 416276001266 RuvA N terminal domain; Region: RuvA_N; pfam01330 416276001267 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 416276001268 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 416276001269 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 416276001270 Walker A motif; other site 416276001271 ATP binding site [chemical binding]; other site 416276001272 Walker B motif; other site 416276001273 arginine finger; other site 416276001274 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 416276001275 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 416276001276 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 416276001277 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276001278 Walker A/P-loop; other site 416276001279 ATP binding site [chemical binding]; other site 416276001280 Q-loop/lid; other site 416276001281 ABC transporter signature motif; other site 416276001282 Walker B; other site 416276001283 D-loop; other site 416276001284 H-loop/switch region; other site 416276001285 muropeptide transporter; Reviewed; Region: ampG; PRK11902 416276001286 muropeptide transporter; Validated; Region: ampG; cl17669 416276001287 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 416276001288 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 416276001289 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276001290 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 416276001291 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 416276001292 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 416276001293 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 416276001294 BON domain; Region: BON; pfam04972 416276001295 BON domain; Region: BON; pfam04972 416276001296 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 416276001297 Iron permease FTR1 family; Region: FTR1; cl00475 416276001298 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 416276001299 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 416276001300 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 416276001301 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 416276001302 active site 416276001303 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 416276001304 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 416276001305 catalytic residues [active] 416276001306 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 416276001307 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 416276001308 tandem repeat interface [polypeptide binding]; other site 416276001309 oligomer interface [polypeptide binding]; other site 416276001310 active site residues [active] 416276001311 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 416276001312 trimer interface [polypeptide binding]; other site 416276001313 active site 416276001314 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 416276001315 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 416276001316 N-acetyl-D-glucosamine binding site [chemical binding]; other site 416276001317 catalytic residue [active] 416276001318 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 416276001319 dimer interface [polypeptide binding]; other site 416276001320 catalytic triad [active] 416276001321 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 416276001322 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 416276001323 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 416276001324 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 416276001325 catalytic triad [active] 416276001326 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 416276001327 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 416276001328 Subunit I/III interface [polypeptide binding]; other site 416276001329 D-pathway; other site 416276001330 Subunit I/VIIc interface [polypeptide binding]; other site 416276001331 Subunit I/IV interface [polypeptide binding]; other site 416276001332 Subunit I/II interface [polypeptide binding]; other site 416276001333 Low-spin heme (heme a) binding site [chemical binding]; other site 416276001334 Subunit I/VIIa interface [polypeptide binding]; other site 416276001335 Subunit I/VIa interface [polypeptide binding]; other site 416276001336 Dimer interface; other site 416276001337 Putative water exit pathway; other site 416276001338 Binuclear center (heme a3/CuB) [ion binding]; other site 416276001339 K-pathway; other site 416276001340 Subunit I/Vb interface [polypeptide binding]; other site 416276001341 Putative proton exit pathway; other site 416276001342 Subunit I/VIb interface; other site 416276001343 Subunit I/VIc interface [polypeptide binding]; other site 416276001344 Electron transfer pathway; other site 416276001345 Subunit I/VIIIb interface [polypeptide binding]; other site 416276001346 Subunit I/VIIb interface [polypeptide binding]; other site 416276001347 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276001348 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 416276001349 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 416276001350 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 416276001351 putative peptidase; Provisional; Region: PRK11649 416276001352 Peptidase family M23; Region: Peptidase_M23; pfam01551 416276001353 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 416276001354 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276001355 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 416276001356 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 416276001357 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 416276001358 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 416276001359 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 416276001360 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 416276001361 cell division protein FtsW; Region: ftsW; TIGR02614 416276001362 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 416276001363 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 416276001364 active site 416276001365 homodimer interface [polypeptide binding]; other site 416276001366 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 416276001367 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 416276001368 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 416276001369 diaminopimelate epimerase; Region: DapF; TIGR00652 416276001370 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 416276001371 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 416276001372 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 416276001373 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 416276001374 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 416276001375 FeS/SAM binding site; other site 416276001376 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 416276001377 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 416276001378 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 416276001379 dimer interface [polypeptide binding]; other site 416276001380 motif 1; other site 416276001381 active site 416276001382 motif 2; other site 416276001383 motif 3; other site 416276001384 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 416276001385 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 416276001386 putative tRNA-binding site [nucleotide binding]; other site 416276001387 B3/4 domain; Region: B3_4; pfam03483 416276001388 tRNA synthetase B5 domain; Region: B5; smart00874 416276001389 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 416276001390 dimer interface [polypeptide binding]; other site 416276001391 motif 1; other site 416276001392 motif 3; other site 416276001393 motif 2; other site 416276001394 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 416276001395 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 416276001396 DNA polymerase III subunit beta; Validated; Region: PRK05643 416276001397 putative DNA binding surface [nucleotide binding]; other site 416276001398 dimer interface [polypeptide binding]; other site 416276001399 beta-clamp/clamp loader binding surface; other site 416276001400 beta-clamp/translesion DNA polymerase binding surface; other site 416276001401 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 416276001402 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 416276001403 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 416276001404 HIGH motif; other site 416276001405 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 416276001406 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 416276001407 active site 416276001408 KMSKS motif; other site 416276001409 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 416276001410 tRNA binding surface [nucleotide binding]; other site 416276001411 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 416276001412 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 416276001413 catalytic site [active] 416276001414 putative active site [active] 416276001415 putative substrate binding site [chemical binding]; other site 416276001416 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 416276001417 Septum formation initiator; Region: DivIC; pfam04977 416276001418 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 416276001419 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 416276001420 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 416276001421 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 416276001422 catalytic residue [active] 416276001423 putative FPP diphosphate binding site; other site 416276001424 putative FPP binding hydrophobic cleft; other site 416276001425 dimer interface [polypeptide binding]; other site 416276001426 putative IPP diphosphate binding site; other site 416276001427 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 416276001428 HAMP domain; Region: HAMP; pfam00672 416276001429 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 416276001430 dimer interface [polypeptide binding]; other site 416276001431 phosphorylation site [posttranslational modification] 416276001432 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 416276001433 ATP binding site [chemical binding]; other site 416276001434 Mg2+ binding site [ion binding]; other site 416276001435 G-X-G motif; other site 416276001436 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 416276001437 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 416276001438 active site 416276001439 phosphorylation site [posttranslational modification] 416276001440 intermolecular recognition site; other site 416276001441 dimerization interface [polypeptide binding]; other site 416276001442 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 416276001443 DNA binding site [nucleotide binding] 416276001444 branched-chain amino acid aminotransferase; Validated; Region: PRK06606 416276001445 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 416276001446 homodimer interface [polypeptide binding]; other site 416276001447 substrate-cofactor binding pocket; other site 416276001448 pyridoxal 5'-phosphate binding site [chemical binding]; other site 416276001449 catalytic residue [active] 416276001450 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 416276001451 dihydrodipicolinate synthase; Region: dapA; TIGR00674 416276001452 dimer interface [polypeptide binding]; other site 416276001453 active site 416276001454 catalytic residue [active] 416276001455 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 416276001456 SmpB-tmRNA interface; other site 416276001457 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 416276001458 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 416276001459 catalytic residues [active] 416276001460 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 416276001461 CoA binding domain; Region: CoA_binding; pfam02629 416276001462 CoA-ligase; Region: Ligase_CoA; pfam00549 416276001463 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 416276001464 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 416276001465 CoA-ligase; Region: Ligase_CoA; pfam00549 416276001466 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 416276001467 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 416276001468 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 416276001469 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 416276001470 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 416276001471 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 416276001472 Predicted membrane protein [Function unknown]; Region: COG1238 416276001473 Predicted membrane protein/domain [Function unknown]; Region: COG1714 416276001474 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 416276001475 RecR protein; Region: RecR; pfam02132 416276001476 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 416276001477 putative active site [active] 416276001478 putative metal-binding site [ion binding]; other site 416276001479 tetramer interface [polypeptide binding]; other site 416276001480 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 416276001481 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 416276001482 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 416276001483 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 416276001484 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 416276001485 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 416276001486 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 416276001487 Predicted permeases [General function prediction only]; Region: COG0679 416276001488 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 416276001489 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 416276001490 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 416276001491 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 416276001492 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 416276001493 