-- dump date 20140620_034930 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105101000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 1105101000002 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 1105101000003 catalytic residues [active] 1105101000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105101000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 1105101000006 Walker A/P-loop; other site 1105101000007 ATP binding site [chemical binding]; other site 1105101000008 Q-loop/lid; other site 1105101000009 ABC transporter signature motif; other site 1105101000010 Walker B; other site 1105101000011 D-loop; other site 1105101000012 H-loop/switch region; other site 1105101000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1105101000014 ABC-2 type transporter; Region: ABC2_membrane; cl17235 1105101000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105101000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105101000017 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 1105101000018 FAD binding pocket [chemical binding]; other site 1105101000019 FAD binding motif [chemical binding]; other site 1105101000020 phosphate binding motif [ion binding]; other site 1105101000021 beta-alpha-beta structure motif; other site 1105101000022 NAD binding pocket [chemical binding]; other site 1105101000023 Iron coordination center [ion binding]; other site 1105101000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 1105101000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 1105101000026 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 1105101000027 active site 1105101000028 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 1105101000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105101000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105101000031 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 1105101000032 trimer interface [polypeptide binding]; other site 1105101000033 active site 1105101000034 UDP-GlcNAc binding site [chemical binding]; other site 1105101000035 lipid binding site [chemical binding]; lipid-binding site 1105101000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105101000037 active site 1105101000038 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105101000039 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101000040 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1105101000041 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 1105101000042 FMN binding site [chemical binding]; other site 1105101000043 active site 1105101000044 catalytic residues [active] 1105101000045 substrate binding site [chemical binding]; other site 1105101000046 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 1105101000047 NodB motif; other site 1105101000048 putative active site [active] 1105101000049 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1105101000050 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 1105101000051 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 1105101000052 intersubunit interface [polypeptide binding]; other site 1105101000053 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105101000054 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105101000055 active site 1105101000056 NTP binding site [chemical binding]; other site 1105101000057 metal binding triad [ion binding]; metal-binding site 1105101000058 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105101000059 Competence protein; Region: Competence; pfam03772 1105101000060 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105101000061 AAA domain; Region: AAA_22; pfam13401 1105101000062 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105101000063 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105101000064 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 1105101000065 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 1105101000066 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105101000067 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 1105101000068 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1105101000069 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 1105101000070 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 1105101000071 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105101000072 Thioredoxin; Region: Thioredoxin_4; pfam13462 1105101000073 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 1105101000074 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105101000075 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 1105101000076 S-adenosylmethionine binding site [chemical binding]; other site 1105101000077 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105101000078 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105101000079 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 1105101000080 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000081 Walker A/P-loop; other site 1105101000082 ATP binding site [chemical binding]; other site 1105101000083 Q-loop/lid; other site 1105101000084 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000085 ABC transporter signature motif; other site 1105101000086 Walker B; other site 1105101000087 D-loop; other site 1105101000088 H-loop/switch region; other site 1105101000089 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 1105101000090 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 1105101000091 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1105101000092 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 1105101000093 folate binding site [chemical binding]; other site 1105101000094 NADP+ binding site [chemical binding]; other site 1105101000095 potential frameshift: common BLAST hit: gi|157827907|ref|YP_001494149.1| folate synthesis bifunctional protein 1105101000096 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105101000097 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 1105101000098 Cu(I) binding site [ion binding]; other site 1105101000099 Putative transcriptional regulator [Transcription]; Region: COG1678 1105101000100 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1105101000101 Colicin V production protein; Region: Colicin_V; pfam02674 1105101000102 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105101000103 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105101000104 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101000105 active site 1105101000106 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101000107 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105101000108 Clp amino terminal domain; Region: Clp_N; pfam02861 1105101000109 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 1105101000110 Walker A motif; other site 1105101000111 ATP binding site [chemical binding]; other site 1105101000112 Walker B motif; other site 1105101000113 arginine finger; other site 1105101000114 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 1105101000115 Walker A motif; other site 1105101000116 ATP binding site [chemical binding]; other site 1105101000117 Walker B motif; other site 1105101000118 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1105101000119 UGMP family protein; Validated; Region: PRK09604 1105101000120 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1105101000121 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 1105101000122 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105101000123 Di-iron ligands [ion binding]; other site 1105101000124 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 1105101000125 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105101000126 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cl17355 1105101000127 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1105101000128 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1105101000129 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105101000130 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105101000131 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105101000132 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1105101000133 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 1105101000134 Ligand Binding Site [chemical binding]; other site 1105101000135 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000136 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105101000137 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105101000138 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 1105101000139 Walker A motif; other site 1105101000140 ATP binding site [chemical binding]; other site 1105101000141 Walker B motif; other site 1105101000142 arginine finger; other site 1105101000143 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105101000144 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 1105101000145 cofactor binding site; other site 1105101000146 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 1105101000147 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105101000148 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1105101000149 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105101000150 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000151 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1105101000152 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1105101000153 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105101000154 membrane protein insertase; Provisional; Region: PRK01318 1105101000155 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1105101000156 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105101000157 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 1105101000158 S-adenosylmethionine binding site [chemical binding]; other site 1105101000159 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105101000160 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 1105101000161 active site 1105101000162 catalytic residues [active] 1105101000163 metal binding site [ion binding]; metal-binding site 1105101000164 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101000165 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105101000166 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 1105101000167 putative substrate translocation pore; other site 1105101000168 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 1105101000169 active site 1105101000170 multimer interface [polypeptide binding]; other site 1105101000171 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105101000172 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1105101000173 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105101000174 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1105101000175 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1105101000176 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105101000177 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 1105101000178 P-loop; other site 1105101000179 Magnesium ion binding site [ion binding]; other site 1105101000180 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 1105101000181 Magnesium ion binding site [ion binding]; other site 1105101000182 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1105101000183 ParB-like nuclease domain; Region: ParBc; pfam02195 1105101000184 KorB domain; Region: KorB; pfam08535 1105101000185 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105101000186 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105101000187 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105101000188 ABC transporter; Region: ABC_tran_2; pfam12848 1105101000189 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105101000190 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105101000191 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 1105101000192 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105101000193 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105101000194 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105101000195 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1105101000196 Zn2+ binding site [ion binding]; other site 1105101000197 Mg2+ binding site [ion binding]; other site 1105101000198 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105101000199 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1105101000200 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1105101000201 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105101000202 active site 1105101000203 HIGH motif; other site 1105101000204 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101000205 KMSK motif region; other site 1105101000206 tRNA binding surface [nucleotide binding]; other site 1105101000207 DALR anticodon binding domain; Region: DALR_1; smart00836 1105101000208 anticodon binding site; other site 1105101000209 Sporulation related domain; Region: SPOR; pfam05036 1105101000210 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105101000211 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 1105101000212 CAP-like domain; other site 1105101000213 active site 1105101000214 primary dimer interface [polypeptide binding]; other site 1105101000215 Gram-negative porin; Region: Porin_4; pfam13609 1105101000216 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105101000217 trimer interface [polypeptide binding]; other site 1105101000218 active site 1105101000219 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 1105101000220 SecA binding site; other site 1105101000221 Preprotein binding site; other site 1105101000222 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105101000223 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 1105101000224 active site 1105101000225 phosphorylation site [posttranslational modification] 1105101000226 intermolecular recognition site; other site 1105101000227 dimerization interface [polypeptide binding]; other site 1105101000228 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 1105101000229 DNA binding site [nucleotide binding] 1105101000230 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 1105101000231 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105101000232 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 1105101000233 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105101000234 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 1105101000235 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105101000236 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 1105101000237 EamA-like transporter family; Region: EamA; pfam00892 1105101000238 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1105101000239 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 1105101000240 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101000241 putative substrate translocation pore; other site 1105101000242 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1105101000243 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105101000244 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105101000245 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105101000246 active site 1105101000247 HIGH motif; other site 1105101000248 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105101000249 KMSKS motif; other site 1105101000250 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105101000251 tRNA binding surface [nucleotide binding]; other site 1105101000252 anticodon binding site; other site 1105101000253 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 1105101000254 rRNA interaction site [nucleotide binding]; other site 1105101000255 S8 interaction site; other site 1105101000256 putative laminin-1 binding site; other site 1105101000257 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105101000258 UBA/TS-N domain; Region: UBA; pfam00627 1105101000259 Elongation factor TS; Region: EF_TS; pfam00889 1105101000260 Elongation factor TS; Region: EF_TS; pfam00889 1105101000261 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 1105101000262 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000263 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105101000264 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 1105101000265 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105101000266 putative acyl-acceptor binding pocket; other site 1105101000267 aspartate aminotransferase; Provisional; Region: PRK05764 1105101000268 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 1105101000269 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105101000270 homodimer interface [polypeptide binding]; other site 1105101000271 catalytic residue [active] 1105101000272 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105101000273 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105101000274 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 1105101000275 binding surface 1105101000276 TPR motif; other site 1105101000277 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1105101000278 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 1105101000279 S-adenosylmethionine binding site [chemical binding]; other site 1105101000280 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1105101000281 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 1105101000282 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105101000283 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105101000284 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105101000285 active site 1105101000286 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000287 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1105101000288 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105101000289 active site 1105101000290 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105101000291 dimer interface [polypeptide binding]; other site 1105101000292 substrate binding site [chemical binding]; other site 1105101000293 catalytic residues [active] 1105101000294 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1105101000295 Permease; Region: Permease; pfam02405 1105101000296 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105101000297 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000298 Walker A/P-loop; other site 1105101000299 ATP binding site [chemical binding]; other site 1105101000300 Q-loop/lid; other site 1105101000301 ABC transporter signature motif; other site 1105101000302 Walker B; other site 1105101000303 D-loop; other site 1105101000304 H-loop/switch region; other site 1105101000305 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 1105101000306 50S ribosomal protein L31; Provisional; Region: PRK01397 1105101000307 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105101000308 G1 box; other site 1105101000309 GTP/Mg2+ binding site [chemical binding]; other site 1105101000310 Switch I region; other site 1105101000311 G2 box; other site 1105101000312 G3 box; other site 1105101000313 Switch II region; other site 1105101000314 G4 box; other site 1105101000315 G5 box; other site 1105101000316 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 1105101000317 nucleotide binding site [chemical binding]; other site 1105101000318 substrate binding site [chemical binding]; other site 1105101000319 type IV secretion system protein VirB3; Provisional; Region: PRK13899 1105101000320 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105101000321 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105101000322 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000323 Walker A/P-loop; other site 1105101000324 ATP binding site [chemical binding]; other site 1105101000325 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105101000326 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105101000327 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105101000328 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105101000329 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105101000330 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105101000331 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105101000332 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105101000333 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 1105101000334 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1105101000335 hypothetical protein; Provisional; Region: PRK13694 1105101000336 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105101000337 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105101000338 Protein export membrane protein; Region: SecD_SecF; pfam02355 1105101000339 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105101000340 SLBB domain; Region: SLBB; pfam10531 1105101000341 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 1105101000342 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105101000343 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 1105101000344 Catalytic site [active] 1105101000345 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 1105101000346 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105101000347 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 1105101000348 dimerization interface [polypeptide binding]; other site 1105101000349 active site 1105101000350 metal binding site [ion binding]; metal-binding site 1105101000351 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 1105101000352 dsRNA binding site [nucleotide binding]; other site 1105101000353 GTPase Era; Provisional; Region: era; PRK15494 1105101000354 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000355 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105101000356 G1 box; other site 1105101000357 GTP/Mg2+ binding site [chemical binding]; other site 1105101000358 Switch I region; other site 1105101000359 G2 box; other site 1105101000360 Switch II region; other site 1105101000361 G3 box; other site 1105101000362 G4 box; other site 1105101000363 G5 box; other site 1105101000364 KH domain; Region: KH_2; pfam07650 1105101000365 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 1105101000366 active site 1105101000367 putative DNA-binding cleft [nucleotide binding]; other site 1105101000368 dimer interface [polypeptide binding]; other site 1105101000369 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105101000370 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1105101000371 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 1105101000372 potential frameshift: common BLAST hit: gi|165932732|ref|YP_001649521.1| nucleotidyltransferase 1105101000373 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105101000374 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105101000375 AAA domain; Region: AAA_31; pfam13614 1105101000376 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 1105101000377 Walker A motif; other site 1105101000378 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 