-- dump date 20140620_035039 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105109000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 1105109000002 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 1105109000003 catalytic residues [active] 1105109000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105109000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 1105109000006 Walker A/P-loop; other site 1105109000007 ATP binding site [chemical binding]; other site 1105109000008 Q-loop/lid; other site 1105109000009 ABC transporter signature motif; other site 1105109000010 Walker B; other site 1105109000011 D-loop; other site 1105109000012 H-loop/switch region; other site 1105109000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1105109000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1105109000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105109000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105109000017 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 1105109000018 FAD binding pocket [chemical binding]; other site 1105109000019 FAD binding motif [chemical binding]; other site 1105109000020 phosphate binding motif [ion binding]; other site 1105109000021 beta-alpha-beta structure motif; other site 1105109000022 NAD binding pocket [chemical binding]; other site 1105109000023 Iron coordination center [ion binding]; other site 1105109000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 1105109000025 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 1105109000026 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 1105109000027 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 1105109000028 active site 1105109000029 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 1105109000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105109000031 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105109000032 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 1105109000033 trimer interface [polypeptide binding]; other site 1105109000034 active site 1105109000035 UDP-GlcNAc binding site [chemical binding]; other site 1105109000036 lipid binding site [chemical binding]; lipid-binding site 1105109000037 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105109000038 active site 1105109000039 potential frameshift: common BLAST hit: gi|67458401|ref|YP_246025.1| alpha-beta hydrolase family esterase 1105109000040 COG0666 FOG: Ankyrin repeat. Overlaps tRNA on same strand. 1105109000041 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1105109000042 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 1105109000043 FMN binding site [chemical binding]; other site 1105109000044 active site 1105109000045 catalytic residues [active] 1105109000046 substrate binding site [chemical binding]; other site 1105109000047 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 1105109000048 NodB motif; other site 1105109000049 putative active site [active] 1105109000050 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1105109000051 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 1105109000052 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 1105109000053 intersubunit interface [polypeptide binding]; other site 1105109000054 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105109000055 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105109000056 active site 1105109000057 NTP binding site [chemical binding]; other site 1105109000058 metal binding triad [ion binding]; metal-binding site 1105109000059 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105109000060 Competence protein; Region: Competence; pfam03772 1105109000061 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105109000062 AAA domain; Region: AAA_22; pfam13401 1105109000063 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105109000064 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105109000065 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 1105109000066 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 1105109000067 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105109000068 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 1105109000069 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109000070 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1105109000071 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 1105109000072 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 1105109000073 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105109000074 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 1105109000075 catalytic residues [active] 1105109000076 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 1105109000077 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105109000078 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105109000079 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 1105109000080 S-adenosylmethionine binding site [chemical binding]; other site 1105109000081 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105109000082 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105109000083 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 1105109000084 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109000085 Walker A/P-loop; other site 1105109000086 ATP binding site [chemical binding]; other site 1105109000087 Q-loop/lid; other site 1105109000088 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109000089 ABC transporter signature motif; other site 1105109000090 Walker B; other site 1105109000091 D-loop; other site 1105109000092 H-loop/switch region; other site 1105109000093 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 1105109000094 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1105109000095 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 1105109000096 folate binding site [chemical binding]; other site 1105109000097 NADP+ binding site [chemical binding]; other site 1105109000098 potential frameshift: common BLAST hit: gi|67458431|ref|YP_246055.1| folate synthesis bifunctional protein 1105109000099 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase [Coenzyme metabolism]; Region: FolK; COG0801 1105109000100 tetratricopeptide repeat protein; Provisional; Region: PRK11788 1105109000101 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105109000102 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 1105109000103 Cu(I) binding site [ion binding]; other site 1105109000104 Putative transcriptional regulator [Transcription]; Region: COG1678 1105109000105 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1105109000106 Colicin V production protein; Region: Colicin_V; pfam02674 1105109000107 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105109000108 potential frameshift: common BLAST hit: gi|229586268|ref|YP_002844769.1| acetoacetyl-CoA reductase 1105109000109 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105109000110 Clp amino terminal domain; Region: Clp_N; pfam02861 1105109000111 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 1105109000112 Walker A motif; other site 1105109000113 ATP binding site [chemical binding]; other site 1105109000114 Walker B motif; other site 1105109000115 arginine finger; other site 1105109000116 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 1105109000117 Walker A motif; other site 1105109000118 ATP binding site [chemical binding]; other site 1105109000119 Walker B motif; other site 1105109000120 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1105109000121 UGMP family protein; Validated; Region: PRK09604 1105109000122 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1105109000123 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 1105109000124 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105109000125 Di-iron ligands [ion binding]; other site 1105109000126 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 1105109000127 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105109000128 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 1105109000129 DNA binding site [nucleotide binding] 1105109000130 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1105109000131 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1105109000132 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105109000133 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105109000134 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105109000135 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1105109000136 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 1105109000137 Ligand Binding Site [chemical binding]; other site 1105109000138 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109000139 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105109000140 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105109000141 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 1105109000142 Walker A motif; other site 1105109000143 ATP binding site [chemical binding]; other site 1105109000144 Walker B motif; other site 1105109000145 arginine finger; other site 1105109000146 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105109000147 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 1105109000148 cofactor binding site; other site 1105109000149 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 1105109000150 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105109000151 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1105109000152 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3755 1105109000153 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105109000154 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109000155 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1105109000156 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1105109000157 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105109000158 membrane protein insertase; Provisional; Region: PRK01318 1105109000159 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1105109000160 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105109000161 potential frameshift: common BLAST hit: gi|67458519|ref|YP_246143.1| tellurite resistance protein-like protein 1105109000162 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 1105109000163 active site 1105109000164 catalytic residues [active] 1105109000165 metal binding site [ion binding]; metal-binding site 1105109000166 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105109000167 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105109000168 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 1105109000169 putative substrate translocation pore; other site 1105109000170 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 1105109000171 active site 1105109000172 multimer interface [polypeptide binding]; other site 1105109000173 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105109000174 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1105109000175 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105109000176 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1105109000177 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1105109000178 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105109000179 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 1105109000180 P-loop; other site 1105109000181 Magnesium ion binding site [ion binding]; other site 1105109000182 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 1105109000183 Magnesium ion binding site [ion binding]; other site 1105109000184 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1105109000185 ParB-like nuclease domain; Region: ParB; smart00470 1105109000186 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105109000187 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105109000188 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105109000189 ABC transporter; Region: ABC_tran_2; pfam12848 1105109000190 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105109000191 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105109000192 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 1105109000193 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105109000194 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105109000195 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105109000196 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1105109000197 Zn2+ binding site [ion binding]; other site 1105109000198 Mg2+ binding site [ion binding]; other site 1105109000199 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105109000200 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1105109000201 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1105109000202 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105109000203 active site 1105109000204 HIGH motif; other site 1105109000205 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105109000206 KMSK motif region; other site 1105109000207 tRNA binding surface [nucleotide binding]; other site 1105109000208 DALR anticodon binding domain; Region: DALR_1; smart00836 1105109000209 anticodon binding site; other site 1105109000210 Sporulation related domain; Region: SPOR; pfam05036 1105109000211 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105109000212 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 1105109000213 CAP-like domain; other site 1105109000214 active site 1105109000215 primary dimer interface [polypeptide binding]; other site 1105109000216 Gram-negative porin; Region: Porin_4; pfam13609 1105109000217 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105109000218 trimer interface [polypeptide binding]; other site 1105109000219 active site 1105109000220 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 1105109000221 SecA binding site; other site 1105109000222 Preprotein binding site; other site 1105109000223 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105109000224 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 1105109000225 active site 1105109000226 phosphorylation site [posttranslational modification] 1105109000227 intermolecular recognition site; other site 1105109000228 dimerization interface [polypeptide binding]; other site 1105109000229 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 1105109000230 DNA binding site [nucleotide binding] 1105109000231 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 1105109000232 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105109000233 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 1105109000234 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105109000235 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 1105109000236 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105109000237 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 1105109000238 EamA-like transporter family; Region: EamA; pfam00892 1105109000239 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1105109000240 EamA-like transporter family; Region: EamA; pfam00892 1105109000241 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 1105109000242 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109000243 putative substrate translocation pore; other site 1105109000244 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1105109000245 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105109000246 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105109000247 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105109000248 active site 1105109000249 HIGH motif; other site 1105109000250 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105109000251 KMSKS motif; other site 1105109000252 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105109000253 tRNA binding surface [nucleotide binding]; other site 1105109000254 anticodon binding site; other site 1105109000255 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 1105109000256 rRNA interaction site [nucleotide binding]; other site 1105109000257 S8 interaction site; other site 1105109000258 putative laminin-1 binding site; other site 1105109000259 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105109000260 UBA/TS-N domain; Region: UBA; pfam00627 1105109000261 Elongation factor TS; Region: EF_TS; pfam00889 1105109000262 Elongation factor TS; Region: EF_TS; pfam00889 1105109000263 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105109000264 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 1105109000265 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109000266 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105109000267 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 1105109000268 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105109000269 putative acyl-acceptor binding pocket; other site 1105109000270 aspartate aminotransferase; Provisional; Region: PRK05764 1105109000271 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 1105109000272 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105109000273 homodimer interface [polypeptide binding]; other site 1105109000274 catalytic residue [active] 1105109000275 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 1105109000276 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105109000277 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 1105109000278 binding surface 1105109000279 TPR motif; other site 1105109000280 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1105109000281 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 1105109000282 S-adenosylmethionine binding site [chemical binding]; other site 1105109000283 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1105109000284 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 1105109000285 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105109000286 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105109000287 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105109000288 active site 1105109000289 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109000290 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1105109000291 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105109000292 active site 1105109000293 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105109000294 dimer interface [polypeptide binding]; other site 1105109000295 substrate binding site [chemical binding]; other site 1105109000296 catalytic residues [active] 1105109000297 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1105109000298 Permease; Region: Permease; pfam02405 1105109000299 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105109000300 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109000301 Walker A/P-loop; other site 1105109000302 ATP binding site [chemical binding]; other site 1105109000303 Q-loop/lid; other site 1105109000304 ABC transporter signature motif; other site 1105109000305 Walker B; other site 1105109000306 D-loop; other site 1105109000307 H-loop/switch region; other site 1105109000308 CheD chemotactic sensory transduction; Region: CheD; cl00810 1105109000309 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 1105109000310 50S ribosomal protein L31; Provisional; Region: PRK01397 1105109000311 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105109000312 G1 box; other site 1105109000313 GTP/Mg2+ binding site [chemical binding]; other site 1105109000314 Switch I region; other site 1105109000315 G2 box; other site 1105109000316 G3 box; other site 1105109000317 Switch II region; other site 1105109000318 G4 box; other site 1105109000319 G5 box; other site 1105109000320 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 1105109000321 nucleotide binding site [chemical binding]; other site 1105109000322 substrate binding site [chemical binding]; other site 1105109000323 type IV secretion system protein VirB3; Provisional; Region: PRK13899 1105109000324 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105109000325 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105109000326 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109000327 Walker A/P-loop; other site 1105109000328 ATP binding site [chemical binding]; other site 1105109000329 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105109000330 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105109000331 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105109000332 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105109000333 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105109000334 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105109000335 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105109000336 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105109000337 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 1105109000338 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1105109000339 hypothetical protein; Provisional; Region: PRK13694 1105109000340 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105109000341 Protein export membrane protein; Region: SecD_SecF; pfam02355 1105109000342 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105109000343 SLBB domain; Region: SLBB; pfam10531 1105109000344 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 1105109000345 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105109000346 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 1105109000347 Catalytic site [active] 1105109000348 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 1105109000349 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105109000350 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 1105109000351 dimerization interface [polypeptide binding]; other site 1105109000352 active site 1105109000353 metal binding site [ion binding]; metal-binding site 1105109000354 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 1105109000355 dsRNA binding site [nucleotide binding]; other site 1105109000356 GTPase Era; Provisional; Region: era; PRK15494 1105109000357 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109000358 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105109000359 G1 box; other site 1105109000360 GTP/Mg2+ binding site [chemical binding]; other site 1105109000361 Switch I region; other site 1105109000362 G2 box; other site 1105109000363 Switch II region; other site 1105109000364 G3 box; other site 1105109000365 G4 box; other site 1105109000366 G5 box; other site 1105109000367 KH domain; Region: KH_2; pfam07650 1105109000368 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 1105109000369 active site 1105109000370 putative DNA-binding cleft [nucleotide binding]; other site 1105109000371 dimer interface [polypeptide binding]; other site 1105109000372 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105109000373 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1105109000374 potential frameshift: common BLAST hit: gi|229586359|ref|YP_002844860.1| nucleotidyltransferase substrate binding protein 1105109000375 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105109000376 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105109000377 AAA domain; Region: AAA_31; pfam13614 1105109000378 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 1105109000379 Walker A motif; other site 1105109000380 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 1105109000381 HflK protein; Region: hflK; TIGR01933 1105109000382 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105109000383 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 1105109000384 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 1105109000385 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105109000386 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 1105109000387 protein binding site [polypeptide binding]; other site 1105109000388 hypothetical protein; Validated; Region: PRK01415 1105109000389 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105109000390 active site residue [active] 1105109000391 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 1105109000392 Iron-sulfur protein interface; other site 1105109000393 proximal quinone binding site [chemical binding]; other site 1105109000394 SdhD (CybS) interface [polypeptide binding]; other site 1105109000395 proximal heme binding site [chemical binding]; other site 1105109000396 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 1105109000397 putative SdhC subunit interface [polypeptide binding]; other site 1105109000398 putative proximal heme binding site [chemical binding]; other site 1105109000399 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105109000400 putative proximal quinone binding site; other site 1105109000401 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105109000402 L-aspartate oxidase; Provisional; Region: PRK06175 1105109000403 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105109000404 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105109000405 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 1105109000406 dimer interface [polypeptide binding]; other site 1105109000407 conserved gate region; other site 1105109000408 putative PBP binding loops; other site 1105109000409 ABC-ATPase