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 416276001494 tetramerization interface [polypeptide binding]; other site 416276001495 NAD(P) binding site [chemical binding]; other site 416276001496 catalytic residues [active] 416276001497 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 416276001498 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 416276001499 active site 416276001500 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 416276001501 Part of AAA domain; Region: AAA_19; pfam13245 416276001502 Family description; Region: UvrD_C_2; pfam13538 416276001503 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 416276001504 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 416276001505 tetramer interface [polypeptide binding]; other site 416276001506 pyridoxal 5'-phosphate binding site [chemical binding]; other site 416276001507 catalytic residue [active] 416276001508 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 416276001509 Found in ATP-dependent protease La (LON); Region: LON; smart00464 416276001510 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 416276001511 Walker A motif; other site 416276001512 ATP binding site [chemical binding]; other site 416276001513 Walker B motif; other site 416276001514 arginine finger; other site 416276001515 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 416276001516 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 416276001517 30S subunit binding site; other site 416276001518 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 416276001519 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 416276001520 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 416276001521 homodimer interface [polypeptide binding]; other site 416276001522 NADP binding site [chemical binding]; other site 416276001523 substrate binding site [chemical binding]; other site 416276001524 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 416276001525 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 416276001526 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 416276001527 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 416276001528 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 416276001529 Class I ribonucleotide reductase; Region: RNR_I; cd01679 416276001530 active site 416276001531 dimer interface [polypeptide binding]; other site 416276001532 catalytic residues [active] 416276001533 effector binding site; other site 416276001534 R2 peptide binding site; other site 416276001535 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 416276001536 dimer interface [polypeptide binding]; other site 416276001537 putative radical transfer pathway; other site 416276001538 diiron center [ion binding]; other site 416276001539 tyrosyl radical; other site 416276001540 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 416276001541 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 416276001542 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 416276001543 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 416276001544 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 416276001545 active site 416276001546 substrate binding site [chemical binding]; other site 416276001547 metal binding site [ion binding]; metal-binding site 416276001548 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 416276001549 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 416276001550 Walker A/P-loop; other site 416276001551 ATP binding site [chemical binding]; other site 416276001552 Q-loop/lid; other site 416276001553 ABC transporter signature motif; other site 416276001554 Walker B; other site 416276001555 D-loop; other site 416276001556 H-loop/switch region; other site 416276001557 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276001558 OstA-like protein; Region: OstA; pfam03968 416276001559 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 416276001560 KpsF/GutQ family protein; Region: kpsF; TIGR00393 416276001561 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 416276001562 putative active site [active] 416276001563 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 416276001564 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 416276001565 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 416276001566 RNase E interface [polypeptide binding]; other site 416276001567 trimer interface [polypeptide binding]; other site 416276001568 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 416276001569 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 416276001570 RNase E interface [polypeptide binding]; other site 416276001571 trimer interface [polypeptide binding]; other site 416276001572 active site 416276001573 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 416276001574 putative nucleic acid binding region [nucleotide binding]; other site 416276001575 G-X-X-G motif; other site 416276001576 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 416276001577 RNA binding site [nucleotide binding]; other site 416276001578 domain interface; other site 416276001579 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 416276001580 16S/18S rRNA binding site [nucleotide binding]; other site 416276001581 S13e-L30e interaction site [polypeptide binding]; other site 416276001582 25S rRNA binding site [nucleotide binding]; other site 416276001583 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 416276001584 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 416276001585 RNA binding site [nucleotide binding]; other site 416276001586 active site 416276001587 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276001588 TLC ATP/ADP transporter; Region: TLC; pfam03219 416276001589 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 416276001590 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 416276001591 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 416276001592 non-specific DNA binding site [nucleotide binding]; other site 416276001593 salt bridge; other site 416276001594 sequence-specific DNA binding site [nucleotide binding]; other site 416276001595 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 416276001596 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 416276001597 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 416276001598 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 416276001599 uncharacterized protein, YfiH family; Region: TIGR00726 416276001600 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 416276001601 active site 416276001602 catalytic residues [active] 416276001603 metal binding site [ion binding]; metal-binding site 416276001604 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 416276001605 hypothetical protein; Provisional; Region: PRK06661 416276001606 intersubunit interface [polypeptide binding]; other site 416276001607 active site 416276001608 Zn2+ binding site [ion binding]; other site 416276001609 pyruvate phosphate dikinase; Provisional; Region: PRK09279 416276001610 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 416276001611 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 416276001612 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 416276001613 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 416276001614 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 416276001615 GSH binding site (G-site) [chemical binding]; other site 416276001616 C-terminal domain interface [polypeptide binding]; other site 416276001617 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 416276001618 N-terminal domain interface [polypeptide binding]; other site 416276001619 dimer interface [polypeptide binding]; other site 416276001620 substrate binding pocket (H-site) [chemical binding]; other site 416276001621 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 416276001622 conserved cys residue [active] 416276001623 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 416276001624 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 416276001625 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 416276001626 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 416276001627 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 416276001628 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 416276001629 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 416276001630 active site 416276001631 nucleophile elbow; other site 416276001632 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 416276001633 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 416276001634 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 416276001635 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 416276001636 Predicted membrane protein [Function unknown]; Region: COG5346 416276001637 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 416276001638 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 416276001639 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 416276001640 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 416276001641 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 416276001642 E3 interaction surface; other site 416276001643 lipoyl attachment site [posttranslational modification]; other site 416276001644 e3 binding domain; Region: E3_binding; pfam02817 416276001645 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 416276001646 peptide chain release factor 1; Validated; Region: prfA; PRK00591 416276001647 This domain is found in peptide chain release factors; Region: PCRF; smart00937 416276001648 RF-1 domain; Region: RF-1; pfam00472 416276001649 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 416276001650 DHH family; Region: DHH; pfam01368 416276001651 DHHA1 domain; Region: DHHA1; pfam02272 416276001652 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 416276001653 S-adenosylmethionine binding site [chemical binding]; other site 416276001654 Methyltransferase domain; Region: Methyltransf_31; pfam13847 416276001655 transcription termination factor Rho; Provisional; Region: rho; PRK09376 416276001656 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 416276001657 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 416276001658 RNA binding site [nucleotide binding]; other site 416276001659 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 416276001660 multimer interface [polypeptide binding]; other site 416276001661 Walker A motif; other site 416276001662 ATP binding site [chemical binding]; other site 416276001663 Walker B motif; other site 416276001664 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 416276001665 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 416276001666 tandem repeat interface [polypeptide binding]; other site 416276001667 oligomer interface [polypeptide binding]; other site 416276001668 active site residues [active] 416276001669 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 416276001670 IHF - DNA interface [nucleotide binding]; other site 416276001671 IHF dimer interface [polypeptide binding]; other site 416276001672 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 416276001673 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 416276001674 active site 416276001675 DNA binding site [nucleotide binding] 416276001676 Int/Topo IB signature motif; other site 416276001677 Protein of unknown function (DUF4065); Region: DUF4065; pfam13274 416276001678 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 416276001679 TraE protein; Region: TraE; cl05060 416276001680 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 416276001681 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 416276001682 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 416276001683 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 416276001684 Walker A motif; other site 416276001685 ATP binding site [chemical binding]; other site 416276001686 AAA ATPase domain; Region: AAA_16; pfam13191 416276001687 Archaeal ATPase; Region: Arch_ATPase; pfam01637 416276001688 TraU protein; Region: TraU; pfam06834 416276001689 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 416276001690 Type-1V conjugative transfer system mating pair stabilisation; Region: TraN; pfam06986 416276001691 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 416276001692 F plasmid transfer operon protein; Region: TraF; pfam13728 416276001693 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 416276001694 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 416276001695 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 416276001696 TPR repeat; Region: TPR_11; pfam13414 416276001697 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 416276001698 binding surface 416276001699 TPR motif; other site 416276001700 TPR repeat; Region: TPR_11; pfam13414 416276001701 TPR repeat; Region: TPR_11; pfam13414 416276001702 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 416276001703 binding surface 416276001704 TPR motif; other site 416276001705 TPR repeat; Region: TPR_11; pfam13414 416276001706 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 416276001707 binding surface 416276001708 TPR motif; other site 416276001709 TPR repeat; Region: TPR_11; pfam13414 416276001710 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 416276001711 binding surface 416276001712 TPR motif; other site 416276001713 TPR repeat; Region: TPR_11; pfam13414 416276001714 F sex factor protein N terminal; Region: TraD_N; pfam12615 416276001715 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 416276001716 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 416276001717 Walker A motif; other site 416276001718 ATP binding site [chemical binding]; other site 416276001719 Walker B motif; other site 416276001720 hypothetical protein; Provisional; Region: PRK09956 416276001721 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 416276001722 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 