-- dump date 20140620_035018 -- class Genbank::misc_feature -- table misc_feature_note -- id note 941638000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 941638000002 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 941638000003 catalytic residues [active] 941638000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 941638000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 941638000006 Walker A/P-loop; other site 941638000007 ATP binding site [chemical binding]; other site 941638000008 Q-loop/lid; other site 941638000009 ABC transporter signature motif; other site 941638000010 Walker B; other site 941638000011 D-loop; other site 941638000012 H-loop/switch region; other site 941638000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 941638000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 941638000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 941638000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 941638000017 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 941638000018 FAD binding pocket [chemical binding]; other site 941638000019 FAD binding motif [chemical binding]; other site 941638000020 phosphate binding motif [ion binding]; other site 941638000021 beta-alpha-beta structure motif; other site 941638000022 NAD binding pocket [chemical binding]; other site 941638000023 Iron coordination center [ion binding]; other site 941638000024 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 941638000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 941638000026 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 941638000027 active site 941638000028 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 941638000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 941638000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 941638000031 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 941638000032 trimer interface [polypeptide binding]; other site 941638000033 active site 941638000034 UDP-GlcNAc binding site [chemical binding]; other site 941638000035 lipid binding site [chemical binding]; lipid-binding site 941638000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 941638000037 active site 941638000038 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 941638000039 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 941638000040 FMN binding site [chemical binding]; other site 941638000041 active site 941638000042 catalytic residues [active] 941638000043 substrate binding site [chemical binding]; other site 941638000044 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 941638000045 NodB motif; other site 941638000046 putative active site [active] 941638000047 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 941638000048 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 941638000049 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 941638000050 intersubunit interface [polypeptide binding]; other site 941638000051 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 941638000052 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 941638000053 active site 941638000054 NTP binding site [chemical binding]; other site 941638000055 metal binding triad [ion binding]; metal-binding site 941638000056 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 941638000057 Autotransporter beta-domain; Region: Autotransporter; pfam03797 941638000058 AAA domain; Region: AAA_22; pfam13401 941638000059 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 941638000060 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 941638000061 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 941638000062 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 941638000063 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 941638000064 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638000065 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 941638000066 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 941638000067 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 941638000068 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 941638000069 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 941638000070 catalytic residues [active] 941638000071 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 941638000072 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 941638000073 Methyltransferase domain; Region: Methyltransf_31; pfam13847 941638000074 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 941638000075 S-adenosylmethionine binding site [chemical binding]; other site 941638000076 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 941638000077 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 941638000078 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 941638000079 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638000080 Walker A/P-loop; other site 941638000081 ATP binding site [chemical binding]; other site 941638000082 Q-loop/lid; other site 941638000083 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638000084 ABC transporter signature motif; other site 941638000085 Walker B; other site 941638000086 D-loop; other site 941638000087 H-loop/switch region; other site 941638000088 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 941638000089 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 941638000090 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 941638000091 Cu(I) binding site [ion binding]; other site 941638000092 Putative transcriptional regulator [Transcription]; Region: COG1678 941638000093 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 941638000094 Colicin V production protein; Region: Colicin_V; pfam02674 941638000095 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 941638000096 UGMP family protein; Validated; Region: PRK09604 941638000097 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 941638000098 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 941638000099 Fatty acid desaturase; Region: FA_desaturase; pfam00487 941638000100 Di-iron ligands [ion binding]; other site 941638000101 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 941638000102 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 941638000103 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 941638000104 DNA binding site [nucleotide binding] 941638000105 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 941638000106 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 941638000107 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 941638000108 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 941638000109 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 941638000110 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 941638000111 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 941638000112 Ligand Binding Site [chemical binding]; other site 941638000113 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638000114 FtsH Extracellular; Region: FtsH_ext; pfam06480 941638000115 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 941638000116 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 941638000117 Walker A motif; other site 941638000118 ATP binding site [chemical binding]; other site 941638000119 Walker B motif; other site 941638000120 arginine finger; other site 941638000121 Peptidase family M41; Region: Peptidase_M41; pfam01434 941638000122 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 941638000123 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 941638000124 Uncharacterized conserved protein [Function unknown]; Region: COG1565 941638000125 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638000126 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 941638000127 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 941638000128 Mechanosensitive ion channel; Region: MS_channel; pfam00924 941638000129 membrane protein insertase; Provisional; Region: PRK01318 941638000130 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 941638000131 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 941638000132 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 941638000133 active site 941638000134 catalytic residues [active] 941638000135 metal binding site [ion binding]; metal-binding site 941638000136 TLC ATP/ADP transporter; Region: TLC; pfam03219 941638000137 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 941638000138 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 941638000139 putative substrate translocation pore; other site 941638000140 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 941638000141 active site 941638000142 multimer interface [polypeptide binding]; other site 941638000143 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 941638000144 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 941638000145 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 941638000146 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 941638000147 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 941638000148 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 941638000149 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 941638000150 P-loop; other site 941638000151 Magnesium ion binding site [ion binding]; other site 941638000152 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 941638000153 Magnesium ion binding site [ion binding]; other site 941638000154 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 941638000155 ParB-like nuclease domain; Region: ParB; smart00470 941638000156 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 941638000157 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 941638000158 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 941638000159 ABC transporter; Region: ABC_tran_2; pfam12848 941638000160 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 941638000161 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 941638000162 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 941638000163 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 941638000164 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 941638000165 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 941638000166 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 941638000167 Zn2+ binding site [ion binding]; other site 941638000168 Mg2+ binding site [ion binding]; other site 941638000169 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 941638000170 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 941638000171 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 941638000172 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 941638000173 active site 941638000174 HIGH motif; other site 941638000175 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 941638000176 KMSK motif region; other site 941638000177 tRNA binding surface [nucleotide binding]; other site 941638000178 DALR anticodon binding domain; Region: DALR_1; smart00836 941638000179 anticodon binding site; other site 941638000180 Sporulation related domain; Region: SPOR; pfam05036 941638000181 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 941638000182 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 941638000183 CAP-like domain; other site 941638000184 active site 941638000185 primary dimer interface [polypeptide binding]; other site 941638000186 Gram-negative porin; Region: Porin_4; pfam13609 941638000187 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 941638000188 trimer interface [polypeptide binding]; other site 941638000189 active site 941638000190 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 941638000191 SecA binding site; other site 941638000192 Preprotein binding site; other site 941638000193 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 941638000194 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 941638000195 active site 941638000196 phosphorylation site [posttranslational modification] 941638000197 intermolecular recognition site; other site 941638000198 dimerization interface [polypeptide binding]; other site 941638000199 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 941638000200 DNA binding site [nucleotide binding] 941638000201 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 941638000202 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 941638000203 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 941638000204 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 941638000205 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 941638000206 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 941638000207 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 941638000208 EamA-like transporter family; Region: EamA; pfam00892 941638000209 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 941638000210 EamA-like transporter family; Region: EamA; pfam00892 941638000211 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 941638000212 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638000213 putative substrate translocation pore; other site 941638000214 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 941638000215 Autotransporter beta-domain; Region: Autotransporter; pfam03797 941638000216 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 941638000217 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 941638000218 active site 941638000219 HIGH motif; other site 941638000220 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 941638000221 KMSKS motif; other site 941638000222 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 941638000223 tRNA binding surface [nucleotide binding]; other site 941638000224 anticodon binding site; other site 941638000225 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 941638000226 rRNA interaction site [nucleotide binding]; other site 941638000227 S8 interaction site; other site 941638000228 putative laminin-1 binding site; other site 941638000229 elongation factor Ts; Provisional; Region: tsf; PRK09377 941638000230 UBA/TS-N domain; Region: UBA; pfam00627 941638000231 Elongation factor TS; Region: EF_TS; pfam00889 941638000232 Elongation factor TS; Region: EF_TS; pfam00889 941638000233 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 941638000234 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638000235 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 941638000236 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 941638000237 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 941638000238 putative acyl-acceptor binding pocket; other site 941638000239 aspartate aminotransferase; Provisional; Region: PRK05764 941638000240 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 941638000241 pyridoxal 5'-phosphate binding site [chemical binding]; other site 941638000242 homodimer interface [polypeptide binding]; other site 941638000243 catalytic residue [active] 941638000244 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 941638000245 Tetratricopeptide repeat; Region: TPR_12; pfam13424 941638000246 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 941638000247 binding surface 941638000248 TPR motif; other site 941638000249 Methyltransferase domain; Region: Methyltransf_23; pfam13489 941638000250 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 941638000251 S-adenosylmethionine binding site [chemical binding]; other site 941638000252 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 941638000253 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 941638000254 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 941638000255 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 941638000256 active site 941638000257 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 941638000258 dimer interface [polypeptide binding]; other site 941638000259 substrate binding site [chemical binding]; other site 941638000260 catalytic residues [active] 941638000261 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 941638000262 Permease; Region: Permease; pfam02405 941638000263 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 941638000264 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638000265 Walker A/P-loop; other site 941638000266 ATP binding site [chemical binding]; other site 941638000267 Q-loop/lid; other site 941638000268 ABC transporter signature motif; other site 941638000269 Walker B; other site 941638000270 D-loop; other site 941638000271 H-loop/switch region; other site 941638000272 CheD chemotactic sensory transduction; Region: CheD; cl00810 941638000273 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 941638000274 50S ribosomal protein L31; Provisional; Region: PRK01397 941638000275 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 941638000276 G1 box; other site 941638000277 GTP/Mg2+ binding site [chemical binding]; other site 941638000278 Switch I region; other site 941638000279 G2 box; other site 941638000280 G3 box; other site 941638000281 Switch II region; other site 941638000282 G4 box; other site 941638000283 G5 box; other site 941638000284 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 941638000285 nucleotide binding site [chemical binding]; other site 941638000286 substrate binding site [chemical binding]; other site 941638000287 type IV secretion system protein VirB3; Provisional; Region: PRK13899 941638000288 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 941638000289 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 941638000290 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638000291 Walker A/P-loop; other site 941638000292 ATP binding site [chemical binding]; other site 941638000293 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 941638000294 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 941638000295 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 941638000296 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 941638000297 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 941638000298 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 941638000299 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 941638000300 hypothetical protein; Provisional; Region: PRK13694 941638000301 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 941638000302 Protein export membrane protein; Region: SecD_SecF; pfam02355 941638000303 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 941638000304 SLBB domain; Region: SLBB; pfam10531 941638000305 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 941638000306 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 941638000307 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 941638000308 Catalytic site [active] 941638000309 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 941638000310 ribonuclease III; Reviewed; Region: rnc; PRK00102 941638000311 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 941638000312 dimerization interface [polypeptide binding]; other site 941638000313 active site 941638000314 metal binding site [ion binding]; metal-binding site 941638000315 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 941638000316 dsRNA binding site [nucleotide binding]; other site 941638000317 GTPase Era; Provisional; Region: era; PRK15494 941638000318 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638000319 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 941638000320 G1 box; other site 941638000321 GTP/Mg2+ binding site [chemical binding]; other site 941638000322 Switch I region; other site 941638000323 G2 box; other site 941638000324 Switch II region; other site 941638000325 G3 box; other site 941638000326 G4 box; other site 941638000327 G5 box; other site 941638000328 KH domain; Region: KH_2; pfam07650 941638000329 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 941638000330 active site 941638000331 putative DNA-binding cleft [nucleotide binding]; other site 941638000332 dimer interface [polypeptide binding]; other site 941638000333 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 941638000334 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 941638000335 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 941638000336 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 941638000337 AAA domain; Region: AAA_31; pfam13614 941638000338 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 941638000339 Walker A motif; other site 941638000340 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 941638000341 HflK protein; Region: hflK; TIGR01933 941638000342 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 941638000343 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 941638000344 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 941638000345 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 941638000346 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 941638000347 protein binding site [polypeptide binding]; other site 941638000348 hypothetical protein; Validated; Region: PRK01415 941638000349 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 941638000350 active site residue [active] 941638000351 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 941638000352 Iron-sulfur protein interface; other site 941638000353 proximal quinone binding site [chemical binding]; other site 941638000354 SdhD (CybS) interface [polypeptide binding]; other site 941638000355 proximal heme binding site [chemical binding]; other site 941638000356 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 941638000357 putative SdhC subunit interface [polypeptide binding]; other site 941638000358 putative proximal heme binding site [chemical binding]; other site 941638000359 putative Iron-sulfur protein interface [polypeptide binding]; other site 941638000360 putative proximal quinone binding site; other site 941638000361 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 941638000362 L-aspartate oxidase; Provisional; Region: PRK06175 941638000363 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 941638000364 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 941638000365 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 941638000366 dimer interface [polypeptide binding]; other site 941638000367 conserved gate region; other site 941638000368 putative PBP binding loops; other site 941638000369 ABC-ATPase subunit interface; other site 941638000370 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 941638000371 S17 interaction site [polypeptide binding]; other site 941638000372 S8 interaction site; other site 941638000373 16S rRNA interaction site [nucleotide binding]; other site 941638000374 streptomycin interaction site [chemical binding]; other site 941638000375 23S rRNA interaction site [nucleotide binding]; other site 941638000376 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 