subunit interface; other site 1105109000410 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 1105109000411 S17 interaction site [polypeptide binding]; other site 1105109000412 S8 interaction site; other site 1105109000413 16S rRNA interaction site [nucleotide binding]; other site 1105109000414 streptomycin interaction site [chemical binding]; other site 1105109000415 23S rRNA interaction site [nucleotide binding]; other site 1105109000416 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105109000417 30S ribosomal protein S7; Validated; Region: PRK05302 1105109000418 elongation factor G; Reviewed; Region: PRK00007 1105109000419 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105109000420 G1 box; other site 1105109000421 putative GEF interaction site [polypeptide binding]; other site 1105109000422 GTP/Mg2+ binding site [chemical binding]; other site 1105109000423 Switch I region; other site 1105109000424 G2 box; other site 1105109000425 G3 box; other site 1105109000426 Switch II region; other site 1105109000427 G4 box; other site 1105109000428 G5 box; other site 1105109000429 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 1105109000430 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 1105109000431 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 1105109000432 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 1105109000433 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105109000434 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105109000435 putative homodimer interface [polypeptide binding]; other site 1105109000436 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1105109000437 heterodimer interface [polypeptide binding]; other site 1105109000438 homodimer interface [polypeptide binding]; other site 1105109000439 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105109000440 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 1105109000441 23S rRNA interface [nucleotide binding]; other site 1105109000442 putative thiostrepton binding site; other site 1105109000443 L7/L12 interface [polypeptide binding]; other site 1105109000444 L25 interface [polypeptide binding]; other site 1105109000445 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 1105109000446 mRNA/rRNA interface [nucleotide binding]; other site 1105109000447 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 1105109000448 23S rRNA interface [nucleotide binding]; other site 1105109000449 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105109000450 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 1105109000451 core dimer interface [polypeptide binding]; other site 1105109000452 peripheral dimer interface [polypeptide binding]; other site 1105109000453 L10 interface [polypeptide binding]; other site 1105109000454 L11 interface [polypeptide binding]; other site 1105109000455 putative EF-Tu interaction site [polypeptide binding]; other site 1105109000456 putative EF-G interaction site [polypeptide binding]; other site 1105109000457 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1105109000458 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 1105109000459 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105109000460 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 1105109000461 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1105109000462 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 1105109000463 RPB3 interaction site [polypeptide binding]; other site 1105109000464 RPB1 interaction site [polypeptide binding]; other site 1105109000465 RPB11 interaction site [polypeptide binding]; other site 1105109000466 RPB10 interaction site [polypeptide binding]; other site 1105109000467 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105109000468 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105109000469 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1105109000470 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105109000471 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105109000472 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105109000473 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105109000474 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105109000475 DNA binding site [nucleotide binding] 1105109000476 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105109000477 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 1105109000478 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109000479 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105109000480 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 1105109000481 interface (dimer of trimers) [polypeptide binding]; other site 1105109000482 Substrate-binding/catalytic site; other site 1105109000483 Zn-binding sites [ion binding]; other site 1105109000484 ATPase MipZ; Region: MipZ; pfam09140 1105109000485 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 1105109000486 P-loop; other site 1105109000487 Magnesium ion binding site [ion binding]; other site 1105109000488 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 1105109000489 Magnesium ion binding site [ion binding]; other site 1105109000490 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105109000491 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 1105109000492 dimer interface [polypeptide binding]; other site 1105109000493 anticodon binding site; other site 1105109000494 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 1105109000495 homodimer interface [polypeptide binding]; other site 1105109000496 motif 1; other site 1105109000497 active site 1105109000498 motif 2; other site 1105109000499 GAD domain; Region: GAD; pfam02938 1105109000500 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 1105109000501 active site 1105109000502 motif 3; other site 1105109000503 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1105109000504 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105109000505 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105109000506 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1105109000507 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105109000508 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 1105109000509 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105109000510 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 1105109000511 substrate binding pocket [chemical binding]; other site 1105109000512 membrane-bound complex binding site; other site 1105109000513 hinge residues; other site 1105109000514 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105109000515 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105109000516 GatB domain; Region: GatB_Yqey; smart00845 1105109000517 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105109000518 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1105109000519 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1105109000520 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 1105109000521 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105109000522 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 1105109000523 hinge region; other site 1105109000524 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 1105109000525 putative nucleotide binding site [chemical binding]; other site 1105109000526 uridine monophosphate binding site [chemical binding]; other site 1105109000527 homohexameric interface [polypeptide binding]; other site 1105109000528 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 1105109000529 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105109000530 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 1105109000531 putative substrate translocation pore; other site 1105109000532 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 1105109000533 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105109000534 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1105109000535 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105109000536 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105109000537 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105109000538 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105109000539 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105109000540 Surface antigen; Region: Bac_surface_Ag; pfam01103 1105109000541 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105109000542 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 1105109000543 active site 1105109000544 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 1105109000545 protein binding site [polypeptide binding]; other site 1105109000546 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 1105109000547 putative substrate binding region [chemical binding]; other site 1105109000548 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1105109000549 putative RNA binding site [nucleotide binding]; other site 1105109000550 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105109000551 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 1105109000552 S-adenosylmethionine binding site [chemical binding]; other site 1105109000553 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105109000554 putative coenzyme Q binding site [chemical binding]; other site 1105109000555 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109000556 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105109000557 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105109000558 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 1105109000559 RNA methyltransferase, RsmE family; Region: TIGR00046 1105109000560 Uncharacterized conserved protein [Function unknown]; Region: COG2155 1105109000561 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105109000562 Protein export membrane protein; Region: SecD_SecF; cl14618 1105109000563 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 1105109000564 IHF dimer interface [polypeptide binding]; other site 1105109000565 IHF - DNA interface [nucleotide binding]; other site 1105109000566 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105109000567 signal recognition particle protein; Provisional; Region: PRK10867 1105109000568 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1105109000569 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 1105109000570 P loop; other site 1105109000571 GTP binding site [chemical binding]; other site 1105109000572 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105109000573 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105109000574 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105109000575 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105109000576 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105109000577 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105109000578 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105109000579 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105109000580 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 1105109000581 FeS/SAM binding site; other site 1105109000582 HemN C-terminal domain; Region: HemN_C; pfam06969 1105109000583 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 1105109000584 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105109000585 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 1105109000586 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105109000587 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1105109000588 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 1105109000589 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 1105109000590 active site 1105109000591 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105109000592 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 1105109000593 E3 interaction surface; other site 1105109000594 lipoyl attachment site [posttranslational modification]; other site 1105109000595 e3 binding domain; Region: E3_binding; pfam02817 1105109000596 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105109000597 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105109000598 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 1105109000599 TPP-binding site [chemical binding]; other site 1105109000600 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1105109000601 dimer interface [polypeptide binding]; other site 1105109000602 PYR/PP interface [polypeptide binding]; other site 1105109000603 TPP binding site [chemical binding]; other site 1105109000604 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 1105109000605 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 1105109000606 active site 1105109000607 Zn binding site [ion binding]; other site 1105109000608 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105109000609 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105109000610 Walker A/P-loop; other site 1105109000611 ATP binding site [chemical binding]; other site 1105109000612 Q-loop/lid; other site 1105109000613 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105109000614 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105109000615 ABC transporter signature motif; other site 1105109000616 Walker B; other site 1105109000617 D-loop; other site 1105109000618 H-loop/switch region; other site 1105109000619 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105109000620 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105109000621 ChaB; Region: ChaB; cl01887 1105109000622 ChaB; Region: ChaB; cl01887 1105109000623 chaperone protein DnaJ; Provisional; Region: PRK14300 1105109000624 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 1105109000625 HSP70 interaction site [polypeptide binding]; other site 1105109000626 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105109000627 substrate binding site [polypeptide binding]; other site 1105109000628 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105109000629 Zn binding sites [ion binding]; other site 1105109000630 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105109000631 dimer interface [polypeptide binding]; other site 1105109000632 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105109000633 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105109000634 nucleotide binding site [chemical binding]; other site 1105109000635 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 1105109000636 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105109000637 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 1105109000638 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105109000639 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105109000640 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105109000641 diiron binding motif [ion binding]; other site 1105109000642 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 1105109000643 Subunit III/VIIa interface [polypeptide binding]; other site 1105109000644 Phospholipid binding site [chemical binding]; other site 1105109000645 Subunit I/III interface [polypeptide binding]; other site 1105109000646 Subunit III/VIb interface [polypeptide binding]; other site 1105109000647 Subunit III/VIa interface; other site 1105109000648 Subunit III/Vb interface [polypeptide binding]; other site 1105109000649 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1105109000650 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 1105109000651 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105109000652 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 1105109000653 trimer interface [polypeptide binding]; other site 1105109000654 active site 1105109000655 substrate binding site [chemical binding]; other site 1105109000656 CoA binding site [chemical binding]; other site 1105109000657 Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]; Region: PbpC; COG4953 1105109000658 Transglycosylase; Region: Transgly; pfam00912 1105109000659 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105109000660 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 1105109000661 potential frameshift: common BLAST hit: gi|157828132|ref|YP_001494374.1| cell surface antigen-like protein Sca8 1105109000662 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105109000663 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 1105109000664 Ligand Binding Site [chemical binding]; other site 1105109000665 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105109000666 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1105109000667 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1105109000668 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 1105109000669 catalytic loop [active] 1105109000670 iron binding site [ion binding]; other site 1105109000671 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105109000672 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105109000673 nucleotide binding site [chemical binding]; other site 1105109000674 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105109000675 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 1105109000676 HSP70 interaction site [polypeptide binding]; other site 1105109000677 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105109000678 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105109000679 active site 1105109000680 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105109000681 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 1105109000682 ATP binding site [chemical binding]; other site 1105109000683 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 1105109000684 nucleotide binding region [chemical binding]; other site 1105109000685 ATP-binding site [chemical binding]; other site 1105109000686 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105109000687 UvrB/uvrC motif; Region: UVR; pfam02151 1105109000688 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 1105109000689 GSH binding site [chemical binding]; other site 1105109000690 catalytic residues [active] 1105109000691 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105109000692 potential frameshift: common BLAST hit: gi|157964270|ref|YP_001499094.1| multidrug resistance protein Atm1 1105109000693 DNA gyrase subunit A; Validated; Region: PRK05560 1105109000694 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 1105109000695 CAP-like domain; other site 1105109000696 active site 1105109000697 primary dimer interface [polypeptide binding]; other site 1105109000698 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105109000699 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105109000700 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105109000701 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105109000702 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105109000703 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105109000704 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105109000705 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105109000706 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 1105109000707 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 1105109000708 active site 1105109000709 catalytic residues [active] 1105109000710 metal binding site [ion binding]; metal-binding site 1105109000711 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105109000712 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105109000713 putative active site [active] 1105109000714 substrate binding site [chemical binding]; other site 1105109000715 putative cosubstrate binding site; other site 1105109000716 catalytic site [active] 1105109000717 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105109000718 substrate binding site [chemical binding]; other site 1105109000719 Protein of unknown function (DUF563); Region: DUF563; cl15705 1105109000720 Predicted ATPase [General function prediction only]; Region: COG1485 1105109000721 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 1105109000722 Walker A motif; other site 1105109000723 ATP binding site [chemical binding]; other site 1105109000724 Walker B motif; other site 1105109000725 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 1105109000726 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1105109000727 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 1105109000728 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105109000729 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105109000730 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109000731 Walker A/P-loop; other site 1105109000732 ATP binding site [chemical binding]; other site 1105109000733 Q-loop/lid; other site 1105109000734 ABC transporter signature motif; other site 1105109000735 Walker B; other site 1105109000736 D-loop; other site 1105109000737 H-loop/switch region; other site 1105109000738 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105109000739 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 1105109000740 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105109000741 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105109000742 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105109000743 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 1105109000744 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105109000745 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105109000746 putative metal binding site; other site 1105109000747 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105109000748 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105109000749 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105109000750 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105109000751 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105109000752 ATP binding site [chemical binding]; other site 1105109000753 active site 1105109000754 substrate binding site [chemical binding]; other site 1105109000755 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105109000756 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 1105109000757 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105109000758 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 1105109000759 active site 1105109000760 dimer interface [polypeptide binding]; other site 1105109000761 motif 1; other site 1105109000762 motif 2; other site 1105109000763 motif 3; other site 1105109000764 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 1105109000765 anticodon binding site; other site 1105109000766 potential frameshift: common BLAST hit: gi|67459373|ref|YP_246997.1| multidrug ABC transporter ATPase and permease 1105109000767 potential frameshift: common BLAST hit: gi|67459373|ref|YP_246997.1| multidrug ABC transporter ATPase and permease 1105109000768 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 1105109000769 Walker A/P-loop; other site 1105109000770 ATP binding site [chemical binding]; other site 1105109000771 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109000772 ABC transporter signature motif; other site 1105109000773 Walker B; other site 1105109000774 D-loop; other site 1105109000775 H-loop/switch region; other site 1105109000776 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 1105109000777 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105109000778 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105109000779 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 1105109000780 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 1105109000781 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105109000782 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105109000783 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105109000784 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 1105109000785 ATP binding site [chemical binding]; other site 1105109000786 Mg2+ binding site [ion binding]; other site 1105109000787 G-X-G motif; other site 1105109000788 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 1105109000789 anchoring element; other site 1105109000790 dimer interface [polypeptide binding]; other site 1105109000791 ATP binding site [chemical binding]; other site 1105109000792 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 1105109000793 active site 1105109000794 metal binding site [ion binding]; metal-binding site 1105109000795 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105109000796 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105109000797 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105109000798 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 1105109000799 protein binding site [polypeptide binding]; other site 1105109000800 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105109000801 Catalytic dyad [active] 1105109000802 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1105109000803 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 1105109000804 dimer interface [polypeptide binding]; other site 1105109000805 phosphorylation site [posttranslational modification] 1105109000806 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 1105109000807 ATP binding site [chemical binding]; other site 1105109000808 Mg2+ binding site [ion binding]; other site 1105109000809 