416276001723 Ti-type conjugative transfer relaxase TraA; Region: TraA_Ti; TIGR02768 416276001724 MobA/MobL family; Region: MobA_MobL; pfam03389 416276001725 AAA domain; Region: AAA_30; pfam13604 416276001726 Family description; Region: UvrD_C_2; pfam13538 416276001727 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 416276001728 active site 416276001729 metal binding site [ion binding]; metal-binding site 416276001730 interdomain interaction site; other site 416276001731 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 416276001732 Transposase; Region: DEDD_Tnp_IS110; pfam01548 416276001733 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 416276001734 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 416276001735 helix-hairpin-helix signature motif; other site 416276001736 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 416276001737 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 416276001738 Walker A motif; other site 416276001739 ATP binding site [chemical binding]; other site 416276001740 Walker B motif; other site 416276001741 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276001742 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 416276001743 Transposase; Region: HTH_Tnp_1; pfam01527 416276001744 putative transposase OrfB; Reviewed; Region: PHA02517 416276001745 HTH-like domain; Region: HTH_21; pfam13276 416276001746 Integrase core domain; Region: rve; pfam00665 416276001747 Integrase core domain; Region: rve_3; pfam13683 416276001748 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 416276001749 Helix-turn-helix domain; Region: HTH_38; pfam13936 416276001750 Integrase core domain; Region: rve; pfam00665 416276001751 Helix-turn-helix domain; Region: HTH_28; pfam13518 416276001752 Winged helix-turn helix; Region: HTH_29; pfam13551 416276001753 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 416276001754 Integrase core domain; Region: rve; pfam00665 416276001755 Integrase core domain; Region: rve_3; pfam13683 416276001756 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 416276001757 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 416276001758 Walker A motif; other site 416276001759 ATP binding site [chemical binding]; other site 416276001760 Walker B motif; other site 416276001761 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 416276001762 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 416276001763 Conjugal transfer protein TraD; Region: TraD; pfam06412 416276001764 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 416276001765 HD domain; Region: HD_4; pfam13328 416276001766 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 416276001767 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 416276001768 ATP binding site [chemical binding]; other site 416276001769 Mg2+ binding site [ion binding]; other site 416276001770 G-X-G motif; other site 416276001771 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 416276001772 DnaA N-terminal domain; Region: DnaA_N; pfam11638 416276001773 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 416276001774 sequence-specific DNA binding site [nucleotide binding]; other site 416276001775 salt bridge; other site 416276001776 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 416276001777 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 416276001778 CMP-binding site; other site 416276001779 The sites determining sugar specificity; other site 416276001780 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 416276001781 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 416276001782 RNA binding site [nucleotide binding]; other site 416276001783 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 416276001784 RNA binding site [nucleotide binding]; other site 416276001785 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 416276001786 RNA binding site [nucleotide binding]; other site 416276001787 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 416276001788 RNA binding site [nucleotide binding]; other site 416276001789 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 416276001790 RNA binding site [nucleotide binding]; other site 416276001791 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 416276001792 RNA binding site [nucleotide binding]; other site 416276001793 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 416276001794 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 416276001795 oligomer interface [polypeptide binding]; other site 416276001796 active site residues [active] 416276001797 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 416276001798 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 416276001799 homotetramer interface [polypeptide binding]; other site 416276001800 FMN binding site [chemical binding]; other site 416276001801 homodimer contacts [polypeptide binding]; other site 416276001802 putative active site [active] 416276001803 putative substrate binding site [chemical binding]; other site 416276001804 Predicted acetyltransferase [General function prediction only]; Region: COG5628 416276001805 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 416276001806 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 416276001807 Coenzyme A binding pocket [chemical binding]; other site 416276001808 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 416276001809 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 416276001810 Substrate binding site; other site 416276001811 Mg++ binding site; other site 416276001812 hypothetical protein; Validated; Region: PRK00110 416276001813 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 416276001814 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 416276001815 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 416276001816 N-acetyl-D-glucosamine binding site [chemical binding]; other site 416276001817 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 416276001818 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 416276001819 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 416276001820 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 416276001821 S-adenosylmethionine binding site [chemical binding]; other site 416276001822 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 416276001823 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 416276001824 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 416276001825 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 416276001826 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 416276001827 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 416276001828 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 416276001829 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 416276001830 catalytic site [active] 416276001831 putative active site [active] 416276001832 putative substrate binding site [chemical binding]; other site 416276001833 Helicase and RNase D C-terminal; Region: HRDC; smart00341 416276001834 Uncharacterized conserved protein [Function unknown]; Region: COG1723 416276001835 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 416276001836 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 416276001837 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 416276001838 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 416276001839 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 416276001840 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 416276001841 dimer interface [polypeptide binding]; other site 416276001842 catalytic triad [active] 416276001843 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 416276001844 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 416276001845 domain interfaces; other site 416276001846 active site 416276001847 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 416276001848 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 416276001849 active site 416276001850 HIGH motif; other site 416276001851 dimer interface [polypeptide binding]; other site 416276001852 KMSKS motif; other site 416276001853 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 416276001854 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 416276001855 putative acyl-acceptor binding pocket; other site 416276001856 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 416276001857 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 416276001858 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 416276001859 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 416276001860 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 416276001861 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 416276001862 active site 416276001863 Lysine efflux permease [General function prediction only]; Region: COG1279 416276001864 AmpG-like permease; Region: 2A0125; TIGR00901 416276001865 TLC ATP/ADP transporter; Region: TLC; pfam03219 416276001866 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 416276001867 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 416276001868 substrate binding pocket [chemical binding]; other site 416276001869 chain length determination region; other site 416276001870 substrate-Mg2+ binding site; other site 416276001871 catalytic residues [active] 416276001872 aspartate-rich region 1; other site 416276001873 active site lid residues [active] 416276001874 aspartate-rich region 2; other site 416276001875 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 416276001876 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 416276001877 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276001878 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 416276001879 active site 416276001880 arginine:agmatin antiporter; Provisional; Region: PRK10644 416276001881 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 416276001882 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 416276001883 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 416276001884 trimerization site [polypeptide binding]; other site 416276001885 active site 416276001886 cysteine desulfurase; Provisional; Region: PRK14012 416276001887 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 416276001888 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 416276001889 catalytic residue [active] 416276001890 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 416276001891 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 416276001892 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 416276001893 catalytic residue [active] 416276001894 Predicted transcriptional regulator [Transcription]; Region: COG1959 416276001895 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 416276001896 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 416276001897 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 416276001898 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 416276001899 dimer interface [polypeptide binding]; other site 416276001900 allosteric magnesium binding site [ion binding]; other site 416276001901 active site 416276001902 aspartate-rich active site metal binding site; other site 416276001903 Schiff base residues; other site 416276001904 primosome assembly protein PriA; Validated; Region: PRK05580 416276001905 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 416276001906 ATP binding site [chemical binding]; other site 416276001907 putative Mg++ binding site [ion binding]; other site 416276001908 helicase superfamily c-terminal domain; Region: HELICc; smart00490 416276001909 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 416276001910 Flavoprotein; Region: Flavoprotein; pfam02441 416276001911 replicative DNA helicase; Provisional; Region: PRK09165 416276001912 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 416276001913 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 416276001914 Walker A motif; other site 416276001915 ATP binding site [chemical binding]; other site 416276001916 Walker B motif; other site 416276001917 DNA binding loops [nucleotide binding] 416276001918 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 416276001919 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 416276001920 RNA binding surface [nucleotide binding]; other site 416276001921 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 416276001922 active site 416276001923 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 416276001924 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 416276001925 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 416276001926 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 416276001927 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 416276001928 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 416276001929 S-adenosylmethionine binding site [chemical binding]; other site 416276001930 DNA repair protein RadA; Provisional; Region: PRK11823 416276001931 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 416276001932 Walker A motif/ATP binding site; other site 416276001933 ATP binding site [chemical binding]; other site 416276001934 Walker B motif; other site 416276001935 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 416276001936 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 416276001937 Recombination protein O N terminal; Region: RecO_N; pfam11967 416276001938 Recombination protein O C terminal; Region: RecO_C; pfam02565 416276001939 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 416276001940 Glycoprotease family; Region: Peptidase_M22; pfam00814 416276001941 translation initiation factor IF-2; Validated; Region: infB; PRK05306 416276001942 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 416276001943 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 416276001944 G1 box; other site 416276001945 putative GEF interaction site [polypeptide binding]; other site 416276001946 GTP/Mg2+ binding site [chemical