1105101000379 HflK protein; Region: hflK; TIGR01933 1105101000380 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105101000381 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 1105101000382 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105101000383 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105101000384 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 1105101000385 protein binding site [polypeptide binding]; other site 1105101000386 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 1105101000387 protein binding site [polypeptide binding]; other site 1105101000388 hypothetical protein; Validated; Region: PRK01415 1105101000389 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105101000390 active site residue [active] 1105101000391 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 1105101000392 Iron-sulfur protein interface; other site 1105101000393 proximal quinone binding site [chemical binding]; other site 1105101000394 SdhD (CybS) interface [polypeptide binding]; other site 1105101000395 proximal heme binding site [chemical binding]; other site 1105101000396 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 1105101000397 putative SdhC subunit interface [polypeptide binding]; other site 1105101000398 putative proximal heme binding site [chemical binding]; other site 1105101000399 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105101000400 putative proximal quinone binding site; other site 1105101000401 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105101000402 L-aspartate oxidase; Provisional; Region: PRK06175 1105101000403 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105101000404 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105101000405 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 1105101000406 dimer interface [polypeptide binding]; other site 1105101000407 conserved gate region; other site 1105101000408 putative PBP binding loops; other site 1105101000409 ABC-ATPase subunit interface; other site 1105101000410 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 1105101000411 S17 interaction site [polypeptide binding]; other site 1105101000412 S8 interaction site; other site 1105101000413 16S rRNA interaction site [nucleotide binding]; other site 1105101000414 streptomycin interaction site [chemical binding]; other site 1105101000415 23S rRNA interaction site [nucleotide binding]; other site 1105101000416 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105101000417 30S ribosomal protein S7; Validated; Region: PRK05302 1105101000418 elongation factor G; Reviewed; Region: PRK00007 1105101000419 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105101000420 G1 box; other site 1105101000421 putative GEF interaction site [polypeptide binding]; other site 1105101000422 GTP/Mg2+ binding site [chemical binding]; other site 1105101000423 Switch I region; other site 1105101000424 G2 box; other site 1105101000425 G3 box; other site 1105101000426 Switch II region; other site 1105101000427 G4 box; other site 1105101000428 G5 box; other site 1105101000429 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 1105101000430 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 1105101000431 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 1105101000432 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 1105101000433 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105101000434 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105101000435 putative homodimer interface [polypeptide binding]; other site 1105101000436 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1105101000437 heterodimer interface [polypeptide binding]; other site 1105101000438 homodimer interface [polypeptide binding]; other site 1105101000439 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105101000440 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 1105101000441 23S rRNA interface [nucleotide binding]; other site 1105101000442 putative thiostrepton binding site; other site 1105101000443 L7/L12 interface [polypeptide binding]; other site 1105101000444 L25 interface [polypeptide binding]; other site 1105101000445 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 1105101000446 mRNA/rRNA interface [nucleotide binding]; other site 1105101000447 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 1105101000448 23S rRNA interface [nucleotide binding]; other site 1105101000449 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105101000450 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 1105101000451 core dimer interface [polypeptide binding]; other site 1105101000452 peripheral dimer interface [polypeptide binding]; other site 1105101000453 L10 interface [polypeptide binding]; other site 1105101000454 L11 interface [polypeptide binding]; other site 1105101000455 putative EF-Tu interaction site [polypeptide binding]; other site 1105101000456 putative EF-G interaction site [polypeptide binding]; other site 1105101000457 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1105101000458 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 1105101000459 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105101000460 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 1105101000461 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1105101000462 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 1105101000463 RPB3 interaction site [polypeptide binding]; other site 1105101000464 RPB1 interaction site [polypeptide binding]; other site 1105101000465 RPB11 interaction site [polypeptide binding]; other site 1105101000466 RPB10 interaction site [polypeptide binding]; other site 1105101000467 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105101000468 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105101000469 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1105101000470 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105101000471 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105101000472 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105101000473 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105101000474 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105101000475 DNA binding site [nucleotide binding] 1105101000476 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105101000477 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000478 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105101000479 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 1105101000480 interface (dimer of trimers) [polypeptide binding]; other site 1105101000481 Substrate-binding/catalytic site; other site 1105101000482 Zn-binding sites [ion binding]; other site 1105101000483 ATPase MipZ; Region: MipZ; pfam09140 1105101000484 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 1105101000485 P-loop; other site 1105101000486 Magnesium ion binding site [ion binding]; other site 1105101000487 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 1105101000488 Magnesium ion binding site [ion binding]; other site 1105101000489 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105101000490 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 1105101000491 dimer interface [polypeptide binding]; other site 1105101000492 anticodon binding site; other site 1105101000493 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 1105101000494 homodimer interface [polypeptide binding]; other site 1105101000495 motif 1; other site 1105101000496 active site 1105101000497 motif 2; other site 1105101000498 GAD domain; Region: GAD; pfam02938 1105101000499 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 1105101000500 active site 1105101000501 motif 3; other site 1105101000502 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1105101000503 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105101000504 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105101000505 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1105101000506 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105101000507 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 1105101000508 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105101000509 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 1105101000510 substrate binding pocket [chemical binding]; other site 1105101000511 membrane-bound complex binding site; other site 1105101000512 hinge residues; other site 1105101000513 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105101000514 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105101000515 GatB domain; Region: GatB_Yqey; smart00845 1105101000516 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105101000517 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1105101000518 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1105101000519 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 1105101000520 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105101000521 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 1105101000522 hinge region; other site 1105101000523 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 1105101000524 putative nucleotide binding site [chemical binding]; other site 1105101000525 uridine monophosphate binding site [chemical binding]; other site 1105101000526 homohexameric interface [polypeptide binding]; other site 1105101000527 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 1105101000528 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105101000529 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 1105101000530 putative substrate translocation pore; other site 1105101000531 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 1105101000532 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105101000533 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1105101000534 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105101000535 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105101000536 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105101000537 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105101000538 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105101000539 Surface antigen; Region: Bac_surface_Ag; pfam01103 1105101000540 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105101000541 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 1105101000542 active site 1105101000543 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 1105101000544 protein binding site [polypeptide binding]; other site 1105101000545 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 1105101000546 putative substrate binding region [chemical binding]; other site 1105101000547 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1105101000548 putative RNA binding site [nucleotide binding]; other site 1105101000549 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105101000550 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 1105101000551 S-adenosylmethionine binding site [chemical binding]; other site 1105101000552 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105101000553 putative coenzyme Q binding site [chemical binding]; other site 1105101000554 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101000555 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105101000556 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105101000557 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 1105101000558 RNA methyltransferase, RsmE family; Region: TIGR00046 1105101000559 Uncharacterized conserved protein [Function unknown]; Region: COG2155 1105101000560 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105101000561 Protein export membrane protein; Region: SecD_SecF; cl14618 1105101000562 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 1105101000563 IHF dimer interface [polypeptide binding]; other site 1105101000564 IHF - DNA interface [nucleotide binding]; other site 1105101000565 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105101000566 signal recognition particle protein; Provisional; Region: PRK10867 1105101000567 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1105101000568 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 1105101000569 P loop; other site 1105101000570 GTP binding site [chemical binding]; other site 1105101000571 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105101000572 potential frameshift: common BLAST hit: gi|51473374|ref|YP_067131.1| post-proline cleaving enzyme 1105101000573 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105101000574 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105101000575 potential frameshift: common BLAST hit: gi|67459496|ref|YP_247120.1| prolyl endopeptidase 1105101000576 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105101000577 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 1105101000578 FeS/SAM binding site; other site 1105101000579 HemN C-terminal domain; Region: HemN_C; pfam06969 1105101000580 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 1105101000581 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105101000582 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 1105101000583 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105101000584 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1105101000585 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 1105101000586 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 1105101000587 active site 1105101000588 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105101000589 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 1105101000590 E3 interaction surface; other site 1105101000591 lipoyl attachment site [posttranslational modification]; other site 1105101000592 e3 binding domain; Region: E3_binding; pfam02817 1105101000593 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105101000594 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105101000595 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 1105101000596 TPP-binding site [chemical binding]; other site 1105101000597 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1105101000598 dimer interface [polypeptide binding]; other site 1105101000599 PYR/PP interface [polypeptide binding]; other site 1105101000600 TPP binding site [chemical binding]; other site 1105101000601 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 1105101000602 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 1105101000603 active site 1105101000604 Zn binding site [ion binding]; other site 1105101000605 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105101000606 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105101000607 Walker A/P-loop; other site 1105101000608 ATP binding site [chemical binding]; other site 1105101000609 Q-loop/lid; other site 1105101000610 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105101000611 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105101000612 ABC transporter signature motif; other site 1105101000613 Walker B; other site 1105101000614 D-loop; other site 1105101000615 H-loop/switch region; other site 1105101000616 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105101000617 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105101000618 ChaB; Region: ChaB; cl01887 1105101000619 ChaB; Region: ChaB; cl01887 1105101000620 chaperone protein DnaJ; Provisional; Region: PRK14300 1105101000621 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 1105101000622 HSP70 interaction site [polypeptide binding]; other site 1105101000623 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105101000624 substrate binding site [polypeptide binding]; other site 1105101000625 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105101000626 Zn binding sites [ion binding]; other site 1105101000627 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105101000628 dimer interface [polypeptide binding]; other site 1105101000629 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105101000630 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105101000631 nucleotide binding site [chemical binding]; other site 1105101000632 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 1105101000633 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105101000634 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 1105101000635 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105101000636 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105101000637 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105101000638 diiron binding motif [ion binding]; other site 1105101000639 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 1105101000640 Subunit III/VIIa interface [polypeptide binding]; other site 1105101000641 Phospholipid binding site [chemical binding]; other site 1105101000642 Subunit I/III interface [polypeptide binding]; other site 1105101000643 Subunit III/VIb interface [polypeptide binding]; other site 1105101000644 Subunit III/VIa interface; other site 1105101000645 Subunit III/Vb interface [polypeptide binding]; other site 1105101000646 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1105101000647 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 1105101000648 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105101000649 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 1105101000650 trimer interface [polypeptide binding]; other site 1105101000651 active site 1105101000652 substrate binding site [chemical binding]; other site 1105101000653 CoA binding site [chemical binding]; other site 1105101000654 potential frameshift: common BLAST hit: gi|15892172|ref|NP_359886.1| bifunctional penicillin-binding protein 1C 1105101000655 potential frameshift: common BLAST hit: gi|229586439|ref|YP_002844940.1| Bifunctional penicillin-binding protein 1C 1105101000656 potential frameshift: common BLAST hit: gi|15892172|ref|NP_359886.1| bifunctional penicillin-binding protein 1C 1105101000657 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105101000658 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 1105101000659 Ligand Binding Site [chemical binding]; other site 1105101000660 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105101000661 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1105101000662 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1105101000663 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 1105101000664 catalytic loop [active] 1105101000665 iron binding site [ion binding]; other site 1105101000666 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105101000667 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105101000668 nucleotide binding site [chemical binding]; other site 1105101000669 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105101000670 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 1105101000671 HSP70 interaction site [polypeptide binding]; other site 1105101000672 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105101000673 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105101000674 active site 1105101000675 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105101000676 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 1105101000677 ATP binding site [chemical binding]; other site 1105101000678 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 1105101000679 nucleotide binding region [chemical binding]; other site 1105101000680 ATP-binding site [chemical binding]; other site 1105101000681 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105101000682 UvrB/uvrC motif; Region: UVR; pfam02151 1105101000683 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 1105101000684 GSH binding site [chemical binding]; other site 1105101000685 catalytic residues [active] 1105101000686 potential frameshift: common BLAST hit: gi|157964270|ref|YP_001499094.1| multidrug resistance protein Atm1 1105101000687 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105101000688 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000689 Walker A/P-loop; other site 1105101000690 ATP binding site [chemical binding]; other site 1105101000691 Q-loop/lid; other site 1105101000692 Pleckstrin homology-like domain; Region: PH-like; cl17171 1105101000693 DNA gyrase subunit A; Validated; Region: PRK05560 1105101000694 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 1105101000695 CAP-like domain; other site 1105101000696 active site 1105101000697 primary dimer interface [polypeptide binding]; other site 1105101000698 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000699 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000700 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000701 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000702 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105101000703 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105101000704 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105101000705 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105101000706 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 1105101000707 active site 1105101000708 catalytic residues [active] 1105101000709 metal binding site [ion binding]; metal-binding site 1105101000710 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105101000711 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105101000712 putative active site [active] 1105101000713 substrate binding site [chemical binding]; other site 1105101000714 putative cosubstrate binding site; other site 1105101000715 catalytic site [active] 1105101000716 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105101000717 substrate binding site [chemical binding]; other site 1105101000718 potential RNA of insufficient length (23S ribosomal RNA) 1105101000719 potential frameshift: common BLAST hit: gi|157826977|ref|YP_001496041.1| capsular polysaccharide biosynthesis protein 1105101000720 Predicted ATPase [General function prediction only]; Region: COG1485 1105101000721 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 1105101000722 Walker A motif; other site 1105101000723 ATP binding site [chemical binding]; other site 1105101000724 Walker B motif; other site 1105101000725 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 1105101000726 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1105101000727 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 1105101000728 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105101000729 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105101000730 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105101000731 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000732 Walker A/P-loop; other site 1105101000733 ATP binding site [chemical binding]; other site 1105101000734 Q-loop/lid; other site 1105101000735 ABC transporter