G-X-G motif; other site 1105109000810 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105109000811 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105109000812 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105109000813 Trp docking motif [polypeptide binding]; other site 1105109000814 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 1105109000815 23S rRNA interface [nucleotide binding]; other site 1105109000816 L3 interface [polypeptide binding]; other site 1105109000817 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1105109000818 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 1105109000819 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 1105109000820 DCoH dimer interaction site [polypeptide binding]; other site 1105109000821 aromatic arch; other site 1105109000822 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105109000823 DCoH tetramer interaction site [polypeptide binding]; other site 1105109000824 substrate binding site [chemical binding]; other site 1105109000825 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 1105109000826 putative active site [active] 1105109000827 Ap4A binding site [chemical binding]; other site 1105109000828 nudix motif; other site 1105109000829 putative metal binding site [ion binding]; other site 1105109000830 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105109000831 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 1105109000832 active site 1105109000833 phosphorylation site [posttranslational modification] 1105109000834 intermolecular recognition site; other site 1105109000835 dimerization interface [polypeptide binding]; other site 1105109000836 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 1105109000837 active site 1105109000838 phosphorylation site [posttranslational modification] 1105109000839 intermolecular recognition site; other site 1105109000840 dimerization interface [polypeptide binding]; other site 1105109000841 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105109000842 metal binding site [ion binding]; metal-binding site 1105109000843 active site 1105109000844 I-site; other site 1105109000845 elongation factor P; Validated; Region: PRK00529 1105109000846 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105109000847 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 1105109000848 RNA binding site [nucleotide binding]; other site 1105109000849 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 1105109000850 RNA binding site [nucleotide binding]; other site 1105109000851 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105109000852 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 1105109000853 active site 1105109000854 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105109000855 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 1105109000856 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105109000857 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1105109000858 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1105109000859 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105109000860 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105109000861 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105109000862 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 1105109000863 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105109000864 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105109000865 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105109000866 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105109000867 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105109000868 FAD binding domain; Region: FAD_binding_4; pfam01565 1105109000869 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105109000870 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105109000871 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105109000872 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1105109000873 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1105109000874 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105109000875 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105109000876 cell division protein FtsA; Region: ftsA; TIGR01174 1105109000877 Cell division protein FtsA; Region: FtsA; smart00842 1105109000878 Cell division protein FtsA; Region: FtsA; pfam14450 1105109000879 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1105109000880 Cytochrome c2 [Energy production and conversion]; Region: COG3474 1105109000881 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1105109000882 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105109000883 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 1105109000884 RNA binding site [nucleotide binding]; other site 1105109000885 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 1105109000886 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 1105109000887 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105109000888 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 1105109000889 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105109000890 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 1105109000891 RNA binding surface [nucleotide binding]; other site 1105109000892 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105109000893 active site 1105109000894 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 1105109000895 Beta-lactamase; Region: Beta-lactamase; pfam00144 1105109000896 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 1105109000897 putative catalytic site [active] 1105109000898 putative phosphate binding site [ion binding]; other site 1105109000899 active site 1105109000900 metal binding site A [ion binding]; metal-binding site 1105109000901 DNA binding site [nucleotide binding] 1105109000902 putative AP binding site [nucleotide binding]; other site 1105109000903 putative metal binding site B [ion binding]; other site 1105109000904 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105109000905 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 1105109000906 tetramer interface [polypeptide binding]; other site 1105109000907 TPP-binding site [chemical binding]; other site 1105109000908 heterodimer interface [polypeptide binding]; other site 1105109000909 phosphorylation loop region [posttranslational modification] 1105109000910 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105109000911 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 1105109000912 alpha subunit interface [polypeptide binding]; other site 1105109000913 TPP binding site [chemical binding]; other site 1105109000914 heterodimer interface [polypeptide binding]; other site 1105109000915 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105109000916 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1105109000917 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105109000918 G1 box; other site 1105109000919 putative GEF interaction site [polypeptide binding]; other site 1105109000920 GTP/Mg2+ binding site [chemical binding]; other site 1105109000921 Switch I region; other site 1105109000922 G2 box; other site 1105109000923 G3 box; other site 1105109000924 Switch II region; other site 1105109000925 G4 box; other site 1105109000926 G5 box; other site 1105109000927 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 1105109000928 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 1105109000929 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 1105109000930 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105109000931 isocitrate dehydrogenase; Validated; Region: PRK09222 1105109000932 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 1105109000933 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 1105109000934 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105109000935 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 1105109000936 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105109000937 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105109000938 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105109000939 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105109000940 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 1105109000941 [2Fe-2S] cluster binding site [ion binding]; other site 1105109000942 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 1105109000943 Qi binding site; other site 1105109000944 cytochrome b; Provisional; Region: CYTB; MTH00191 1105109000945 intrachain domain interface; other site 1105109000946 interchain domain interface [polypeptide binding]; other site 1105109000947 heme bH binding site [chemical binding]; other site 1105109000948 heme bL binding site [chemical binding]; other site 1105109000949 Qo binding site; other site 1105109000950 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 1105109000951 interchain domain interface [polypeptide binding]; other site 1105109000952 intrachain domain interface; other site 1105109000953 Qi binding site; other site 1105109000954 Qo binding site; other site 1105109000955 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105109000956 catalytic site [active] 1105109000957 metal binding site [ion binding]; metal-binding site 1105109000958 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105109000959 Cytochrome c; Region: Cytochrom_C; cl11414 1105109000960 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1105109000961 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 1105109000962 putative dimer interface [polypeptide binding]; other site 1105109000963 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105109000964 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105109000965 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105109000966 PCRF domain; Region: PCRF; pfam03462 1105109000967 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105109000968 RF-1 domain; Region: RF-1; pfam00472 1105109000969 GTP-binding protein LepA; Provisional; Region: PRK05433 1105109000970 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105109000971 G1 box; other site 1105109000972 putative GEF interaction site [polypeptide binding]; other site 1105109000973 GTP/Mg2+ binding site [chemical binding]; other site 1105109000974 Switch I region; other site 1105109000975 G2 box; other site 1105109000976 G3 box; other site 1105109000977 Switch II region; other site 1105109000978 G4 box; other site 1105109000979 G5 box; other site 1105109000980 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 1105109000981 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 1105109000982 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105109000983 Overlaps tRNA on opposite strand. 1105109000984 Phage capsid family; Region: Phage_capsid; pfam05065 1105109000985 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105109000986 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105109000987 HD domain; Region: HD_4; pfam13328 1105109000988 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109000989 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1105109000990 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105109000991 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105109000992 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105109000993 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105109000994 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105109000995 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 1105109000996 oligomeric interface; other site 1105109000997 putative active site [active] 1105109000998 homodimer interface [polypeptide binding]; other site 1105109000999 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105109001000 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105109001001 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105109001002 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105109001003 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 1105109001004 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105109001005 VirB7 interaction site; other site 1105109001006 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105109001007 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105109001008 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105109001009 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1105109001010 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1105109001011 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 1105109001012 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 1105109001013 Walker A motif; other site 1105109001014 hexamer interface [polypeptide binding]; other site 1105109001015 ATP binding site [chemical binding]; other site 1105109001016 Walker B motif; other site 1105109001017 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105109001018 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 1105109001019 Walker A motif; other site 1105109001020 ATP binding site [chemical binding]; other site 1105109001021 Walker B motif; other site 1105109001022 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105109001023 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1105109001024 Phage-related protein [Function unknown]; Region: COG4695; cl01923 1105109001025 Phage portal protein; Region: Phage_portal; pfam04860 1105109001026 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105109001027 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105109001028 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105109001029 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 1105109001030 active site 1105109001031 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105109001032 MutS domain I; Region: MutS_I; pfam01624 1105109001033 MutS domain II; Region: MutS_II; pfam05188 1105109001034 MutS domain III; Region: MutS_III; pfam05192 1105109001035 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1105109001036 Walker A/P-loop; other site 1105109001037 ATP binding site [chemical binding]; other site 1105109001038 Q-loop/lid; other site 1105109001039 ABC transporter signature motif; other site 1105109001040 Walker B; other site 1105109001041 D-loop; other site 1105109001042 H-loop/switch region; other site 1105109001043 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105109001044 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105109001045 Protein of unknown function DUF45; Region: DUF45; pfam01863 1105109001046 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1105109001047 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105109001048 TolB amino-terminal domain; Region: TolB_N; pfam04052 1105109001049 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105109001050 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105109001051 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105109001052 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105109001053 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105109001054 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105109001055 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 1105109001056 DNA binding residues [nucleotide binding] 1105109001057 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 1105109001058 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1105109001059 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 1105109001060 Ligand Binding Site [chemical binding]; other site 1105109001061 amino acid transporter; Region: 2A0306; TIGR00909 1105109001062 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105109001063 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 1105109001064 dimer interface [polypeptide binding]; other site 1105109001065 motif 1; other site 1105109001066 active site 1105109001067 motif 2; other site 1105109001068 motif 3; other site 1105109001069 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 1105109001070 anticodon binding site; other site 1105109001071 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109001072 Walker A/P-loop; other site 1105109001073 ATP binding site [chemical binding]; other site 1105109001074 Q-loop/lid; other site 1105109001075 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105109001076 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105109001077 TolQ protein; Region: tolQ; TIGR02796 1105109001078 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1105109001079 TolR protein; Region: tolR; TIGR02801 1105109001080 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1105109001081 CAAX protease self-immunity; Region: Abi; cl00558 1105109001082 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105109001083 HD domain; Region: HD_4; pfam13328 1105109001084 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 1105109001085 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109001086 putative substrate translocation pore; other site 1105109001087 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105109001088 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 1105109001089 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105109001090 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105109001091 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1105109001092 Walker A/P-loop; other site 1105109001093 ATP binding site [chemical binding]; other site 1105109001094 Q-loop/lid; other site 1105109001095 ABC transporter signature motif; other site 1105109001096 Walker B; other site 1105109001097 D-loop; other site 1105109001098 H-loop/switch region; other site 1105109001099 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105109001100 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1105109001101 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 1105109001102 nucleotide binding site/active site [active] 1105109001103 HIT family signature motif; other site 1105109001104 catalytic residue [active] 1105109001105 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105109001106 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105109001107 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 1105109001108 active site 1105109001109 HslU subunit interaction site [polypeptide binding]; other site 1105109001110 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105109001111 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 1105109001112 Walker A motif; other site 1105109001113 ATP binding site [chemical binding]; other site 1105109001114 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1105109001115 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105109001116 potential frameshift: common BLAST hit: gi|91205630|ref|YP_537985.1| Mg chelatase-like protein 1105109001117 potential frameshift: common BLAST hit: gi|67458910|ref|YP_246534.1| Mg chelatase-like protein 1105109001118 potential frameshift: common BLAST hit: gi|157827341|ref|YP_001496405.1| Mg chelatase-like protein 1105109001119 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105109001120 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105109001121 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105109001122 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105109001123 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1105109001124 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105109001125 dimerization interface [polypeptide binding]; other site 1105109001126 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 1105109001127 putative iron binding site [ion binding]; other site 1105109001128 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105109001129 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 1105109001130 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 1105109001131 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105109001132 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105109001133 HIGH motif; other site 1105109001134 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105109001135 active site 1105109001136 KMSKS motif; other site 1105109001137 DNA topoisomerase I; Validated; Region: PRK06599 1105109001138 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 1105109001139 active site 1105109001140 interdomain interaction site; other site 1105109001141 putative metal-binding site [ion binding]; other site 1105109001142 nucleotide binding site [chemical binding]; other site 1105109001143 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 1105109001144 domain I; other site 1105109001145 DNA binding groove [nucleotide binding] 1105109001146 phosphate binding site [ion binding]; other site 1105109001147 domain II; other site 1105109001148 domain III; other site 1105109001149 nucleotide binding site [chemical binding]; other site 1105109001150 catalytic site [active] 1105109001151 domain IV; other site 1105109001152 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105109001153 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 1105109001154 DNA protecting protein DprA; Region: dprA; TIGR00732 1105109001155 DNA protecting protein DprA; Region: dprA; TIGR00732 1105109001156 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105109001157 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 1105109001158 dimer interface [polypeptide binding]; other site 1105109001159 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105109001160 catalytic triad [active] 1105109001161 peroxidatic and resolving cysteines [active] 1105109001162 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105109001163 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 1105109001164 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105109001165 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105109001166 Sulfatase; Region: Sulfatase; pfam00884 1105109001167 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 1105109001168 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 1105109001169 sequence-specific DNA binding site [nucleotide binding]; other site 1105109001170 salt bridge; other site 1105109001171 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105109001172 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105109001173 NADP binding site [chemical binding]; other site 1105109001174 active site 1105109001175 putative substrate binding site [chemical binding]; other site 1105109001176 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105109001177 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105109001178 NAD(P) binding site [chemical binding]; other site 1105109001179 homodimer interface [polypeptide binding]; other site 1105109001180 substrate binding site [chemical binding]; other site 1105109001181 active site 1105109001182 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105109001183 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105109001184 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 1105109001185 active site 1105109001186 homodimer interface [polypeptide binding]; other site 1105109001187 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105109001188 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 1105109001189 S-adenosylmethionine binding site [chemical binding]; other site 1105109001190 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105109001191 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 1105109001192 active site 1105109001193 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105109001194 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 1105109001195 active site 1105109001196 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 1105109001197 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105109001198 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105109001199 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105109001200 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 1105109001201 catalytic site [active] 1105109001202 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105109001203 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 1105109001204 putative ADP-binding pocket [chemical binding]; other site 1105109001205 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105109001206 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105109001207 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 1105109001208 RNA binding surface [nucleotide binding]; other site 1105109001209 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 1105109001210 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105109001211 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 1105109001212 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105109001213 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105109001214 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 1105109001215 TPR motif; other site 1105109001216 binding surface 1105109001217 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105109001218 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105109001219 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105109001220 RimM N-terminal domain; Region: RimM; pfam01782 1105109001221 PRC-barrel domain; Region: PRC; pfam05239 1105109001222 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105109001223 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1105109001224 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 1105109001225 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105109001226 active site 1105109001227 DNA binding site [nucleotide binding] 1105109001228 hypothetical protein; Provisional; Region: PRK14388 1105109001229 NADH dehydrogenase subunit E; Validated; Region: PRK07539 1105109001230 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 1105109001231 putative dimer interface [polypeptide binding]; other site 1105109001232 [2Fe-2S] cluster binding site [ion binding]; other site 1105109001233 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 1105109001234 GIY-YIG motif/motif A; other site 1105109001235 putative active site [active] 1105109001236 putative metal binding site [ion binding]; other site 1105109001237 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 1105109001238 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1105109001239 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105109001240 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1105109001241 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1105109001242 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1105109001243 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105109001244 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 1105109001245 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105109001246 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105109001247 Overlaps tRNA on same strand. 