binding]; other site 416276001947 Switch I region; other site 416276001948 G2 box; other site 416276001949 G3 box; other site 416276001950 Switch II region; other site 416276001951 G4 box; other site 416276001952 G5 box; other site 416276001953 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 416276001954 Translation-initiation factor 2; Region: IF-2; pfam11987 416276001955 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 416276001956 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 416276001957 NusA N-terminal domain; Region: NusA_N; pfam08529 416276001958 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 416276001959 RNA binding site [nucleotide binding]; other site 416276001960 homodimer interface [polypeptide binding]; other site 416276001961 NusA-like KH domain; Region: KH_5; pfam13184 416276001962 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 416276001963 G-X-X-G motif; other site 416276001964 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 416276001965 Sm and related proteins; Region: Sm_like; cl00259 416276001966 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 416276001967 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 416276001968 putative oligomer interface [polypeptide binding]; other site 416276001969 putative RNA binding site [nucleotide binding]; other site 416276001970 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 416276001971 FAD binding pocket [chemical binding]; other site 416276001972 conserved FAD binding motif [chemical binding]; other site 416276001973 phosphate binding motif [ion binding]; other site 416276001974 beta-alpha-beta structure motif; other site 416276001975 NAD binding pocket [chemical binding]; other site 416276001976 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 416276001977 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 416276001978 RNA binding surface [nucleotide binding]; other site 416276001979 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 416276001980 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 416276001981 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 416276001982 active site 416276001983 HIGH motif; other site 416276001984 dimer interface [polypeptide binding]; other site 416276001985 KMSKS motif; other site 416276001986 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 416276001987 RNA binding surface [nucleotide binding]; other site 416276001988 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 416276001989 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 416276001990 MG2 domain; Region: A2M_N; pfam01835 416276001991 Alpha-2-macroglobulin family; Region: A2M; pfam00207 416276001992 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 416276001993 surface patch; other site 416276001994 thioester region; other site 416276001995 specificity defining residues; other site 416276001996 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 416276001997 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 416276001998 active site 416276001999 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276002000 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 416276002001 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 416276002002 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 416276002003 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 416276002004 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 416276002005 active site 416276002006 phosphorylation site [posttranslational modification] 416276002007 intermolecular recognition site; other site 416276002008 dimerization interface [polypeptide binding]; other site 416276002009 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 416276002010 Walker A motif; other site 416276002011 ATP binding site [chemical binding]; other site 416276002012 Walker B motif; other site 416276002013 arginine finger; other site 416276002014 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 416276002015 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 416276002016 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 416276002017 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 416276002018 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 416276002019 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 416276002020 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 416276002021 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 416276002022 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 416276002023 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 416276002024 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 416276002025 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 416276002026 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 416276002027 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 416276002028 S-adenosylmethionine binding site [chemical binding]; other site 416276002029 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 416276002030 MraZ protein; Region: MraZ; pfam02381 416276002031 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 416276002032 Na binding site [ion binding]; other site 416276002033 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 416276002034 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 416276002035 GIY-YIG motif/motif A; other site 416276002036 active site 416276002037 catalytic site [active] 416276002038 putative DNA binding site [nucleotide binding]; other site 416276002039 metal binding site [ion binding]; metal-binding site 416276002040 UvrB/uvrC motif; Region: UVR; pfam02151 416276002041 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 416276002042 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 416276002043 A new structural DNA glycosylase; Region: AlkD_like; cd06561 416276002044 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 416276002045 active site 416276002046 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 416276002047 DEAD/DEAH box helicase; Region: DEAD; pfam00270 416276002048 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 416276002049 SEC-C motif; Region: SEC-C; pfam02810 416276002050 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03095 416276002051 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 416276002052 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 416276002053 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 416276002054 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 416276002055 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 416276002056 hinge; other site 416276002057 active site 416276002058 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 416276002059 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 416276002060 ATP binding site [chemical binding]; other site 416276002061 Mg2+ binding site [ion binding]; other site 416276002062 G-X-G motif; other site 416276002063 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 416276002064 anchoring element; other site 416276002065 dimer interface [polypeptide binding]; other site 416276002066 ATP binding site [chemical binding]; other site 416276002067 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 416276002068 active site 416276002069 putative metal-binding site [ion binding]; other site 416276002070 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 416276002071 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 416276002072 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 416276002073 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 416276002074 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 416276002075 MgtE intracellular N domain; Region: MgtE_N; pfam03448 416276002076 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 416276002077 Divalent cation transporter; Region: MgtE; pfam01769 416276002078 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 416276002079 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 416276002080 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 416276002081 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 416276002082 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 416276002083 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 416276002084 Cu(I) binding site [ion binding]; other site 416276002085 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 416276002086 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 416276002087 dimer interface [polypeptide binding]; other site 416276002088 substrate binding site [chemical binding]; other site 416276002089 metal binding sites [ion binding]; metal-binding site 416276002090 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276002091 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 416276002092 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 416276002093 TraX protein; Region: TraX; pfam05857 416276002094 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 416276002095 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 416276002096 ssDNA binding site; other site 416276002097 generic binding surface II; other site 416276002098 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 416276002099 ATP binding site [chemical binding]; other site 416276002100 putative Mg++ binding site [ion binding]; other site 416276002101 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 416276002102 nucleotide binding region [chemical binding]; other site 416276002103 ATP-binding site [chemical binding]; other site 416276002104 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 416276002105 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 416276002106 V-type ATP synthase subunit I; Validated; Region: PRK05771 416276002107 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 416276002108 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 416276002109 Mg++ binding site [ion binding]; other site 416276002110 putative catalytic motif [active] 416276002111 putative substrate binding site [chemical binding]; other site 416276002112 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 416276002113 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 416276002114 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 416276002115 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 416276002116 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 416276002117 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 416276002118 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 416276002119 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 416276002120 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 416276002121 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 416276002122 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 416276002123 ATP binding site [chemical binding]; other site 416276002124 putative Mg++ binding site [ion binding]; other site 416276002125 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 416276002126 nucleotide binding region [chemical binding]; other site 416276002127 ATP-binding site [chemical binding]; other site 416276002128 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 416276002129 Uncharacterized conserved protein [Function unknown]; Region: COG2938 416276002130 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 416276002131 active site residue [active] 416276002132 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 416276002133 DnaA N-terminal domain; Region: DnaA_N; pfam11638 416276002134 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 416276002135 Walker A motif; other site 416276002136 ATP binding site [chemical binding]; other site 416276002137 Walker B motif; other site 416276002138 arginine finger; other site 416276002139 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 416276002140 DnaA box-binding interface [nucleotide binding]; other site 416276002141 Patatin [General function prediction only]; Region: COG3621 416276002142 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 416276002143 active site 416276002144 nucleophile elbow; other site 416276002145 GTP-binding protein YchF; Reviewed; Region: PRK09601 416276002146 YchF GTPase; Region: YchF; cd01900 416276002147 G1 box; other site 416276002148 GTP/Mg2+ binding site [chemical binding]; other site 416276002149 Switch I region; other site 416276002150 G2 box; other site 416276002151 Switch II region; other site 416276002152 G3 box; other site 416276002153 G4 box; other site 416276002154 G5 box; other site 416276002155 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 416276002156 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 416276002157 putative active site [active] 416276002158 catalytic residue [active] 416276002159 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 416276002160 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 416276002161 5S rRNA interface [nucleotide binding]; other site 416276002162 CTC domain interface [polypeptide binding]; other site 416276002163 L16 interface [polypeptide binding]; other site 416276002164 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 416276002165 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 416276002166 FeS/SAM binding site; other site 416276002167 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 416276002168 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 416276002169 23S rRNA binding site [nucleotide binding]; other site 416276002170 L21 binding site [polypeptide binding]; other site 416276002171 L13 binding site [polypeptide binding]; other site 416276002172 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 416276002173 ribonuclease P; Reviewed; Region: rnpA; PRK01492 416276002174 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276002175 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 416276002176 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 