941638000377 30S ribosomal protein S7; Validated; Region: PRK05302 941638000378 elongation factor G; Reviewed; Region: PRK00007 941638000379 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 941638000380 G1 box; other site 941638000381 putative GEF interaction site [polypeptide binding]; other site 941638000382 GTP/Mg2+ binding site [chemical binding]; other site 941638000383 Switch I region; other site 941638000384 G2 box; other site 941638000385 G3 box; other site 941638000386 Switch II region; other site 941638000387 G4 box; other site 941638000388 G5 box; other site 941638000389 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 941638000390 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 941638000391 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 941638000392 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 941638000393 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 941638000394 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 941638000395 putative homodimer interface [polypeptide binding]; other site 941638000396 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 941638000397 heterodimer interface [polypeptide binding]; other site 941638000398 homodimer interface [polypeptide binding]; other site 941638000399 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 941638000400 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 941638000401 23S rRNA interface [nucleotide binding]; other site 941638000402 putative thiostrepton binding site; other site 941638000403 L7/L12 interface [polypeptide binding]; other site 941638000404 L25 interface [polypeptide binding]; other site 941638000405 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 941638000406 mRNA/rRNA interface [nucleotide binding]; other site 941638000407 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 941638000408 23S rRNA interface [nucleotide binding]; other site 941638000409 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 941638000410 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 941638000411 core dimer interface [polypeptide binding]; other site 941638000412 peripheral dimer interface [polypeptide binding]; other site 941638000413 L10 interface [polypeptide binding]; other site 941638000414 L11 interface [polypeptide binding]; other site 941638000415 putative EF-Tu interaction site [polypeptide binding]; other site 941638000416 putative EF-G interaction site [polypeptide binding]; other site 941638000417 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 941638000418 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 941638000419 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 941638000420 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 941638000421 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 941638000422 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 941638000423 RPB3 interaction site [polypeptide binding]; other site 941638000424 RPB1 interaction site [polypeptide binding]; other site 941638000425 RPB11 interaction site [polypeptide binding]; other site 941638000426 RPB10 interaction site [polypeptide binding]; other site 941638000427 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 941638000428 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 941638000429 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 941638000430 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 941638000431 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 941638000432 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 941638000433 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 941638000434 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 941638000435 DNA binding site [nucleotide binding] 941638000436 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 941638000437 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 941638000438 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638000439 multifunctional aminopeptidase A; Provisional; Region: PRK00913 941638000440 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 941638000441 interface (dimer of trimers) [polypeptide binding]; other site 941638000442 Substrate-binding/catalytic site; other site 941638000443 Zn-binding sites [ion binding]; other site 941638000444 ATPase MipZ; Region: MipZ; pfam09140 941638000445 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 941638000446 P-loop; other site 941638000447 Magnesium ion binding site [ion binding]; other site 941638000448 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 941638000449 Magnesium ion binding site [ion binding]; other site 941638000450 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 941638000451 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 941638000452 dimer interface [polypeptide binding]; other site 941638000453 anticodon binding site; other site 941638000454 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 941638000455 homodimer interface [polypeptide binding]; other site 941638000456 motif 1; other site 941638000457 active site 941638000458 motif 2; other site 941638000459 GAD domain; Region: GAD; pfam02938 941638000460 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 941638000461 active site 941638000462 motif 3; other site 941638000463 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 941638000464 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 941638000465 dihydrodipicolinate reductase; Provisional; Region: PRK00048 941638000466 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 941638000467 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 941638000468 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 941638000469 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 941638000470 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 941638000471 substrate binding pocket [chemical binding]; other site 941638000472 membrane-bound complex binding site; other site 941638000473 hinge residues; other site 941638000474 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 941638000475 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 941638000476 GatB domain; Region: GatB_Yqey; smart00845 941638000477 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 941638000478 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 941638000479 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 941638000480 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 941638000481 ribosome recycling factor; Reviewed; Region: frr; PRK00083 941638000482 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 941638000483 hinge region; other site 941638000484 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 941638000485 putative nucleotide binding site [chemical binding]; other site 941638000486 uridine monophosphate binding site [chemical binding]; other site 941638000487 homohexameric interface [polypeptide binding]; other site 941638000488 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 941638000489 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 941638000490 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 941638000491 putative substrate translocation pore; other site 941638000492 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 941638000493 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 941638000494 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 941638000495 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 941638000496 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 941638000497 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 941638000498 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 941638000499 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 941638000500 Surface antigen; Region: Bac_surface_Ag; pfam01103 941638000501 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 941638000502 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 941638000503 active site 941638000504 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 941638000505 protein binding site [polypeptide binding]; other site 941638000506 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 941638000507 putative substrate binding region [chemical binding]; other site 941638000508 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 941638000509 putative RNA binding site [nucleotide binding]; other site 941638000510 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 941638000511 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 941638000512 S-adenosylmethionine binding site [chemical binding]; other site 941638000513 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 941638000514 putative coenzyme Q binding site [chemical binding]; other site 941638000515 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638000516 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 941638000517 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 941638000518 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 941638000519 RNA methyltransferase, RsmE family; Region: TIGR00046 941638000520 Uncharacterized conserved protein [Function unknown]; Region: COG2155 941638000521 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 941638000522 Protein export membrane protein; Region: SecD_SecF; cl14618 941638000523 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 941638000524 IHF dimer interface [polypeptide binding]; other site 941638000525 IHF - DNA interface [nucleotide binding]; other site 941638000526 DNA polymerase III subunit delta'; Validated; Region: PRK06581 941638000527 signal recognition particle protein; Provisional; Region: PRK10867 941638000528 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 941638000529 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 941638000530 P loop; other site 941638000531 GTP binding site [chemical binding]; other site 941638000532 Signal peptide binding domain; Region: SRP_SPB; pfam02978 941638000533 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 941638000534 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 941638000535 FeS/SAM binding site; other site 941638000536 HemN C-terminal domain; Region: HemN_C; pfam06969 941638000537 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 941638000538 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 941638000539 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 941638000540 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 941638000541 active site 941638000542 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 941638000543 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 941638000544 E3 interaction surface; other site 941638000545 lipoyl attachment site [posttranslational modification]; other site 941638000546 e3 binding domain; Region: E3_binding; pfam02817 941638000547 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 941638000548 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 941638000549 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 941638000550 TPP-binding site [chemical binding]; other site 941638000551 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 941638000552 dimer interface [polypeptide binding]; other site 941638000553 PYR/PP interface [polypeptide binding]; other site 941638000554 TPP binding site [chemical binding]; other site 941638000555 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 941638000556 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 941638000557 active site 941638000558 Zn binding site [ion binding]; other site 941638000559 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 941638000560 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 941638000561 Walker A/P-loop; other site 941638000562 ATP binding site [chemical binding]; other site 941638000563 Q-loop/lid; other site 941638000564 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 941638000565 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 941638000566 ABC transporter signature motif; other site 941638000567 Walker B; other site 941638000568 D-loop; other site 941638000569 H-loop/switch region; other site 941638000570 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 941638000571 Tetratricopeptide repeat; Region: TPR_6; pfam13174 941638000572 ChaB; Region: ChaB; cl01887 941638000573 chaperone protein DnaJ; Provisional; Region: PRK14300 941638000574 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 941638000575 HSP70 interaction site [polypeptide binding]; other site 941638000576 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 941638000577 substrate binding site [polypeptide binding]; other site 941638000578 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 941638000579 Zn binding sites [ion binding]; other site 941638000580 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 941638000581 dimer interface [polypeptide binding]; other site 941638000582 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 941638000583 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 941638000584 nucleotide binding site [chemical binding]; other site 941638000585 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 941638000586 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 941638000587 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 941638000588 Lipopolysaccharide-assembly; Region: LptE; cl01125 941638000589 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 941638000590 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 941638000591 diiron binding motif [ion binding]; other site 941638000592 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 941638000593 Subunit III/VIIa interface [polypeptide binding]; other site 941638000594 Phospholipid binding site [chemical binding]; other site 941638000595 Subunit I/III interface [polypeptide binding]; other site 941638000596 Subunit III/VIb interface [polypeptide binding]; other site 941638000597 Subunit III/VIa interface; other site 941638000598 Subunit III/Vb interface [polypeptide binding]; other site 941638000599 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 941638000600 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 941638000601 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 941638000602 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 941638000603 trimer interface [polypeptide binding]; other site 941638000604 active site 941638000605 substrate binding site [chemical binding]; other site 941638000606 CoA binding site [chemical binding]; other site 941638000607 Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]; Region: PbpC; COG4953 941638000608 Transglycosylase; Region: Transgly; pfam00912 941638000609 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 941638000610 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 941638000611 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 941638000612 Ligand Binding Site [chemical binding]; other site 941638000613 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 941638000614 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 941638000615 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 941638000616 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 941638000617 catalytic loop [active] 941638000618 iron binding site [ion binding]; other site 941638000619 chaperone protein HscA; Provisional; Region: hscA; PRK01433 941638000620 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 941638000621 nucleotide binding site [chemical binding]; other site 941638000622 co-chaperone HscB; Provisional; Region: hscB; PRK01356 941638000623 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 941638000624 HSP70 interaction site [polypeptide binding]; other site 941638000625 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 941638000626 RNA/DNA hybrid binding site [nucleotide binding]; other site 941638000627 active site 941638000628 excinuclease ABC subunit B; Provisional; Region: PRK05298 941638000629 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 941638000630 ATP binding site [chemical binding]; other site 941638000631 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 941638000632 nucleotide binding region [chemical binding]; other site 941638000633 ATP-binding site [chemical binding]; other site 941638000634 Ultra-violet resistance protein B; Region: UvrB; pfam12344 941638000635 UvrB/uvrC motif; Region: UVR; pfam02151 941638000636 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 941638000637 GSH binding site [chemical binding]; other site 941638000638 catalytic residues [active] 941638000639 DNA gyrase subunit A; Validated; Region: PRK05560 941638000640 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 941638000641 CAP-like domain; other site 941638000642 active site 941638000643 primary dimer interface [polypeptide binding]; other site 941638000644 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 941638000645 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 941638000646 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 941638000647 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 941638000648 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 941638000649 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 941638000650 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 941638000651 active site 941638000652 catalytic residues [active] 941638000653 metal binding site [ion binding]; metal-binding site 941638000654 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 941638000655 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 941638000656 putative active site [active] 941638000657 substrate binding site [chemical binding]; other site 941638000658 putative cosubstrate binding site; other site 941638000659 catalytic site [active] 941638000660 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 941638000661 substrate binding site [chemical binding]; other site 941638000662 Protein of unknown function (DUF563); Region: DUF563; cl15705 941638000663 Predicted ATPase [General function prediction only]; Region: COG1485 941638000664 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 941638000665 Walker A motif; other site 941638000666 ATP binding site [chemical binding]; other site 941638000667 Walker B motif; other site 941638000668 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 941638000669 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 941638000670 potential frameshift: common BLAST hit: gi|350273268|ref|YP_004884581.1| ankyrin repeat 941638000671 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 941638000672 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 941638000673 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 941638000674 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638000675 Walker A/P-loop; other site 941638000676 ATP binding site [chemical binding]; other site 941638000677 Q-loop/lid; other site 941638000678 ABC transporter signature motif; other site 941638000679 Walker B; other site 941638000680 D-loop; other site 941638000681 H-loop/switch region; other site 941638000682 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 941638000683 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 941638000684 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 941638000685 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 941638000686 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 941638000687 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 941638000688 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 941638000689 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 941638000690 putative metal binding site; other site 941638000691 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 941638000692 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 941638000693 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 941638000694 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 941638000695 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 941638000696 ATP binding site [chemical binding]; other site 941638000697 active site 941638000698 substrate binding site [chemical binding]; other site 941638000699 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 941638000700 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 941638000701 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 941638000702 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 941638000703 active site 941638000704 dimer interface [polypeptide binding]; other site 941638000705 motif 1; other site 941638000706 motif 2; other site 941638000707 motif 3; other site 941638000708 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 941638000709 anticodon binding site; other site 941638000710 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 941638000711 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 941638000712 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 941638000713 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 941638000714 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 941638000715 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 941638000716 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 941638000717 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 941638000718 ATP binding site [chemical binding]; other site 941638000719 Mg2+ binding site [ion binding]; other site 941638000720 G-X-G motif; other site 941638000721 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 941638000722 anchoring element; other site 941638000723 dimer interface [polypeptide binding]; other site 941638000724 ATP binding site [chemical binding]; other site 941638000725 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 941638000726 active site 941638000727 metal binding site [ion binding]; metal-binding site 941638000728 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 941638000729 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 941638000730 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 941638000731 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 941638000732 protein binding site [polypeptide binding]; other site 941638000733 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 941638000734 Catalytic dyad [active] 941638000735 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 941638000736 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 941638000737 dimer interface [polypeptide binding]; other site 941638000738 phosphorylation site [posttranslational modification] 941638000739 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 941638000740 ATP binding site [chemical binding]; other site 941638000741 Mg2+ binding site [ion binding]; other site 941638000742 G-X-G motif; other site 941638000743 