signature motif; other site 1105101000736 Walker B; other site 1105101000737 D-loop; other site 1105101000738 H-loop/switch region; other site 1105101000739 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105101000740 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 1105101000741 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105101000742 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105101000743 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105101000744 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 1105101000745 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105101000746 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105101000747 putative metal binding site; other site 1105101000748 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105101000749 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105101000750 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105101000751 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105101000752 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105101000753 ATP binding site [chemical binding]; other site 1105101000754 active site 1105101000755 substrate binding site [chemical binding]; other site 1105101000756 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105101000757 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 1105101000758 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105101000759 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 1105101000760 active site 1105101000761 dimer interface [polypeptide binding]; other site 1105101000762 motif 1; other site 1105101000763 motif 2; other site 1105101000764 motif 3; other site 1105101000765 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 1105101000766 anticodon binding site; other site 1105101000767 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000768 Walker A/P-loop; other site 1105101000769 ATP binding site [chemical binding]; other site 1105101000770 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000771 ABC transporter signature motif; other site 1105101000772 Walker B; other site 1105101000773 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101000774 H-loop/switch region; other site 1105101000775 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 1105101000776 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105101000777 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated; Region: PRK04028 1105101000778 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105101000779 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 1105101000780 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 1105101000781 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105101000782 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105101000783 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 1105101000784 ATP binding site [chemical binding]; other site 1105101000785 Mg2+ binding site [ion binding]; other site 1105101000786 G-X-G motif; other site 1105101000787 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 1105101000788 anchoring element; other site 1105101000789 dimer interface [polypeptide binding]; other site 1105101000790 ATP binding site [chemical binding]; other site 1105101000791 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 1105101000792 active site 1105101000793 metal binding site [ion binding]; metal-binding site 1105101000794 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105101000795 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105101000796 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105101000797 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 1105101000798 protein binding site [polypeptide binding]; other site 1105101000799 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105101000800 Catalytic dyad [active] 1105101000801 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1105101000802 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 1105101000803 dimer interface [polypeptide binding]; other site 1105101000804 phosphorylation site [posttranslational modification] 1105101000805 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 1105101000806 ATP binding site [chemical binding]; other site 1105101000807 Mg2+ binding site [ion binding]; other site 1105101000808 G-X-G motif; other site 1105101000809 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105101000810 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105101000811 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105101000812 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105101000813 Trp docking motif [polypeptide binding]; other site 1105101000814 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 1105101000815 23S rRNA interface [nucleotide binding]; other site 1105101000816 L3 interface [polypeptide binding]; other site 1105101000817 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1105101000818 potential protein location (hypothetical protein RPK_01760 [Rickettsia rickettsii str. Hlp#2]) that overlaps RNA (tRNA-M) 1105101000819 Pterin 4 alpha carbinolamine dehydratase; Region: Pterin_4a; pfam01329 1105101000820 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105101000821 DCoH tetramer interaction site [polypeptide binding]; other site 1105101000822 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 1105101000823 putative active site [active] 1105101000824 Ap4A binding site [chemical binding]; other site 1105101000825 nudix motif; other site 1105101000826 putative metal binding site [ion binding]; other site 1105101000827 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105101000828 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 1105101000829 active site 1105101000830 phosphorylation site [posttranslational modification] 1105101000831 intermolecular recognition site; other site 1105101000832 dimerization interface [polypeptide binding]; other site 1105101000833 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 1105101000834 active site 1105101000835 phosphorylation site [posttranslational modification] 1105101000836 intermolecular recognition site; other site 1105101000837 dimerization interface [polypeptide binding]; other site 1105101000838 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105101000839 metal binding site [ion binding]; metal-binding site 1105101000840 active site 1105101000841 I-site; other site 1105101000842 elongation factor P; Validated; Region: PRK00529 1105101000843 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105101000844 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 1105101000845 RNA binding site [nucleotide binding]; other site 1105101000846 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 1105101000847 RNA binding site [nucleotide binding]; other site 1105101000848 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105101000849 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 1105101000850 active site 1105101000851 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105101000852 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 1105101000853 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105101000854 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1105101000855 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1105101000856 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105101000857 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105101000858 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101000859 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105101000860 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 1105101000861 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105101000862 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105101000863 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105101000864 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105101000865 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105101000866 FAD binding domain; Region: FAD_binding_4; pfam01565 1105101000867 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105101000868 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105101000869 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105101000870 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1105101000871 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1105101000872 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105101000873 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105101000874 cell division protein FtsA; Region: ftsA; TIGR01174 1105101000875 Cell division protein FtsA; Region: FtsA; smart00842 1105101000876 Cell division protein FtsA; Region: FtsA; pfam14450 1105101000877 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1105101000878 Cytochrome c2 [Energy production and conversion]; Region: COG3474 1105101000879 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1105101000880 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105101000881 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 1105101000882 RNA binding site [nucleotide binding]; other site 1105101000883 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 1105101000884 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 1105101000885 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105101000886 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 1105101000887 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105101000888 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 1105101000889 RNA binding surface [nucleotide binding]; other site 1105101000890 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105101000891 active site 1105101000892 potential frameshift: common BLAST hit: gi|15892268|ref|NP_359982.1| penicillin-binding protein 4* 1105101000893 potential frameshift: common BLAST hit: gi|341583576|ref|YP_004764067.1| penicillin-binding protein 4* 1105101000894 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 1105101000895 putative catalytic site [active] 1105101000896 putative phosphate binding site [ion binding]; other site 1105101000897 active site 1105101000898 metal binding site A [ion binding]; metal-binding site 1105101000899 DNA binding site [nucleotide binding] 1105101000900 putative AP binding site [nucleotide binding]; other site 1105101000901 putative metal binding site B [ion binding]; other site 1105101000902 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105101000903 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 1105101000904 tetramer interface [polypeptide binding]; other site 1105101000905 TPP-binding site [chemical binding]; other site 1105101000906 heterodimer interface [polypeptide binding]; other site 1105101000907 phosphorylation loop region [posttranslational modification] 1105101000908 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105101000909 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 1105101000910 alpha subunit interface [polypeptide binding]; other site 1105101000911 TPP binding site [chemical binding]; other site 1105101000912 heterodimer interface [polypeptide binding]; other site 1105101000913 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105101000914 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1105101000915 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105101000916 G1 box; other site 1105101000917 putative GEF interaction site [polypeptide binding]; other site 1105101000918 GTP/Mg2+ binding site [chemical binding]; other site 1105101000919 Switch I region; other site 1105101000920 G2 box; other site 1105101000921 G3 box; other site 1105101000922 Switch II region; other site 1105101000923 G4 box; other site 1105101000924 G5 box; other site 1105101000925 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 1105101000926 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 1105101000927 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105101000928 isocitrate dehydrogenase; Validated; Region: PRK09222 1105101000929 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 1105101000930 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 1105101000931 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105101000932 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 1105101000933 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105101000934 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105101000935 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105101000936 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105101000937 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 1105101000938 [2Fe-2S] cluster binding site [ion binding]; other site 1105101000939 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 1105101000940 Qi binding site; other site 1105101000941 cytochrome b; Provisional; Region: CYTB; MTH00191 1105101000942 intrachain domain interface; other site 1105101000943 interchain domain interface [polypeptide binding]; other site 1105101000944 heme bH binding site [chemical binding]; other site 1105101000945 heme bL binding site [chemical binding]; other site 1105101000946 Qo binding site; other site 1105101000947 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 1105101000948 interchain domain interface [polypeptide binding]; other site 1105101000949 intrachain domain interface; other site 1105101000950 Qi binding site; other site 1105101000951 Qo binding site; other site 1105101000952 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105101000953 catalytic site [active] 1105101000954 metal binding site [ion binding]; metal-binding site 1105101000955 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105101000956 Cytochrome c; Region: Cytochrom_C; cl11414 1105101000957 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1105101000958 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 1105101000959 putative dimer interface [polypeptide binding]; other site 1105101000960 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105101000961 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105101000962 PCRF domain; Region: PCRF; pfam03462 1105101000963 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105101000964 RF-1 domain; Region: RF-1; pfam00472 1105101000965 GTP-binding protein LepA; Provisional; Region: PRK05433 1105101000966 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105101000967 G1 box; other site 1105101000968 putative GEF interaction site [polypeptide binding]; other site 1105101000969 GTP/Mg2+ binding site [chemical binding]; other site 1105101000970 Switch I region; other site 1105101000971 G2 box; other site 1105101000972 G3 box; other site 1105101000973 Switch II region; other site 1105101000974 G4 box; other site 1105101000975 G5 box; other site 1105101000976 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 1105101000977 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 1105101000978 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105101000979 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 1105101000980 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105101000981 AAA domain; Region: AAA_17; pfam13207 1105101000982 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 1105101000983 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 1105101000984 active site 1105101000985 homodimer interface [polypeptide binding]; other site 1105101000986 putative chemical substrate binding site [chemical binding]; other site 1105101000987 metal binding site [ion binding]; metal-binding site 1105101000988 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105101000989 Substrate binding site; other site 1105101000990 Mg++ binding site; other site 1105101000991 hypothetical protein; Validated; Region: PRK00110 1105101000992 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 1105101000993 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105101000994 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 1105101000995 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105101000996 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105101000997 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 1105101000998 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1105101000999 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1105101001000 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 1105101001001 S-adenosylmethionine binding site [chemical binding]; other site 1105101001002 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105101001003 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1105101001004 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105101001005 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105101001006 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1105101001007 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1105101001008 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105101001009 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105101001010 catalytic site [active] 1105101001011 putative active site [active] 1105101001012 putative substrate binding site [chemical binding]; other site 1105101001013 Helicase and RNase D C-terminal; Region: HRDC; smart00341 1105101001014 Uncharacterized conserved protein [Function unknown]; Region: COG1723 1105101001015 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105101001016 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105101001017 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105101001018 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105101001019 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 1105101001020 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105101001021 potential frameshift: common BLAST hit: gi|15892625|ref|NP_360339.1| sodium/pantothenate symporter 1105101001022 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 1105101001023 dimer interface [polypeptide binding]; other site 1105101001024 phosphorylation site [posttranslational modification] 1105101001025 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 1105101001026 G-X-G motif; other site 1105101001027 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105101001028 dimer interface [polypeptide binding]; other site 1105101001029 catalytic triad [active] 1105101001030 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105101001031 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 1105101001032 domain interfaces; other site 1105101001033 active site 1105101001034 AAA domain; Region: AAA_14; pfam13173 1105101001035 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105101001036 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105101001037 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105101001038 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105101001039 active site 1105101001040 HIGH motif; other site 1105101001041 dimer interface [polypeptide binding]; other site 1105101001042 KMSKS motif; other site 1105101001043 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1105101001044 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105101001045 putative acyl-acceptor binding pocket; other site 1105101001046 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 1105101001047 RelB antitoxin; Region: RelB; cl01171 1105101001048 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105101001049 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105101001050 HemY protein N-terminus; Region: HemY_N; pfam07219 1105101001051 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105101001052 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105101001053 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 1105101001054 active site 1105101001055 Lysine efflux permease [General function prediction only]; Region: COG1279 1105101001056 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105101001057 AmpG-like permease; Region: 2A0125; TIGR00901 1105101001058 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105101001059 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1105101001060 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 1105101001061 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101001062 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105101001063 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105101001064 substrate binding pocket [chemical binding]; other site 1105101001065 chain length determination region; other site 1105101001066 substrate-Mg2+ binding site; other site 1105101001067 catalytic residues [active] 1105101001068 aspartate-rich region 1; other site 1105101001069 active site lid residues [active] 1105101001070 aspartate-rich region 2; other site 1105101001071 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105101001072 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105101001073 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 1105101001074 active site 1105101001075 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105101001076 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105101001077 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105101001078 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105101001079 trimerization site [polypeptide binding]; other site 1105101001080 active site 1105101001081 cysteine desulfurase; Provisional; Region: PRK14012 1105101001082 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105101001083 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105101001084 catalytic residue [active] 1105101001085 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1105101001086 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105101001087 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105101001088 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105101001089 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 1105101001090 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105101001091 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105101001092 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1105101001093 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105101001094 Coenzyme A binding pocket [chemical binding]; other site 1105101001095 Predicted acetyltransferase [General function prediction only]; Region: COG5628 1105101001096 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105101001097 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 1105101001098 homotetramer interface [polypeptide binding]; other site 1105101001099 FMN binding site [chemical binding]; other site 1105101001100 homodimer contacts [polypeptide binding]; other site 1105101001101 putative active site [active] 1105101001102 putative substrate binding site [chemical binding]; other site 1105101001103 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1105101001104 