416276002177 Cl binding site [ion binding]; other site 416276002178 oligomer interface [polypeptide binding]; other site 416276002179 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276002180 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 416276002181 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 416276002182 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 416276002183 dimerization interface [polypeptide binding]; other site 416276002184 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 416276002185 dimer interface [polypeptide binding]; other site 416276002186 phosphorylation site [posttranslational modification] 416276002187 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 416276002188 ATP binding site [chemical binding]; other site 416276002189 Mg2+ binding site [ion binding]; other site 416276002190 G-X-G motif; other site 416276002191 ribosomal protein S21; Region: S21p; TIGR00030 416276002192 Uncharacterized conserved protein [Function unknown]; Region: COG5590 416276002193 COQ9; Region: COQ9; pfam08511 416276002194 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 416276002195 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 416276002196 HIGH motif; other site 416276002197 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 416276002198 active site 416276002199 KMSKS motif; other site 416276002200 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 416276002201 tRNA binding surface [nucleotide binding]; other site 416276002202 anticodon binding site; other site 416276002203 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 416276002204 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 416276002205 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 416276002206 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 416276002207 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 416276002208 carboxyltransferase (CT) interaction site; other site 416276002209 biotinylation site [posttranslational modification]; other site 416276002210 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 416276002211 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 416276002212 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 416276002213 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276002214 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 416276002215 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 416276002216 putative substrate translocation pore; other site 416276002217 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 416276002218 putative acyl-acceptor binding pocket; other site 416276002219 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 416276002220 acyl-activating enzyme (AAE) consensus motif; other site 416276002221 putative AMP binding site [chemical binding]; other site 416276002222 TfoX N-terminal domain; Region: TfoX_N; cl17592 416276002223 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 416276002224 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 416276002225 ABC-ATPase subunit interface; other site 416276002226 dimer interface [polypeptide binding]; other site 416276002227 putative PBP binding regions; other site 416276002228 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 416276002229 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276002230 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 416276002231 S-adenosylmethionine binding site [chemical binding]; other site 416276002232 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 416276002233 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 416276002234 HIGH motif; other site 416276002235 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 416276002236 active site 416276002237 KMSKS motif; other site 416276002238 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276002239 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 416276002240 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276002241 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 416276002242 HD domain; Region: HD_4; pfam13328 416276002243 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 416276002244 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 416276002245 synthetase active site [active] 416276002246 NTP binding site [chemical binding]; other site 416276002247 metal binding site [ion binding]; metal-binding site 416276002248 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 416276002249 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 416276002250 ring oligomerisation interface [polypeptide binding]; other site 416276002251 ATP/Mg binding site [chemical binding]; other site 416276002252 stacking interactions; other site 416276002253 hinge regions; other site 416276002254 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 416276002255 oligomerisation interface [polypeptide binding]; other site 416276002256 mobile loop; other site 416276002257 roof hairpin; other site 416276002258 ribonuclease PH; Reviewed; Region: rph; PRK00173 416276002259 Ribonuclease PH; Region: RNase_PH_bact; cd11362 416276002260 hexamer interface [polypeptide binding]; other site 416276002261 active site 416276002262 GrpE; Region: GrpE; pfam01025 416276002263 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 416276002264 dimer interface [polypeptide binding]; other site 416276002265 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 416276002266 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 416276002267 Domain of unknown function DUF20; Region: UPF0118; pfam01594 416276002268 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 416276002269 hypothetical protein; Validated; Region: PRK06620 416276002270 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 416276002271 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 416276002272 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 416276002273 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 416276002274 alphaNTD - beta interaction site [polypeptide binding]; other site 416276002275 alphaNTD homodimer interface [polypeptide binding]; other site 416276002276 alphaNTD - beta' interaction site [polypeptide binding]; other site 416276002277 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 416276002278 30S ribosomal protein S11; Validated; Region: PRK05309 416276002279 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 416276002280 30S ribosomal protein S13; Region: bact_S13; TIGR03631 416276002281 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 416276002282 adenylate kinase; Reviewed; Region: adk; PRK00279 416276002283 AMP-binding site [chemical binding]; other site 416276002284 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 416276002285 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 416276002286 SecY translocase; Region: SecY; pfam00344 416276002287 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 416276002288 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 416276002289 23S rRNA binding site [nucleotide binding]; other site 416276002290 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 416276002291 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 416276002292 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 416276002293 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 416276002294 5S rRNA interface [nucleotide binding]; other site 416276002295 23S rRNA interface [nucleotide binding]; other site 416276002296 L5 interface [polypeptide binding]; other site 416276002297 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 416276002298 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 416276002299 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 416276002300 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 416276002301 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 416276002302 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 416276002303 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 416276002304 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 416276002305 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 416276002306 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 416276002307 RNA binding site [nucleotide binding]; other site 416276002308 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 416276002309 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 416276002310 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 416276002311 L23 interface [polypeptide binding]; other site 416276002312 trigger factor interaction site; other site 416276002313 23S rRNA interface [nucleotide binding]; other site 416276002314 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 416276002315 23S rRNA interface [nucleotide binding]; other site 416276002316 5S rRNA interface [nucleotide binding]; other site 416276002317 putative antibiotic binding site [chemical binding]; other site 416276002318 L25 interface [polypeptide binding]; other site 416276002319 L27 interface [polypeptide binding]; other site 416276002320 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 416276002321 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 416276002322 G-X-X-G motif; other site 416276002323 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 416276002324 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 416276002325 putative translocon binding site; other site 416276002326 protein-rRNA interface [nucleotide binding]; other site 416276002327 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 416276002328 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 416276002329 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 416276002330 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 416276002331 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 416276002332 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 416276002333 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 416276002334 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 416276002335 elongation factor Tu; Reviewed; Region: PRK00049 416276002336 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 416276002337 G1 box; other site 416276002338 GEF interaction site [polypeptide binding]; other site 416276002339 GTP/Mg2+ binding site [chemical binding]; other site 416276002340 Switch I region; other site 416276002341 G2 box; other site 416276002342 G3 box; other site 416276002343 Switch II region; other site 416276002344 G4 box; other site 416276002345 G5 box; other site 416276002346 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 416276002347 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 416276002348 Antibiotic Binding Site [chemical binding]; other site 416276002349 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 416276002350 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 416276002351 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 416276002352 fumarate hydratase; Reviewed; Region: fumC; PRK00485 416276002353 Class II fumarases; Region: Fumarase_classII; cd01362 416276002354 active site 416276002355 tetramer interface [polypeptide binding]; other site 416276002356 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 416276002357 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 416276002358 putative active site [active] 416276002359 homotetrameric interface [polypeptide binding]; other site 416276002360 metal binding site [ion binding]; metal-binding site 416276002361 cell division protein FtsZ; Validated; Region: PRK09330 416276002362 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 416276002363 nucleotide binding site [chemical binding]; other site 416276002364 SulA interaction site; other site 416276002365 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 416276002366 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 416276002367 muropeptide transporter; Reviewed; Region: ampG; PRK11902 416276002368 muropeptide transporter; Validated; Region: ampG; cl17669 416276002369 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 416276002370 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 416276002371 ATP binding site [chemical binding]; other site 416276002372 Mg++ binding site [ion binding]; other site 416276002373 motif III; other site 416276002374 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 416276002375 nucleotide binding region [chemical binding]; other site 416276002376 ATP-binding site [chemical binding]; other site 416276002377 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 416276002378 DNA-binding site [nucleotide binding]; DNA binding site 416276002379 RNA-binding motif; other site 416276002380 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 416276002381 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 416276002382 S-adenosylmethionine binding site [chemical binding]; other site 416276002383 SurA N-terminal domain; Region: SurA_N_3; cl07813 416276002384 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 416276002385 Organic solvent tolerance protein; Region: OstA_C; pfam04453 416276002386 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 416276002387 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 416276002388 generic binding surface II; other site 416276002389 generic binding surface I; other site 416276002390 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 416276002391 putative catalytic site [active] 416276002392 putative phosphate binding site [ion binding]; other site 416276002393 active site 416276002394 metal binding site A [ion binding]; metal-binding site 416276002395 DNA binding site [nucleotide binding] 416276002396 putative AP binding site [nucleotide binding]; other site 416276002397 putative metal binding site B [ion binding]; other site 416276002398 GTP-binding protein Der; Reviewed; Region: PRK00093 416276002399 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 