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 941638000744 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 941638000745 FOG: WD40-like repeat [Function unknown]; Region: COG1520 941638000746 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 941638000747 Trp docking motif [polypeptide binding]; other site 941638000748 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 941638000749 23S rRNA interface [nucleotide binding]; other site 941638000750 L3 interface [polypeptide binding]; other site 941638000751 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 941638000752 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cl00942 941638000753 DCoH dimer interaction site [polypeptide binding]; other site 941638000754 aromatic arch; other site 941638000755 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 941638000756 DCoH tetramer interaction site [polypeptide binding]; other site 941638000757 substrate binding site [chemical binding]; other site 941638000758 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 941638000759 putative active site [active] 941638000760 Ap4A binding site [chemical binding]; other site 941638000761 nudix motif; other site 941638000762 putative metal binding site [ion binding]; other site 941638000763 response regulator PleD; Reviewed; Region: pleD; PRK09581 941638000764 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 941638000765 active site 941638000766 phosphorylation site [posttranslational modification] 941638000767 intermolecular recognition site; other site 941638000768 dimerization interface [polypeptide binding]; other site 941638000769 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 941638000770 active site 941638000771 phosphorylation site [posttranslational modification] 941638000772 intermolecular recognition site; other site 941638000773 dimerization interface [polypeptide binding]; other site 941638000774 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 941638000775 metal binding site [ion binding]; metal-binding site 941638000776 active site 941638000777 I-site; other site 941638000778 elongation factor P; Validated; Region: PRK00529 941638000779 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 941638000780 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 941638000781 RNA binding site [nucleotide binding]; other site 941638000782 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 941638000783 RNA binding site [nucleotide binding]; other site 941638000784 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 941638000785 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 941638000786 active site 941638000787 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 941638000788 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 941638000789 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 941638000790 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 941638000791 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 941638000792 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 941638000793 HlyD family secretion protein; Region: HlyD_3; pfam13437 941638000794 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 941638000795 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 941638000796 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 941638000797 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 941638000798 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 941638000799 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 941638000800 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 941638000801 FAD binding domain; Region: FAD_binding_4; pfam01565 941638000802 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 941638000803 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 941638000804 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 941638000805 ATP-grasp domain; Region: ATP-grasp_4; cl17255 941638000806 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 941638000807 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 941638000808 Cell division protein FtsQ; Region: FtsQ; pfam03799 941638000809 cell division protein FtsA; Region: ftsA; TIGR01174 941638000810 Cell division protein FtsA; Region: FtsA; smart00842 941638000811 Cell division protein FtsA; Region: FtsA; pfam14450 941638000812 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 941638000813 Cytochrome c2 [Energy production and conversion]; Region: COG3474 941638000814 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 941638000815 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 941638000816 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 941638000817 RNA binding site [nucleotide binding]; other site 941638000818 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 941638000819 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 941638000820 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 941638000821 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 941638000822 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 941638000823 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 941638000824 RNA binding surface [nucleotide binding]; other site 941638000825 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 941638000826 active site 941638000827 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 941638000828 Beta-lactamase; Region: Beta-lactamase; pfam00144 941638000829 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 941638000830 putative catalytic site [active] 941638000831 putative phosphate binding site [ion binding]; other site 941638000832 active site 941638000833 metal binding site A [ion binding]; metal-binding site 941638000834 DNA binding site [nucleotide binding] 941638000835 putative AP binding site [nucleotide binding]; other site 941638000836 putative metal binding site B [ion binding]; other site 941638000837 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 941638000838 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 941638000839 tetramer interface [polypeptide binding]; other site 941638000840 TPP-binding site [chemical binding]; other site 941638000841 heterodimer interface [polypeptide binding]; other site 941638000842 phosphorylation loop region [posttranslational modification] 941638000843 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 941638000844 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 941638000845 alpha subunit interface [polypeptide binding]; other site 941638000846 TPP binding site [chemical binding]; other site 941638000847 heterodimer interface [polypeptide binding]; other site 941638000848 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 941638000849 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 941638000850 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 941638000851 G1 box; other site 941638000852 putative GEF interaction site [polypeptide binding]; other site 941638000853 GTP/Mg2+ binding site [chemical binding]; other site 941638000854 Switch I region; other site 941638000855 G2 box; other site 941638000856 G3 box; other site 941638000857 Switch II region; other site 941638000858 G4 box; other site 941638000859 G5 box; other site 941638000860 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 941638000861 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 941638000862 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 941638000863 isocitrate dehydrogenase; Validated; Region: PRK09222 941638000864 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 941638000865 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 941638000866 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 941638000867 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 941638000868 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 941638000869 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 941638000870 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 941638000871 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 941638000872 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 941638000873 [2Fe-2S] cluster binding site [ion binding]; other site 941638000874 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 941638000875 Qi binding site; other site 941638000876 cytochrome b; Provisional; Region: CYTB; MTH00191 941638000877 intrachain domain interface; other site 941638000878 interchain domain interface [polypeptide binding]; other site 941638000879 heme bH binding site [chemical binding]; other site 941638000880 heme bL binding site [chemical binding]; other site 941638000881 Qo binding site; other site 941638000882 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 941638000883 interchain domain interface [polypeptide binding]; other site 941638000884 intrachain domain interface; other site 941638000885 Qi binding site; other site 941638000886 Qo binding site; other site 941638000887 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 941638000888 Cytochrome c; Region: Cytochrom_C; cl11414 941638000889 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 941638000890 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 941638000891 putative dimer interface [polypeptide binding]; other site 941638000892 PCRF domain; Region: PCRF; pfam03462 941638000893 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 941638000894 RF-1 domain; Region: RF-1; pfam00472 941638000895 GTP-binding protein LepA; Provisional; Region: PRK05433 941638000896 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 941638000897 G1 box; other site 941638000898 putative GEF interaction site [polypeptide binding]; other site 941638000899 GTP/Mg2+ binding site [chemical binding]; other site 941638000900 Switch I region; other site 941638000901 G2 box; other site 941638000902 G3 box; other site 941638000903 Switch II region; other site 941638000904 G4 box; other site 941638000905 G5 box; other site 941638000906 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 941638000907 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 941638000908 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 941638000909 potential protein location (hypothetical protein Rsl_434 [Rickettsia slovaca 13-B]) that overlaps RNA (tRNA-N) 941638000910 Phage capsid family; Region: Phage_capsid; pfam05065 941638000911 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 941638000912 HD domain; Region: HD_4; pfam13328 941638000913 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638000914 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 941638000915 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 941638000916 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 941638000917 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 941638000918 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 941638000919 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 941638000920 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 941638000921 oligomeric interface; other site 941638000922 putative active site [active] 941638000923 homodimer interface [polypeptide binding]; other site 941638000924 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 941638000925 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 941638000926 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 941638000927 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 941638000928 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 941638000929 VirB7 interaction site; other site 941638000930 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 941638000931 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 941638000932 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 941638000933 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 941638000934 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 941638000935 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 941638000936 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 941638000937 Walker A motif; other site 941638000938 hexamer interface [polypeptide binding]; other site 941638000939 ATP binding site [chemical binding]; other site 941638000940 Walker B motif; other site 941638000941 type IV secretion system component VirD4; Provisional; Region: PRK13897 941638000942 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 941638000943 Walker A motif; other site 941638000944 ATP binding site [chemical binding]; other site 941638000945 Walker B motif; other site 941638000946 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 941638000947 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 941638000948 Phage-related protein [Function unknown]; Region: COG4695; cl01923 941638000949 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 941638000950 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 941638000951 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 941638000952 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 941638000953 active site 941638000954 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 941638000955 MutS domain I; Region: MutS_I; pfam01624 941638000956 MutS domain II; Region: MutS_II; pfam05188 941638000957 MutS domain III; Region: MutS_III; pfam05192 941638000958 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 941638000959 Walker A/P-loop; other site 941638000960 ATP binding site [chemical binding]; other site 941638000961 Q-loop/lid; other site 941638000962 ABC transporter signature motif; other site 941638000963 Walker B; other site 941638000964 D-loop; other site 941638000965 H-loop/switch region; other site 941638000966 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 941638000967 Peptidase family M23; Region: Peptidase_M23; pfam01551 941638000968 Protein of unknown function DUF45; Region: DUF45; pfam01863 941638000969 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 941638000970 translocation protein TolB; Provisional; Region: tolB; PRK05137 941638000971 TolB amino-terminal domain; Region: TolB_N; pfam04052 941638000972 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 941638000973 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 941638000974 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 941638000975 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 941638000976 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 941638000977 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 941638000978 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 941638000979 DNA binding residues [nucleotide binding] 941638000980 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 941638000981 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 941638000982 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 941638000983 Ligand Binding Site [chemical binding]; other site 941638000984 amino acid transporter; Region: 2A0306; TIGR00909 941638000985 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 941638000986 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 941638000987 dimer interface [polypeptide binding]; other site 941638000988 motif 1; other site 941638000989 active site 941638000990 motif 2; other site 941638000991 motif 3; other site 941638000992 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 941638000993 anticodon binding site; other site 941638000994 TolQ protein; Region: tolQ; TIGR02796 941638000995 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 941638000996 TolR protein; Region: tolR; TIGR02801 941638000997 Gram-negative bacterial tonB protein; Region: TonB; cl10048 941638000998 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 941638000999 HD domain; Region: HD_4; pfam13328 941638001000 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 941638001001 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638001002 putative substrate translocation pore; other site 941638001003 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 941638001004 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 941638001005 HlyD family secretion protein; Region: HlyD_3; pfam13437 941638001006 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 941638001007 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 941638001008 Walker A/P-loop; other site 941638001009 ATP binding site [chemical binding]; other site 941638001010 Q-loop/lid; other site 941638001011 ABC transporter signature motif; other site 941638001012 Walker B; other site 941638001013 D-loop; other site 941638001014 H-loop/switch region; other site 941638001015 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 941638001016 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 941638001017 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 941638001018 nucleotide binding site/active site [active] 941638001019 HIT family signature motif; other site 941638001020 catalytic residue [active] 941638001021 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 941638001022 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 941638001023 active site 941638001024 HslU subunit interaction site [polypeptide binding]; other site 941638001025 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 941638001026 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 941638001027 Walker A motif; other site 941638001028 ATP binding site [chemical binding]; other site 941638001029 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 941638001030 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 941638001031 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 941638001032 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 941638001033 Lipid-A-disaccharide synthetase; Region: LpxB; pfam02684 941638001034 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 941638001035 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 941638001036 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 941638001037 dimerization interface [polypeptide binding]; other site 941638001038 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 941638001039 putative iron binding site [ion binding]; other site 941638001040 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 941638001041 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 941638001042 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 941638001043 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 941638001044 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 941638001045 HIGH motif; other site 941638001046 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 941638001047 active site 941638001048 KMSKS motif; other site 941638001049 DNA topoisomerase I; Validated; Region: PRK06599 941638001050 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 941638001051 active site 941638001052 interdomain interaction site; other site 941638001053 putative metal-binding site [ion binding]; other site 941638001054 nucleotide binding site [chemical binding]; other site 941638001055 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 941638001056 domain I; other site 941638001057 DNA binding groove [nucleotide binding] 941638001058 phosphate binding site [ion binding]; other site 941638001059 domain II; other site 941638001060 domain III; other site 941638001061 nucleotide binding site [chemical binding]; other site 941638001062 catalytic site [active] 941638001063 domain IV; other site 941638001064 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 941638001065 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 941638001066 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 941638001067 dimer interface [polypeptide binding]; other site 941638001068 decamer (pentamer of dimers) interface [polypeptide binding]; other site 941638001069 catalytic triad [active] 941638001070 peroxidatic and resolving cysteines [active] 941638001071 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 941638001072 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 941638001073 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 941638001074 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 941638001075 Sulfatase; Region: Sulfatase; pfam00884 941638001076 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 941638001077 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 941638001078 sequence-specific DNA binding site [nucleotide binding]; other site 941638001079 salt bridge; other site 941638001080 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 941638001081 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 941638001082 NADP binding site [chemical binding]; other site 941638001083 active site 941638001084 putative substrate binding site [chemical binding]; other site 941638001085 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 941638001086 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 941638001087 NAD(P) binding site [chemical binding]; other site 941638001088 homodimer interface [polypeptide binding]; other site 941638001089 substrate binding site [chemical binding]; other site 941638001090 active site 941638001091 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 941638001092 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 941638001093 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 941638001094 active site 941638001095 homodimer interface [polypeptide binding]; other site 941638001096 Methyltransferase domain; Region: Methyltransf_31; pfam13847 941638001097 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 941638001098 S-adenosylmethionine binding site [chemical binding]; other site 941638001099 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 941638001100 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 941638001101 active site 941638001102 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 941638001103 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 941638001104 active site 941638001105 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 941638001106 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 941638001107 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 941638001108 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 941638001109 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 941638001110 catalytic site [active] 941638001111 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 941638001112 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 941638001113 putative ADP-binding pocket [chemical binding]; other site 941638001114 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 941638001115 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 941638001116 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 941638001117 RNA binding surface [nucleotide binding]; other site 941638001118 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 