1105109001248 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105109001249 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 1105109001250 active site 1105109001251 DNA binding site [nucleotide binding] 1105109001252 Int/Topo IB signature motif; other site 1105109001253 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 1105109001254 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105109001255 NAD binding site [chemical binding]; other site 1105109001256 homotetramer interface [polypeptide binding]; other site 1105109001257 homodimer interface [polypeptide binding]; other site 1105109001258 substrate binding site [chemical binding]; other site 1105109001259 active site 1105109001260 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105109001261 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105109001262 putative active site [active] 1105109001263 catalytic triad [active] 1105109001264 putative dimer interface [polypeptide binding]; other site 1105109001265 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105109001266 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 1105109001267 amidase catalytic site [active] 1105109001268 Zn binding residues [ion binding]; other site 1105109001269 substrate binding site [chemical binding]; other site 1105109001270 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105109001271 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 1105109001272 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 1105109001273 TM-ABC transporter signature motif; other site 1105109001274 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1105109001275 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 1105109001276 Walker A/P-loop; other site 1105109001277 ATP binding site [chemical binding]; other site 1105109001278 Q-loop/lid; other site 1105109001279 ABC transporter signature motif; other site 1105109001280 Walker B; other site 1105109001281 D-loop; other site 1105109001282 H-loop/switch region; other site 1105109001283 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 1105109001284 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 1105109001285 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105109001286 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105109001287 active site 1105109001288 HIGH motif; other site 1105109001289 KMSKS motif; other site 1105109001290 Predicted permeases [General function prediction only]; Region: COG0679 1105109001291 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105109001292 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105109001293 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105109001294 putative NAD(P) binding site [chemical binding]; other site 1105109001295 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 1105109001296 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 1105109001297 putative active site [active] 1105109001298 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105109001299 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109001300 malate dehydrogenase; Reviewed; Region: PRK06223 1105109001301 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105109001302 NAD(P) binding site [chemical binding]; other site 1105109001303 dimer interface [polypeptide binding]; other site 1105109001304 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105109001305 substrate binding site [chemical binding]; other site 1105109001306 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105109001307 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105109001308 CTP synthetase; Validated; Region: pyrG; PRK05380 1105109001309 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 1105109001310 Catalytic site [active] 1105109001311 active site 1105109001312 UTP binding site [chemical binding]; other site 1105109001313 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105109001314 active site 1105109001315 putative oxyanion hole; other site 1105109001316 catalytic triad [active] 1105109001317 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1105109001318 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105109001319 Ligand binding site; other site 1105109001320 oligomer interface; other site 1105109001321 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 1105109001322 nudix motif; other site 1105109001323 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 1105109001324 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105109001325 active site 1105109001326 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105109001327 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 1105109001328 dimer interface [polypeptide binding]; other site 1105109001329 motif 1; other site 1105109001330 active site 1105109001331 motif 2; other site 1105109001332 motif 3; other site 1105109001333 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 1105109001334 anticodon binding site; other site 1105109001335 Fic family protein [Function unknown]; Region: COG3177 1105109001336 Fic/DOC family; Region: Fic; pfam02661 1105109001337 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105109001338 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105109001339 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105109001340 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 1105109001341 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 1105109001342 Walker A motif; other site 1105109001343 ATP binding site [chemical binding]; other site 1105109001344 Walker B motif; other site 1105109001345 arginine finger; other site 1105109001346 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105109001347 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105109001348 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105109001349 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109001350 Walker A/P-loop; other site 1105109001351 ATP binding site [chemical binding]; other site 1105109001352 Q-loop/lid; other site 1105109001353 ABC transporter signature motif; other site 1105109001354 Walker B; other site 1105109001355 D-loop; other site 1105109001356 H-loop/switch region; other site 1105109001357 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105109001358 muropeptide transporter; Validated; Region: ampG; cl17669 1105109001359 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1105109001360 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105109001361 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109001362 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105109001363 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1105109001364 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1105109001365 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105109001366 BON domain; Region: BON; pfam04972 1105109001367 BON domain; Region: BON; pfam04972 1105109001368 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 1105109001369 Iron permease FTR1 family; Region: FTR1; cl00475 1105109001370 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 1105109001371 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105109001372 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105109001373 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 1105109001374 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 1105109001375 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1105109001376 catalytic residues [active] 1105109001377 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 1105109001378 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105109001379 tandem repeat interface [polypeptide binding]; other site 1105109001380 oligomer interface [polypeptide binding]; other site 1105109001381 active site residues [active] 1105109001382 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105109001383 trimer interface [polypeptide binding]; other site 1105109001384 active site 1105109001385 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105109001386 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 1105109001387 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105109001388 catalytic residue [active] 1105109001389 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105109001390 dimer interface [polypeptide binding]; other site 1105109001391 catalytic triad [active] 1105109001392 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105109001393 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 1105109001394 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105109001395 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105109001396 catalytic triad [active] 1105109001397 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105109001398 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 1105109001399 Subunit I/III interface [polypeptide binding]; other site 1105109001400 D-pathway; other site 1105109001401 Subunit I/VIIc interface [polypeptide binding]; other site 1105109001402 Subunit I/IV interface [polypeptide binding]; other site 1105109001403 Subunit I/II interface [polypeptide binding]; other site 1105109001404 Low-spin heme (heme a) binding site [chemical binding]; other site 1105109001405 Subunit I/VIIa interface [polypeptide binding]; other site 1105109001406 Subunit I/VIa interface [polypeptide binding]; other site 1105109001407 Dimer interface; other site 1105109001408 Putative water exit pathway; other site 1105109001409 Binuclear center (heme a3/CuB) [ion binding]; other site 1105109001410 K-pathway; other site 1105109001411 Subunit I/Vb interface [polypeptide binding]; other site 1105109001412 Putative proton exit pathway; other site 1105109001413 Subunit I/VIb interface; other site 1105109001414 Subunit I/VIc interface [polypeptide binding]; other site 1105109001415 Electron transfer pathway; other site 1105109001416 Subunit I/VIIIb interface [polypeptide binding]; other site 1105109001417 Subunit I/VIIb interface [polypeptide binding]; other site 1105109001418 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 1105109001419 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 1105109001420 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 1105109001421 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109001422 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105109001423 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105109001424 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1105109001425 putative peptidase; Provisional; Region: PRK11649 1105109001426 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105109001427 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1105109001428 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1105109001429 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105109001430 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105109001431 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105109001432 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105109001433 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105109001434 cell division protein FtsW; Region: ftsW; TIGR02614 1105109001435 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105109001436 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 1105109001437 active site 1105109001438 homodimer interface [polypeptide binding]; other site 1105109001439 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105109001440 potential frameshift: common BLAST hit: gi|378723966|ref|YP_005288850.1| acriflavin resistance plasma membrane protein 1105109001441 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105109001442 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105109001443 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105109001444 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105109001445 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105109001446 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1105109001447 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105109001448 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1105109001449 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 1105109001450 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 1105109001451 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105109001452 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105109001453 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105109001454 diaminopimelate epimerase; Region: DapF; TIGR00652 1105109001455 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105109001456 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105109001457 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105109001458 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105109001459 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 1105109001460 FeS/SAM binding site; other site 1105109001461 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105109001462 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105109001463 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 1105109001464 dimer interface [polypeptide binding]; other site 1105109001465 motif 1; other site 1105109001466 active site 1105109001467 motif 2; other site 1105109001468 motif 3; other site 1105109001469 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105109001470 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 1105109001471 putative tRNA-binding site [nucleotide binding]; other site 1105109001472 B3/4 domain; Region: B3_4; pfam03483 1105109001473 tRNA synthetase B5 domain; Region: B5; smart00874 1105109001474 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 1105109001475 dimer interface [polypeptide binding]; other site 1105109001476 motif 1; other site 1105109001477 motif 3; other site 1105109001478 motif 2; other site 1105109001479 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1105109001480 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 1105109001481 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105109001482 putative DNA binding surface [nucleotide binding]; other site 1105109001483 dimer interface [polypeptide binding]; other site 1105109001484 beta-clamp/clamp loader binding surface; other site 1105109001485 beta-clamp/translesion DNA polymerase binding surface; other site 1105109001486 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105109001487 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105109001488 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105109001489 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105109001490 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105109001491 HIGH motif; other site 1105109001492 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105109001493 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105109001494 active site 1105109001495 KMSKS motif; other site 1105109001496 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105109001497 tRNA binding surface [nucleotide binding]; other site 1105109001498 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109001499 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105109001500 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105109001501 catalytic site [active] 1105109001502 putative active site [active] 1105109001503 putative substrate binding site [chemical binding]; other site 1105109001504 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 1105109001505 Septum formation initiator; Region: DivIC; pfam04977 1105109001506 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1105109001507 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1105109001508 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 1105109001509 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105109001510 catalytic residue [active] 1105109001511 putative FPP diphosphate binding site; other site 1105109001512 putative FPP binding hydrophobic cleft; other site 1105109001513 dimer interface [polypeptide binding]; other site 1105109001514 putative IPP diphosphate binding site; other site 1105109001515 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105109001516 HAMP domain; Region: HAMP; pfam00672 1105109001517 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 1105109001518 dimer interface [polypeptide binding]; other site 1105109001519 phosphorylation site [posttranslational modification] 1105109001520 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 1105109001521 ATP binding site [chemical binding]; other site 1105109001522 Mg2+ binding site [ion binding]; other site 1105109001523 G-X-G motif; other site 1105109001524 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105109001525 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 1105109001526 active site 1105109001527 phosphorylation site [posttranslational modification] 1105109001528 intermolecular recognition site; other site 1105109001529 dimerization interface [polypeptide binding]; other site 1105109001530 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 1105109001531 DNA binding site [nucleotide binding] 1105109001532 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1105109001533 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 1105109001534 homodimer interface [polypeptide binding]; other site 1105109001535 substrate-cofactor binding pocket; other site 1105109001536 catalytic residue [active] 1105109001537 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105109001538 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105109001539 dimer interface [polypeptide binding]; other site 1105109001540 active site 1105109001541 catalytic residue [active] 1105109001542 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 1105109001543 SmpB-tmRNA interface; other site 1105109001544 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 1105109001545 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105109001546 catalytic residues [active] 1105109001547 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105109001548 CoA binding domain; Region: CoA_binding; pfam02629 1105109001549 CoA-ligase; Region: Ligase_CoA; pfam00549 1105109001550 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105109001551 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1105109001552 CoA-ligase; Region: Ligase_CoA; pfam00549 1105109001553 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 1105109001554 putative active site [active] 1105109001555 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 1105109001556 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105109001557 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 1105109001558 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105109001559 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105109001560 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 1105109001561 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105109001562 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1105109001563 Predicted membrane protein [Function unknown]; Region: COG1238 1105109001564 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1105109001565 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 1105109001566 RecR protein; Region: RecR; pfam02132 1105109001567 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 1105109001568 putative active site [active] 1105109001569 putative metal-binding site [ion binding]; other site 1105109001570 tetramer interface [polypeptide binding]; other site 1105109001571 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 1105109001572 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105109001573 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1105109001574 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105109001575 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105109001576 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1105109001577 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105109001578 Predicted permeases [General function prediction only]; Region: COG0679 1105109001579 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1105109001580 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105109001581 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105109001582 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105109001583 potential frameshift: common BLAST hit: gi|15892544|ref|NP_360258.1| succinate semialdehyde dehydrogenase 1105109001584 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105109001585 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 1105109001586 active site 1105109001587 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1105109001588 Part of AAA domain; Region: AAA_19; pfam13245 1105109001589 Family description; Region: UvrD_C_2; pfam13538 1105109001590 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 1105109001591 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105109001592 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 1105109001593 tetramer interface [polypeptide binding]; other site 1105109001594 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105109001595 catalytic residue [active] 1105109001596 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105109001597 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105109001598 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 1105109001599 Walker A motif; other site 1105109001600 ATP binding site [chemical binding]; other site 1105109001601 Walker B motif; other site 1105109001602 arginine finger; other site 1105109001603 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1105109001604 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 1105109001605 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 1105109001606 30S subunit binding site; other site 1105109001607 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 1105109001608 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 1105109001609 trimer interface [polypeptide binding]; other site 1105109001610 putative metal binding site [ion binding]; other site 1105109001611 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105109001612 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105109001613 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105109001614 homodimer interface [polypeptide binding]; other site 1105109001615 NADP binding site [chemical binding]; other site 1105109001616 substrate binding site [chemical binding]; other site 1105109001617 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105109001618 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105109001619 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105109001620 potential frameshift: common BLAST hit: gi|165933233|ref|YP_001650022.1| protein U 1105109001621 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105109001622 potential frameshift: common BLAST hit: gi|157827080|ref|YP_001496144.1| P pilus assembly, fimbrial usher protein 1105109001623 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105109001624 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105109001625 Spore Coat Protein U domain; Region: SCPU; pfam05229 1105109001626 Chitin binding domain; Region: Chitin_bind_3; cl03871 1105109001627 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105109001628 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105109001629 active site 1105109001630 dimer interface [polypeptide binding]; other site 1105109001631 catalytic residues [active] 1105109001632 effector binding site; other site 