416276002400 G1 box; other site 416276002401 GTP/Mg2+ binding site [chemical binding]; other site 416276002402 Switch I region; other site 416276002403 G2 box; other site 416276002404 Switch II region; other site 416276002405 G3 box; other site 416276002406 G4 box; other site 416276002407 G5 box; other site 416276002408 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 416276002409 G1 box; other site 416276002410 GTP/Mg2+ binding site [chemical binding]; other site 416276002411 Switch I region; other site 416276002412 G2 box; other site 416276002413 G3 box; other site 416276002414 Switch II region; other site 416276002415 G4 box; other site 416276002416 G5 box; other site 416276002417 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 416276002418 ABC1 family; Region: ABC1; cl17513 416276002419 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 416276002420 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 416276002421 S-adenosylmethionine binding site [chemical binding]; other site 416276002422 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 416276002423 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 416276002424 DNA binding site [nucleotide binding] 416276002425 catalytic residue [active] 416276002426 H2TH interface [polypeptide binding]; other site 416276002427 putative catalytic residues [active] 416276002428 turnover-facilitating residue; other site 416276002429 intercalation triad [nucleotide binding]; other site 416276002430 8OG recognition residue [nucleotide binding]; other site 416276002431 putative reading head residues; other site 416276002432 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 416276002433 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 416276002434 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276002435 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 416276002436 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 416276002437 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 416276002438 active site 416276002439 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 416276002440 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 416276002441 HIGH motif; other site 416276002442 active site 416276002443 KMSKS motif; other site 416276002444 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 416276002445 tRNA binding surface [nucleotide binding]; other site 416276002446 anticodon binding site; other site 416276002447 thymidylate kinase; Validated; Region: tmk; PRK00698 416276002448 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 416276002449 TMP-binding site; other site 416276002450 ATP-binding site [chemical binding]; other site 416276002451 metabolite-proton symporter; Region: 2A0106; TIGR00883 416276002452 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 416276002453 UbiA prenyltransferase family; Region: UbiA; pfam01040 416276002454 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 416276002455 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 416276002456 active site 416276002457 HIGH motif; other site 416276002458 nucleotide binding site [chemical binding]; other site 416276002459 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 416276002460 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 416276002461 active site 416276002462 KMSKS motif; other site 416276002463 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 416276002464 tRNA binding surface [nucleotide binding]; other site 416276002465 anticodon binding site; other site 416276002466 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 416276002467 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 416276002468 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 416276002469 RmuC family; Region: RmuC; pfam02646 416276002470 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 416276002471 putative NAD(P) binding site [chemical binding]; other site 416276002472 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 416276002473 active site 416276002474 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 416276002475 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 416276002476 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 416276002477 Walker A motif; other site 416276002478 ATP binding site [chemical binding]; other site 416276002479 Walker B motif; other site 416276002480 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 416276002481 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 416276002482 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 416276002483 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 416276002484 Ligand Binding Site [chemical binding]; other site 416276002485 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 416276002486 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 416276002487 HicB family; Region: HicB; pfam05534 416276002488 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 416276002489 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 416276002490 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276002491 Walker A/P-loop; other site 416276002492 ATP binding site [chemical binding]; other site 416276002493 Q-loop/lid; other site 416276002494 ABC transporter signature motif; other site 416276002495 Walker B; other site 416276002496 D-loop; other site 416276002497 H-loop/switch region; other site 416276002498 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 416276002499 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 416276002500 putative substrate translocation pore; other site 416276002501 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 416276002502 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 416276002503 FtsX-like permease family; Region: FtsX; pfam02687 416276002504 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 416276002505 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 416276002506 Walker A/P-loop; other site 416276002507 ATP binding site [chemical binding]; other site 416276002508 Q-loop/lid; other site 416276002509 ABC transporter signature motif; other site 416276002510 Walker B; other site 416276002511 D-loop; other site 416276002512 H-loop/switch region; other site 416276002513 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 416276002514 Domain of unknown function DUF21; Region: DUF21; pfam01595 416276002515 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 416276002516 Transporter associated domain; Region: CorC_HlyC; smart01091 416276002517 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 416276002518 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 416276002519 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 416276002520 Autotransporter beta-domain; Region: Autotransporter; smart00869 416276002521 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 416276002522 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 416276002523 synthetase active site [active] 416276002524 NTP binding site [chemical binding]; other site 416276002525 metal binding site [ion binding]; metal-binding site 416276002526 Transposase IS200 like; Region: Y1_Tnp; pfam01797 416276002527 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 416276002528 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 416276002529 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 416276002530 DNA binding residues [nucleotide binding] 416276002531 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 416276002532 IHF dimer interface [polypeptide binding]; other site 416276002533 IHF - DNA interface [nucleotide binding]; other site 416276002534 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 416276002535 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 416276002536 catalytic triad [active] 416276002537 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 416276002538 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 416276002539 putative acyl-acceptor binding pocket; other site 416276002540 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 416276002541 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 416276002542 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 416276002543 Peptidase family M23; Region: Peptidase_M23; pfam01551 416276002544 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 416276002545 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 416276002546 nucleotide binding pocket [chemical binding]; other site 416276002547 K-X-D-G motif; other site 416276002548 catalytic site [active] 416276002549 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 416276002550 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 416276002551 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 416276002552 Dimer interface [polypeptide binding]; other site 416276002553 BRCT sequence motif; other site 416276002554 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 416276002555 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 416276002556 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 416276002557 mce related protein; Region: MCE; pfam02470 416276002558 hypothetical protein; Provisional; Region: PRK06630 416276002559 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 416276002560 RNA/DNA hybrid binding site [nucleotide binding]; other site 416276002561 active site 416276002562 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 416276002563 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 416276002564 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 416276002565 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 416276002566 CoA-binding site [chemical binding]; other site 416276002567 ATP-binding [chemical binding]; other site 416276002568 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 416276002569 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 416276002570 active site 416276002571 catalytic site [active] 416276002572 substrate binding site [chemical binding]; other site 416276002573 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 416276002574 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 416276002575 Part of AAA domain; Region: AAA_19; pfam13245 416276002576 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 416276002577 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 416276002578 Family description; Region: UvrD_C_2; pfam13538 416276002579 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 416276002580 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 416276002581 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 416276002582 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 416276002583 TLC ATP/ADP transporter; Region: TLC; pfam03219 416276002584 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 416276002585 nudix motif; other site 416276002586 FOG: CBS domain [General function prediction only]; Region: COG0517 416276002587 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 416276002588 Transporter associated domain; Region: CorC_HlyC; smart01091 416276002589 metal-binding heat shock protein; Provisional; Region: PRK00016 416276002590 PemK-like protein; Region: PemK; cl00995 416276002591 lipoyl synthase; Provisional; Region: PRK05481 416276002592 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 416276002593 FeS/SAM binding site; other site 416276002594 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 416276002595 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 416276002596 dimer interface [polypeptide binding]; other site 416276002597 active site 416276002598 glycine-pyridoxal phosphate binding site [chemical binding]; other site 416276002599 folate binding site [chemical binding]; other site 416276002600 Predicted esterase [General function prediction only]; Region: COG0400 416276002601 putative hydrolase; Provisional; Region: PRK11460 416276002602 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 416276002603 putative GSH binding site [chemical binding]; other site 416276002604 catalytic residues [active] 416276002605 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 416276002606 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 416276002607 minor groove reading motif; other site 416276002608 helix-hairpin-helix signature motif; other site 416276002609 substrate binding pocket [chemical binding]; other site 416276002610 active site 416276002611 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 416276002612 Predicted small secreted protein [Function unknown]; Region: COG5510 416276002613 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 416276002614 Predicted methyltransferases [General function prediction only]; Region: COG0313 416276002615 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 416276002616 putative SAM binding site [chemical binding]; other site 416276002617 putative homodimer interface [polypeptide binding]; other site 416276002618 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 416276002619 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 416276002620 putative ligand binding site [chemical binding]; other site 416276002621 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 416276002622 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 416276002623 tetramer interfaces [polypeptide binding]; other site 416276002624 binuclear metal-binding site [ion binding]; other site 416276002625 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 416276002626 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 416276002627 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 416276002628 aspartate kinase; Reviewed; Region: PRK06635 416276002629 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 416276002630 putative nucleotide binding site [chemical binding]; other site 416276002631 putative catalytic residues [active] 416276002632 putative Mg ion binding site [ion binding]; other site 