941638001119 UbiA prenyltransferase family; Region: UbiA; pfam01040 941638001120 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 941638001121 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 941638001122 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 941638001123 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 941638001124 TPR motif; other site 941638001125 binding surface 941638001126 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 941638001127 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 941638001128 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 941638001129 RimM N-terminal domain; Region: RimM; pfam01782 941638001130 PRC-barrel domain; Region: PRC; pfam05239 941638001131 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 941638001132 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 941638001133 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 941638001134 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 941638001135 active site 941638001136 DNA binding site [nucleotide binding] 941638001137 Haemolytic domain; Region: Haemolytic; cl00506 941638001138 NADH dehydrogenase subunit E; Validated; Region: PRK07539 941638001139 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 941638001140 putative dimer interface [polypeptide binding]; other site 941638001141 [2Fe-2S] cluster binding site [ion binding]; other site 941638001142 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 941638001143 GIY-YIG motif/motif A; other site 941638001144 putative active site [active] 941638001145 putative metal binding site [ion binding]; other site 941638001146 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 941638001147 NADH dehydrogenase subunit D; Validated; Region: PRK06075 941638001148 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 941638001149 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 941638001150 NADH dehydrogenase subunit B; Validated; Region: PRK06411 941638001151 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 941638001152 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 941638001153 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 941638001154 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 941638001155 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 941638001156 active site 941638001157 DNA binding site [nucleotide binding] 941638001158 Int/Topo IB signature motif; other site 941638001159 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 941638001160 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 941638001161 NAD binding site [chemical binding]; other site 941638001162 homotetramer interface [polypeptide binding]; other site 941638001163 homodimer interface [polypeptide binding]; other site 941638001164 substrate binding site [chemical binding]; other site 941638001165 active site 941638001166 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 941638001167 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 941638001168 putative active site [active] 941638001169 catalytic triad [active] 941638001170 putative dimer interface [polypeptide binding]; other site 941638001171 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 941638001172 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 941638001173 amidase catalytic site [active] 941638001174 Zn binding residues [ion binding]; other site 941638001175 substrate binding site [chemical binding]; other site 941638001176 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 941638001177 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 941638001178 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 941638001179 TM-ABC transporter signature motif; other site 941638001180 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 941638001181 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 941638001182 Walker A/P-loop; other site 941638001183 ATP binding site [chemical binding]; other site 941638001184 Q-loop/lid; other site 941638001185 ABC transporter signature motif; other site 941638001186 Walker B; other site 941638001187 D-loop; other site 941638001188 H-loop/switch region; other site 941638001189 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 941638001190 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cl02529 941638001191 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 941638001192 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 941638001193 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 941638001194 active site 941638001195 HIGH motif; other site 941638001196 KMSKS motif; other site 941638001197 Predicted permeases [General function prediction only]; Region: COG0679 941638001198 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 941638001199 Malic enzyme, N-terminal domain; Region: malic; pfam00390 941638001200 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 941638001201 putative NAD(P) binding site [chemical binding]; other site 941638001202 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 941638001203 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 941638001204 putative active site [active] 941638001205 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 941638001206 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638001207 malate dehydrogenase; Reviewed; Region: PRK06223 941638001208 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 941638001209 NAD(P) binding site [chemical binding]; other site 941638001210 dimer interface [polypeptide binding]; other site 941638001211 tetramer (dimer of dimers) interface [polypeptide binding]; other site 941638001212 substrate binding site [chemical binding]; other site 941638001213 TLC ATP/ADP transporter; Region: TLC; pfam03219 941638001214 CTP synthetase; Validated; Region: pyrG; PRK05380 941638001215 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 941638001216 Catalytic site [active] 941638001217 active site 941638001218 UTP binding site [chemical binding]; other site 941638001219 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 941638001220 active site 941638001221 putative oxyanion hole; other site 941638001222 catalytic triad [active] 941638001223 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 941638001224 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 941638001225 Ligand binding site; other site 941638001226 oligomer interface; other site 941638001227 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 941638001228 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 941638001229 nudix motif; other site 941638001230 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 941638001231 GTP cyclohydrolase I; Provisional; Region: PLN03044 941638001232 active site 941638001233 prolyl-tRNA synthetase; Provisional; Region: PRK12325 941638001234 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 941638001235 dimer interface [polypeptide binding]; other site 941638001236 motif 1; other site 941638001237 active site 941638001238 motif 2; other site 941638001239 motif 3; other site 941638001240 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 941638001241 anticodon binding site; other site 941638001242 Fic family protein [Function unknown]; Region: COG3177 941638001243 Fic/DOC family; Region: Fic; pfam02661 941638001244 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 941638001245 RuvA N terminal domain; Region: RuvA_N; pfam01330 941638001246 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 941638001247 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 941638001248 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 941638001249 Walker A motif; other site 941638001250 ATP binding site [chemical binding]; other site 941638001251 Walker B motif; other site 941638001252 arginine finger; other site 941638001253 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 941638001254 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 941638001255 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 941638001256 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638001257 Walker A/P-loop; other site 941638001258 ATP binding site [chemical binding]; other site 941638001259 Q-loop/lid; other site 941638001260 ABC transporter signature motif; other site 941638001261 Walker B; other site 941638001262 D-loop; other site 941638001263 H-loop/switch region; other site 941638001264 muropeptide transporter; Reviewed; Region: ampG; PRK11902 941638001265 muropeptide transporter; Validated; Region: ampG; cl17669 941638001266 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 941638001267 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 941638001268 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638001269 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 941638001270 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 941638001271 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 941638001272 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 941638001273 BON domain; Region: BON; pfam04972 941638001274 BON domain; Region: BON; pfam04972 941638001275 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 941638001276 Iron permease FTR1 family; Region: FTR1; cl00475 941638001277 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 941638001278 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 941638001279 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 941638001280 Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion...; Region: 3,4-PCD; cd03459 941638001281 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 941638001282 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 941638001283 catalytic residues [active] 941638001284 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 941638001285 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 941638001286 tandem repeat interface [polypeptide binding]; other site 941638001287 oligomer interface [polypeptide binding]; other site 941638001288 active site residues [active] 941638001289 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 941638001290 trimer interface [polypeptide binding]; other site 941638001291 active site 941638001292 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 941638001293 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 941638001294 N-acetyl-D-glucosamine binding site [chemical binding]; other site 941638001295 catalytic residue [active] 941638001296 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 941638001297 dimer interface [polypeptide binding]; other site 941638001298 catalytic triad [active] 941638001299 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 941638001300 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 941638001301 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 941638001302 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 941638001303 catalytic triad [active] 941638001304 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 941638001305 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 941638001306 Subunit I/III interface [polypeptide binding]; other site 941638001307 D-pathway; other site 941638001308 Subunit I/VIIc interface [polypeptide binding]; other site 941638001309 Subunit I/IV interface [polypeptide binding]; other site 941638001310 Subunit I/II interface [polypeptide binding]; other site 941638001311 Low-spin heme (heme a) binding site [chemical binding]; other site 941638001312 Subunit I/VIIa interface [polypeptide binding]; other site 941638001313 Subunit I/VIa interface [polypeptide binding]; other site 941638001314 Dimer interface; other site 941638001315 Putative water exit pathway; other site 941638001316 Binuclear center (heme a3/CuB) [ion binding]; other site 941638001317 K-pathway; other site 941638001318 Subunit I/Vb interface [polypeptide binding]; other site 941638001319 Putative proton exit pathway; other site 941638001320 Subunit I/VIb interface; other site 941638001321 Subunit I/VIc interface [polypeptide binding]; other site 941638001322 Electron transfer pathway; other site 941638001323 Subunit I/VIIIb interface [polypeptide binding]; other site 941638001324 Subunit I/VIIb interface [polypeptide binding]; other site 941638001325 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 941638001326 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 941638001327 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 941638001328 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638001329 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 941638001330 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 941638001331 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 941638001332 putative peptidase; Provisional; Region: PRK11649 941638001333 Peptidase family M23; Region: Peptidase_M23; pfam01551 941638001334 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 941638001335 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 941638001336 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 941638001337 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 941638001338 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 941638001339 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 941638001340 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 941638001341 cell division protein FtsW; Region: ftsW; TIGR02614 941638001342 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 941638001343 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 941638001344 active site 941638001345 homodimer interface [polypeptide binding]; other site 941638001346 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 941638001347 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 941638001348 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 941638001349 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 941638001350 diaminopimelate epimerase; Region: DapF; TIGR00652 941638001351 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 941638001352 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 941638001353 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 941638001354 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 941638001355 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 941638001356 FeS/SAM binding site; other site 941638001357 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 941638001358 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 941638001359 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 941638001360 dimer interface [polypeptide binding]; other site 941638001361 motif 1; other site 941638001362 active site 941638001363 motif 2; other site 941638001364 motif 3; other site 941638001365 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 941638001366 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 941638001367 putative tRNA-binding site [nucleotide binding]; other site 941638001368 B3/4 domain; Region: B3_4; pfam03483 941638001369 tRNA synthetase B5 domain; Region: B5; smart00874 941638001370 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 941638001371 dimer interface [polypeptide binding]; other site 941638001372 motif 1; other site 941638001373 motif 3; other site 941638001374 motif 2; other site 941638001375 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 941638001376 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 941638001377 DNA polymerase III subunit beta; Validated; Region: PRK05643 941638001378 putative DNA binding surface [nucleotide binding]; other site 941638001379 dimer interface [polypeptide binding]; other site 941638001380 beta-clamp/clamp loader binding surface; other site 941638001381 beta-clamp/translesion DNA polymerase binding surface; other site 941638001382 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 941638001383 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 941638001384 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638001385 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 941638001386 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 941638001387 catalytic site [active] 941638001388 putative active site [active] 941638001389 putative substrate binding site [chemical binding]; other site 941638001390 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 941638001391 Septum formation initiator; Region: DivIC; pfam04977 941638001392 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 941638001393 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 941638001394 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 941638001395 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 941638001396 catalytic residue [active] 941638001397 putative FPP diphosphate binding site; other site 941638001398 putative FPP binding hydrophobic cleft; other site 941638001399 dimer interface [polypeptide binding]; other site 941638001400 putative IPP diphosphate binding site; other site 941638001401 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 941638001402 HAMP domain; Region: HAMP; pfam00672 941638001403 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 941638001404 dimer interface [polypeptide binding]; other site 941638001405 phosphorylation site [posttranslational modification] 941638001406 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 941638001407 ATP binding site [chemical binding]; other site 941638001408 Mg2+ binding site [ion binding]; other site 941638001409 G-X-G motif; other site 941638001410 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 941638001411 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 941638001412 active site 941638001413 phosphorylation site [posttranslational modification] 941638001414 intermolecular recognition site; other site 941638001415 dimerization interface [polypeptide binding]; other site 941638001416 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 941638001417 DNA binding site [nucleotide binding] 941638001418 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 941638001419 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 941638001420 homodimer interface [polypeptide binding]; other site 941638001421 substrate-cofactor binding pocket; other site 941638001422 catalytic residue [active] 941638001423 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 941638001424 dihydrodipicolinate synthase; Region: dapA; TIGR00674 941638001425 dimer interface [polypeptide binding]; other site 941638001426 active site 941638001427 catalytic residue [active] 941638001428 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 941638001429 SmpB-tmRNA interface; other site 941638001430 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 941638001431 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 941638001432 catalytic residues [active] 941638001433 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 941638001434 CoA binding domain; Region: CoA_binding; pfam02629 941638001435 CoA-ligase; Region: Ligase_CoA; pfam00549 941638001436 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 941638001437 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 941638001438 CoA-ligase; Region: Ligase_CoA; pfam00549 941638001439 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 941638001440 putative active site [active] 941638001441 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 941638001442 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 941638001443 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 941638001444 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 941638001445 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 941638001446 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 941638001447 Predicted membrane protein [Function unknown]; Region: COG1238 941638001448 Predicted membrane protein/domain [Function unknown]; Region: COG1714 941638001449 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 941638001450 RecR protein; Region: RecR; pfam02132 941638001451 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 941638001452 putative active site [active] 941638001453 putative metal-binding site [ion binding]; other site 941638001454 tetramer interface [polypeptide binding]; other site 941638001455 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 941638001456 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 941638001457 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 941638001458 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 941638001459 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 941638001460 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 941638001461 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 941638001462 Predicted permeases [General function prediction only]; Region: COG0679 941638001463 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 941638001464 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 941638001465 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 941638001466 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 941638001467 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 941638001468 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 941638001469 active site 941638001470 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 941638001471 Part of AAA domain; Region: AAA_19; pfam13245 941638001472 Family description; Region: UvrD_C_2; pfam13538 941638001473 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 941638001474 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 941638001475 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 941638001476 tetramer interface [polypeptide binding]; other site 941638001477 pyridoxal 5'-phosphate binding site [chemical binding]; other site 941638001478 catalytic residue [active] 941638001479 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 941638001480 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 941638001481 Walker A motif; other site 941638001482 ATP binding site [chemical binding]; other site 941638001483 Walker B motif; other site 941638001484 arginine finger; other site 941638001485 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 941638001486 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 941638001487 30S subunit binding site; other site 941638001488 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 941638001489 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 941638001490 trimer interface [polypeptide binding]; other site 941638001491 putative metal binding site [ion binding]; other site 941638001492 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 941638001493 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 941638001494 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 941638001495 homodimer interface [polypeptide binding]; other