1105109001633 R2 peptide binding site; other site 1105109001634 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105109001635 dimer interface [polypeptide binding]; other site 1105109001636 putative radical transfer pathway; other site 1105109001637 diiron center [ion binding]; other site 1105109001638 tyrosyl radical; other site 1105109001639 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1105109001640 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1105109001641 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105109001642 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105109001643 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 1105109001644 active site 1105109001645 substrate binding site [chemical binding]; other site 1105109001646 metal binding site [ion binding]; metal-binding site 1105109001647 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105109001648 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109001649 Walker A/P-loop; other site 1105109001650 ATP binding site [chemical binding]; other site 1105109001651 Q-loop/lid; other site 1105109001652 ABC transporter signature motif; other site 1105109001653 Walker B; other site 1105109001654 D-loop; other site 1105109001655 H-loop/switch region; other site 1105109001656 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109001657 OstA-like protein; Region: OstA; pfam03968 1105109001658 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105109001659 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 1105109001660 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 1105109001661 putative active site [active] 1105109001662 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 1105109001663 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105109001664 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 1105109001665 oligomer interface [polypeptide binding]; other site 1105109001666 RNA binding site [nucleotide binding]; other site 1105109001667 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105109001668 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105109001669 RNase E interface [polypeptide binding]; other site 1105109001670 trimer interface [polypeptide binding]; other site 1105109001671 active site 1105109001672 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 1105109001673 putative nucleic acid binding region [nucleotide binding]; other site 1105109001674 G-X-X-G motif; other site 1105109001675 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 1105109001676 RNA binding site [nucleotide binding]; other site 1105109001677 domain interface; other site 1105109001678 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 1105109001679 16S/18S rRNA binding site [nucleotide binding]; other site 1105109001680 S13e-L30e interaction site [polypeptide binding]; other site 1105109001681 25S rRNA binding site [nucleotide binding]; other site 1105109001682 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105109001683 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105109001684 RNA binding site [nucleotide binding]; other site 1105109001685 active site 1105109001686 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109001687 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105109001688 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105109001689 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1105109001690 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 1105109001691 non-specific DNA binding site [nucleotide binding]; other site 1105109001692 salt bridge; other site 1105109001693 sequence-specific DNA binding site [nucleotide binding]; other site 1105109001694 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 1105109001695 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1105109001696 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105109001697 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105109001698 uncharacterized protein, YfiH family; Region: TIGR00726 1105109001699 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 1105109001700 active site 1105109001701 catalytic residues [active] 1105109001702 metal binding site [ion binding]; metal-binding site 1105109001703 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109001704 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105109001705 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105109001706 putative active site [active] 1105109001707 homotetrameric interface [polypeptide binding]; other site 1105109001708 metal binding site [ion binding]; metal-binding site 1105109001709 hypothetical protein; Provisional; Region: PRK06661 1105109001710 intersubunit interface [polypeptide binding]; other site 1105109001711 active site 1105109001712 Zn2+ binding site [ion binding]; other site 1105109001713 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105109001714 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105109001715 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1105109001716 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1105109001717 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105109001718 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 1105109001719 GSH binding site (G-site) [chemical binding]; other site 1105109001720 C-terminal domain interface [polypeptide binding]; other site 1105109001721 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105109001722 N-terminal domain interface [polypeptide binding]; other site 1105109001723 dimer interface [polypeptide binding]; other site 1105109001724 substrate binding pocket (H-site) [chemical binding]; other site 1105109001725 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105109001726 conserved cys residue [active] 1105109001727 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 1105109001728 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1105109001729 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105109001730 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105109001731 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105109001732 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105109001733 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105109001734 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105109001735 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105109001736 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105109001737 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1105109001738 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105109001739 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 1105109001740 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1105109001741 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105109001742 Predicted membrane protein [Function unknown]; Region: COG5346 1105109001743 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1105109001744 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105109001745 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105109001746 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 1105109001747 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105109001748 E3 interaction surface; other site 1105109001749 lipoyl attachment site [posttranslational modification]; other site 1105109001750 e3 binding domain; Region: E3_binding; pfam02817 1105109001751 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105109001752 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105109001753 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1105109001754 RF-1 domain; Region: RF-1; pfam00472 1105109001755 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105109001756 DHH family; Region: DHH; pfam01368 1105109001757 DHHA1 domain; Region: DHHA1; pfam02272 1105109001758 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 1105109001759 S-adenosylmethionine binding site [chemical binding]; other site 1105109001760 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105109001761 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105109001762 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1105109001763 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 1105109001764 RNA binding site [nucleotide binding]; other site 1105109001765 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 1105109001766 multimer interface [polypeptide binding]; other site 1105109001767 Walker A motif; other site 1105109001768 ATP binding site [chemical binding]; other site 1105109001769 Walker B motif; other site 1105109001770 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1105109001771 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105109001772 tandem repeat interface [polypeptide binding]; other site 1105109001773 oligomer interface [polypeptide binding]; other site 1105109001774 active site residues [active] 1105109001775 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 1105109001776 IHF - DNA interface [nucleotide binding]; other site 1105109001777 IHF dimer interface [polypeptide binding]; other site 1105109001778 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 1105109001779 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 1105109001780 non-specific DNA binding site [nucleotide binding]; other site 1105109001781 salt bridge; other site 1105109001782 sequence-specific DNA binding site [nucleotide binding]; other site 1105109001783 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 1105109001784 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 1105109001785 CMP-binding site; other site 1105109001786 The sites determining sugar specificity; other site 1105109001787 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105109001788 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 1105109001789 RNA binding site [nucleotide binding]; other site 1105109001790 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 1105109001791 RNA binding site [nucleotide binding]; other site 1105109001792 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 1105109001793 RNA binding site [nucleotide binding]; other site 1105109001794 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 1105109001795 RNA binding site [nucleotide binding]; other site 1105109001796 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 1105109001797 RNA binding site [nucleotide binding]; other site 1105109001798 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 1105109001799 RNA binding site [nucleotide binding]; other site 1105109001800 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1105109001801 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105109001802 oligomer interface [polypeptide binding]; other site 1105109001803 active site residues [active] 1105109001804 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105109001805 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 1105109001806 homotetramer interface [polypeptide binding]; other site 1105109001807 FMN binding site [chemical binding]; other site 1105109001808 homodimer contacts [polypeptide binding]; other site 1105109001809 putative active site [active] 1105109001810 putative substrate binding site [chemical binding]; other site 1105109001811 Predicted acetyltransferase [General function prediction only]; Region: COG5628 1105109001812 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105109001813 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1105109001814 Coenzyme A binding pocket [chemical binding]; other site 1105109001815 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105109001816 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105109001817 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105109001818 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105109001819 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 1105109001820 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1105109001821 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105109001822 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105109001823 catalytic residue [active] 1105109001824 cysteine desulfurase; Provisional; Region: PRK14012 1105109001825 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105109001826 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105109001827 catalytic residue [active] 1105109001828 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105109001829 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105109001830 trimerization site [polypeptide binding]; other site 1105109001831 active site 1105109001832 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105109001833 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1105109001834 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105109001835 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105109001836 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105109001837 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 1105109001838 active site 1105109001839 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105109001840 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105109001841 substrate binding pocket [chemical binding]; other site 1105109001842 chain length determination region; other site 1105109001843 substrate-Mg2+ binding site; other site 1105109001844 catalytic residues [active] 1105109001845 aspartate-rich region 1; other site 1105109001846 active site lid residues [active] 1105109001847 aspartate-rich region 2; other site 1105109001848 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105109001849 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1105109001850 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1105109001851 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 1105109001852 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105109001853 potential frameshift: common BLAST hit: gi|157828595|ref|YP_001494837.1| transposase 1105109001854 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105109001855 AmpG-like permease; Region: 2A0125; TIGR00901 1105109001856 Lysine efflux permease [General function prediction only]; Region: COG1279 1105109001857 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105109001858 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 1105109001859 active site 1105109001860 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105109001861 HemY protein N-terminus; Region: HemY_N; pfam07219 1105109001862 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105109001863 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105109001864 RelB antitoxin; Region: RelB; cl01171 1105109001865 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 1105109001866 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1105109001867 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105109001868 putative acyl-acceptor binding pocket; other site 1105109001869 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105109001870 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105109001871 active site 1105109001872 HIGH motif; other site 1105109001873 dimer interface [polypeptide binding]; other site 1105109001874 KMSKS motif; other site 1105109001875 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 1105109001876 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105109001877 AAA domain; Region: AAA_14; pfam13173 1105109001878 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105109001879 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 1105109001880 domain interfaces; other site 1105109001881 active site 1105109001882 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105109001883 dimer interface [polypeptide binding]; other site 1105109001884 catalytic triad [active] 1105109001885 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 1105109001886 ATP binding site [chemical binding]; other site 1105109001887 G-X-G motif; other site 1105109001888 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 1105109001889 dimer interface [polypeptide binding]; other site 1105109001890 phosphorylation site [posttranslational modification] 1105109001891 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105109001892 Na binding site [ion binding]; other site 1105109001893 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105109001894 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105109001895 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105109001896 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105109001897 Uncharacterized conserved protein [Function unknown]; Region: COG1723 1105109001898 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105109001899 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105109001900 catalytic site [active] 1105109001901 putative active site [active] 1105109001902 putative substrate binding site [chemical binding]; other site 1105109001903 Helicase and RNase D C-terminal; Region: HRDC; smart00341 1105109001904 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1105109001905 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1105109001906 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105109001907 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1105109001908 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105109001909 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105109001910 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1105109001911 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 1105109001912 S-adenosylmethionine binding site [chemical binding]; other site 1105109001913 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1105109001914 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 1105109001915 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105109001916 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105109001917 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 1105109001918 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105109001919 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 1105109001920 hypothetical protein; Validated; Region: PRK00110 1105109001921 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 1105109001922 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105109001923 Substrate binding site; other site 1105109001924 Mg++ binding site; other site 1105109001925 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 1105109001926 active site 1105109001927 homodimer interface [polypeptide binding]; other site 1105109001928 putative chemical substrate binding site [chemical binding]; other site 1105109001929 metal binding site [ion binding]; metal-binding site 1105109001930 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 1105109001931 Coenzyme A binding pocket [chemical binding]; other site 1105109001932 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105109001933 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105109001934 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 1105109001935 dimer interface [polypeptide binding]; other site 1105109001936 allosteric magnesium binding site [ion binding]; other site 1105109001937 active site 1105109001938 aspartate-rich active site metal binding site; other site 1105109001939 Schiff base residues; other site 1105109001940 primosome assembly protein PriA; Validated; Region: PRK05580 1105109001941 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 1105109001942 ATP binding site [chemical binding]; other site 1105109001943 putative Mg++ binding site [ion binding]; other site 1105109001944 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1105109001945 polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; Region: ubiX_pad; TIGR00421 1105109001946 Flavoprotein; Region: Flavoprotein; pfam02441 1105109001947 SacI restriction endonuclease; Region: RE_SacI; pfam09566 1105109001948 replicative DNA helicase; Provisional; Region: PRK09165 1105109001949 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105109001950 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 1105109001951 Walker A motif; other site 1105109001952 ATP binding site [chemical binding]; other site 1105109001953 Walker B motif; other site 1105109001954 DNA binding loops [nucleotide binding] 1105109001955 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105109001956 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105109001957 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105109001958 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 1105109001959 RNA binding surface [nucleotide binding]; other site 1105109001960 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105109001961 active site 1105109001962 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105109001963 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105109001964 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105109001965 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105109001966 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105109001967 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1105109001968 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 1105109001969 S-adenosylmethionine binding site [chemical binding]; other site 1105109001970 DNA repair protein RadA; Provisional; Region: PRK11823 1105109001971 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 1105109001972 Walker A motif/ATP binding site; other site 1105109001973 ATP binding site [chemical binding]; other site 1105109001974 Walker B motif; other site 1105109001975 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1105109001976 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105109001977 Recombination protein O N terminal; Region: RecO_N; pfam11967 1105109001978 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105109001979 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 1105109001980 Glycoprotease family; Region: Peptidase_M22; pfam00814 1105109001981 translation initiation factor IF-2; Validated; Region: infB; PRK05306 1105109001982 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105109001983 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105109001984 G1 box; other site 1105109001985 putative GEF interaction site [polypeptide binding]; other site 1105109001986 GTP/Mg2+ binding site [chemical binding]; other site 1105109001987 Switch I region; other site 1105109001988 G2 box; other site 1105109001989 G3 box; other site 1105109001990 Switch II region; other site 1105109001991 G4 box; other site 1105109001992 G5 box; other site 1105109001993 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 1105109001994 Translation-initiation factor 2; Region: IF-2; pfam11987 1105109001995 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 1105109001996 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105109001997 NusA N-terminal domain; Region: NusA_N; pfam08529 1105109001998 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 1105109001999 RNA binding site [nucleotide binding]; other site 1105109002000 homodimer interface [polypeptide binding]; other site 1105109002001 NusA-like KH domain; Region: KH_5; pfam13184 1105109002002 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 1105109002003 G-X-X-G motif; other site 1105109002004 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105109002005 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 1105109002006 Sm and related proteins; Region: Sm_like; cl00259 1105109002007 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1105109002008 putative oligomer interface [polypeptide binding]; other site 1105109002009 putative RNA binding site [nucleotide binding]; other site 1105109002010 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 1105109002011 NAD binding pocket [chemical binding]; other site 1105109002012 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105109002013 Transcriptional regulator; Region: Rrf2; cl17282 1105109002014 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105109002015 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 1105109002016 RNA binding surface [nucleotide binding]; other site 1105109002017 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1105109002018 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105109002019 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105109002020 active site 1105109002021 HIGH motif; other site 1105109002022 dimer interface [polypeptide binding]; other site 1105109002023 KMSKS motif; other site 1105109002024 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 1105109002025 RNA binding surface [nucleotide binding]; other site 1105109002026 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105109002027 phosphoenolpyruvate synthase; Validated; Region: PRK06241 1105109002028 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109002029 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 1105109002030 MG2 domain; Region: A2M_N; pfam01835 1105109002031 Alpha-2-macroglobulin family; Region: A2M; pfam00207 1105109002032 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 1105109002033 surface patch; other site 1105109002034 thioester region; other site 1105109002035 