416276002633 putative aspartate binding site [chemical binding]; other site 416276002634 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 416276002635 putative allosteric regulatory residue; other site 416276002636 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 416276002637 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 416276002638 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 416276002639 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 416276002640 metabolite-proton symporter; Region: 2A0106; TIGR00883 416276002641 putative substrate translocation pore; other site 416276002642 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 416276002643 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276002644 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 416276002645 Helix-turn-helix domain; Region: HTH_25; pfam13413 416276002646 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 416276002647 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 416276002648 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 416276002649 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 416276002650 trmE is a tRNA modification GTPase; Region: trmE; cd04164 416276002651 G1 box; other site 416276002652 GTP/Mg2+ binding site [chemical binding]; other site 416276002653 Switch I region; other site 416276002654 G2 box; other site 416276002655 Switch II region; other site 416276002656 G3 box; other site 416276002657 G4 box; other site 416276002658 G5 box; other site 416276002659 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 416276002660 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 416276002661 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 416276002662 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 416276002663 hexamer interface [polypeptide binding]; other site 416276002664 Walker A motif; other site 416276002665 ATP binding site [chemical binding]; other site 416276002666 Walker B motif; other site 416276002667 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 416276002668 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 416276002669 NAD(P) binding site [chemical binding]; other site 416276002670 homotetramer interface [polypeptide binding]; other site 416276002671 homodimer interface [polypeptide binding]; other site 416276002672 active site 416276002673 acyl carrier protein; Provisional; Region: acpP; PRK00982 416276002674 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 416276002675 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 416276002676 dimer interface [polypeptide binding]; other site 416276002677 active site 416276002678 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 416276002679 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 416276002680 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 416276002681 AAA domain; Region: AAA_14; pfam13173 416276002682 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 416276002683 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 416276002684 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 416276002685 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 416276002686 catalytic site [active] 416276002687 G-X2-G-X-G-K; other site 416276002688 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 416276002689 sequence-specific DNA binding site [nucleotide binding]; other site 416276002690 salt bridge; other site 416276002691 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 416276002692 rod shape-determining protein MreC; Region: MreC; pfam04085 416276002693 rod shape-determining protein MreB; Provisional; Region: PRK13927 416276002694 MreB and similar proteins; Region: MreB_like; cd10225 416276002695 nucleotide binding site [chemical binding]; other site 416276002696 Mg binding site [ion binding]; other site 416276002697 putative protofilament interaction site [polypeptide binding]; other site 416276002698 RodZ interaction site [polypeptide binding]; other site 416276002699 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 416276002700 Predicted permeases [General function prediction only]; Region: COG0795 416276002701 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 416276002702 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 416276002703 ligand binding site [chemical binding]; other site 416276002704 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 416276002705 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 416276002706 dimer interface [polypeptide binding]; other site 416276002707 active site 416276002708 CoA binding pocket [chemical binding]; other site 416276002709 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 416276002710 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 416276002711 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 416276002712 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 416276002713 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 416276002714 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 416276002715 P loop; other site 416276002716 GTP binding site [chemical binding]; other site 416276002717 DNA polymerase I; Provisional; Region: PRK05755 416276002718 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 416276002719 active site 416276002720 metal binding site 1 [ion binding]; metal-binding site 416276002721 putative 5' ssDNA interaction site; other site 416276002722 metal binding site 3; metal-binding site 416276002723 metal binding site 2 [ion binding]; metal-binding site 416276002724 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 416276002725 putative DNA binding site [nucleotide binding]; other site 416276002726 putative metal binding site [ion binding]; other site 416276002727 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 416276002728 active site 416276002729 substrate binding site [chemical binding]; other site 416276002730 catalytic site [active] 416276002731 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 416276002732 active site 416276002733 DNA binding site [nucleotide binding] 416276002734 catalytic site [active] 416276002735 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 416276002736 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 416276002737 putative active site [active] 416276002738 putative PHP Thumb interface [polypeptide binding]; other site 416276002739 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 416276002740 generic binding surface I; other site 416276002741 generic binding surface II; other site 416276002742 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 416276002743 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 416276002744 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 416276002745 Protein of unknown function; Region: DUF3971; pfam13116 416276002746 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 416276002747 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 416276002748 muropeptide transporter; Reviewed; Region: ampG; PRK11902 416276002749 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 416276002750 seryl-tRNA synthetase; Provisional; Region: PRK05431 416276002751 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 416276002752 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 416276002753 dimer interface [polypeptide binding]; other site 416276002754 active site 416276002755 motif 1; other site 416276002756 motif 2; other site 416276002757 motif 3; other site 416276002758 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 416276002759 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 416276002760 Integral membrane protein TerC family; Region: TerC; cl10468 416276002761 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 416276002762 Methyltransferase domain; Region: Methyltransf_31; pfam13847 416276002763 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 416276002764 S-adenosylmethionine binding site [chemical binding]; other site 416276002765 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 416276002766 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 416276002767 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 416276002768 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 416276002769 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 416276002770 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 416276002771 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 416276002772 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 416276002773 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 416276002774 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 416276002775 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276002776 Walker A/P-loop; other site 416276002777 ATP binding site [chemical binding]; other site 416276002778 Q-loop/lid; other site 416276002779 ABC transporter signature motif; other site 416276002780 Walker B; other site 416276002781 D-loop; other site 416276002782 H-loop/switch region; other site 416276002783 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 416276002784 4Fe-4S binding domain; Region: Fer4; cl02805 416276002785 4Fe-4S binding domain; Region: Fer4; pfam00037 416276002786 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 416276002787 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 416276002788 NADH dehydrogenase subunit G; Validated; Region: PRK09130 416276002789 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 416276002790 catalytic loop [active] 416276002791 iron binding site [ion binding]; other site 416276002792 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 416276002793 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 416276002794 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 416276002795 Predicted membrane protein [Function unknown]; Region: COG3671 416276002796 aconitate hydratase; Validated; Region: PRK09277 416276002797 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 416276002798 substrate binding site [chemical binding]; other site 416276002799 ligand binding site [chemical binding]; other site 416276002800 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 416276002801 substrate binding site [chemical binding]; other site 416276002802 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 416276002803 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 416276002804 gamma subunit interface [polypeptide binding]; other site 416276002805 epsilon subunit interface [polypeptide binding]; other site 416276002806 LBP interface [polypeptide binding]; other site 416276002807 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 416276002808 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 416276002809 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 416276002810 alpha subunit interaction interface [polypeptide binding]; other site 416276002811 Walker A motif; other site 416276002812 ATP binding site [chemical binding]; other site 416276002813 Walker B motif; other site 416276002814 inhibitor binding site; inhibition site 416276002815 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 416276002816 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 416276002817 core domain interface [polypeptide binding]; other site 416276002818 delta subunit interface [polypeptide binding]; other site 416276002819 epsilon subunit interface [polypeptide binding]; other site 416276002820 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 416276002821 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 416276002822 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 416276002823 beta subunit interaction interface [polypeptide binding]; other site 416276002824 Walker A motif; other site 416276002825 ATP binding site [chemical binding]; other site 416276002826 Walker B motif; other site 416276002827 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 416276002828 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 416276002829 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 416276002830 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 416276002831 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 416276002832 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 416276002833 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 416276002834 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 416276002835 Transglycosylase; Region: Transgly; pfam00912 416276002836 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 416276002837 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 416276002838 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 416276002839 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 416276002840 FeS/SAM binding site; other site 416276002841 TRAM domain; Region: TRAM; pfam01938 416276002842 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 416276002843 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 416276002844 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 416276002845 Bacterial SH3 domain; Region: SH3_4; pfam06347 416276002846 Bacterial SH3 domain; Region: SH3_4; pfam06347 416276002847 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 416276002848 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 416276002849 TrkA-N domain; Region: TrkA_N; pfam02254 416276002850 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 416276002851 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 416276002852 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 416276002853 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 416276002854 rRNA binding site [nucleotide binding]; other site 416276002855 predicted 30S ribosome binding site; other site 416276002856 Maf-like protein; Region: Maf; pfam02545 416276002857 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 416276002858 active site 416276002859 dimer interface [polypeptide