site 941638001496 NADP binding site [chemical binding]; other site 941638001497 substrate binding site [chemical binding]; other site 941638001498 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 941638001499 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 941638001500 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 941638001501 Spore Coat Protein U domain; Region: SCPU; pfam05229 941638001502 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 941638001503 Class I ribonucleotide reductase; Region: RNR_I; cd01679 941638001504 active site 941638001505 dimer interface [polypeptide binding]; other site 941638001506 catalytic residues [active] 941638001507 effector binding site; other site 941638001508 R2 peptide binding site; other site 941638001509 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 941638001510 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 941638001511 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 941638001512 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 941638001513 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 941638001514 active site 941638001515 substrate binding site [chemical binding]; other site 941638001516 metal binding site [ion binding]; metal-binding site 941638001517 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 941638001518 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638001519 Walker A/P-loop; other site 941638001520 ATP binding site [chemical binding]; other site 941638001521 Q-loop/lid; other site 941638001522 ABC transporter signature motif; other site 941638001523 Walker B; other site 941638001524 D-loop; other site 941638001525 H-loop/switch region; other site 941638001526 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638001527 OstA-like protein; Region: OstA; pfam03968 941638001528 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 941638001529 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 941638001530 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 941638001531 putative active site [active] 941638001532 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 941638001533 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 941638001534 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 941638001535 oligomer interface [polypeptide binding]; other site 941638001536 RNA binding site [nucleotide binding]; other site 941638001537 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 941638001538 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 941638001539 RNase E interface [polypeptide binding]; other site 941638001540 trimer interface [polypeptide binding]; other site 941638001541 active site 941638001542 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 941638001543 putative nucleic acid binding region [nucleotide binding]; other site 941638001544 G-X-X-G motif; other site 941638001545 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 941638001546 RNA binding site [nucleotide binding]; other site 941638001547 domain interface; other site 941638001548 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 941638001549 16S/18S rRNA binding site [nucleotide binding]; other site 941638001550 S13e-L30e interaction site [polypeptide binding]; other site 941638001551 25S rRNA binding site [nucleotide binding]; other site 941638001552 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 941638001553 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 941638001554 RNA binding site [nucleotide binding]; other site 941638001555 active site 941638001556 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638001557 TLC ATP/ADP transporter; Region: TLC; pfam03219 941638001558 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 941638001559 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 941638001560 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 941638001561 non-specific DNA binding site [nucleotide binding]; other site 941638001562 salt bridge; other site 941638001563 sequence-specific DNA binding site [nucleotide binding]; other site 941638001564 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 941638001565 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 941638001566 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 941638001567 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 941638001568 uncharacterized protein, YfiH family; Region: TIGR00726 941638001569 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 941638001570 active site 941638001571 catalytic residues [active] 941638001572 metal binding site [ion binding]; metal-binding site 941638001573 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 941638001574 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 941638001575 putative active site [active] 941638001576 homotetrameric interface [polypeptide binding]; other site 941638001577 metal binding site [ion binding]; metal-binding site 941638001578 hypothetical protein; Provisional; Region: PRK06661 941638001579 intersubunit interface [polypeptide binding]; other site 941638001580 active site 941638001581 Zn2+ binding site [ion binding]; other site 941638001582 pyruvate phosphate dikinase; Provisional; Region: PRK09279 941638001583 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 941638001584 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 941638001585 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 941638001586 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 941638001587 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 941638001588 GSH binding site (G-site) [chemical binding]; other site 941638001589 C-terminal domain interface [polypeptide binding]; other site 941638001590 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 941638001591 N-terminal domain interface [polypeptide binding]; other site 941638001592 dimer interface [polypeptide binding]; other site 941638001593 substrate binding pocket (H-site) [chemical binding]; other site 941638001594 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 941638001595 conserved cys residue [active] 941638001596 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 941638001597 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 941638001598 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 941638001599 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 941638001600 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 941638001601 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 941638001602 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 941638001603 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 941638001604 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 941638001605 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 941638001606 Predicted membrane protein [Function unknown]; Region: COG5346 941638001607 translation initiation factor IF-3; Region: infC; TIGR00168 941638001608 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 941638001609 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 941638001610 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 941638001611 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 941638001612 E3 interaction surface; other site 941638001613 lipoyl attachment site [posttranslational modification]; other site 941638001614 e3 binding domain; Region: E3_binding; pfam02817 941638001615 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 941638001616 peptide chain release factor 1; Validated; Region: prfA; PRK00591 941638001617 This domain is found in peptide chain release factors; Region: PCRF; smart00937 941638001618 RF-1 domain; Region: RF-1; pfam00472 941638001619 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 941638001620 DHH family; Region: DHH; pfam01368 941638001621 DHHA1 domain; Region: DHHA1; pfam02272 941638001622 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 941638001623 S-adenosylmethionine binding site [chemical binding]; other site 941638001624 Methyltransferase domain; Region: Methyltransf_31; pfam13847 941638001625 transcription termination factor Rho; Provisional; Region: rho; PRK09376 941638001626 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 941638001627 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 941638001628 RNA binding site [nucleotide binding]; other site 941638001629 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 941638001630 multimer interface [polypeptide binding]; other site 941638001631 Walker A motif; other site 941638001632 ATP binding site [chemical binding]; other site 941638001633 Walker B motif; other site 941638001634 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 941638001635 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 941638001636 tandem repeat interface [polypeptide binding]; other site 941638001637 oligomer interface [polypeptide binding]; other site 941638001638 active site residues [active] 941638001639 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 941638001640 IHF - DNA interface [nucleotide binding]; other site 941638001641 IHF dimer interface [polypeptide binding]; other site 941638001642 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 941638001643 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 941638001644 non-specific DNA binding site [nucleotide binding]; other site 941638001645 salt bridge; other site 941638001646 sequence-specific DNA binding site [nucleotide binding]; other site 941638001647 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 941638001648 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 941638001649 CMP-binding site; other site 941638001650 The sites determining sugar specificity; other site 941638001651 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 941638001652 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 941638001653 RNA binding site [nucleotide binding]; other site 941638001654 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 941638001655 RNA binding site [nucleotide binding]; other site 941638001656 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 941638001657 RNA binding site [nucleotide binding]; other site 941638001658 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 941638001659 RNA binding site [nucleotide binding]; other site 941638001660 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 941638001661 RNA binding site [nucleotide binding]; other site 941638001662 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 941638001663 RNA binding site [nucleotide binding]; other site 941638001664 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 941638001665 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 941638001666 oligomer interface [polypeptide binding]; other site 941638001667 active site residues [active] 941638001668 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 941638001669 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 941638001670 homotetramer interface [polypeptide binding]; other site 941638001671 FMN binding site [chemical binding]; other site 941638001672 homodimer contacts [polypeptide binding]; other site 941638001673 putative active site [active] 941638001674 putative substrate binding site [chemical binding]; other site 941638001675 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 941638001676 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 941638001677 Coenzyme A binding pocket [chemical binding]; other site 941638001678 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 941638001679 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 941638001680 Transcriptional regulator; Region: Rrf2; cl17282 941638001681 Rrf2 family protein; Region: rrf2_super; TIGR00738 941638001682 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 941638001683 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 941638001684 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 941638001685 catalytic residue [active] 941638001686 cysteine desulfurase; Provisional; Region: PRK14012 941638001687 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 941638001688 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 941638001689 catalytic residue [active] 941638001690 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 941638001691 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 941638001692 trimerization site [polypeptide binding]; other site 941638001693 active site 941638001694 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 941638001695 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 941638001696 arginine:agmatin antiporter; Provisional; Region: PRK10644 941638001697 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 941638001698 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 941638001699 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 941638001700 active site 941638001701 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 941638001702 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 941638001703 substrate binding pocket [chemical binding]; other site 941638001704 chain length determination region; other site 941638001705 substrate-Mg2+ binding site; other site 941638001706 catalytic residues [active] 941638001707 aspartate-rich region 1; other site 941638001708 active site lid residues [active] 941638001709 aspartate-rich region 2; other site 941638001710 TLC ATP/ADP transporter; Region: TLC; pfam03219 941638001711 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 941638001712 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 941638001713 muropeptide transporter; Reviewed; Region: ampG; PRK11902 941638001714 AmpG-like permease; Region: 2A0125; TIGR00901 941638001715 Lysine efflux permease [General function prediction only]; Region: COG1279 941638001716 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 941638001717 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 941638001718 active site 941638001719 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 941638001720 HemY protein N-terminus; Region: HemY_N; pfam07219 941638001721 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 941638001722 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 941638001723 RelB antitoxin; Region: RelB; cl01171 941638001724 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 941638001725 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 941638001726 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 941638001727 putative acyl-acceptor binding pocket; other site 941638001728 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 941638001729 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 941638001730 active site 941638001731 HIGH motif; other site 941638001732 dimer interface [polypeptide binding]; other site 941638001733 KMSKS motif; other site 941638001734 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 941638001735 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 941638001736 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 941638001737 domain interfaces; other site 941638001738 active site 941638001739 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 941638001740 dimer interface [polypeptide binding]; other site 941638001741 catalytic triad [active] 941638001742 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 941638001743 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 941638001744 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 941638001745 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 941638001746 Uncharacterized conserved protein [Function unknown]; Region: COG1723 941638001747 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 941638001748 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 941638001749 catalytic site [active] 941638001750 putative active site [active] 941638001751 putative substrate binding site [chemical binding]; other site 941638001752 Helicase and RNase D C-terminal; Region: HRDC; smart00341 941638001753 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 941638001754 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 941638001755 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 941638001756 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 941638001757 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 941638001758 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 941638001759 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 941638001760 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 941638001761 S-adenosylmethionine binding site [chemical binding]; other site 941638001762 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 941638001763 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 941638001764 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 941638001765 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 941638001766 N-acetyl-D-glucosamine binding site [chemical binding]; other site 941638001767 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 941638001768 hypothetical protein; Validated; Region: PRK00110 941638001769 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 941638001770 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 941638001771 Substrate binding site; other site 941638001772 Mg++ binding site; other site 941638001773 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 941638001774 active site 941638001775 homodimer interface [polypeptide binding]; other site 941638001776 putative chemical substrate binding site [chemical binding]; other site 941638001777 metal binding site [ion binding]; metal-binding site 941638001778 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 941638001779 Coenzyme A binding pocket [chemical binding]; other site 941638001780 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 941638001781 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 941638001782 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 941638001783 dimer interface [polypeptide binding]; other site 941638001784 allosteric magnesium binding site [ion binding]; other site 941638001785 active site 941638001786 aspartate-rich active site metal binding site; other site 941638001787 Schiff base residues; other site 941638001788 primosome assembly protein PriA; Validated; Region: PRK05580 941638001789 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 941638001790 ATP binding site [chemical binding]; other site 941638001791 putative Mg++ binding site [ion binding]; other site 941638001792 helicase superfamily c-terminal domain; Region: HELICc; smart00490 941638001793 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 941638001794 Flavoprotein; Region: Flavoprotein; pfam02441 941638001795 replicative DNA helicase; Provisional; Region: PRK09165 941638001796 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 941638001797 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 941638001798 Walker A motif; other site 941638001799 ATP binding site [chemical binding]; other site 941638001800 Walker B motif; other site 941638001801 DNA binding loops [nucleotide binding] 941638001802 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 941638001803 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 941638001804 RNA binding surface [nucleotide binding]; other site 941638001805 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 941638001806 active site 941638001807 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 941638001808 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 941638001809 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 941638001810 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 941638001811 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 941638001812 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 941638001813 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 941638001814 S-adenosylmethionine binding site [chemical binding]; other site 941638001815 DNA repair protein RadA; Provisional; Region: PRK11823 941638001816 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 941638001817 Walker A motif/ATP binding site; other site 941638001818 ATP binding site [chemical binding]; other site 941638001819 Walker B motif; other site 941638001820 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 941638001821 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 941638001822 Recombination protein O N terminal; Region: RecO_N; pfam11967 941638001823 Recombination protein O C terminal; Region: RecO_C; pfam02565 941638001824 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 941638001825 Glycoprotease family; Region: Peptidase_M22; pfam00814 941638001826 translation initiation factor IF-2; Validated; Region: infB; PRK05306 941638001827 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 941638001828 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 941638001829 G1 box; other site 941638001830 putative GEF interaction site [polypeptide binding]; other site 941638001831 GTP/Mg2+ binding site [chemical binding]; other site 941638001832 Switch I region; other site 941638001833 G2 box; other site 941638001834 G3 box; other site 941638001835 Switch II region; other site 941638001836 G4 box; other site 941638001837 G5 box; other site 941638001838 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 941638001839 Translation-initiation factor 2; Region: IF-2; pfam11987 941638001840 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 941638001841 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 941638001842 NusA N-terminal domain; Region: NusA_N; pfam08529 941638001843 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 941638001844 RNA binding site [nucleotide binding]; other site 941638001845 homodimer interface [polypeptide binding]; other site 941638001846 NusA-like KH domain; Region: KH_5; pfam13184 941638001847 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 941638001848 G-X-X-G motif; other site 941638001849 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 941638001850 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 941638001851 Sm and related proteins; Region: Sm_like; cl00259 941638001852 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 941638001853 putative oligomer interface [polypeptide binding]; other site 941638001854 putative RNA binding site [nucleotide binding]; other site 941638001855 Predicted transcriptional regulator [Transcription]; Region: COG1959 941638001856 Transcriptional regulator; Region: Rrf2; cl17282 941638001857 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 941638001858 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 941638001859 RNA binding surface [nucleotide binding]; other site 941638001860 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 