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105101001105 oligomer interface [polypeptide binding]; other site 1105101001106 active site residues [active] 1105101001107 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105101001108 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 1105101001109 RNA binding site [nucleotide binding]; other site 1105101001110 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 1105101001111 RNA binding site [nucleotide binding]; other site 1105101001112 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 1105101001113 RNA binding site [nucleotide binding]; other site 1105101001114 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 1105101001115 RNA binding site [nucleotide binding]; other site 1105101001116 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 1105101001117 RNA binding site [nucleotide binding]; other site 1105101001118 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 1105101001119 RNA binding site [nucleotide binding]; other site 1105101001120 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 1105101001121 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 1105101001122 CMP-binding site; other site 1105101001123 The sites determining sugar specificity; other site 1105101001124 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 1105101001125 non-specific DNA binding site [nucleotide binding]; other site 1105101001126 salt bridge; other site 1105101001127 sequence-specific DNA binding site [nucleotide binding]; other site 1105101001128 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 1105101001129 hypothetical protein; Region: PHA00670 1105101001130 hypothetical protein; Region: PHA00670 1105101001131 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 1105101001132 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 1105101001133 IHF - DNA interface [nucleotide binding]; other site 1105101001134 IHF dimer interface [polypeptide binding]; other site 1105101001135 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1105101001136 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105101001137 tandem repeat interface [polypeptide binding]; other site 1105101001138 oligomer interface [polypeptide binding]; other site 1105101001139 active site residues [active] 1105101001140 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105101001141 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1105101001142 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 1105101001143 RNA binding site [nucleotide binding]; other site 1105101001144 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 1105101001145 multimer interface [polypeptide binding]; other site 1105101001146 Walker A motif; other site 1105101001147 ATP binding site [chemical binding]; other site 1105101001148 Walker B motif; other site 1105101001149 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 1105101001150 S-adenosylmethionine binding site [chemical binding]; other site 1105101001151 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105101001152 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105101001153 DHH family; Region: DHH; pfam01368 1105101001154 DHHA1 domain; Region: DHHA1; pfam02272 1105101001155 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105101001156 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1105101001157 RF-1 domain; Region: RF-1; pfam00472 1105101001158 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 1105101001159 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105101001160 E3 interaction surface; other site 1105101001161 lipoyl attachment site [posttranslational modification]; other site 1105101001162 e3 binding domain; Region: E3_binding; pfam02817 1105101001163 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105101001164 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1105101001165 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105101001166 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105101001167 Predicted membrane protein [Function unknown]; Region: COG5346 1105101001168 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105101001169 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1105101001170 Uncharacterized conserved protein [Function unknown]; Region: COG5448 1105101001171 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105101001172 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1105101001173 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105101001174 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105101001175 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105101001176 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105101001177 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105101001178 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105101001179 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105101001180 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1105101001181 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 1105101001182 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105101001183 conserved cys residue [active] 1105101001184 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105101001185 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 1105101001186 GSH binding site (G-site) [chemical binding]; other site 1105101001187 C-terminal domain interface [polypeptide binding]; other site 1105101001188 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105101001189 N-terminal domain interface [polypeptide binding]; other site 1105101001190 dimer interface [polypeptide binding]; other site 1105101001191 substrate binding pocket (H-site) [chemical binding]; other site 1105101001192 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105101001193 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105101001194 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1105101001195 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1105101001196 hypothetical protein; Provisional; Region: PRK06661 1105101001197 intersubunit interface [polypeptide binding]; other site 1105101001198 active site 1105101001199 Zn2+ binding site [ion binding]; other site 1105101001200 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105101001201 putative active site [active] 1105101001202 homotetrameric interface [polypeptide binding]; other site 1105101001203 metal binding site [ion binding]; metal-binding site 1105101001204 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001205 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cl00234 1105101001206 catalytic residues [active] 1105101001207 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105101001208 uncharacterized protein, YfiH family; Region: TIGR00726 1105101001209 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1105101001210 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105101001211 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 1105101001212 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1105101001213 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 1105101001214 non-specific DNA binding site [nucleotide binding]; other site 1105101001215 salt bridge; other site 1105101001216 sequence-specific DNA binding site [nucleotide binding]; other site 1105101001217 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105101001218 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101001219 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105101001220 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105101001221 RNA binding site [nucleotide binding]; other site 1105101001222 active site 1105101001223 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001224 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 1105101001225 16S/18S rRNA binding site [nucleotide binding]; other site 1105101001226 S13e-L30e interaction site [polypeptide binding]; other site 1105101001227 25S rRNA binding site [nucleotide binding]; other site 1105101001228 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105101001229 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105101001230 RNase E interface [polypeptide binding]; other site 1105101001231 trimer interface [polypeptide binding]; other site 1105101001232 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105101001233 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105101001234 RNase E interface [polypeptide binding]; other site 1105101001235 trimer interface [polypeptide binding]; other site 1105101001236 active site 1105101001237 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 1105101001238 putative nucleic acid binding region [nucleotide binding]; other site 1105101001239 G-X-X-G motif; other site 1105101001240 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 1105101001241 RNA binding site [nucleotide binding]; other site 1105101001242 domain interface; other site 1105101001243 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 1105101001244 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 1105101001245 putative active site [active] 1105101001246 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 1105101001247 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105101001248 OstA-like protein; Region: OstA; pfam03968 1105101001249 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105101001250 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101001251 Walker A/P-loop; other site 1105101001252 ATP binding site [chemical binding]; other site 1105101001253 Q-loop/lid; other site 1105101001254 ABC transporter signature motif; other site 1105101001255 Walker B; other site 1105101001256 D-loop; other site 1105101001257 H-loop/switch region; other site 1105101001258 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105101001259 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 1105101001260 active site 1105101001261 substrate binding site [chemical binding]; other site 1105101001262 metal binding site [ion binding]; metal-binding site 1105101001263 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1105101001264 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105101001265 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105101001266 dimer interface [polypeptide binding]; other site 1105101001267 putative radical transfer pathway; other site 1105101001268 diiron center [ion binding]; other site 1105101001269 tyrosyl radical; other site 1105101001270 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105101001271 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105101001272 active site 1105101001273 dimer interface [polypeptide binding]; other site 1105101001274 catalytic residues [active] 1105101001275 effector binding site; other site 1105101001276 R2 peptide binding site; other site 1105101001277 Spore Coat Protein U domain; Region: SCPU; pfam05229 1105101001278 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105101001279 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105101001280 potential frameshift: common BLAST hit: gi|91205792|ref|YP_538147.1| P pilus assembly, fimbrial usher protein 1105101001281 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105101001282 Uncharacterized secreted protein [Function unknown]; Region: COG5430 1105101001283 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105101001284 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105101001285 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105101001286 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105101001287 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105101001288 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105101001289 homodimer interface [polypeptide binding]; other site 1105101001290 NADP binding site [chemical binding]; other site 1105101001291 substrate binding site [chemical binding]; other site 1105101001292 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 1105101001293 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 1105101001294 30S subunit binding site; other site 1105101001295 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 1105101001296 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 1105101001297 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105101001298 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105101001299 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 1105101001300 Walker A motif; other site 1105101001301 ATP binding site [chemical binding]; other site 1105101001302 Walker B motif; other site 1105101001303 arginine finger; other site 1105101001304 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1105101001305 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105101001306 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 1105101001307 tetramer interface [polypeptide binding]; other site 1105101001308 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105101001309 catalytic residue [active] 1105101001310 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 1105101001311 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1105101001312 Part of AAA domain; Region: AAA_19; pfam13245 1105101001313 Family description; Region: UvrD_C_2; pfam13538 1105101001314 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105101001315 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 1105101001316 active site 1105101001317 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1105101001318 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 1105101001319 tetramerization interface [polypeptide binding]; other site 1105101001320 NAD(P) binding site [chemical binding]; other site 1105101001321 catalytic residues [active] 1105101001322 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105101001323 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105101001324 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105101001325 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105101001326 Predicted permeases [General function prediction only]; Region: COG0679 1105101001327 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105101001328 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1105101001329 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105101001330 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105101001331 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1105101001332 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105101001333 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 1105101001334 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 1105101001335 RecR protein; Region: RecR; pfam02132 1105101001336 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 1105101001337 putative active site [active] 1105101001338 putative metal-binding site [ion binding]; other site 1105101001339 tetramer interface [polypeptide binding]; other site 1105101001340 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1105101001341 Predicted membrane protein [Function unknown]; Region: COG1238 1105101001342 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1105101001343 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105101001344 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 1105101001345 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105101001346 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105101001347 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 1105101001348 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105101001349 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105101001350 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1105101001351 CoA-ligase; Region: Ligase_CoA; pfam00549 1105101001352 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105101001353 CoA binding domain; Region: CoA_binding; pfam02629 1105101001354 CoA-ligase; Region: Ligase_CoA; pfam00549 1105101001355 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 1105101001356 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105101001357 catalytic residues [active] 1105101001358 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 1105101001359 SmpB-tmRNA interface; other site 1105101001360 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105101001361 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105101001362 dimer interface [polypeptide binding]; other site 1105101001363 active site 1105101001364 catalytic residue [active] 1105101001365 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1105101001366 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 1105101001367 homodimer interface [polypeptide binding]; other site 1105101001368 substrate-cofactor binding pocket; other site 1105101001369 catalytic residue [active] 1105101001370 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105101001371 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 1105101001372 active site 1105101001373 phosphorylation site [posttranslational modification] 1105101001374 intermolecular recognition site; other site 1105101001375 dimerization interface [polypeptide binding]; other site 1105101001376 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 1105101001377 DNA binding site [nucleotide binding] 1105101001378 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105101001379 HAMP domain; Region: HAMP; pfam00672 1105101001380 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 1105101001381 dimer interface [polypeptide binding]; other site 1105101001382 phosphorylation site [posttranslational modification] 1105101001383 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 1105101001384 ATP binding site [chemical binding]; other site 1105101001385 Mg2+ binding site [ion binding]; other site 1105101001386 G-X-G motif; other site 1105101001387 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 1105101001388 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105101001389 catalytic residue [active] 1105101001390 putative FPP diphosphate binding site; other site 1105101001391 putative FPP binding hydrophobic cleft; other site 1105101001392 dimer interface [polypeptide binding]; other site 1105101001393 putative IPP diphosphate binding site; other site 1105101001394 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1105101001395 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1105101001396 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 1105101001397 Septum formation initiator; Region: DivIC; pfam04977 1105101001398 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105101001399 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105101001400 catalytic site [active] 1105101001401 putative active site [active] 1105101001402 putative substrate binding site [chemical binding]; other site 1105101001403 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105101001404 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105101001405 HIGH motif; other site 1105101001406 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105101001407 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101001408 active site 1105101001409 KMSKS motif; other site 1105101001410 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105101001411 tRNA binding surface [nucleotide binding]; other site 1105101001412 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105101001413 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105101001414 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105101001415 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 1105101001416 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105101001417 putative DNA binding surface [nucleotide binding]; other site 1105101001418 dimer interface [polypeptide binding]; other site 1105101001419 beta-clamp/clamp loader binding surface; other site 1105101001420 beta-clamp/translesion DNA polymerase binding surface; other site 1105101001421 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105101001422 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 1105101001423 putative tRNA-binding site [nucleotide binding]; other site 1105101001424 B3/4 domain; Region: B3_4; pfam03483 1105101001425 tRNA synthetase B5 domain; Region: B5; smart00874 1105101001426 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 1105101001427 dimer interface [polypeptide binding]; other site 1105101001428 motif 1; other site 1105101001429 motif 3; other site 1105101001430 motif 2; other site 1105101001431 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1105101001432 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105101001433 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105101001434 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 1105101001435 dimer interface [polypeptide binding]; other site 1105101001436 motif 1; other site 1105101001437 active site 1105101001438 motif 2; other site 1105101001439 motif 3; other site 1105101001440 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105101001441 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105101001442 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 1105101001443 FeS/SAM binding site; other site 1105101001444 diaminopimelate epimerase; Region: DapF; TIGR00652 1105101001445 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105101001446 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105101001447 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101001448 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101001449 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 1105101001450 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105101001451 potential frameshift: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 1105101001452 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105101001453 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105101001454 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105101001455 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 1105101001456 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105101001457 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105101001458 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105101001459 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105101001460 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105101001461 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 1105101001462 active site 1105101001463 homodimer interface [polypeptide binding]; other site 1105101001464 cell division protein FtsW; Region: ftsW; TIGR02614 1105101001465 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105101001466 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105101001467 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105101001468 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105101001469 