specificity defining residues; other site 1105109002036 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 1105109002037 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105109002038 potential frameshift: common BLAST hit: gi|15892765|ref|NP_360479.1| 3-hydroxyacyl-CoA dehydrogenase (FadB) 1105109002039 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1105109002040 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1105109002041 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002042 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105109002043 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1105109002044 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 1105109002045 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105109002046 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 1105109002047 active site 1105109002048 phosphorylation site [posttranslational modification] 1105109002049 intermolecular recognition site; other site 1105109002050 dimerization interface [polypeptide binding]; other site 1105109002051 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 1105109002052 Walker A motif; other site 1105109002053 ATP binding site [chemical binding]; other site 1105109002054 Walker B motif; other site 1105109002055 arginine finger; other site 1105109002056 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1105109002057 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105109002058 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105109002059 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105109002060 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105109002061 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105109002062 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105109002063 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105109002064 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105109002065 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105109002066 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105109002067 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1105109002068 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 1105109002069 S-adenosylmethionine binding site [chemical binding]; other site 1105109002070 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105109002071 MraZ protein; Region: MraZ; pfam02381 1105109002072 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 1105109002073 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 1105109002074 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105109002075 Na binding site [ion binding]; other site 1105109002076 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105109002077 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105109002078 GIY-YIG motif/motif A; other site 1105109002079 active site 1105109002080 catalytic site [active] 1105109002081 putative DNA binding site [nucleotide binding]; other site 1105109002082 metal binding site [ion binding]; metal-binding site 1105109002083 UvrB/uvrC motif; Region: UVR; pfam02151 1105109002084 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 1105109002085 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105109002086 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 1105109002087 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 1105109002088 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105109002089 active site 1105109002090 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105109002091 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 1105109002092 active site 1105109002093 DNA binding site [nucleotide binding] 1105109002094 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1105109002095 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1105109002096 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1105109002097 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105109002098 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 1105109002099 DNA binding site [nucleotide binding] 1105109002100 active site 1105109002101 potential frameshift: common BLAST hit: gi|91205217|ref|YP_537572.1| Type I site-specific restriction-modification system, R 1105109002102 potential frameshift: common BLAST hit: gi|91205217|ref|YP_537572.1| Type I site-specific restriction-modification system, R 1105109002103 potential frameshift: common BLAST hit: gi|15892796|ref|NP_360510.1| type I restriction enzyme restriction subunit 1105109002104 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105109002105 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1105109002106 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1105109002107 SEC-C motif; Region: SEC-C; pfam02810 1105109002108 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 1105109002109 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1105109002110 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1105109002111 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 1105109002112 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105109002113 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 1105109002114 hinge; other site 1105109002115 active site 1105109002116 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105109002117 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 1105109002118 ATP binding site [chemical binding]; other site 1105109002119 Mg2+ binding site [ion binding]; other site 1105109002120 G-X-G motif; other site 1105109002121 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 1105109002122 anchoring element; other site 1105109002123 dimer interface [polypeptide binding]; other site 1105109002124 ATP binding site [chemical binding]; other site 1105109002125 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 1105109002126 active site 1105109002127 putative metal-binding site [ion binding]; other site 1105109002128 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105109002129 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105109002130 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 1105109002131 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 1105109002132 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105109002133 MgtE intracellular N domain; Region: MgtE_N; pfam03448 1105109002134 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 1105109002135 Divalent cation transporter; Region: MgtE; pfam01769 1105109002136 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105109002137 HD domain; Region: HD_4; pfam13328 1105109002138 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109002139 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105109002140 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1105109002141 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105109002142 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1105109002143 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105109002144 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 1105109002145 Cu(I) binding site [ion binding]; other site 1105109002146 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 1105109002147 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 1105109002148 dimer interface [polypeptide binding]; other site 1105109002149 substrate binding site [chemical binding]; other site 1105109002150 metal binding sites [ion binding]; metal-binding site 1105109002151 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002152 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1105109002153 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1105109002154 TraX protein; Region: TraX; pfam05857 1105109002155 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105109002156 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 1105109002157 ssDNA binding site; other site 1105109002158 generic binding surface II; other site 1105109002159 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 1105109002160 ATP binding site [chemical binding]; other site 1105109002161 putative Mg++ binding site [ion binding]; other site 1105109002162 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 1105109002163 nucleotide binding region [chemical binding]; other site 1105109002164 ATP-binding site [chemical binding]; other site 1105109002165 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1105109002166 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1105109002167 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 1105109002168 V-type ATP synthase subunit I; Validated; Region: PRK05771 1105109002169 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105109002170 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 1105109002171 Mg++ binding site [ion binding]; other site 1105109002172 putative catalytic motif [active] 1105109002173 putative substrate binding site [chemical binding]; other site 1105109002174 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1105109002175 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105109002176 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105109002177 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105109002178 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105109002179 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105109002180 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105109002181 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105109002182 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105109002183 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1105109002184 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 1105109002185 ATP binding site [chemical binding]; other site 1105109002186 putative Mg++ binding site [ion binding]; other site 1105109002187 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 1105109002188 nucleotide binding region [chemical binding]; other site 1105109002189 ATP-binding site [chemical binding]; other site 1105109002190 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1105109002191 Uncharacterized conserved protein [Function unknown]; Region: COG2938 1105109002192 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 1105109002193 active site residue [active] 1105109002194 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105109002195 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105109002196 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 1105109002197 Walker A motif; other site 1105109002198 ATP binding site [chemical binding]; other site 1105109002199 Walker B motif; other site 1105109002200 arginine finger; other site 1105109002201 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 1105109002202 DnaA box-binding interface [nucleotide binding]; other site 1105109002203 Patatin [General function prediction only]; Region: COG3621 1105109002204 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105109002205 active site 1105109002206 nucleophile elbow; other site 1105109002207 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105109002208 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105109002209 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 1105109002210 potential frameshift: common BLAST hit: gi|341584111|ref|YP_004764602.1| nucleotidyltransferase 1105109002211 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1105109002212 active site 1105109002213 NTP binding site [chemical binding]; other site 1105109002214 metal binding triad [ion binding]; metal-binding site 1105109002215 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105109002216 YchF GTPase; Region: YchF; cd01900 1105109002217 G1 box; other site 1105109002218 GTP/Mg2+ binding site [chemical binding]; other site 1105109002219 Switch I region; other site 1105109002220 G2 box; other site 1105109002221 Switch II region; other site 1105109002222 G3 box; other site 1105109002223 G4 box; other site 1105109002224 G5 box; other site 1105109002225 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 1105109002226 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105109002227 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 1105109002228 putative active site [active] 1105109002229 catalytic residue [active] 1105109002230 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105109002231 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105109002232 5S rRNA interface [nucleotide binding]; other site 1105109002233 CTC domain interface [polypeptide binding]; other site 1105109002234 L16 interface [polypeptide binding]; other site 1105109002235 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105109002236 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 1105109002237 FeS/SAM binding site; other site 1105109002238 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1105109002239 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105109002240 23S rRNA binding site [nucleotide binding]; other site 1105109002241 L21 binding site [polypeptide binding]; other site 1105109002242 L13 binding site [polypeptide binding]; other site 1105109002243 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1105109002244 ribonuclease P; Reviewed; Region: rnpA; PRK01492 1105109002245 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 1105109002246 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105109002247 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105109002248 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 1105109002249 Cl binding site [ion binding]; other site 1105109002250 oligomer interface [polypeptide binding]; other site 1105109002251 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 1105109002252 Phosphotransferase enzyme family; Region: APH; pfam01636 1105109002253 substrate binding site [chemical binding]; other site 1105109002254 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 1105109002255 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105109002256 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 1105109002257 dimerization interface [polypeptide binding]; other site 1105109002258 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 1105109002259 dimer interface [polypeptide binding]; other site 1105109002260 phosphorylation site [posttranslational modification] 1105109002261 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 1105109002262 ATP binding site [chemical binding]; other site 1105109002263 Mg2+ binding site [ion binding]; other site 1105109002264 G-X-G motif; other site 1105109002265 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 1105109002266 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105109002267 COQ9; Region: COQ9; pfam08511 1105109002268 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105109002269 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105109002270 HIGH motif; other site 1105109002271 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105109002272 active site 1105109002273 KMSKS motif; other site 1105109002274 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105109002275 tRNA binding surface [nucleotide binding]; other site 1105109002276 anticodon binding site; other site 1105109002277 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 1105109002278 TPR motif; other site 1105109002279 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105109002280 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105109002281 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1105109002282 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1105109002283 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 1105109002284 carboxyltransferase (CT) interaction site; other site 1105109002285 biotinylation site [posttranslational modification]; other site 1105109002286 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1105109002287 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1105109002288 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1105109002289 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105109002290 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 1105109002291 putative substrate translocation pore; other site 1105109002292 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105109002293 putative acyl-acceptor binding pocket; other site 1105109002294 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 1105109002295 acyl-activating enzyme (AAE) consensus motif; other site 1105109002296 putative AMP binding site [chemical binding]; other site 1105109002297 potential frameshift: common BLAST hit: gi|350273712|ref|YP_004885025.1| regulator of competence-specific genes tfoX 1105109002298 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1105109002299 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 1105109002300 ABC-ATPase subunit interface; other site 1105109002301 dimer interface [polypeptide binding]; other site 1105109002302 putative PBP binding regions; other site 1105109002303 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105109002304 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002305 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 1105109002306 S-adenosylmethionine binding site [chemical binding]; other site 1105109002307 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105109002308 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105109002309 HIGH motif; other site 1105109002310 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105109002311 active site 1105109002312 KMSKS motif; other site 1105109002313 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002314 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 1105109002315 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105109002316 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 1105109002317 ring oligomerisation interface [polypeptide binding]; other site 1105109002318 ATP/Mg binding site [chemical binding]; other site 1105109002319 stacking interactions; other site 1105109002320 hinge regions; other site 1105109002321 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 1105109002322 oligomerisation interface [polypeptide binding]; other site 1105109002323 mobile loop; other site 1105109002324 roof hairpin; other site 1105109002325 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 1105109002326 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105109002327 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105109002328 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105109002329 hexamer interface [polypeptide binding]; other site 1105109002330 active site 1105109002331 GrpE; Region: GrpE; pfam01025 1105109002332 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 1105109002333 dimer interface [polypeptide binding]; other site 1105109002334 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105109002335 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1105109002336 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105109002337 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 1105109002338 hypothetical protein; Validated; Region: PRK06620 1105109002339 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109002340 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109002341 potential frameshift: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 1105109002342 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1105109002343 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 1105109002344 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105109002345 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105109002346 alphaNTD - beta interaction site [polypeptide binding]; other site 1105109002347 alphaNTD homodimer interface [polypeptide binding]; other site 1105109002348 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105109002349 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1105109002350 30S ribosomal protein S11; Validated; Region: PRK05309 1105109002351 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105109002352 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1105109002353 adenylate kinase; Reviewed; Region: adk; PRK00279 1105109002354 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 1105109002355 AMP-binding site [chemical binding]; other site 1105109002356 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105109002357 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105109002358 SecY translocase; Region: SecY; pfam00344 1105109002359 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1105109002360 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 1105109002361 23S rRNA binding site [nucleotide binding]; other site 1105109002362 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105109002363 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105109002364 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105109002365 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 1105109002366 5S rRNA interface [nucleotide binding]; other site 1105109002367 23S rRNA interface [nucleotide binding]; other site 1105109002368 L5 interface [polypeptide binding]; other site 1105109002369 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105109002370 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105109002371 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105109002372 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1105109002373 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1105109002374 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105109002375 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105109002376 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105109002377 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105109002378 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1105109002379 RNA binding site [nucleotide binding]; other site 1105109002380 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1105109002381 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1105109002382 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 1105109002383 L23 interface [polypeptide binding]; other site 1105109002384 trigger factor interaction site; other site 1105109002385 23S rRNA interface [nucleotide binding]; other site 1105109002386 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 1105109002387 23S rRNA interface [nucleotide binding]; other site 1105109002388 5S rRNA interface [nucleotide binding]; other site 1105109002389 putative antibiotic binding site [chemical binding]; other site 1105109002390 L25 interface [polypeptide binding]; other site 1105109002391 L27 interface [polypeptide binding]; other site 1105109002392 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105109002393 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 1105109002394 G-X-X-G motif; other site 1105109002395 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105109002396 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 1105109002397 putative translocon binding site; other site 1105109002398 protein-rRNA interface [nucleotide binding]; other site 1105109002399 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1105109002400 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105109002401 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105109002402 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105109002403 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1105109002404 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1105109002405 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1105109002406 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1105109002407 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002408 elongation factor Tu; Reviewed; Region: PRK00049 1105109002409 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105109002410 G1 box; other site 1105109002411 GEF interaction site [polypeptide binding]; other site 1105109002412 GTP/Mg2+ binding site [chemical binding]; other site 1105109002413 Switch I region; other site 1105109002414 G2 box; other site 1105109002415 G3 box; other site 1105109002416 Switch II region; other site 1105109002417 G4 box; other site 1105109002418 G5 box; other site 1105109002419 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 1105109002420 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 1105109002421 Antibiotic Binding Site [chemical binding]; other site 1105109002422 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105109002423 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1105109002424 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1105109002425 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105109002426 Class II fumarases; Region: Fumarase_classII; cd01362 1105109002427 active site 1105109002428 tetramer interface [polypeptide binding]; other site 1105109002429 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105109002430 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105109002431 putative active site [active] 1105109002432 homotetrameric interface [polypeptide binding]; other site 1105109002433 cell division protein FtsZ; Validated; Region: PRK09330 1105109002434 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 