941638001861 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 941638001862 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 941638001863 active site 941638001864 HIGH motif; other site 941638001865 dimer interface [polypeptide binding]; other site 941638001866 KMSKS motif; other site 941638001867 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 941638001868 RNA binding surface [nucleotide binding]; other site 941638001869 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 941638001870 phosphoenolpyruvate synthase; Validated; Region: PRK06241 941638001871 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638001872 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 941638001873 MG2 domain; Region: A2M_N; pfam01835 941638001874 Alpha-2-macroglobulin family; Region: A2M; pfam00207 941638001875 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 941638001876 surface patch; other site 941638001877 thioester region; other site 941638001878 specificity defining residues; other site 941638001879 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 941638001880 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 941638001881 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638001882 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 941638001883 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 941638001884 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 941638001885 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 941638001886 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 941638001887 active site 941638001888 phosphorylation site [posttranslational modification] 941638001889 intermolecular recognition site; other site 941638001890 dimerization interface [polypeptide binding]; other site 941638001891 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 941638001892 Walker A motif; other site 941638001893 ATP binding site [chemical binding]; other site 941638001894 Walker B motif; other site 941638001895 arginine finger; other site 941638001896 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 941638001897 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 941638001898 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 941638001899 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 941638001900 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 941638001901 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 941638001902 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 941638001903 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 941638001904 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 941638001905 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 941638001906 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 941638001907 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 941638001908 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 941638001909 S-adenosylmethionine binding site [chemical binding]; other site 941638001910 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 941638001911 MraZ protein; Region: MraZ; pfam02381 941638001912 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 941638001913 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 941638001914 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 941638001915 Na binding site [ion binding]; other site 941638001916 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 941638001917 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 941638001918 GIY-YIG motif/motif A; other site 941638001919 active site 941638001920 catalytic site [active] 941638001921 putative DNA binding site [nucleotide binding]; other site 941638001922 metal binding site [ion binding]; metal-binding site 941638001923 UvrB/uvrC motif; Region: UVR; pfam02151 941638001924 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 941638001925 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 941638001926 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 941638001927 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 941638001928 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 941638001929 DNA binding site [nucleotide binding] 941638001930 active site 941638001931 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 941638001932 DEAD/DEAH box helicase; Region: DEAD; pfam00270 941638001933 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 941638001934 SEC-C motif; Region: SEC-C; pfam02810 941638001935 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 941638001936 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 941638001937 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 941638001938 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 941638001939 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 941638001940 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 941638001941 hinge; other site 941638001942 active site 941638001943 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 941638001944 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 941638001945 ATP binding site [chemical binding]; other site 941638001946 Mg2+ binding site [ion binding]; other site 941638001947 G-X-G motif; other site 941638001948 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 941638001949 anchoring element; other site 941638001950 dimer interface [polypeptide binding]; other site 941638001951 ATP binding site [chemical binding]; other site 941638001952 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 941638001953 active site 941638001954 putative metal-binding site [ion binding]; other site 941638001955 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 941638001956 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 941638001957 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 941638001958 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 941638001959 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 941638001960 MgtE intracellular N domain; Region: MgtE_N; pfam03448 941638001961 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 941638001962 Divalent cation transporter; Region: MgtE; pfam01769 941638001963 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 941638001964 HD domain; Region: HD_4; pfam13328 941638001965 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638001966 protein-export membrane protein SecD; Region: secD; TIGR01129 941638001967 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 941638001968 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 941638001969 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 941638001970 Cu(I) binding site [ion binding]; other site 941638001971 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 941638001972 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 941638001973 dimer interface [polypeptide binding]; other site 941638001974 substrate binding site [chemical binding]; other site 941638001975 metal binding sites [ion binding]; metal-binding site 941638001976 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638001977 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 941638001978 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 941638001979 TraX protein; Region: TraX; pfam05857 941638001980 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 941638001981 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 941638001982 ssDNA binding site; other site 941638001983 generic binding surface II; other site 941638001984 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 941638001985 ATP binding site [chemical binding]; other site 941638001986 putative Mg++ binding site [ion binding]; other site 941638001987 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 941638001988 nucleotide binding region [chemical binding]; other site 941638001989 ATP-binding site [chemical binding]; other site 941638001990 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 941638001991 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 941638001992 V-type ATP synthase subunit I; Validated; Region: PRK05771 941638001993 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 941638001994 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 941638001995 Mg++ binding site [ion binding]; other site 941638001996 putative catalytic motif [active] 941638001997 putative substrate binding site [chemical binding]; other site 941638001998 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 941638001999 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 941638002000 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 941638002001 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 941638002002 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 941638002003 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 941638002004 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 941638002005 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 941638002006 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 941638002007 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 941638002008 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 941638002009 ATP binding site [chemical binding]; other site 941638002010 putative Mg++ binding site [ion binding]; other site 941638002011 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 941638002012 nucleotide binding region [chemical binding]; other site 941638002013 ATP-binding site [chemical binding]; other site 941638002014 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 941638002015 Uncharacterized conserved protein [Function unknown]; Region: COG2938 941638002016 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 941638002017 active site residue [active] 941638002018 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 941638002019 DnaA N-terminal domain; Region: DnaA_N; pfam11638 941638002020 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 941638002021 Walker A motif; other site 941638002022 ATP binding site [chemical binding]; other site 941638002023 Walker B motif; other site 941638002024 arginine finger; other site 941638002025 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 941638002026 DnaA box-binding interface [nucleotide binding]; other site 941638002027 Patatin [General function prediction only]; Region: COG3621 941638002028 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 941638002029 active site 941638002030 nucleophile elbow; other site 941638002031 GTP-binding protein YchF; Reviewed; Region: PRK09601 941638002032 YchF GTPase; Region: YchF; cd01900 941638002033 G1 box; other site 941638002034 GTP/Mg2+ binding site [chemical binding]; other site 941638002035 Switch I region; other site 941638002036 G2 box; other site 941638002037 Switch II region; other site 941638002038 G3 box; other site 941638002039 G4 box; other site 941638002040 G5 box; other site 941638002041 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 941638002042 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 941638002043 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 941638002044 putative active site [active] 941638002045 catalytic residue [active] 941638002046 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 941638002047 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 941638002048 5S rRNA interface [nucleotide binding]; other site 941638002049 CTC domain interface [polypeptide binding]; other site 941638002050 L16 interface [polypeptide binding]; other site 941638002051 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 941638002052 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 941638002053 FeS/SAM binding site; other site 941638002054 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 941638002055 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 941638002056 23S rRNA binding site [nucleotide binding]; other site 941638002057 L21 binding site [polypeptide binding]; other site 941638002058 L13 binding site [polypeptide binding]; other site 941638002059 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 941638002060 ribonuclease P; Reviewed; Region: rnpA; PRK01492 941638002061 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 941638002062 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 941638002063 Cl binding site [ion binding]; other site 941638002064 oligomer interface [polypeptide binding]; other site 941638002065 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 941638002066 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 941638002067 dimerization interface [polypeptide binding]; other site 941638002068 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 941638002069 dimer interface [polypeptide binding]; other site 941638002070 phosphorylation site [posttranslational modification] 941638002071 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 941638002072 ATP binding site [chemical binding]; other site 941638002073 Mg2+ binding site [ion binding]; other site 941638002074 G-X-G motif; other site 941638002075 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 941638002076 Uncharacterized conserved protein [Function unknown]; Region: COG5590 941638002077 COQ9; Region: COQ9; pfam08511 941638002078 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 941638002079 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 941638002080 HIGH motif; other site 941638002081 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 941638002082 active site 941638002083 KMSKS motif; other site 941638002084 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 941638002085 tRNA binding surface [nucleotide binding]; other site 941638002086 anticodon binding site; other site 941638002087 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 941638002088 TPR motif; other site 941638002089 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 941638002090 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 941638002091 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 941638002092 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 941638002093 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 941638002094 carboxyltransferase (CT) interaction site; other site 941638002095 biotinylation site [posttranslational modification]; other site 941638002096 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 941638002097 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 941638002098 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 941638002099 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 941638002100 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 941638002101 putative substrate translocation pore; other site 941638002102 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 941638002103 putative acyl-acceptor binding pocket; other site 941638002104 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 941638002105 acyl-activating enzyme (AAE) consensus motif; other site 941638002106 putative AMP binding site [chemical binding]; other site 941638002107 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 941638002108 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 941638002109 ABC-ATPase subunit interface; other site 941638002110 dimer interface [polypeptide binding]; other site 941638002111 putative PBP binding regions; other site 941638002112 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 941638002113 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638002114 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 941638002115 S-adenosylmethionine binding site [chemical binding]; other site 941638002116 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 941638002117 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 941638002118 HIGH motif; other site 941638002119 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 941638002120 active site 941638002121 KMSKS motif; other site 941638002122 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638002123 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 941638002124 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 941638002125 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 941638002126 ring oligomerisation interface [polypeptide binding]; other site 941638002127 ATP/Mg binding site [chemical binding]; other site 941638002128 stacking interactions; other site 941638002129 hinge regions; other site 941638002130 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 941638002131 oligomerisation interface [polypeptide binding]; other site 941638002132 mobile loop; other site 941638002133 roof hairpin; other site 941638002134 ribonuclease PH; Reviewed; Region: rph; PRK00173 941638002135 Ribonuclease PH; Region: RNase_PH_bact; cd11362 941638002136 hexamer interface [polypeptide binding]; other site 941638002137 active site 941638002138 GrpE; Region: GrpE; pfam01025 941638002139 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 941638002140 dimer interface [polypeptide binding]; other site 941638002141 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 941638002142 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 941638002143 Domain of unknown function DUF20; Region: UPF0118; pfam01594 941638002144 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 941638002145 hypothetical protein; Validated; Region: PRK06620 941638002146 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 941638002147 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 941638002148 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 941638002149 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 941638002150 alphaNTD - beta interaction site [polypeptide binding]; other site 941638002151 alphaNTD homodimer interface [polypeptide binding]; other site 941638002152 alphaNTD - beta' interaction site [polypeptide binding]; other site 941638002153 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 941638002154 30S ribosomal protein S11; Validated; Region: PRK05309 941638002155 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 941638002156 30S ribosomal protein S13; Region: bact_S13; TIGR03631 941638002157 adenylate kinase; Reviewed; Region: adk; PRK00279 941638002158 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 941638002159 AMP-binding site [chemical binding]; other site 941638002160 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 941638002161 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 941638002162 SecY translocase; Region: SecY; pfam00344 941638002163 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 941638002164 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 941638002165 23S rRNA binding site [nucleotide binding]; other site 941638002166 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 941638002167 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 941638002168 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 941638002169 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 941638002170 5S rRNA interface [nucleotide binding]; other site 941638002171 23S rRNA interface [nucleotide binding]; other site 941638002172 L5 interface [polypeptide binding]; other site 941638002173 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 941638002174 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 941638002175 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 941638002176 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 941638002177 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 941638002178 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 941638002179 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 941638002180 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 941638002181 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 941638002182 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 941638002183 RNA binding site [nucleotide binding]; other site 941638002184 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 941638002185 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 941638002186 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 941638002187 L23 interface [polypeptide binding]; other site 941638002188 trigger factor interaction site; other site 941638002189 23S rRNA interface [nucleotide binding]; other site 941638002190 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 941638002191 23S rRNA interface [nucleotide binding]; other site 941638002192 5S rRNA interface [nucleotide binding]; other site 941638002193 putative antibiotic binding site [chemical binding]; other site 941638002194 L25 interface [polypeptide binding]; other site 941638002195 L27 interface [polypeptide binding]; other site 941638002196 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 941638002197 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 941638002198 G-X-X-G motif; other site 941638002199 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 941638002200 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 941638002201 putative translocon binding site; other site 941638002202 protein-rRNA interface [nucleotide binding]; other site 941638002203 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 941638002204 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 941638002205 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 941638002206 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 941638002207 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 941638002208 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 941638002209 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 941638002210 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 941638002211 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638002212 elongation factor Tu; Reviewed; Region: PRK00049 941638002213 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 941638002214 G1 box; other site 941638002215 GEF interaction site [polypeptide binding]; other site 941638002216 GTP/Mg2+ binding site [chemical binding]; other site 941638002217 Switch I region; other site 941638002218 G2 box; other site 941638002219 G3 box; other site 941638002220 Switch II region; other site 941638002221 G4 box; other site 941638002222 G5 box; other site 941638002223 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 941638002224 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 941638002225 Antibiotic Binding Site [chemical binding]; other site 941638002226 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 941638002227 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 941638002228 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 941638002229 fumarate hydratase; Reviewed; Region: fumC; PRK00485 941638002230 Class II fumarases; Region: Fumarase_classII; cd01362 941638002231 active site 941638002232 tetramer interface [polypeptide binding]; other site 941638002233 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 941638002234 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 941638002235 putative active site [active] 941638002236 homotetrameric interface [polypeptide binding]; other site 941638002237 cell division protein FtsZ; Validated; Region: PRK09330 941638002238 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 941638002239 nucleotide binding site [chemical binding]; other site 941638002240 SulA interaction site; other site 941638002241 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 941638002242 secondary substrate binding site; other site 941638002243 primary substrate binding site; other site 941638002244 inhibition loop; other site 941638002245 dimerization interface [polypeptide binding]; other site 941638002246 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 941638002247 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 941638002248 muropeptide transporter; Validated; Region: ampG; cl17669 941638002249 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 941638002250 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 941638002251 ATP binding site [chemical binding]; other site 941638002252 Mg++ binding site [ion binding]; other site 941638002253 motif III; other site 941638002254 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 941638002255 nucleotide binding region [chemical binding]; other site 941638002256 ATP-binding site [chemical binding]; other site 941638002257 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 941638002258 DNA-binding site [nucleotide binding]; DNA binding site 941638002259 RNA-binding motif; other site 941638002260 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 941638002261 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 941638002262 S-adenosylmethionine binding site [chemical binding]; other site 941638002263 SurA N-terminal domain; Region: SurA_N_3; cl07813 941638002264 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 941638002265 Organic solvent tolerance protein; Region: OstA_C; pfam04453 941638002266 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 941638002267 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 941638002268 generic binding surface II; other site 941638002269 generic binding surface I; other site 941638002270 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 941638002271 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 941638002272 putative catalytic site [active] 941638002273 putative phosphate binding site [ion binding]; other site 941638002274 active site 941638002275 metal binding site A [ion binding]; metal-binding site 941638002276 DNA binding site [nucleotide binding] 941638002277 putative AP binding site [nucleotide binding]; other site 941638002278 putative metal binding site B [ion binding]; other site 941638002279 GTP-binding protein Der; Reviewed; Region: PRK00093 941638002280 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 941638002281 G1 box; other site 941638002282 GTP/Mg2+ binding site [chemical binding]; other site 941638002283 Switch I region; other site 941638002284 G2 box; other site 941638002285 Switch II region; other site 941638002286 G3 box; other site 941638002287 G4 box; other site 941638002288 G5 box; other site 941638002289 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 941638002290 G1 box; other site 941638002291 GTP/Mg2+ binding site [chemical binding]; other site 941638002292 Switch I region; other site 941638002293 G2 box; other site 941638002294 G3 box; other site 941638002295 Switch II region; other site 941638002296 G4 box; other site 941638002297 G5 box; other site 941638002298 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 941638002299 AAA domain; Region: AAA_14; pfam13173 941638002300 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 941638002301 ABC1 family; Region: ABC1; cl17513 941638002302 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 941638002303 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 941638002304 S-adenosylmethionine binding site [chemical binding]; other site 941638002305 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 941638002306 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 941638002307 DNA binding site [nucleotide binding] 941638002308 catalytic residue [active] 941638002309 H2TH interface [polypeptide binding]; other site 941638002310 putative catalytic residues [active] 941638002311 turnover-facilitating residue; other site 941638002312 intercalation triad [nucleotide binding]; other site 941638002313 8OG recognition residue [nucleotide binding]; other site 941638002314 putative reading head residues; other site 941638002315 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 941638002316 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 941638002317 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 941638002318 active site 941638002319 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 941638002320 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 941638002321 HIGH motif; other site 941638002322 active site 941638002323 KMSKS motif; other site 941638002324 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 941638002325 tRNA binding surface [nucleotide binding]; other site 941638002326 anticodon binding site; other site 941638002327 thymidylate kinase; Validated; Region: tmk; PRK00698 941638002328 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 941638002329 TMP-binding site; other site 941638002330 ATP-binding site [chemical binding]; other site 941638002331 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638002332 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 941638002333 UbiA prenyltransferase family; Region: UbiA; pfam01040 941638002334 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 941638002335 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 941638002336 active site 941638002337 HIGH motif; other site 941638002338 nucleotide binding site [chemical binding]; other site 941638002339 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 941638002340 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 941638002341 active site 941638002342 KMSKS motif; other site 941638002343 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 941638002344 tRNA binding surface [nucleotide binding]; other site 941638002345 anticodon binding site; other site 941638002346 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 941638002347 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 941638002348 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 941638002349 RmuC family; Region: RmuC; pfam02646 941638002350 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 941638002351 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 941638002352 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 941638002353 Peptidase family M23; Region: Peptidase_M23; pfam01551 941638002354 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 941638002355 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 941638002356 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 941638002357 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 941638002358 putative acyl-acceptor binding pocket; other site 941638002359 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 941638002360 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 941638002361 catalytic triad [active] 941638002362 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 941638002363 IHF dimer interface [polypeptide binding]; other site 941638002364 IHF - DNA interface [nucleotide binding]; other site 941638002365 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 941638002366 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 941638002367 DNA binding residues [nucleotide binding] 941638002368 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 941638002369 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 941638002370 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 941638002371 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 941638002372 synthetase active site [active] 941638002373 NTP binding site [chemical binding]; other site 941638002374 metal binding site [ion binding]; metal-binding site 941638002375 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 941638002376 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 941638002377 Autotransporter beta-domain; Region: Autotransporter; smart00869 941638002378 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 941638002379 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 941638002380 Domain of unknown function DUF21; Region: DUF21; pfam01595 941638002381 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 941638002382 Transporter associated domain; Region: CorC_HlyC; smart01091 941638002383 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 941638002384 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 941638002385 Walker A/P-loop; other site 941638002386 ATP binding site [chemical binding]; other site 941638002387 Q-loop/lid; other site 941638002388 ABC transporter signature motif; other site 941638002389 Walker B; other site 941638002390 D-loop; other site 941638002391 H-loop/switch region; other site 941638002392 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 941638002393 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 941638002394 FtsX-like permease family; Region: FtsX; pfam02687 941638002395 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 941638002396 putative substrate translocation pore; other site 941638002397 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 941638002398 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 941638002399 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 941638002400 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638002401 Walker A/P-loop; other site 941638002402 ATP binding site [chemical binding]; other site 941638002403 Q-loop/lid; other site 941638002404 ABC transporter signature motif; other site 941638002405 Walker B; other site 941638002406 D-loop; other site 941638002407 H-loop/switch region; other site 941638002408 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 941638002409 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 941638002410 HicB family; Region: HicB; pfam05534 941638002411 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 941638002412 Ligand Binding Site [chemical binding]; other site 941638002413 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 941638002414 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 941638002415 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 941638002416 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 941638002417 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 941638002418 Walker A motif; other site 941638002419 ATP binding site [chemical binding]; other site 941638002420 Walker B motif; other site 941638002421 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 941638002422 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 941638002423 DoxX-like family; Region: DoxX_3; pfam13781 941638002424 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 941638002425 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 941638002426 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 941638002427 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 941638002428 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 941638002429 nucleotide binding pocket [chemical binding]; other site 941638002430 K-X-D-G motif; other site 941638002431 catalytic site [active] 941638002432 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 941638002433 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 941638002434 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 941638002435 Dimer interface [polypeptide binding]; other site 941638002436 BRCT sequence motif; other site 941638002437 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 941638002438 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 941638002439 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 941638002440 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 941638002441 mce related protein; Region: MCE; pfam02470 941638002442 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 941638002443 RNA/DNA hybrid binding site [nucleotide binding]; other site 941638002444 active site 941638002445 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 941638002446 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 941638002447 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 941638002448 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 941638002449 CoA-binding site [chemical binding]; other site 941638002450 ATP-binding [chemical binding]; other site 941638002451 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 941638002452 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 941638002453 active site 941638002454 catalytic site [active] 941638002455 substrate binding site [chemical binding]; other site 941638002456 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 941638002457 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 941638002458 Part of AAA domain; Region: AAA_19; pfam13245 941638002459 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 941638002460 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 941638002461 Family description; Region: UvrD_C_2; pfam13538 941638002462 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 941638002463 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 941638002464 acetyl-CoA acetyltransferase; Provisional; Region: PRK06633 941638002465 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 941638002466 dimer interface [polypeptide binding]; other site 941638002467 active site 941638002468 TLC ATP/ADP transporter; Region: TLC; pfam03219 941638002469 FOG: CBS domain [General function prediction only]; Region: COG0517 941638002470 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 941638002471 Transporter associated domain; Region: CorC_HlyC; smart01091 941638002472 metal-binding heat shock protein; Provisional; Region: PRK00016 941638002473 PemK-like protein; Region: PemK; cl00995 941638002474 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 941638002475 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 941638002476 FeS/SAM binding site; other site 941638002477 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 941638002478 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 941638002479 dimer interface [polypeptide binding]; other site 941638002480 active site 941638002481 glycine-pyridoxal phosphate binding site [chemical binding]; other site 941638002482 folate binding site [chemical binding]; other site 941638002483 Predicted esterase [General function prediction only]; Region: COG0400 941638002484 putative hydrolase; Provisional; Region: PRK11460 941638002485 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 941638002486 putative GSH binding site [chemical binding]; other site 941638002487 catalytic residues [active] 941638002488 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 941638002489 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 941638002490 minor groove reading motif; other site 941638002491 helix-hairpin-helix signature motif; other site 941638002492 substrate binding pocket [chemical binding]; other site 941638002493 active site 941638002494 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 941638002495 Predicted small secreted protein [Function unknown]; Region: COG5510 941638002496 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 941638002497 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 941638002498 Predicted methyltransferases [General function prediction only]; Region: COG0313 941638002499 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 941638002500 putative SAM binding site [chemical binding]; other site 941638002501 putative homodimer interface [polypeptide binding]; other site 941638002502 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 941638002503 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 941638002504 putative ligand binding site [chemical binding]; other site 941638002505 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 941638002506 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 941638002507 tetramer interfaces [polypeptide binding]; other site 941638002508 binuclear metal-binding site [ion binding]; other site 941638002509 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 941638002510 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 941638002511 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 941638002512 aspartate kinase; Reviewed; Region: PRK06635 941638002513 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 941638002514 putative nucleotide binding site [chemical binding]; other site 941638002515 putative catalytic residues [active] 941638002516 putative Mg ion binding site [ion binding]; other site 941638002517 putative aspartate binding site [chemical binding]; other site 941638002518 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 941638002519 putative allosteric regulatory residue; other site 941638002520 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 941638002521 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 941638002522 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 941638002523 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 941638002524 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638002525 putative substrate translocation pore; other site 941638002526 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 941638002527 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638002528 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 941638002529 Helix-turn-helix domain; Region: HTH_25; pfam13413 941638002530 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 941638002531 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 941638002532 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 941638002533 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 941638002534 trmE is a tRNA modification GTPase; Region: trmE; cd04164 941638002535 G1 box; other site 941638002536 GTP/Mg2+ binding site [chemical binding]; other site 941638002537 Switch I region; other site 941638002538 G2 box; other site 941638002539 Switch II region; other site 941638002540 G3 box; other site 941638002541 G4 box; other site 941638002542 G5 box; other site 941638002543 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 941638002544 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 941638002545 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 941638002546 hexamer interface [polypeptide binding]; other site 941638002547 Walker A motif; other site 941638002548 ATP binding site [chemical binding]; other site 941638002549 Walker B motif; other site 941638002550 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 941638002551 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 941638002552 NAD(P) binding site [chemical binding]; other site 941638002553 active site 941638002554 acyl carrier protein; Provisional; Region: acpP; PRK00982 941638002555 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 941638002556 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 941638002557 dimer interface [polypeptide binding]; other site 941638002558 active site 941638002559 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 941638002560 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 941638002561 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 941638002562 AAA domain; Region: AAA_14; pfam13173 941638002563 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 941638002564 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 941638002565 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 941638002566 catalytic site [active] 941638002567 G-X2-G-X-G-K; other site 941638002568 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 941638002569 sequence-specific DNA binding site [nucleotide binding]; other site 941638002570 salt bridge; other site 941638002571 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 941638002572 rod shape-determining protein MreC; Region: MreC; pfam04085 941638002573 rod shape-determining protein MreB; Provisional; Region: PRK13927 941638002574 MreB and similar proteins; Region: MreB_like; cd10225 941638002575 nucleotide binding site [chemical binding]; other site 941638002576 Mg binding site [ion binding]; other site 941638002577 putative protofilament interaction site [polypeptide binding]; other site 941638002578 RodZ interaction site [polypeptide binding]; other site 941638002579 Predicted permeases [General function prediction only]; Region: COG0795 941638002580 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 941638002581 putative outer membrane lipoprotein; Provisional; Region: PRK09967 941638002582 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 941638002583 ligand binding site [chemical binding]; other site 941638002584 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 941638002585 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 941638002586 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 941638002587 dimer interface [polypeptide binding]; other site 941638002588 active site 941638002589 CoA binding pocket [chemical binding]; other site 941638002590 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 941638002591 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 941638002592 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 941638002593 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 941638002594 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 941638002595 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 941638002596 P loop; other site 941638002597 GTP binding site [chemical binding]; other site 941638002598 DNA polymerase I; Provisional; Region: PRK05755 941638002599 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 941638002600 active site 941638002601 metal binding site 1 [ion binding]; metal-binding site 941638002602 putative 5' ssDNA interaction site; other site 941638002603 metal binding site 3; metal-binding site 941638002604 metal binding site 2 [ion binding]; metal-binding site 941638002605 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 941638002606 putative DNA binding site [nucleotide binding]; other site 941638002607 putative metal binding site [ion binding]; other site 941638002608 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 941638002609 active site 