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1105101001470 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105101001471 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1105101001472 putative peptidase; Provisional; Region: PRK11649 1105101001473 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105101001474 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001475 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105101001476 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105101001477 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1105101001478 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 1105101001479 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 1105101001480 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 1105101001481 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105101001482 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 1105101001483 Subunit I/III interface [polypeptide binding]; other site 1105101001484 D-pathway; other site 1105101001485 Subunit I/VIIc interface [polypeptide binding]; other site 1105101001486 Subunit I/IV interface [polypeptide binding]; other site 1105101001487 Subunit I/II interface [polypeptide binding]; other site 1105101001488 Low-spin heme (heme a) binding site [chemical binding]; other site 1105101001489 Subunit I/VIIa interface [polypeptide binding]; other site 1105101001490 Subunit I/VIa interface [polypeptide binding]; other site 1105101001491 Dimer interface; other site 1105101001492 Putative water exit pathway; other site 1105101001493 Binuclear center (heme a3/CuB) [ion binding]; other site 1105101001494 K-pathway; other site 1105101001495 Subunit I/Vb interface [polypeptide binding]; other site 1105101001496 Putative proton exit pathway; other site 1105101001497 Subunit I/VIb interface; other site 1105101001498 Subunit I/VIc interface [polypeptide binding]; other site 1105101001499 Electron transfer pathway; other site 1105101001500 Subunit I/VIIIb interface [polypeptide binding]; other site 1105101001501 Subunit I/VIIb interface [polypeptide binding]; other site 1105101001502 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105101001503 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105101001504 catalytic triad [active] 1105101001505 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105101001506 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 1105101001507 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105101001508 dimer interface [polypeptide binding]; other site 1105101001509 catalytic triad [active] 1105101001510 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105101001511 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 1105101001512 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105101001513 catalytic residue [active] 1105101001514 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105101001515 trimer interface [polypeptide binding]; other site 1105101001516 active site 1105101001517 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 1105101001518 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105101001519 tandem repeat interface [polypeptide binding]; other site 1105101001520 oligomer interface [polypeptide binding]; other site 1105101001521 active site residues [active] 1105101001522 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 1105101001523 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1105101001524 catalytic residues [active] 1105101001525 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105101001526 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 1105101001527 active site 1105101001528 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105101001529 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 1105101001530 Iron permease FTR1 family; Region: FTR1; cl00475 1105101001531 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 1105101001532 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105101001533 BON domain; Region: BON; pfam04972 1105101001534 BON domain; Region: BON; pfam04972 1105101001535 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101001536 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101001537 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1105101001538 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1105101001539 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1105101001540 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105101001541 muropeptide transporter; Validated; Region: ampG; cl17669 1105101001542 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105101001543 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105101001544 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105101001545 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101001546 Walker A/P-loop; other site 1105101001547 ATP binding site [chemical binding]; other site 1105101001548 Q-loop/lid; other site 1105101001549 ABC transporter signature motif; other site 1105101001550 Walker B; other site 1105101001551 D-loop; other site 1105101001552 H-loop/switch region; other site 1105101001553 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 1105101001554 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 1105101001555 Walker A motif; other site 1105101001556 ATP binding site [chemical binding]; other site 1105101001557 Walker B motif; other site 1105101001558 arginine finger; other site 1105101001559 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105101001560 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105101001561 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105101001562 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105101001563 Fic family protein [Function unknown]; Region: COG3177 1105101001564 Fic/DOC family; Region: Fic; pfam02661 1105101001565 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105101001566 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 1105101001567 dimer interface [polypeptide binding]; other site 1105101001568 motif 1; other site 1105101001569 active site 1105101001570 motif 2; other site 1105101001571 motif 3; other site 1105101001572 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 1105101001573 anticodon binding site; other site 1105101001574 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 1105101001575 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105101001576 active site 1105101001577 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 1105101001578 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1105101001579 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105101001580 Ligand binding site; other site 1105101001581 oligomer interface; other site 1105101001582 CTP synthetase; Validated; Region: pyrG; PRK05380 1105101001583 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 1105101001584 Catalytic site [active] 1105101001585 active site 1105101001586 UTP binding site [chemical binding]; other site 1105101001587 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105101001588 active site 1105101001589 putative oxyanion hole; other site 1105101001590 catalytic triad [active] 1105101001591 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101001592 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 1105101001593 malate dehydrogenase; Reviewed; Region: PRK06223 1105101001594 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105101001595 NAD(P) binding site [chemical binding]; other site 1105101001596 dimer interface [polypeptide binding]; other site 1105101001597 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105101001598 substrate binding site [chemical binding]; other site 1105101001599 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101001600 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105101001601 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 1105101001602 putative active site [active] 1105101001603 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105101001604 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105101001605 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105101001606 putative NAD(P) binding site [chemical binding]; other site 1105101001607 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 1105101001608 Predicted permeases [General function prediction only]; Region: COG0679 1105101001609 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105101001610 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105101001611 active site 1105101001612 HIGH motif; other site 1105101001613 KMSKS motif; other site 1105101001614 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 1105101001615 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 1105101001616 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1105101001617 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101001618 Walker A/P-loop; other site 1105101001619 ATP binding site [chemical binding]; other site 1105101001620 Q-loop/lid; other site 1105101001621 ABC transporter signature motif; other site 1105101001622 Walker B; other site 1105101001623 D-loop; other site 1105101001624 H-loop/switch region; other site 1105101001625 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 1105101001626 TM-ABC transporter signature motif; other site 1105101001627 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 1105101001628 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105101001629 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 1105101001630 amidase catalytic site [active] 1105101001631 Zn binding residues [ion binding]; other site 1105101001632 substrate binding site [chemical binding]; other site 1105101001633 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105101001634 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105101001635 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105101001636 putative active site [active] 1105101001637 catalytic triad [active] 1105101001638 putative dimer interface [polypeptide binding]; other site 1105101001639 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 1105101001640 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105101001641 NAD binding site [chemical binding]; other site 1105101001642 homotetramer interface [polypeptide binding]; other site 1105101001643 homodimer interface [polypeptide binding]; other site 1105101001644 substrate binding site [chemical binding]; other site 1105101001645 active site 1105101001646 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105101001647 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 1105101001648 active site 1105101001649 DNA binding site [nucleotide binding] 1105101001650 Int/Topo IB signature motif; other site 1105101001651 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105101001652 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 1105101001653 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105101001654 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1105101001655 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1105101001656 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105101001657 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1105101001658 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 1105101001659 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1105101001660 NADH dehydrogenase subunit E; Validated; Region: PRK07539 1105101001661 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 1105101001662 putative dimer interface [polypeptide binding]; other site 1105101001663 [2Fe-2S] cluster binding site [ion binding]; other site 1105101001664 hypothetical protein; Provisional; Region: PRK14388 1105101001665 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105101001666 active site 1105101001667 DNA binding site [nucleotide binding] 1105101001668 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105101001669 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1105101001670 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105101001671 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105101001672 RimM N-terminal domain; Region: RimM; pfam01782 1105101001673 PRC-barrel domain; Region: PRC; pfam05239 1105101001674 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105101001675 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105101001676 TPR repeat; Region: TPR_11; pfam13414 1105101001677 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 1105101001678 TPR motif; other site 1105101001679 binding surface 1105101001680 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105101001681 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 1105101001682 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105101001683 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 1105101001684 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105101001685 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105101001686 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105101001687 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 1105101001688 RNA binding surface [nucleotide binding]; other site 1105101001689 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105101001690 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 1105101001691 putative ADP-binding pocket [chemical binding]; other site 1105101001692 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105101001693 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 1105101001694 catalytic site [active] 1105101001695 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105101001696 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 1105101001697 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105101001698 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105101001699 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105101001700 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 1105101001701 active site 1105101001702 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105101001703 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 1105101001704 active site 1105101001705 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105101001706 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 1105101001707 S-adenosylmethionine binding site [chemical binding]; other site 1105101001708 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105101001709 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 1105101001710 active site 1105101001711 homodimer interface [polypeptide binding]; other site 1105101001712 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105101001713 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105101001714 NAD(P) binding site [chemical binding]; other site 1105101001715 homodimer interface [polypeptide binding]; other site 1105101001716 substrate binding site [chemical binding]; other site 1105101001717 active site 1105101001718 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105101001719 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105101001720 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105101001721 NADP binding site [chemical binding]; other site 1105101001722 active site 1105101001723 putative substrate binding site [chemical binding]; other site 1105101001724 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 1105101001725 sequence-specific DNA binding site [nucleotide binding]; other site 1105101001726 salt bridge; other site 1105101001727 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 1105101001728 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105101001729 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105101001730 Sulfatase; Region: Sulfatase; pfam00884 1105101001731 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105101001732 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 1105101001733 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105101001734 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 1105101001735 dimer interface [polypeptide binding]; other site 1105101001736 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105101001737 catalytic triad [active] 1105101001738 peroxidatic and resolving cysteines [active] 1105101001739 DNA protecting protein DprA; Region: dprA; TIGR00732 1105101001740 DNA protecting protein DprA; Region: dprA; TIGR00732 1105101001741 DNA topoisomerase I; Validated; Region: PRK06599 1105101001742 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 1105101001743 active site 1105101001744 interdomain interaction site; other site 1105101001745 putative metal-binding site [ion binding]; other site 1105101001746 nucleotide binding site [chemical binding]; other site 1105101001747 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 1105101001748 domain I; other site 1105101001749 DNA binding groove [nucleotide binding] 1105101001750 phosphate binding site [ion binding]; other site 1105101001751 domain II; other site 1105101001752 domain III; other site 1105101001753 nucleotide binding site [chemical binding]; other site 1105101001754 catalytic site [active] 1105101001755 domain IV; other site 1105101001756 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105101001757 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1105101001758 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105101001759 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105101001760 HIGH motif; other site 1105101001761 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101001762 active site 1105101001763 KMSKS motif; other site 1105101001764 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 1105101001765 putative iron binding site [ion binding]; other site 1105101001766 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1105101001767 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105101001768 dimerization interface [polypeptide binding]; other site 1105101001769 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105101001770 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105101001771 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105101001772 Uncharacterized conserved protein [Function unknown]; Region: COG5464 1105101001773 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101001774 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101001775 potential frameshift: common BLAST hit: gi|67458910|ref|YP_246534.1| Mg chelatase-like protein 1105101001776 potential frameshift: common BLAST hit: gi|157827341|ref|YP_001496405.1| Mg chelatase-like protein 1105101001777 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105101001778 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 1105101001779 Walker A motif; other site 1105101001780 ATP binding site [chemical binding]; other site 1105101001781 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1105101001782 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105101001783 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 1105101001784 active site 1105101001785 HslU subunit interaction site [polypeptide binding]; other site 1105101001786 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101001787 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105101001788 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 1105101001789 nucleotide binding site/active site [active] 1105101001790 HIT family signature motif; other site 1105101001791 catalytic residue [active] 1105101001792 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105101001793 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1105101001794 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105101001795 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1105101001796 Walker A/P-loop; other site 1105101001797 ATP binding site [chemical binding]; other site 1105101001798 Q-loop/lid; other site 1105101001799 ABC transporter signature motif; other site 1105101001800 Walker B; other site 1105101001801 D-loop; other site 1105101001802 H-loop/switch region; other site 1105101001803 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105101001804 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 1105101001805 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105101001806 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 1105101001807 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101001808 putative substrate translocation pore; other site 1105101001809 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105101001810 HD domain; Region: HD_4; pfam13328 1105101001811 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1105101001812 TolR protein; Region: tolR; TIGR02801 1105101001813 TolQ protein; Region: tolQ; TIGR02796 1105101001814 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105101001815 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105101001816 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105101001817 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105101001818 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105101001819 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 1105101001820 dimer interface [polypeptide binding]; other site 1105101001821 motif 1; other site 1105101001822 active site 1105101001823 motif 2; other site 1105101001824 motif 3; other site 1105101001825 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 1105101001826 anticodon binding site; other site 1105101001827 amino acid transporter; Region: 2A0306; TIGR00909 1105101001828 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1105101001829 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 1105101001830 Ligand Binding Site [chemical binding]; other site 1105101001831 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 1105101001832 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105101001833 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105101001834 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105101001835 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 1105101001836 DNA binding residues [nucleotide binding] 1105101001837 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105101001838 TolB amino-terminal domain; Region: TolB_N; pfam04052 1105101001839 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105101001840 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105101001841 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105101001842 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1105101001843 Protein of unknown function DUF45; Region: DUF45; pfam01863 1105101001844 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105101001845 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105101001846 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105101001847 MutS domain I; Region: MutS_I; pfam01624 1105101001848 MutS domain II; Region: MutS_II; pfam05188 1105101001849 MutS domain