binding]; other site 416276002860 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 416276002861 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 416276002862 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 416276002863 active site 416276002864 DNA binding site [nucleotide binding] 416276002865 Int/Topo IB signature motif; other site 416276002866 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 416276002867 PLD-like domain; Region: PLDc_2; pfam13091 416276002868 putative active site [active] 416276002869 catalytic site [active] 416276002870 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 416276002871 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 416276002872 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 416276002873 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 416276002874 Autotransporter beta-domain; Region: Autotransporter; pfam03797 416276002875 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 416276002876 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 416276002877 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 416276002878 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 416276002879 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 416276002880 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 416276002881 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 416276002882 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 416276002883 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 416276002884 active site 416276002885 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 416276002886 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 416276002887 Mg++ binding site [ion binding]; other site 416276002888 putative catalytic motif [active] 416276002889 putative substrate binding site [chemical binding]; other site 416276002890 Protein of unknown function (DUF721); Region: DUF721; pfam05258 416276002891 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 416276002892 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 416276002893 Ferredoxin [Energy production and conversion]; Region: COG1146 416276002894 4Fe-4S binding domain; Region: Fer4; cl02805 416276002895 heme exporter protein CcmC; Region: ccmC; TIGR01191 416276002896 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 416276002897 nucleoside/Zn binding site; other site 416276002898 dimer interface [polypeptide binding]; other site 416276002899 catalytic motif [active] 416276002900 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 416276002901 Cation efflux family; Region: Cation_efflux; cl00316 416276002902 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 416276002903 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 416276002904 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 416276002905 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 416276002906 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 416276002907 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 416276002908 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 416276002909 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 416276002910 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 416276002911 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 416276002912 dimer interface [polypeptide binding]; other site 416276002913 ssDNA binding site [nucleotide binding]; other site 416276002914 tetramer (dimer of dimers) interface [polypeptide binding]; other site 416276002915 hypothetical protein; Reviewed; Region: PRK01530 416276002916 heat shock protein 90; Provisional; Region: PRK05218 416276002917 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 416276002918 ATP binding site [chemical binding]; other site 416276002919 Mg2+ binding site [ion binding]; other site 416276002920 G-X-G motif; other site 416276002921 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 416276002922 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 416276002923 substrate-cofactor binding pocket; other site 416276002924 pyridoxal 5'-phosphate binding site [chemical binding]; other site 416276002925 catalytic residue [active] 416276002926 trigger factor; Provisional; Region: tig; PRK01490 416276002927 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 416276002928 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 416276002929 GTPase CgtA; Reviewed; Region: obgE; PRK12299 416276002930 GTP1/OBG; Region: GTP1_OBG; pfam01018 416276002931 Obg GTPase; Region: Obg; cd01898 416276002932 G1 box; other site 416276002933 GTP/Mg2+ binding site [chemical binding]; other site 416276002934 Switch I region; other site 416276002935 G2 box; other site 416276002936 G3 box; other site 416276002937 Switch II region; other site 416276002938 G4 box; other site 416276002939 G5 box; other site 416276002940 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 416276002941 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 416276002942 dimer interface [polypeptide binding]; other site 416276002943 active site 416276002944 citrylCoA binding site [chemical binding]; other site 416276002945 NADH binding [chemical binding]; other site 416276002946 cationic pore residues; other site 416276002947 oxalacetate/citrate binding site [chemical binding]; other site 416276002948 coenzyme A binding site [chemical binding]; other site 416276002949 catalytic triad [active] 416276002950 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 416276002951 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 416276002952 Fe-S cluster binding site [ion binding]; other site 416276002953 active site 416276002954 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 416276002955 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 416276002956 RNA binding surface [nucleotide binding]; other site 416276002957 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 416276002958 active site 416276002959 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 416276002960 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 416276002961 S-adenosylmethionine binding site [chemical binding]; other site 416276002962 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 416276002963 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 416276002964 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 416276002965 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 416276002966 DALR anticodon binding domain; Region: DALR_1; pfam05746 416276002967 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 416276002968 motif 1; other site 416276002969 dimer interface [polypeptide binding]; other site 416276002970 active site 416276002971 motif 2; other site 416276002972 motif 3; other site 416276002973 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 416276002974 oligomeric interface; other site 416276002975 putative active site [active] 416276002976 homodimer interface [polypeptide binding]; other site 416276002977 prevent-host-death family protein; Region: phd_fam; TIGR01552 416276002978 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 416276002979 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 416276002980 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 416276002981 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 416276002982 ATP binding site [chemical binding]; other site 416276002983 Mg2+ binding site [ion binding]; other site 416276002984 G-X-G motif; other site 416276002985 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 416276002986 ATP binding site [chemical binding]; other site 416276002987 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 416276002988 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 416276002989 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 416276002990 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 416276002991 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 416276002992 amidase catalytic site [active] 416276002993 Zn binding residues [ion binding]; other site 416276002994 substrate binding site [chemical binding]; other site 416276002995 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 416276002996 lipoate-protein ligase B; Provisional; Region: PRK14347 416276002997 Uncharacterized conserved protein [Function unknown]; Region: COG1434 416276002998 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 416276002999 putative active site [active] 416276003000 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 416276003001 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 416276003002 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 416276003003 metal binding site [ion binding]; metal-binding site 416276003004 dimer interface [polypeptide binding]; other site 416276003005 DNA polymerase III subunit chi; Provisional; Region: PRK06646 416276003006 Predicted permeases [General function prediction only]; Region: COG0795 416276003007 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 416276003008 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 416276003009 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 416276003010 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 416276003011 active site 416276003012 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 416276003013 putative hydrolase; Provisional; Region: PRK02113 416276003014 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 416276003015 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 416276003016 Walker A/P-loop; other site 416276003017 ATP binding site [chemical binding]; other site 416276003018 Q-loop/lid; other site 416276003019 ABC transporter signature motif; other site 416276003020 Walker B; other site 416276003021 D-loop; other site 416276003022 H-loop/switch region; other site 416276003023 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 416276003024 Predicted aspartyl protease [General function prediction only]; Region: COG3577 416276003025 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 416276003026 catalytic motif [active] 416276003027 Catalytic residue [active] 416276003028 hypothetical protein; Validated; Region: PRK00153 416276003029 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 416276003030 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 416276003031 Walker A motif; other site 416276003032 ATP binding site [chemical binding]; other site 416276003033 Walker B motif; other site 416276003034 arginine finger; other site 416276003035 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 416276003036 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 416276003037 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 416276003038 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 416276003039 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 416276003040 ligand binding site [chemical binding]; other site 416276003041 homodimer interface [polypeptide binding]; other site 416276003042 NAD(P) binding site [chemical binding]; other site 416276003043 trimer interface B [polypeptide binding]; other site 416276003044 trimer interface A [polypeptide binding]; other site 416276003045 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 416276003046 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 416276003047 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 416276003048 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 416276003049 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 416276003050 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 416276003051 DNA primase, catalytic core; Region: dnaG; TIGR01391 416276003052 CHC2 zinc finger; Region: zf-CHC2; pfam01807 416276003053 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 416276003054 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 416276003055 active site 416276003056 metal binding site [ion binding]; metal-binding site 416276003057 interdomain interaction site; other site 416276003058 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 416276003059 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 416276003060 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 416276003061 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 416276003062 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 416276003063 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 416276003064 DNA binding residues [nucleotide binding] 416276003065 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 416276003066 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 416276003067 dimerization interface 3.5A [polypeptide binding]; other site 416276003068 active site 416276003069 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 416276003070 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 416276003071 motif 1; other site 416276003072 active site 416276003073 motif 2; other site 416276003074 motif 3; other site 416276003075 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 416276003076 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 416276003077 metabolite-proton symporter; Region: 2A0106; TIGR00883 416276003078 putative substrate translocation pore; other site 416276003079 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 416276003080 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 416276003081 TIGR00701 family protein; Region: TIGR00701 416276003082 ferrochelatase; Reviewed; Region: hemH; PRK00035 416276003083 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 416276003084 C-terminal domain interface [polypeptide binding]; other site 416276003085 active site 416276003086 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 416276003087 active site 416276003088 N-terminal domain interface [polypeptide binding]; other site 416276003089 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 416276003090 substrate binding site [chemical binding]; other site 416276003091 active site