941638002610 substrate binding site [chemical binding]; other site 941638002611 catalytic site [active] 941638002612 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 941638002613 active site 941638002614 DNA binding site [nucleotide binding] 941638002615 catalytic site [active] 941638002616 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 941638002617 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 941638002618 putative active site [active] 941638002619 putative PHP Thumb interface [polypeptide binding]; other site 941638002620 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 941638002621 generic binding surface I; other site 941638002622 generic binding surface II; other site 941638002623 Protein of unknown function; Region: DUF3971; pfam13116 941638002624 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 941638002625 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 941638002626 putative substrate translocation pore; other site 941638002627 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 941638002628 seryl-tRNA synthetase; Provisional; Region: PRK05431 941638002629 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 941638002630 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 941638002631 dimer interface [polypeptide binding]; other site 941638002632 active site 941638002633 motif 1; other site 941638002634 motif 2; other site 941638002635 motif 3; other site 941638002636 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 941638002637 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 941638002638 Integral membrane protein TerC family; Region: TerC; cl10468 941638002639 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 941638002640 Methyltransferase domain; Region: Methyltransf_31; pfam13847 941638002641 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 941638002642 S-adenosylmethionine binding site [chemical binding]; other site 941638002643 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 941638002644 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 941638002645 Predicted transcriptional regulator [Transcription]; Region: COG2944 941638002646 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 941638002647 salt bridge; other site 941638002648 non-specific DNA binding site [nucleotide binding]; other site 941638002649 sequence-specific DNA binding site [nucleotide binding]; other site 941638002650 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 941638002651 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 941638002652 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 941638002653 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 941638002654 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 941638002655 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 941638002656 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 941638002657 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 941638002658 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 941638002659 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638002660 Walker A/P-loop; other site 941638002661 ATP binding site [chemical binding]; other site 941638002662 Q-loop/lid; other site 941638002663 ABC transporter signature motif; other site 941638002664 Walker B; other site 941638002665 D-loop; other site 941638002666 H-loop/switch region; other site 941638002667 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 941638002668 4Fe-4S binding domain; Region: Fer4; cl02805 941638002669 4Fe-4S binding domain; Region: Fer4; pfam00037 941638002670 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 941638002671 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 941638002672 NADH dehydrogenase subunit G; Validated; Region: PRK09130 941638002673 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 941638002674 catalytic loop [active] 941638002675 iron binding site [ion binding]; other site 941638002676 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 941638002677 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 941638002678 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 941638002679 Predicted membrane protein [Function unknown]; Region: COG3671 941638002680 aconitate hydratase; Validated; Region: PRK09277 941638002681 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 941638002682 substrate binding site [chemical binding]; other site 941638002683 ligand binding site [chemical binding]; other site 941638002684 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 941638002685 substrate binding site [chemical binding]; other site 941638002686 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 941638002687 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 941638002688 gamma subunit interface [polypeptide binding]; other site 941638002689 epsilon subunit interface [polypeptide binding]; other site 941638002690 LBP interface [polypeptide binding]; other site 941638002691 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 941638002692 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 941638002693 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 941638002694 alpha subunit interaction interface [polypeptide binding]; other site 941638002695 Walker A motif; other site 941638002696 ATP binding site [chemical binding]; other site 941638002697 Walker B motif; other site 941638002698 inhibitor binding site; inhibition site 941638002699 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 941638002700 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 941638002701 core domain interface [polypeptide binding]; other site 941638002702 delta subunit interface [polypeptide binding]; other site 941638002703 epsilon subunit interface [polypeptide binding]; other site 941638002704 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 941638002705 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 941638002706 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 941638002707 beta subunit interaction interface [polypeptide binding]; other site 941638002708 Walker A motif; other site 941638002709 ATP binding site [chemical binding]; other site 941638002710 Walker B motif; other site 941638002711 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 941638002712 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 941638002713 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 941638002714 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 941638002715 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 941638002716 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 941638002717 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 941638002718 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 941638002719 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 941638002720 dinuclear metal binding motif [ion binding]; other site 941638002721 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 941638002722 Transglycosylase; Region: Transgly; pfam00912 941638002723 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 941638002724 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 941638002725 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 941638002726 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 941638002727 FeS/SAM binding site; other site 941638002728 TRAM domain; Region: TRAM; pfam01938 941638002729 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 941638002730 Bacterial SH3 domain; Region: SH3_4; pfam06347 941638002731 Bacterial SH3 domain; Region: SH3_4; pfam06347 941638002732 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 941638002733 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 941638002734 TrkA-N domain; Region: TrkA_N; pfam02254 941638002735 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 941638002736 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 941638002737 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 941638002738 rRNA binding site [nucleotide binding]; other site 941638002739 predicted 30S ribosome binding site; other site 941638002740 Maf-like protein; Region: Maf; pfam02545 941638002741 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 941638002742 active site 941638002743 dimer interface [polypeptide binding]; other site 941638002744 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 941638002745 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 941638002746 active site 941638002747 DNA binding site [nucleotide binding] 941638002748 Int/Topo IB signature motif; other site 941638002749 Phasin protein; Region: Phasin_2; pfam09361 941638002750 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 941638002751 PLD-like domain; Region: PLDc_2; pfam13091 941638002752 putative active site [active] 941638002753 catalytic site [active] 941638002754 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 941638002755 SurA N-terminal domain; Region: SurA_N_3; cl07813 941638002756 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 941638002757 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 941638002758 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 941638002759 Autotransporter beta-domain; Region: Autotransporter; pfam03797 941638002760 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 941638002761 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 941638002762 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 941638002763 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 941638002764 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 941638002765 active site 941638002766 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 941638002767 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 941638002768 Mg++ binding site [ion binding]; other site 941638002769 putative catalytic motif [active] 941638002770 putative substrate binding site [chemical binding]; other site 941638002771 Protein of unknown function (DUF721); Region: DUF721; pfam05258 941638002772 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 941638002773 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 941638002774 Ferredoxin [Energy production and conversion]; Region: COG1146 941638002775 4Fe-4S binding domain; Region: Fer4; cl02805 941638002776 heme exporter protein CcmC; Region: ccmC; TIGR01191 941638002777 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 941638002778 nucleoside/Zn binding site; other site 941638002779 dimer interface [polypeptide binding]; other site 941638002780 catalytic motif [active] 941638002781 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 941638002782 Cation efflux family; Region: Cation_efflux; cl00316 941638002783 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 941638002784 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 941638002785 substrate binding site [chemical binding]; other site 941638002786 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 941638002787 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 941638002788 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 941638002789 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 941638002790 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 941638002791 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 941638002792 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 941638002793 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 941638002794 dimer interface [polypeptide binding]; other site 941638002795 ssDNA binding site [nucleotide binding]; other site 941638002796 tetramer (dimer of dimers) interface [polypeptide binding]; other site 941638002797 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 941638002798 hypothetical protein; Reviewed; Region: PRK01530 941638002799 heat shock protein 90; Provisional; Region: PRK05218 941638002800 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 941638002801 ATP binding site [chemical binding]; other site 941638002802 Mg2+ binding site [ion binding]; other site 941638002803 G-X-G motif; other site 941638002804 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 941638002805 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 941638002806 substrate-cofactor binding pocket; other site 941638002807 pyridoxal 5'-phosphate binding site [chemical binding]; other site 941638002808 catalytic residue [active] 941638002809 trigger factor; Provisional; Region: tig; PRK01490 941638002810 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 941638002811 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 941638002812 GTPase CgtA; Reviewed; Region: obgE; PRK12299 941638002813 GTP1/OBG; Region: GTP1_OBG; pfam01018 941638002814 Obg GTPase; Region: Obg; cd01898 941638002815 G1 box; other site 941638002816 GTP/Mg2+ binding site [chemical binding]; other site 941638002817 Switch I region; other site 941638002818 G2 box; other site 941638002819 G3 box; other site 941638002820 Switch II region; other site 941638002821 G4 box; other site 941638002822 G5 box; other site 941638002823 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 941638002824 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 941638002825 dimer interface [polypeptide binding]; other site 941638002826 active site 941638002827 citrylCoA binding site [chemical binding]; other site 941638002828 NADH binding [chemical binding]; other site 941638002829 cationic pore residues; other site 941638002830 oxalacetate/citrate binding site [chemical binding]; other site 941638002831 coenzyme A binding site [chemical binding]; other site 941638002832 catalytic triad [active] 941638002833 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 941638002834 Fe-S cluster binding site [ion binding]; other site 941638002835 active site 941638002836 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 941638002837 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 941638002838 RNA binding surface [nucleotide binding]; other site 941638002839 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 941638002840 active site 941638002841 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 941638002842 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 941638002843 S-adenosylmethionine binding site [chemical binding]; other site 941638002844 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 941638002845 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 941638002846 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 941638002847 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 941638002848 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 941638002849 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 941638002850 motif 1; other site 941638002851 dimer interface [polypeptide binding]; other site 941638002852 active site 941638002853 motif 2; other site 941638002854 motif 3; other site 941638002855 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 941638002856 oligomeric interface; other site 941638002857 putative active site [active] 941638002858 homodimer interface [polypeptide binding]; other site 941638002859 prevent-host-death family protein; Region: phd_fam; TIGR01552 941638002860 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 941638002861 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 941638002862 metabolite-proton symporter; Region: 2A0106; TIGR00883 941638002863 putative substrate translocation pore; other site 941638002864 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 941638002865 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 941638002866 motif 1; other site 941638002867 active site 941638002868 motif 2; other site 941638002869 motif 3; other site 941638002870 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 941638002871 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 941638002872 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 941638002873 dimerization interface 3.5A [polypeptide binding]; other site 941638002874 active site 941638002875 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 941638002876 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 941638002877 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 941638002878 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 941638002879 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 941638002880 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 941638002881 DNA binding residues [nucleotide binding] 941638002882 DNA primase, catalytic core; Region: dnaG; TIGR01391 941638002883 CHC2 zinc finger; Region: zf-CHC2; pfam01807 941638002884 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 941638002885 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 941638002886 active site 941638002887 metal binding site [ion binding]; metal-binding site 941638002888 interdomain interaction site; other site 941638002889 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 941638002890 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 941638002891 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 941638002892 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 941638002893 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 941638002894 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 941638002895 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 941638002896 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 941638002897 ligand binding site [chemical binding]; other site 941638002898 homodimer interface [polypeptide binding]; other site 941638002899 NAD(P) binding site [chemical binding]; other site 941638002900 trimer interface B [polypeptide binding]; other site 941638002901 trimer interface A [polypeptide binding]; other site 941638002902 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 941638002903 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 941638002904 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 941638002905 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 941638002906 Walker A motif; other site 941638002907 ATP binding site [chemical binding]; other site 941638002908 Walker B motif; other site 941638002909 arginine finger; other site 941638002910 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 941638002911 hypothetical protein; Validated; Region: PRK00153 941638002912 Predicted aspartyl protease [General function prediction only]; Region: COG3577 941638002913 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 941638002914 catalytic motif [active] 941638002915 Catalytic residue [active] 941638002916 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 941638002917 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 941638002918 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 941638002919 Walker A/P-loop; other site 941638002920 ATP binding site [chemical binding]; other site 941638002921 Q-loop/lid; other site 941638002922 ABC transporter signature motif; other site 941638002923 Walker B; other site 941638002924 D-loop; other site 941638002925 H-loop/switch region; other site 941638002926 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 941638002927 putative hydrolase; Provisional; Region: PRK02113 941638002928 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 941638002929 active site 941638002930 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 941638002931 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 941638002932 Predicted permeases [General function prediction only]; Region: COG0795 941638002933 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 941638002934 DNA polymerase III subunit chi; Provisional; Region: PRK06646 941638002935 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 941638002936 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 941638002937 metal binding site [ion binding]; metal-binding site 941638002938 dimer interface [polypeptide binding]; other site 941638002939 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 941638002940 Uncharacterized conserved protein [Function unknown]; Region: COG1434 941638002941 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 941638002942 putative active site [active] 941638002943 lipoate-protein ligase B; Provisional; Region: PRK14347 941638002944 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 941638002945 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 941638002946 amidase catalytic site [active] 941638002947 Zn binding residues [ion binding]; other site 941638002948 substrate binding site [chemical binding]; other site 941638002949 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 941638002950 potential protein location (hypothetical protein Rsl_1551 [Rickettsia slovaca 13-B]) that overlaps RNA (tRNA-T) 941638002951 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 941638002952 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 941638002953 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 941638002954 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 941638002955 ATP binding site [chemical binding]; other site 941638002956 Mg2+ binding site [ion binding]; other site 941638002957 G-X-G motif; other site 941638002958 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 941638002959 ATP binding site [chemical binding]; other site 941638002960 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 941638002961 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 941638002962 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 941638002963 Tetratricopeptide repeat; Region: TPR_12; pfam13424 941638002964 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 941638002965 binding surface 941638002966 TPR repeat; Region: TPR_11; pfam13414 941638002967 TPR motif; other site 941638002968 Tetratricopeptide repeat; Region: TPR_12; pfam13424 941638002969 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 941638002970 binding surface 941638002971 TPR motif; other site 941638002972 TPR repeat; Region: TPR_11; pfam13414 941638002973 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 941638002974 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 941638002975 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 941638002976 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 941638002977 ferrochelatase; Reviewed; Region: hemH; PRK00035 941638002978 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 941638002979 C-terminal domain interface [polypeptide binding]; other site 941638002980 active site 941638002981 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 941638002982 active site 941638002983 N-terminal domain interface [polypeptide binding]; other site 941638002984 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 941638002985 substrate binding site [chemical binding]; other site 941638002986 active site