III; Region: MutS_III; pfam05192 1105101001850 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1105101001851 Walker A/P-loop; other site 1105101001852 ATP binding site [chemical binding]; other site 1105101001853 Q-loop/lid; other site 1105101001854 ABC transporter signature motif; other site 1105101001855 Walker B; other site 1105101001856 D-loop; other site 1105101001857 H-loop/switch region; other site 1105101001858 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105101001859 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 1105101001860 active site 1105101001861 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105101001862 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105101001863 Phage portal protein; Region: Phage_portal; pfam04860 1105101001864 Phage-related protein [Function unknown]; Region: COG4695; cl01923 1105101001865 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105101001866 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1105101001867 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105101001868 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 1105101001869 Walker A motif; other site 1105101001870 ATP binding site [chemical binding]; other site 1105101001871 Walker B motif; other site 1105101001872 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 1105101001873 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 1105101001874 Walker A motif; other site 1105101001875 hexamer interface [polypeptide binding]; other site 1105101001876 ATP binding site [chemical binding]; other site 1105101001877 Walker B motif; other site 1105101001878 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1105101001879 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1105101001880 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105101001881 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105101001882 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105101001883 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105101001884 VirB7 interaction site; other site 1105101001885 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 1105101001886 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105101001887 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105101001888 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105101001889 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105101001890 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 1105101001891 oligomeric interface; other site 1105101001892 putative active site [active] 1105101001893 homodimer interface [polypeptide binding]; other site 1105101001894 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105101001895 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105101001896 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105101001897 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105101001898 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105101001899 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1105101001900 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105101001901 HD domain; Region: HD_4; pfam13328 1105101001902 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105101001903 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105101001904 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 1105101001905 dimer interface [polypeptide binding]; other site 1105101001906 allosteric magnesium binding site [ion binding]; other site 1105101001907 active site 1105101001908 aspartate-rich active site metal binding site; other site 1105101001909 Schiff base residues; other site 1105101001910 primosome assembly protein PriA; Validated; Region: PRK05580 1105101001911 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 1105101001912 ATP binding site [chemical binding]; other site 1105101001913 putative Mg++ binding site [ion binding]; other site 1105101001914 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1105101001915 aromatic acid decarboxylase; Validated; Region: PRK05920 1105101001916 Flavoprotein; Region: Flavoprotein; pfam02441 1105101001917 SacI restriction endonuclease; Region: RE_SacI; pfam09566 1105101001918 replicative DNA helicase; Provisional; Region: PRK09165 1105101001919 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105101001920 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 1105101001921 Walker A motif; other site 1105101001922 ATP binding site [chemical binding]; other site 1105101001923 Walker B motif; other site 1105101001924 DNA binding loops [nucleotide binding] 1105101001925 potential frameshift: common BLAST hit: gi|67459254|ref|YP_246878.1| to amino acid permeases 1105101001926 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105101001927 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105101001928 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 1105101001929 RNA binding surface [nucleotide binding]; other site 1105101001930 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105101001931 active site 1105101001932 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105101001933 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001934 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105101001935 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001936 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105101001937 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1105101001938 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 1105101001939 S-adenosylmethionine binding site [chemical binding]; other site 1105101001940 DNA repair protein RadA; Provisional; Region: PRK11823 1105101001941 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 1105101001942 Walker A motif/ATP binding site; other site 1105101001943 ATP binding site [chemical binding]; other site 1105101001944 Walker B motif; other site 1105101001945 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1105101001946 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105101001947 Recombination protein O N terminal; Region: RecO_N; pfam11967 1105101001948 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105101001949 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 1105101001950 Glycoprotease family; Region: Peptidase_M22; pfam00814 1105101001951 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105101001952 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 1105101001953 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105101001954 G1 box; other site 1105101001955 putative GEF interaction site [polypeptide binding]; other site 1105101001956 GTP/Mg2+ binding site [chemical binding]; other site 1105101001957 Switch I region; other site 1105101001958 G2 box; other site 1105101001959 G3 box; other site 1105101001960 Switch II region; other site 1105101001961 G4 box; other site 1105101001962 G5 box; other site 1105101001963 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 1105101001964 Translation-initiation factor 2; Region: IF-2; pfam11987 1105101001965 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 1105101001966 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105101001967 NusA N-terminal domain; Region: NusA_N; pfam08529 1105101001968 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 1105101001969 RNA binding site [nucleotide binding]; other site 1105101001970 homodimer interface [polypeptide binding]; other site 1105101001971 NusA-like KH domain; Region: KH_5; pfam13184 1105101001972 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 1105101001973 G-X-X-G motif; other site 1105101001974 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105101001975 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 1105101001976 Sm and related proteins; Region: Sm_like; cl00259 1105101001977 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1105101001978 putative oligomer interface [polypeptide binding]; other site 1105101001979 putative RNA binding site [nucleotide binding]; other site 1105101001980 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 1105101001981 NAD binding pocket [chemical binding]; other site 1105101001982 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105101001983 Transcriptional regulator; Region: Rrf2; cl17282 1105101001984 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105101001985 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 1105101001986 RNA binding surface [nucleotide binding]; other site 1105101001987 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1105101001988 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105101001989 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105101001990 active site 1105101001991 HIGH motif; other site 1105101001992 dimer interface [polypeptide binding]; other site 1105101001993 KMSKS motif; other site 1105101001994 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 1105101001995 RNA binding surface [nucleotide binding]; other site 1105101001996 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105101001997 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 1105101001998 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 1105101001999 Substrate binding site [chemical binding]; other site 1105101002000 proline/glycine betaine transporter; Provisional; Region: PRK10642 1105101002001 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105101002002 potential frameshift: common BLAST hit: gi|157964695|ref|YP_001499519.1| large extracellular alpha-helical protein 1105101002003 potential frameshift: common BLAST hit: gi|350273648|ref|YP_004884961.1| large extracellular alpha-helical protein 1105101002004 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105101002005 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105101002006 potential frameshift: common BLAST hit: gi|341584023|ref|YP_004764514.1| large extracellular alpha-helical protein 1105101002007 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105101002008 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105101002009 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105101002010 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 1105101002011 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1105101002012 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1105101002013 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002014 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105101002015 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1105101002016 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 1105101002017 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105101002018 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 1105101002019 active site 1105101002020 phosphorylation site [posttranslational modification] 1105101002021 intermolecular recognition site; other site 1105101002022 dimerization interface [polypeptide binding]; other site 1105101002023 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 1105101002024 Walker A motif; other site 1105101002025 ATP binding site [chemical binding]; other site 1105101002026 Walker B motif; other site 1105101002027 arginine finger; other site 1105101002028 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1105101002029 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105101002030 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105101002031 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105101002032 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105101002033 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105101002034 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105101002035 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105101002036 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105101002037 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105101002038 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105101002039 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105101002040 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1105101002041 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 1105101002042 S-adenosylmethionine binding site [chemical binding]; other site 1105101002043 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105101002044 MraZ protein; Region: MraZ; pfam02381 1105101002045 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105101002046 Na binding site [ion binding]; other site 1105101002047 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105101002048 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105101002049 GIY-YIG motif/motif A; other site 1105101002050 active site 1105101002051 catalytic site [active] 1105101002052 putative DNA binding site [nucleotide binding]; other site 1105101002053 metal binding site [ion binding]; metal-binding site 1105101002054 UvrB/uvrC motif; Region: UVR; pfam02151 1105101002055 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105101002056 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 1105101002057 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 1105101002058 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105101002059 active site 1105101002060 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 1105101002061 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105101002062 active site 1105101002063 DNA binding site [nucleotide binding] 1105101002064 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1105101002065 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1105101002066 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105101002067 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 1105101002068 DNA binding site [nucleotide binding] 1105101002069 active site 1105101002070 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 1105101002071 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105101002072 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1105101002073 ATP binding site [chemical binding]; other site 1105101002074 putative Mg++ binding site [ion binding]; other site 1105101002075 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1105101002076 SEC-C motif; Region: SEC-C; pfam02810 1105101002077 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 1105101002078 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1105101002079 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1105101002080 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 1105101002081 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105101002082 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 1105101002083 hinge; other site 1105101002084 active site 1105101002085 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105101002086 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 1105101002087 ATP binding site [chemical binding]; other site 1105101002088 Mg2+ binding site [ion binding]; other site 1105101002089 G-X-G motif; other site 1105101002090 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 1105101002091 anchoring element; other site 1105101002092 dimer interface [polypeptide binding]; other site 1105101002093 ATP binding site [chemical binding]; other site 1105101002094 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 1105101002095 active site 1105101002096 putative metal-binding site [ion binding]; other site 1105101002097 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105101002098 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105101002099 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 1105101002100 active site 1105101002101 motif I; other site 1105101002102 motif II; other site 1105101002103 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 1105101002104 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105101002105 MgtE intracellular N domain; Region: MgtE_N; pfam03448 1105101002106 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 1105101002107 Divalent cation transporter; Region: MgtE; pfam01769 1105101002108 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105101002109 HD domain; Region: HD_4; pfam13328 1105101002110 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 1105101002111 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101002112 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1105101002113 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105101002114 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1105101002115 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105101002116 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 1105101002117 Cu(I) binding site [ion binding]; other site 1105101002118 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 1105101002119 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 1105101002120 dimer interface [polypeptide binding]; other site 1105101002121 substrate binding site [chemical binding]; other site 1105101002122 metal binding sites [ion binding]; metal-binding site 1105101002123 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002124 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1105101002125 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1105101002126 TraX protein; Region: TraX; pfam05857 1105101002127 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105101002128 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 1105101002129 ssDNA binding site; other site 1105101002130 generic binding surface II; other site 1105101002131 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 1105101002132 ATP binding site [chemical binding]; other site 1105101002133 putative Mg++ binding site [ion binding]; other site 1105101002134 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 1105101002135 nucleotide binding region [chemical binding]; other site 1105101002136 ATP-binding site [chemical binding]; other site 1105101002137 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1105101002138 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1105101002139 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 1105101002140 V-type ATP synthase subunit I; Validated; Region: PRK05771 1105101002141 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105101002142 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 1105101002143 Mg++ binding site [ion binding]; other site 1105101002144 putative catalytic motif [active] 1105101002145 putative substrate binding site [chemical binding]; other site 1105101002146 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1105101002147 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105101002148 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105101002149 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105101002150 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105101002151 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105101002152 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105101002153 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105101002154 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105101002155 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1105101002156 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 1105101002157 ATP binding site [chemical binding]; other site 1105101002158 putative Mg++ binding site [ion binding]; other site 1105101002159 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 1105101002160 nucleotide binding region [chemical binding]; other site 1105101002161 ATP-binding site [chemical binding]; other site 1105101002162 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1105101002163 Uncharacterized conserved protein [Function unknown]; Region: COG2938 1105101002164 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 1105101002165 active site residue [active] 1105101002166 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105101002167 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105101002168 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 1105101002169 Walker A motif; other site 1105101002170 ATP binding site [chemical binding]; other site 1105101002171 Walker B motif; other site 1105101002172 arginine finger; other site 1105101002173 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 1105101002174 DnaA box-binding interface [nucleotide binding]; other site 1105101002175 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 1105101002176 YT521-B-like domain; Region: YTH; pfam04146 1105101002177 Patatin [General function prediction only]; Region: COG3621 1105101002178 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105101002179 active site 1105101002180 nucleophile elbow; other site 1105101002181 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105101002182 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105101002183 HEPN domain; Region: HEPN; cl00824 1105101002184 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 1105101002185 active site 1105101002186 NTP binding site [chemical binding]; other site 1105101002187 metal binding triad [ion binding]; metal-binding site 1105101002188 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105101002189 YchF GTPase; Region: YchF; cd01900 1105101002190 G1 box; other site 1105101002191 GTP/Mg2+ binding site [chemical binding]; other site 1105101002192 Switch I region; other site 1105101002193 G2 box; other site 1105101002194 Switch II region; other site 1105101002195 G3 box; other site 1105101002196 G4 box; other site 1105101002197 G5 box; other site 1105101002198 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 1105101002199 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105101002200 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 1105101002201 putative active site [active] 1105101002202 catalytic residue [active] 1105101002203 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105101002204 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105101002205 5S rRNA interface [nucleotide binding]; other site 1105101002206 CTC domain interface [polypeptide binding]; other site 1105101002207 L16 interface [polypeptide binding]; other site 1105101002208 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105101002209 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 1105101002210 FeS/SAM binding site; other site 1105101002211 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1105101002212 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105101002213 23S rRNA binding site [nucleotide binding]; other site 1105101002214 L21 binding site [polypeptide binding]; other site 1105101002215 L13 binding site [polypeptide binding]; other site 1105101002216 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1105101002217 ribonuclease P; Reviewed; Region: rnpA; PRK01492 1105101002218 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105101002219 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105101002220 