1105109002435 nucleotide binding site [chemical binding]; other site 1105109002436 SulA interaction site; other site 1105109002437 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 1105109002438 secondary substrate binding site; other site 1105109002439 primary substrate binding site; other site 1105109002440 inhibition loop; other site 1105109002441 dimerization interface [polypeptide binding]; other site 1105109002442 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 1105109002443 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1105109002444 muropeptide transporter; Validated; Region: ampG; cl17669 1105109002445 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 1105109002446 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105109002447 ATP binding site [chemical binding]; other site 1105109002448 Mg++ binding site [ion binding]; other site 1105109002449 motif III; other site 1105109002450 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 1105109002451 nucleotide binding region [chemical binding]; other site 1105109002452 ATP-binding site [chemical binding]; other site 1105109002453 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 1105109002454 DNA-binding site [nucleotide binding]; DNA binding site 1105109002455 RNA-binding motif; other site 1105109002456 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1105109002457 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 1105109002458 S-adenosylmethionine binding site [chemical binding]; other site 1105109002459 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105109002460 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105109002461 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105109002462 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 1105109002463 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 1105109002464 generic binding surface II; other site 1105109002465 generic binding surface I; other site 1105109002466 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105109002467 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 1105109002468 putative catalytic site [active] 1105109002469 putative phosphate binding site [ion binding]; other site 1105109002470 active site 1105109002471 metal binding site A [ion binding]; metal-binding site 1105109002472 DNA binding site [nucleotide binding] 1105109002473 putative AP binding site [nucleotide binding]; other site 1105109002474 putative metal binding site B [ion binding]; other site 1105109002475 Uncharacterized conserved protein [Function unknown]; Region: COG4095 1105109002476 GTP-binding protein Der; Reviewed; Region: PRK00093 1105109002477 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105109002478 G1 box; other site 1105109002479 GTP/Mg2+ binding site [chemical binding]; other site 1105109002480 Switch I region; other site 1105109002481 G2 box; other site 1105109002482 Switch II region; other site 1105109002483 G3 box; other site 1105109002484 G4 box; other site 1105109002485 G5 box; other site 1105109002486 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105109002487 G1 box; other site 1105109002488 GTP/Mg2+ binding site [chemical binding]; other site 1105109002489 Switch I region; other site 1105109002490 G2 box; other site 1105109002491 G3 box; other site 1105109002492 Switch II region; other site 1105109002493 G4 box; other site 1105109002494 G5 box; other site 1105109002495 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105109002496 AAA domain; Region: AAA_14; pfam13173 1105109002497 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 1105109002498 ABC1 family; Region: ABC1; cl17513 1105109002499 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105109002500 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 1105109002501 S-adenosylmethionine binding site [chemical binding]; other site 1105109002502 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105109002503 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105109002504 DNA binding site [nucleotide binding] 1105109002505 catalytic residue [active] 1105109002506 H2TH interface [polypeptide binding]; other site 1105109002507 putative catalytic residues [active] 1105109002508 turnover-facilitating residue; other site 1105109002509 intercalation triad [nucleotide binding]; other site 1105109002510 8OG recognition residue [nucleotide binding]; other site 1105109002511 putative reading head residues; other site 1105109002512 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105109002513 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105109002514 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002515 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105109002516 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 1105109002517 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 1105109002518 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 1105109002519 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 1105109002520 potential frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 1105109002521 potential frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 1105109002522 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105109002523 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105109002524 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105109002525 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105109002526 active site 1105109002527 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105109002528 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105109002529 HIGH motif; other site 1105109002530 active site 1105109002531 KMSKS motif; other site 1105109002532 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105109002533 tRNA binding surface [nucleotide binding]; other site 1105109002534 anticodon binding site; other site 1105109002535 thymidylate kinase; Validated; Region: tmk; PRK00698 1105109002536 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 1105109002537 TMP-binding site; other site 1105109002538 ATP-binding site [chemical binding]; other site 1105109002539 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109002540 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 1105109002541 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105109002542 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105109002543 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105109002544 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105109002545 active site 1105109002546 HIGH motif; other site 1105109002547 nucleotide binding site [chemical binding]; other site 1105109002548 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105109002549 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105109002550 active site 1105109002551 KMSKS motif; other site 1105109002552 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105109002553 tRNA binding surface [nucleotide binding]; other site 1105109002554 anticodon binding site; other site 1105109002555 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105109002556 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105109002557 potential frameshift: common BLAST hit: gi|157804076|ref|YP_001492625.1| ATPase 1105109002558 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 1105109002559 RmuC family; Region: RmuC; pfam02646 1105109002560 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 1105109002561 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 1105109002562 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105109002563 potential frameshift: common BLAST hit: gi|165933666|ref|YP_001650455.1| protein involved in external DNA uptake 1105109002564 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1105109002565 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105109002566 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1105109002567 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1105109002568 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105109002569 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105109002570 putative acyl-acceptor binding pocket; other site 1105109002571 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105109002572 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 1105109002573 catalytic triad [active] 1105109002574 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 1105109002575 IHF dimer interface [polypeptide binding]; other site 1105109002576 IHF - DNA interface [nucleotide binding]; other site 1105109002577 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105109002578 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1105109002579 DNA binding residues [nucleotide binding] 1105109002580 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1105109002581 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105109002582 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105109002583 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105109002584 synthetase active site [active] 1105109002585 NTP binding site [chemical binding]; other site 1105109002586 metal binding site [ion binding]; metal-binding site 1105109002587 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105109002588 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105109002589 synthetase active site [active] 1105109002590 NTP binding site [chemical binding]; other site 1105109002591 metal binding site [ion binding]; metal-binding site 1105109002592 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 1105109002593 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105109002594 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105109002595 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 1105109002596 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105109002597 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105109002598 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 1105109002599 Transporter associated domain; Region: CorC_HlyC; smart01091 1105109002600 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105109002601 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1105109002602 Walker A/P-loop; other site 1105109002603 ATP binding site [chemical binding]; other site 1105109002604 Q-loop/lid; other site 1105109002605 ABC transporter signature motif; other site 1105109002606 Walker B; other site 1105109002607 D-loop; other site 1105109002608 H-loop/switch region; other site 1105109002609 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105109002610 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105109002611 FtsX-like permease family; Region: FtsX; pfam02687 1105109002612 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 1105109002613 putative substrate translocation pore; other site 1105109002614 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105109002615 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105109002616 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105109002617 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109002618 Walker A/P-loop; other site 1105109002619 ATP binding site [chemical binding]; other site 1105109002620 Q-loop/lid; other site 1105109002621 ABC transporter signature motif; other site 1105109002622 Walker B; other site 1105109002623 D-loop; other site 1105109002624 H-loop/switch region; other site 1105109002625 potential protein location (hypothetical protein MC3_06115 [Rickettsia slovaca str. D-CWPP]) that overlaps RNA (tRNA-H) 1105109002626 YcfA-like protein; Region: YcfA; cl00752 1105109002627 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 1105109002628 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 1105109002629 HicB family; Region: HicB; pfam05534 1105109002630 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 1105109002631 Ligand Binding Site [chemical binding]; other site 1105109002632 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105109002633 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105109002634 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105109002635 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1105109002636 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 1105109002637 Walker A motif; other site 1105109002638 ATP binding site [chemical binding]; other site 1105109002639 Walker B motif; other site 1105109002640 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105109002641 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 1105109002642 DoxX-like family; Region: DoxX_3; pfam13781 1105109002643 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 1105109002644 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105109002645 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 1105109002646 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105109002647 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 1105109002648 nucleotide binding pocket [chemical binding]; other site 1105109002649 K-X-D-G motif; other site 1105109002650 catalytic site [active] 1105109002651 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105109002652 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105109002653 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 1105109002654 Dimer interface [polypeptide binding]; other site 1105109002655 BRCT sequence motif; other site 1105109002656 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105109002657 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1105109002658 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105109002659 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105109002660 HD domain; Region: HD_4; pfam13328 1105109002661 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 1105109002662 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1105109002663 mce related protein; Region: MCE; pfam02470 1105109002664 hypothetical protein; Provisional; Region: PRK06630 1105109002665 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105109002666 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105109002667 active site 1105109002668 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 1105109002669 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 1105109002670 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105109002671 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 1105109002672 CoA-binding site [chemical binding]; other site 1105109002673 ATP-binding [chemical binding]; other site 1105109002674 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105109002675 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 1105109002676 active site 1105109002677 catalytic site [active] 1105109002678 substrate binding site [chemical binding]; other site 1105109002679 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 1105109002680 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105109002681 Part of AAA domain; Region: AAA_19; pfam13245 1105109002682 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105109002683 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 1105109002684 Family description; Region: UvrD_C_2; pfam13538 1105109002685 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1105109002686 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105109002687 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105109002688 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105109002689 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105109002690 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105109002691 acetyl-CoA acetyltransferase; Provisional; Region: PRK06633 1105109002692 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 1105109002693 dimer interface [polypeptide binding]; other site 1105109002694 active site 1105109002695 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 1105109002696 potential frameshift: common BLAST hit: gi|238650631|ref|YP_002916483.1| Poly-beta-hydroxybutyrate polymerase 1105109002697 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105109002698 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 1105109002699 nudix motif; other site 1105109002700 FOG: CBS domain [General function prediction only]; Region: COG0517 1105109002701 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 1105109002702 Transporter associated domain; Region: CorC_HlyC; smart01091 1105109002703 metal-binding heat shock protein; Provisional; Region: PRK00016 1105109002704 PemK-like protein; Region: PemK; pfam02452 1105109002705 lipoyl synthase; Provisional; Region: PRK05481 1105109002706 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 1105109002707 FeS/SAM binding site; other site 1105109002708 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105109002709 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 1105109002710 dimer interface [polypeptide binding]; other site 1105109002711 active site 1105109002712 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105109002713 folate binding site [chemical binding]; other site 1105109002714 Predicted esterase [General function prediction only]; Region: COG0400 1105109002715 putative hydrolase; Provisional; Region: PRK11460 1105109002716 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 1105109002717 putative GSH binding site [chemical binding]; other site 1105109002718 catalytic residues [active] 1105109002719 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105109002720 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105109002721 minor groove reading motif; other site 1105109002722 helix-hairpin-helix signature motif; other site 1105109002723 substrate binding pocket [chemical binding]; other site 1105109002724 active site 1105109002725 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1105109002726 Predicted small secreted protein [Function unknown]; Region: COG5510 1105109002727 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105109002728 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105109002729 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105109002730 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1105109002731 putative SAM binding site [chemical binding]; other site 1105109002732 putative homodimer interface [polypeptide binding]; other site 1105109002733 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 1105109002734 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105109002735 putative ligand binding site [chemical binding]; other site 1105109002736 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 1105109002737 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105109002738 tetramer interfaces [polypeptide binding]; other site 1105109002739 binuclear metal-binding site [ion binding]; other site 1105109002740 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 1105109002741 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1105109002742 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1105109002743 aspartate kinase; Reviewed; Region: PRK06635 1105109002744 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 1105109002745 putative nucleotide binding site [chemical binding]; other site 1105109002746 putative catalytic residues [active] 1105109002747 putative Mg ion binding site [ion binding]; other site 1105109002748 putative aspartate binding site [chemical binding]; other site 1105109002749 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 1105109002750 putative allosteric regulatory residue; other site 1105109002751 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA; cl01007 1105109002752 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1105109002753 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1105109002754 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 1105109002755 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109002756 putative substrate translocation pore; other site 1105109002757 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 1105109002758 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002759 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 1105109002760 Helix-turn-helix domain; Region: HTH_25; pfam13413 1105109002761 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105109002762 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 1105109002763 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 1105109002764 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105109002765 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105109002766 G1 box; other site 1105109002767 GTP/Mg2+ binding site [chemical binding]; other site 1105109002768 Switch I region; other site 1105109002769 G2 box; other site 1105109002770 Switch II region; other site 1105109002771 G3 box; other site 1105109002772 G4 box; other site 1105109002773 G5 box; other site 1105109002774 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105109002775 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 1105109002776 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 1105109002777 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 1105109002778 hexamer interface [polypeptide binding]; other site 1105109002779 Walker A motif; other site 1105109002780 ATP binding site [chemical binding]; other site 1105109002781 Walker B motif; other site 1105109002782 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105109002783 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105109002784 NAD(P) binding site [chemical binding]; other site 1105109002785 active site 1105109002786 acyl carrier protein; Provisional; Region: acpP; PRK00982 1105109002787 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105109002788 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 1105109002789 dimer interface [polypeptide binding]; other site 1105109002790 active site 1105109002791 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105109002792 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105109002793 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105109002794 AAA domain; Region: AAA_14; pfam13173 1105109002795 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105109002796 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002797 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105109002798 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 1105109002799 catalytic site [active] 1105109002800 G-X2-G-X-G-K; other site 1105109002801 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 1105109002802 sequence-specific DNA binding site [nucleotide binding]; other site 1105109002803 salt bridge; other site 1105109002804 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 1105109002805 rod shape-determining protein MreC; Region: MreC; pfam04085 1105109002806 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105109002807 MreB and similar proteins; Region: MreB_like; cd10225 1105109002808 nucleotide binding site [chemical binding]; other site 1105109002809 Mg binding site [ion binding]; other site 1105109002810 putative protofilament interaction site [polypeptide binding]; other site 1105109002811 RodZ interaction site [polypeptide binding]; other site 1105109002812 Predicted permeases [General function prediction only]; Region: COG0795 1105109002813 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105109002814 putative outer membrane lipoprotein; Provisional; Region: PRK09967 1105109002815 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105109002816 ligand binding site [chemical binding]; other site 1105109002817 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002818 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105109002819 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 1105109002820 dimer interface [polypeptide binding]; other site 1105109002821 active site 1105109002822 CoA binding pocket [chemical binding]; other site 1105109002823 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 1105109002824 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 1105109002825 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 1105109002826 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105109002827 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1105109002828 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 1105109002829 P loop; other site 1105109002830 GTP binding site [chemical binding]; other site 1105109002831 DNA polymerase I; Provisional; Region: PRK05755 1105109002832 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105109002833 active site 1105109002834 metal binding site 1 [ion binding]; metal-binding site 1105109002835 putative 5' ssDNA interaction site; other site 1105109002836 metal binding site 3; metal-binding site 1105109002837 metal binding site 2 [ion binding]; metal-binding site 1105109002838 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105109002839 putative DNA binding site [nucleotide binding]; other site 1105109002840 putative metal binding site [ion binding]; other site 1105109002841 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105109002842 active site 1105109002843 substrate binding site [chemical binding]; other site 1105109002844 catalytic site [active] 1105109002845 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105109002846 active site 1105109002847 DNA binding site [nucleotide binding] 1105109002848 catalytic site [active] 1105109002849 potential frameshift: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 1105109002850 potential frameshift: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 1105109002851 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 1105109002852 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105109002853 putative active site [active] 1105109002854 putative PHP Thumb interface [polypeptide binding]; other site 1105109002855 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 1105109002856 generic binding surface I; other site 1105109002857 generic binding surface II; other site 1105109002858 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105109002859 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105109002860 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 1105109002861 Protein of unknown function; Region: DUF3971; pfam13116 1105109002862 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105109002863 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 1105109002864 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 1105109002865 putative substrate translocation pore; other site 1105109002866 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1105109002867 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105109002868 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105109002869 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 1105109002870 dimer interface [polypeptide binding]; other site 1105109002871 active site 1105109002872 motif 1; other site 1105109002873 motif 2; other site 1105109002874 motif 3; other site 1105109002875 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105109002876 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105109002877 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105109002878 Integral membrane protein TerC family; Region: TerC; cl10468 1105109002879 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105109002880 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105109002881 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 1105109002882 S-adenosylmethionine binding site [chemical binding]; other site 1105109002883 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105109002884 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 1105109002885 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105109002886 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 1105109002887 salt bridge; other site 1105109002888 non-specific DNA binding site [nucleotide binding]; other site 1105109002889 sequence-specific DNA binding site [nucleotide binding]; other site 1105109002890 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105109002891 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1105109002892 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1105109002893 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105109002894 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105109002895 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105109002896 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105109002897 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105109002898 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105109002899 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109002900 Walker A/P-loop; other site 1105109002901 ATP binding site [chemical binding]; other site 1105109002902 Q-loop/lid; other site 1105109002903 ABC transporter signature motif; other site 1105109002904 Walker B; other site 1105109002905 D-loop; other site 1105109002906 H-loop/switch region; other site 1105109002907 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105109002908 4Fe-4S binding domain; Region: Fer4; cl02805 1105109002909 4Fe-4S binding domain; Region: Fer4; pfam00037 1105109002910 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1105109002911 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1105109002912 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105109002913 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 1105109002914 catalytic loop [active] 1105109002915 iron binding site [ion binding]; other site 1105109002916 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1105109002917 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 1105109002918 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105109002919 Predicted membrane protein [Function unknown]; Region: COG3671 1105109002920 aconitate hydratase; Validated; Region: PRK09277 1105109002921 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105109002922 substrate binding site [chemical binding]; other site 1105109002923 ligand binding site [chemical binding]; other site 1105109002924 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 1105109002925 substrate binding site [chemical binding]; other site 1105109002926 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105109002927 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1105109002928 gamma subunit interface [polypeptide binding]; other site 1105109002929 epsilon subunit interface [polypeptide binding]; other site 1105109002930 LBP interface [polypeptide binding]; other site 1105109002931 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105109002932 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105109002933 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 1105109002934 alpha subunit interaction interface [polypeptide binding]; other site 1105109002935 Walker A motif; other site 1105109002936 ATP binding site [chemical binding]; other site 1105109002937 Walker B motif; other site 1105109002938 inhibitor binding site; inhibition site 1105109002939 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105109002940 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1105109002941 core domain interface [polypeptide binding]; other site 1105109002942 delta subunit interface [polypeptide binding]; other site 1105109002943 epsilon subunit interface [polypeptide binding]; other site 1105109002944 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105109002945 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105109002946 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 1105109002947 beta subunit interaction interface [polypeptide binding]; other site 1105109002948 Walker A motif; other site 1105109002949 ATP binding site [chemical binding]; other site 1105109002950 Walker B motif; other site 1105109002951 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105109002952 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 1105109002953 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105109002954 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105109002955 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1105109002956 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105109002957 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105109002958 potential frameshift: common BLAST hit: gi|238650826|ref|YP_002916681.1| ferroxidase 1105109002959 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105109002960 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 1105109002961 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105109002962 Transglycosylase; Region: Transgly; pfam00912 1105109002963 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105109002964 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105109002965 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105109002966 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 1105109002967 FeS/SAM binding site; other site 1105109002968 TRAM domain; Region: TRAM; pfam01938 1105109002969 HEPN domain; Region: HEPN; cl00824 1105109002970 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105109002971 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 1105109002972 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105109002973 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105109002974 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105109002975 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 1105109002976 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105109002977 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105109002978 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105109002979 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1105109002980 TrkA-N domain; Region: TrkA_N; pfam02254 1105109002981 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 1105109002982 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105109002983 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105109002984 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105109002985 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105109002986 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105109002987 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 1105109002988 rRNA binding site [nucleotide binding]; other site 1105109002989 predicted 30S ribosome binding site; other site 1105109002990 Maf-like protein; Region: Maf; pfam02545 1105109002991 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 1105109002992 active site 1105109002993 dimer interface [polypeptide binding]; other site 1105109002994 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 1105109002995 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105109002996 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 1105109002997 active site 1105109002998 DNA binding site [nucleotide binding] 1105109002999 Int/Topo IB signature motif; other site 1105109003000 Phasin protein; Region: Phasin_2; pfam09361 1105109003001 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105109003002 PLD-like domain; Region: PLDc_2; pfam13091 1105109003003 putative active site [active] 1105109003004 catalytic site [active] 1105109003005 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105109003006 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 1105109003007 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105109003008 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1105109003009 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1105109003010 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105109003011 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105109003012 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105109003013 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 1105109003014 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1105109003015 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1105109003016 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105109003017 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 1105109003018 active site 1105109003019 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105109003020 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105109003021 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105109003022 MPN+ (JAMM) motif; other site 1105109003023 Zinc-binding site [ion binding]; other site 1105109003024 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105109003025 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 1105109003026 Mg++ binding site [ion binding]; other site 1105109003027 putative catalytic motif [active] 1105109003028 putative substrate binding site [chemical binding]; other site 1105109003029 Protein of unknown function (DUF721); Region: DUF721; pfam05258 1105109003030 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105109003031 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105109003032 Ferredoxin [Energy production and conversion]; Region: COG1146 1105109003033 4Fe-4S binding domain; Region: Fer4; cl02805 1105109003034 heme exporter protein CcmC; Region: ccmC; TIGR01191 1105109003035 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 1105109003036 nucleoside/Zn binding site; other site 1105109003037 dimer interface [polypeptide binding]; other site 1105109003038 catalytic motif [active] 1105109003039 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105109003040 Cation efflux family; Region: Cation_efflux; cl00316 1105109003041 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105109003042 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105109003043 substrate binding site [chemical binding]; other site 1105109003044 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105109003045 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 1105109003046 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105109003047 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105109003048 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105109003049 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1105109003050 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105109003051 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 1105109003052 dimer interface [polypeptide binding]; other site 1105109003053 ssDNA binding site [nucleotide binding]; other site 1105109003054 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105109003055 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 1105109003056 hypothetical protein; Reviewed; Region: PRK01530 1105109003057 heat shock protein 90; Provisional; Region: PRK05218 1105109003058 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 1105109003059 ATP binding site [chemical binding]; other site 1105109003060 Mg2+ binding site [ion binding]; other site 1105109003061 G-X-G motif; other site 1105109003062 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1105109003063 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 1105109003064 substrate-cofactor binding pocket; other site 1105109003065 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105109003066 catalytic residue [active] 1105109003067 trigger factor; Provisional; Region: tig; PRK01490 1105109003068 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105109003069 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105109003070 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105109003071 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105109003072 Obg GTPase; Region: Obg; cd01898 1105109003073 G1 box; other site 1105109003074 GTP/Mg2+ binding site [chemical binding]; other site 1105109003075 Switch I region; other site 1105109003076 G2 box; other site 1105109003077 G3 box; other site 1105109003078 Switch II region; other site 1105109003079 G4 box; other site 1105109003080 G5 box; other site 1105109003081 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 1105109003082 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1105109003083 dimer interface [polypeptide binding]; other site 1105109003084 active site 1105109003085 citrylCoA binding site [chemical binding]; other site 1105109003086 NADH binding [chemical binding]; other site 1105109003087 cationic pore residues; other site 1105109003088 oxalacetate/citrate binding site [chemical binding]; other site 1105109003089 coenzyme A binding site [chemical binding]; other site 1105109003090 catalytic triad [active] 1105109003091 potential frameshift: common BLAST hit: gi|67459708|ref|YP_247332.1| transcriptional regulator 1105109003092 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105109003093 Fe-S cluster binding site [ion binding]; other site 1105109003094 active site 1105109003095 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105109003096 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 1105109003097 RNA binding surface [nucleotide binding]; other site 1105109003098 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105109003099 active site 1105109003100 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105109003101 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 1105109003102 S-adenosylmethionine binding site [chemical binding]; other site 1105109003103 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 1105109003104 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1105109003105 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105109003106 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 1105109003107 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105109003108 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 1105109003109 motif 1; other site 1105109003110 dimer interface [polypeptide binding]; other site 1105109003111 active site 1105109003112 motif 2; other site 1105109003113 motif 3; other site 1105109003114 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 1105109003115 oligomeric interface; other site 1105109003116 putative active site [active] 1105109003117 homodimer interface [polypeptide binding]; other site 1105109003118 prevent-host-death family protein; Region: phd_fam; TIGR01552 1105109003119 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 1105109003120 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 1105109003121 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109003122 putative substrate translocation pore; other site 1105109003123 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105109003124 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 1105109003125 motif 1; other site 1105109003126 active site 1105109003127 motif 2; other site 1105109003128 motif 3; other site 1105109003129 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105109003130 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105109003131 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105109003132 dimerization interface 3.5A [polypeptide binding]; other site 1105109003133 active site 1105109003134 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105109003135 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105109003136 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105109003137 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105109003138 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105109003139 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 1105109003140 DNA binding residues [nucleotide binding] 1105109003141 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105109003142 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1105109003143 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105109003144 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 1105109003145 active site 1105109003146 metal binding site [ion binding]; metal-binding site 1105109003147 interdomain interaction site; other site 1105109003148 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 1105109003149 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105109003150 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105109003151 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105109003152 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105109003153 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105109003154 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 1105109003155 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105109003156 ligand binding site [chemical binding]; other site 1105109003157 homodimer interface [polypeptide binding]; other site 1105109003158 NAD(P) binding site [chemical binding]; other site 1105109003159 trimer interface B [polypeptide binding]; other site 1105109003160 trimer interface A [polypeptide binding]; other site 1105109003161 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105109003162 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 1105109003163 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 1105109003164 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 1105109003165 Walker A motif; other site 1105109003166 ATP binding site [chemical binding]; other site 1105109003167 Walker B motif; other site 1105109003168 arginine finger; other site 1105109003169 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1105109003170 hypothetical protein; Validated; Region: PRK00153 1105109003171 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105109003172 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105109003173 catalytic motif [active] 1105109003174 Catalytic residue [active] 1105109003175 Beta-lactamase; Region: Beta-lactamase; cl17358 1105109003176 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 1105109003177 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105109003178 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105109003179 Walker A/P-loop; other site 1105109003180 ATP binding site [chemical binding]; other site 1105109003181 Q-loop/lid; other site 1105109003182 ABC transporter signature motif; other site 1105109003183 Walker B; other site 1105109003184 D-loop; other site 1105109003185 H-loop/switch region; other site 1105109003186 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1105109003187 putative hydrolase; Provisional; Region: PRK02113 1105109003188 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 1105109003189 active site 1105109003190 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 1105109003191 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 1105109003192 Predicted permeases [General function prediction only]; Region: COG0795 1105109003193 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105109003194 DNA polymerase III subunit chi; Provisional; Region: PRK06646 1105109003195 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105109003196 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105109003197 metal binding site [ion binding]; metal-binding site 1105109003198 dimer interface [polypeptide binding]; other site 1105109003199 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1105109003200 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1105109003201 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 1105109003202 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 1105109003203 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1105109003204 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 1105109003205 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1105109003206 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 1105109003207 putative active site [active] 1105109003208 lipoate-protein ligase B; Provisional; Region: PRK14347 1105109003209 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105109003210 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 1105109003211 amidase catalytic site [active] 1105109003212 Zn binding residues [ion binding]; other site 1105109003213 substrate binding site [chemical binding]; other site 1105109003214 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105109003215 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1105109003216 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 1105109003217 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105109003218 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 1105109003219 ATP binding site [chemical binding]; other site 1105109003220 Mg2+ binding site [ion binding]; other site 1105109003221 G-X-G motif; other site 1105109003222 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 1105109003223 ATP binding site [chemical binding]; other site 1105109003224 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1105109003225 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 1105109003226 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105109003227 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 1105109003228 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105109003229 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 1105109003230 binding surface 1105109003231 TPR repeat; Region: TPR_11; pfam13414 1105109003232 TPR motif; other site 1105109003233 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105109003234 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 1105109003235 binding surface 1105109003236 TPR motif; other site 1105109003237 TPR repeat; Region: TPR_11; pfam13414 1105109003238 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 1105109003239 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105109003240 putative substrate translocation pore; other site 1105109003241 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 1105109003242 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 1105109003243 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105109003244 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105109003245 TIGR00701 family protein; Region: TIGR00701 1105109003246 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105109003247 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 1105109003248 C-terminal domain interface [polypeptide binding]; other site 1105109003249 active site 1105109003250 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 1105109003251 active site 1105109003252 N-terminal domain interface [polypeptide binding]; other site 1105109003253 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 1105109003254 substrate binding site [chemical binding]; other site 1105109003255 active site