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 1105101002221 Cl binding site [ion binding]; other site 1105101002222 oligomer interface [polypeptide binding]; other site 1105101002223 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 1105101002224 Phosphotransferase enzyme family; Region: APH; pfam01636 1105101002225 substrate binding site [chemical binding]; other site 1105101002226 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 1105101002227 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105101002228 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 1105101002229 dimerization interface [polypeptide binding]; other site 1105101002230 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 1105101002231 dimer interface [polypeptide binding]; other site 1105101002232 phosphorylation site [posttranslational modification] 1105101002233 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 1105101002234 ATP binding site [chemical binding]; other site 1105101002235 Mg2+ binding site [ion binding]; other site 1105101002236 G-X-G motif; other site 1105101002237 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 1105101002238 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105101002239 COQ9; Region: COQ9; pfam08511 1105101002240 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105101002241 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105101002242 HIGH motif; other site 1105101002243 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105101002244 active site 1105101002245 KMSKS motif; other site 1105101002246 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105101002247 tRNA binding surface [nucleotide binding]; other site 1105101002248 anticodon binding site; other site 1105101002249 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 1105101002250 TPR motif; other site 1105101002251 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105101002252 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105101002253 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1105101002254 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1105101002255 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 1105101002256 carboxyltransferase (CT) interaction site; other site 1105101002257 biotinylation site [posttranslational modification]; other site 1105101002258 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1105101002259 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1105101002260 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1105101002261 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105101002262 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 1105101002263 putative substrate translocation pore; other site 1105101002264 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105101002265 putative acyl-acceptor binding pocket; other site 1105101002266 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 1105101002267 acyl-activating enzyme (AAE) consensus motif; other site 1105101002268 putative AMP binding site [chemical binding]; other site 1105101002269 TfoX N-terminal domain; Region: TfoX_N; pfam04993 1105101002270 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1105101002271 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 1105101002272 ABC-ATPase subunit interface; other site 1105101002273 dimer interface [polypeptide binding]; other site 1105101002274 putative PBP binding regions; other site 1105101002275 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105101002276 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002277 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 1105101002278 S-adenosylmethionine binding site [chemical binding]; other site 1105101002279 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105101002280 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105101002281 HIGH motif; other site 1105101002282 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105101002283 active site 1105101002284 KMSKS motif; other site 1105101002285 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002286 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 1105101002287 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105101002288 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 1105101002289 ring oligomerisation interface [polypeptide binding]; other site 1105101002290 ATP/Mg binding site [chemical binding]; other site 1105101002291 stacking interactions; other site 1105101002292 hinge regions; other site 1105101002293 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 1105101002294 oligomerisation interface [polypeptide binding]; other site 1105101002295 mobile loop; other site 1105101002296 roof hairpin; other site 1105101002297 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105101002298 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 1105101002299 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105101002300 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105101002301 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105101002302 hexamer interface [polypeptide binding]; other site 1105101002303 active site 1105101002304 GrpE; Region: GrpE; pfam01025 1105101002305 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 1105101002306 dimer interface [polypeptide binding]; other site 1105101002307 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105101002308 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1105101002309 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105101002310 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 1105101002311 hypothetical protein; Validated; Region: PRK06620 1105101002312 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101002313 potential frameshift: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 1105101002314 HD domain; Region: HD_4; pfam13328 1105101002315 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1105101002316 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 1105101002317 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105101002318 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105101002319 alphaNTD - beta interaction site [polypeptide binding]; other site 1105101002320 alphaNTD homodimer interface [polypeptide binding]; other site 1105101002321 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105101002322 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1105101002323 30S ribosomal protein S11; Validated; Region: PRK05309 1105101002324 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105101002325 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1105101002326 adenylate kinase; Reviewed; Region: adk; PRK00279 1105101002327 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 1105101002328 AMP-binding site [chemical binding]; other site 1105101002329 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105101002330 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105101002331 SecY translocase; Region: SecY; pfam00344 1105101002332 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1105101002333 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 1105101002334 23S rRNA binding site [nucleotide binding]; other site 1105101002335 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105101002336 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105101002337 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105101002338 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 1105101002339 5S rRNA interface [nucleotide binding]; other site 1105101002340 23S rRNA interface [nucleotide binding]; other site 1105101002341 L5 interface [polypeptide binding]; other site 1105101002342 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105101002343 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105101002344 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105101002345 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1105101002346 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1105101002347 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105101002348 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105101002349 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105101002350 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105101002351 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1105101002352 RNA binding site [nucleotide binding]; other site 1105101002353 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1105101002354 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1105101002355 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 1105101002356 L23 interface [polypeptide binding]; other site 1105101002357 trigger factor interaction site; other site 1105101002358 23S rRNA interface [nucleotide binding]; other site 1105101002359 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 1105101002360 23S rRNA interface [nucleotide binding]; other site 1105101002361 5S rRNA interface [nucleotide binding]; other site 1105101002362 putative antibiotic binding site [chemical binding]; other site 1105101002363 L25 interface [polypeptide binding]; other site 1105101002364 L27 interface [polypeptide binding]; other site 1105101002365 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105101002366 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 1105101002367 G-X-X-G motif; other site 1105101002368 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105101002369 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 1105101002370 putative translocon binding site; other site 1105101002371 protein-rRNA interface [nucleotide binding]; other site 1105101002372 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1105101002373 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105101002374 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105101002375 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105101002376 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1105101002377 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1105101002378 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1105101002379 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1105101002380 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002381 elongation factor Tu; Reviewed; Region: PRK00049 1105101002382 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105101002383 G1 box; other site 1105101002384 GEF interaction site [polypeptide binding]; other site 1105101002385 GTP/Mg2+ binding site [chemical binding]; other site 1105101002386 Switch I region; other site 1105101002387 G2 box; other site 1105101002388 G3 box; other site 1105101002389 Switch II region; other site 1105101002390 G4 box; other site 1105101002391 G5 box; other site 1105101002392 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 1105101002393 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 1105101002394 Antibiotic Binding Site [chemical binding]; other site 1105101002395 potential protein location (hypothetical protein RPK_05560 [Rickettsia rickettsii str. Hlp#2]) that overlaps RNA (tRNA-G) 1105101002396 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105101002397 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1105101002398 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1105101002399 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105101002400 Class II fumarases; Region: Fumarase_classII; cd01362 1105101002401 active site 1105101002402 tetramer interface [polypeptide binding]; other site 1105101002403 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105101002404 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105101002405 putative active site [active] 1105101002406 homotetrameric interface [polypeptide binding]; other site 1105101002407 cell division protein FtsZ; Validated; Region: PRK09330 1105101002408 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 1105101002409 nucleotide binding site [chemical binding]; other site 1105101002410 SulA interaction site; other site 1105101002411 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 1105101002412 secondary substrate binding site; other site 1105101002413 primary substrate binding site; other site 1105101002414 inhibition loop; other site 1105101002415 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 1105101002416 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1105101002417 muropeptide transporter; Validated; Region: ampG; cl17669 1105101002418 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 1105101002419 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105101002420 ATP binding site [chemical binding]; other site 1105101002421 Mg++ binding site [ion binding]; other site 1105101002422 motif III; other site 1105101002423 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 1105101002424 nucleotide binding region [chemical binding]; other site 1105101002425 ATP-binding site [chemical binding]; other site 1105101002426 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 1105101002427 DNA-binding site [nucleotide binding]; DNA binding site 1105101002428 RNA-binding motif; other site 1105101002429 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1105101002430 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 1105101002431 S-adenosylmethionine binding site [chemical binding]; other site 1105101002432 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105101002433 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105101002434 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105101002435 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 1105101002436 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 1105101002437 generic binding surface II; other site 1105101002438 generic binding surface I; other site 1105101002439 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 1105101002440 putative catalytic site [active] 1105101002441 putative phosphate binding site [ion binding]; other site 1105101002442 active site 1105101002443 metal binding site A [ion binding]; metal-binding site 1105101002444 DNA binding site [nucleotide binding] 1105101002445 putative AP binding site [nucleotide binding]; other site 1105101002446 putative metal binding site B [ion binding]; other site 1105101002447 Uncharacterized conserved protein [Function unknown]; Region: COG4095 1105101002448 GTP-binding protein Der; Reviewed; Region: PRK00093 1105101002449 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105101002450 G1 box; other site 1105101002451 GTP/Mg2+ binding site [chemical binding]; other site 1105101002452 Switch I region; other site 1105101002453 G2 box; other site 1105101002454 Switch II region; other site 1105101002455 G3 box; other site 1105101002456 G4 box; other site 1105101002457 G5 box; other site 1105101002458 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105101002459 G1 box; other site 1105101002460 GTP/Mg2+ binding site [chemical binding]; other site 1105101002461 Switch I region; other site 1105101002462 G2 box; other site 1105101002463 G3 box; other site 1105101002464 Switch II region; other site 1105101002465 G4 box; other site 1105101002466 G5 box; other site 1105101002467 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105101002468 AAA domain; Region: AAA_14; pfam13173 1105101002469 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 1105101002470 ABC1 family; Region: ABC1; pfam03109 1105101002471 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 1105101002472 active site 1105101002473 ATP binding site [chemical binding]; other site 1105101002474 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105101002475 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 1105101002476 S-adenosylmethionine binding site [chemical binding]; other site 1105101002477 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105101002478 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105101002479 DNA binding site [nucleotide binding] 1105101002480 catalytic residue [active] 1105101002481 H2TH interface [polypeptide binding]; other site 1105101002482 putative catalytic residues [active] 1105101002483 turnover-facilitating residue; other site 1105101002484 intercalation triad [nucleotide binding]; other site 1105101002485 8OG recognition residue [nucleotide binding]; other site 1105101002486 putative reading head residues; other site 1105101002487 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105101002488 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105101002489 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002490 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101002491 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 1105101002492 active site 1105101002493 potential frameshift: common BLAST hit: gi|15892963|ref|NP_360677.1| mannose-1-phosphate guanylyltransferase 1105101002494 potential frameshift: common BLAST hit: gi|157826925|ref|YP_001495989.1| Poly-beta-hydroxyalkanoate depolymerase 1105101002495 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105101002496 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105101002497 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105101002498 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 1105101002499 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105101002500 active site 1105101002501 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105101002502 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105101002503 HIGH motif; other site 1105101002504 active site 1105101002505 KMSKS motif; other site 1105101002506 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105101002507 tRNA binding surface [nucleotide binding]; other site 1105101002508 anticodon binding site; other site 1105101002509 thymidylate kinase; Validated; Region: tmk; PRK00698 1105101002510 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 1105101002511 TMP-binding site; other site 1105101002512 ATP-binding site [chemical binding]; other site 1105101002513 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101002514 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 1105101002515 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105101002516 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105101002517 potential frameshift: common BLAST hit: gi|67458622|ref|YP_246246.1| transposase 1105101002518 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105101002519 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101002520 active site 1105101002521 HIGH motif; other site 1105101002522 nucleotide binding site [chemical binding]; other site 1105101002523 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105101002524 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105101002525 active site 1105101002526 KMSKS motif; other site 1105101002527 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105101002528 tRNA binding surface [nucleotide binding]; other site 1105101002529 anticodon binding site; other site 1105101002530 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105101002531 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105101002532 potential frameshift: common BLAST hit: gi|157804076|ref|YP_001492625.1| ATPase 1105101002533 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 1105101002534 RmuC family; Region: RmuC; pfam02646 1105101002535 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 1105101002536 DoxX-like family; Region: DoxX_3; pfam13781 1105101002537 potential frameshift: common BLAST hit: gi|157826437|ref|YP_001495501.1| integral membrane protein 1105101002538 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105101002539 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1105101002540 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 1105101002541 Walker A motif; other site 1105101002542 ATP binding site [chemical binding]; other site 1105101002543 Walker B motif; other site 1105101002544 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105101002545 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105101002546 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105101002547 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 1105101002548 Ligand Binding Site [chemical binding]; other site 1105101002549 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 1105101002550 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 1105101002551 HicB family; Region: HicB; pfam05534 1105101002552 YcfA-like protein; Region: YcfA; cl00752 1105101002553 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105101002554 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105101002555 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101002556 Walker A/P-loop; other site 1105101002557 ATP binding site [chemical binding]; other site 1105101002558 Q-loop/lid; other site 1105101002559 ABC transporter signature motif; other site 1105101002560 Walker B; other site 1105101002561 D-loop; other site 1105101002562 H-loop/switch region; other site 1105101002563 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105101002564 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105101002565 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 1105101002566 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105101002567 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105101002568 FtsX-like permease family; Region: FtsX; pfam02687 1105101002569 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105101002570 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1105101002571 Walker A/P-loop; other site 1105101002572 ATP binding site [chemical binding]; other site 1105101002573 Q-loop/lid; other site 1105101002574 ABC transporter signature motif; other site 1105101002575 Walker B; other site 1105101002576 D-loop; other site 1105101002577 H-loop/switch region; other site 1105101002578 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105101002579 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105101002580 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 1105101002581 Transporter associated domain; Region: CorC_HlyC; smart01091 1105101002582 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 1105101002583 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 1105101002584 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105101002585 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105101002586 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105101002587 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105101002588 synthetase active site [active] 1105101002589 NTP binding site [chemical binding]; other site 1105101002590 metal binding site [ion binding]; metal-binding site 1105101002591 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1105101002592 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105101002593 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1105101002594 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105101002595 DNA binding residues [nucleotide binding] 1105101002596 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 1105101002597 IHF dimer interface [polypeptide binding]; other site 1105101002598 IHF - DNA interface [nucleotide binding]; other site 1105101002599 valyl-tRNA synthetase-like protein; Provisional; Region: PTZ00419 1105101002600 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105101002601 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 1105101002602 catalytic triad [active] 1105101002603 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105101002604 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105101002605 putative acyl-acceptor binding pocket; other site 1105101002606 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1105101002607 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1105101002608 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1105101002609 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105101002610 Protein of unknown function (DUF519); Region: DUF519; pfam04378 1105101002611 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105101002612 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 1105101002613 nucleotide binding pocket [chemical binding]; other site 1105101002614 K-X-D-G motif; other site 1105101002615 catalytic site [active] 1105101002616 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105101002617 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105101002618 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 1105101002619 Dimer interface [polypeptide binding]; other site 1105101002620 BRCT sequence motif; other site 1105101002621 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1105101002622 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105101002623 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105101002624 HD domain; Region: HD_4; pfam13328 1105101002625 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 1105101002626 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1105101002627 mce related protein; Region: MCE; pfam02470 1105101002628 hypothetical protein; Provisional; Region: PRK06630 1105101002629 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105101002630 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105101002631 active site 1105101002632 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 1105101002633 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 1105101002634 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105101002635 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 1105101002636 CoA-binding site [chemical binding]; other site 1105101002637 ATP-binding [chemical binding]; other site 1105101002638 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105101002639 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 1105101002640 active site 1105101002641 catalytic site [active] 1105101002642 substrate binding site [chemical binding]; other site 1105101002643 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 1105101002644 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105101002645 Part of AAA domain; Region: AAA_19; pfam13245 1105101002646 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105101002647 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 1105101002648 Family description; Region: UvrD_C_2; pfam13538 1105101002649 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1105101002650 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105101002651 Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]; Region: HtpG; COG0326 1105101002652 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105101002653 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105101002654 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105101002655 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105101002656 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 1105101002657 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105101002658 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105101002659 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 1105101002660 nudix motif; other site 1105101002661 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1105101002662 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 1105101002663 Transporter associated domain; Region: CorC_HlyC; smart01091 1105101002664 metal-binding heat shock protein; Provisional; Region: PRK00016 1105101002665 PemK-like protein; Region: PemK; cl00995 1105101002666 lipoyl synthase; Provisional; Region: PRK05481 1105101002667 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 1105101002668 FeS/SAM binding site; other site 1105101002669 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105101002670 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 1105101002671 dimer interface [polypeptide binding]; other site 1105101002672 active site 1105101002673 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105101002674 folate binding site [chemical binding]; other site 1105101002675 Predicted esterase [General function prediction only]; Region: COG0400 1105101002676 putative hydrolase; Provisional; Region: PRK11460 1105101002677 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 1105101002678 putative GSH binding site [chemical binding]; other site 1105101002679 catalytic residues [active] 1105101002680 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105101002681 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105101002682 minor groove reading motif; other site 1105101002683 helix-hairpin-helix signature motif; other site 1105101002684 substrate binding pocket [chemical binding]; other site 1105101002685 active site 1105101002686 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1105101002687 Predicted small secreted protein [Function unknown]; Region: COG5510 1105101002688 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101002689 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105101002690 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1105101002691 putative SAM binding site [chemical binding]; other site 1105101002692 putative homodimer interface [polypeptide binding]; other site 1105101002693 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105101002694 putative ligand binding site [chemical binding]; other site 1105101002695 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 1105101002696 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105101002697 tetramer interfaces [polypeptide binding]; other site 1105101002698 binuclear metal-binding site [ion binding]; other site 1105101002699 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 1105101002700 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1105101002701 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1105101002702 aspartate kinase; Reviewed; Region: PRK06635 1105101002703 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 1105101002704 putative nucleotide binding site [chemical binding]; other site 1105101002705 putative catalytic residues [active] 1105101002706 putative Mg ion binding site [ion binding]; other site 1105101002707 putative aspartate binding site [chemical binding]; other site 1105101002708 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 1105101002709 putative allosteric regulatory residue; other site 1105101002710 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 1105101002711 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105101002712 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1105101002713 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1105101002714 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1105101002715 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 1105101002716 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101002717 putative substrate translocation pore; other site 1105101002718 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 1105101002719 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002720 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 1105101002721 Helix-turn-helix domain; Region: HTH_25; pfam13413 1105101002722 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105101002723 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 1105101002724 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 1105101002725 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105101002726 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105101002727 G1 box; other site 1105101002728 GTP/Mg2+ binding site [chemical binding]; other site 1105101002729 Switch I region; other site 1105101002730 G2 box; other site 1105101002731 Switch II region; other site 1105101002732 G3 box; other site 1105101002733 G4 box; other site 1105101002734 G5 box; other site 1105101002735 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105101002736 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105101002737 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 1105101002738 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 1105101002739 hexamer interface [polypeptide binding]; other site 1105101002740 Walker A motif; other site 1105101002741 ATP binding site [chemical binding]; other site 1105101002742 Walker B motif; other site 1105101002743 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105101002744 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101002745 NAD(P) binding site [chemical binding]; other site 1105101002746 active site 1105101002747 acyl carrier protein; Provisional; Region: acpP; PRK00982 1105101002748 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105101002749 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 1105101002750 dimer interface [polypeptide binding]; other site 1105101002751 active site 1105101002752 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105101002753 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105101002754 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105101002755 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1105101002756 AAA domain; Region: AAA_14; pfam13173 1105101002757 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105101002758 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002759 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105101002760 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 1105101002761 catalytic site [active] 1105101002762 G-X2-G-X-G-K; other site 1105101002763 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 1105101002764 sequence-specific DNA binding site [nucleotide binding]; other site 1105101002765 salt bridge; other site 1105101002766 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 1105101002767 rod shape-determining protein MreC; Region: MreC; pfam04085 1105101002768 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105101002769 MreB and similar proteins; Region: MreB_like; cd10225 1105101002770 nucleotide binding site [chemical binding]; other site 1105101002771 Mg binding site [ion binding]; other site 1105101002772 putative protofilament interaction site [polypeptide binding]; other site 1105101002773 RodZ interaction site [polypeptide binding]; other site 1105101002774 Predicted permeases [General function prediction only]; Region: COG0795 1105101002775 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105101002776 putative outer membrane lipoprotein; Provisional; Region: PRK09967 1105101002777 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105101002778 ligand binding site [chemical binding]; other site 1105101002779 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105101002780 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105101002781 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 1105101002782 dimer interface [polypeptide binding]; other site 1105101002783 active site 1105101002784 CoA binding pocket [chemical binding]; other site 1105101002785 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 1105101002786 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 1105101002787 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 1105101002788 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105101002789 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1105101002790 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 1105101002791 P loop; other site 1105101002792 GTP binding site [chemical binding]; other site 1105101002793 DNA polymerase I; Provisional; Region: PRK05755 1105101002794 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105101002795 active site 1105101002796 metal binding site 1 [ion binding]; metal-binding site 1105101002797 putative 5' ssDNA interaction site; other site 1105101002798 metal binding site 3; metal-binding site 1105101002799 metal binding site 2 [ion binding]; metal-binding site 1105101002800 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105101002801 putative DNA binding site [nucleotide binding]; other site 1105101002802 putative metal binding site [ion binding]; other site 1105101002803 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105101002804 active site 1105101002805 substrate binding site [chemical binding]; other site 1105101002806 catalytic site [active] 1105101002807 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105101002808 active site 1105101002809 DNA binding site [nucleotide binding] 1105101002810 catalytic site [active] 1105101002811 potential frameshift: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 1105101002812 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1105101002813 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105101002814 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105101002815 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 1105101002816 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105101002817 putative active site [active] 1105101002818 putative PHP Thumb interface [polypeptide binding]; other site 1105101002819 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 1105101002820 generic binding surface I; other site 1105101002821 generic binding surface II; other site 1105101002822 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105101002823 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105101002824 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 1105101002825 Protein of unknown function; Region: DUF3971; pfam13116 1105101002826 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105101002827 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 1105101002828 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 1105101002829 putative substrate translocation pore; other site 1105101002830 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1105101002831 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105101002832 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105101002833 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 1105101002834 dimer interface [polypeptide binding]; other site 1105101002835 active site 1105101002836 motif 1; other site 1105101002837 motif 2; other site 1105101002838 motif 3; other site 1105101002839 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105101002840 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105101002841 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105101002842 Integral membrane protein TerC family; Region: TerC; cl10468 1105101002843 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105101002844 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105101002845 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 1105101002846 S-adenosylmethionine binding site [chemical binding]; other site 1105101002847 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105101002848 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105101002849 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 1105101002850 salt bridge; other site 1105101002851 non-specific DNA binding site [nucleotide binding]; other site 1105101002852 sequence-specific DNA binding site [nucleotide binding]; other site 1105101002853 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105101002854 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1105101002855 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1105101002856 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105101002857 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105101002858 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105101002859 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105101002860 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105101002861 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105101002862 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101002863 Walker A/P-loop; other site 1105101002864 ATP binding site [chemical binding]; other site 1105101002865 Q-loop/lid; other site 1105101002866 ABC transporter signature motif; other site 1105101002867 Walker B; other site 1105101002868 D-loop; other site 1105101002869 H-loop/switch region; other site 1105101002870 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105101002871 4Fe-4S binding domain; Region: Fer4; cl02805 1105101002872 4Fe-4S binding domain; Region: Fer4; pfam00037 1105101002873 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1105101002874 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1105101002875 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105101002876 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 1105101002877 catalytic loop [active] 1105101002878 iron binding site [ion binding]; other site 1105101002879 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1105101002880 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 1105101002881 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105101002882 Predicted membrane protein [Function unknown]; Region: COG3671 1105101002883 aconitate hydratase; Validated; Region: PRK09277 1105101002884 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105101002885 substrate binding site [chemical binding]; other site 1105101002886 ligand binding site [chemical binding]; other site 1105101002887 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 1105101002888 substrate binding site [chemical binding]; other site 1105101002889 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105101002890 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1105101002891 gamma subunit interface [polypeptide binding]; other site 1105101002892 epsilon subunit interface [polypeptide binding]; other site 1105101002893 LBP interface [polypeptide binding]; other site 1105101002894 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105101002895 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105101002896 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 1105101002897 alpha subunit interaction interface [polypeptide binding]; other site 1105101002898 Walker A motif; other site 1105101002899 ATP binding site [chemical binding]; other site 1105101002900 Walker B motif; other site 1105101002901 inhibitor binding site; inhibition site 1105101002902 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105101002903 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1105101002904 core domain interface [polypeptide binding]; other site 1105101002905 delta subunit interface [polypeptide binding]; other site 1105101002906 epsilon subunit interface [polypeptide binding]; other site 1105101002907 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105101002908 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105101002909 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 1105101002910 beta subunit interaction interface [polypeptide binding]; other site 1105101002911 Walker A motif; other site 1105101002912 ATP binding site [chemical binding]; other site 1105101002913 Walker B motif; other site 1105101002914 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105101002915 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 1105101002916 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105101002917 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105101002918 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1105101002919 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105101002920 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105101002921 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1105101002922 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1105101002923 dimerization interface [polypeptide binding]; other site 1105101002924 DPS ferroxidase diiron center [ion binding]; other site 1105101002925 ion pore; other site 1105101002926 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105101002927 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 1105101002928 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105101002929 Transglycosylase; Region: Transgly; pfam00912 1105101002930 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105101002931 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105101002932 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105101002933 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 1105101002934 FeS/SAM binding site; other site 1105101002935 TRAM domain; Region: TRAM; pfam01938 1105101002936 HEPN domain; Region: HEPN; cl00824 1105101002937 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105101002938 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101002939 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105101002940 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 1105101002941 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105101002942 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105101002943 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105101002944 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1105101002945 TrkA-N domain; Region: TrkA_N; pfam02254 1105101002946 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 1105101002947 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105101002948 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105101002949 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105101002950 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105101002951 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105101002952 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 1105101002953 rRNA binding site [nucleotide binding]; other site 1105101002954 predicted 30S ribosome binding site; other site 1105101002955 Maf-like protein; Region: Maf; pfam02545 1105101002956 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 1105101002957 active site 1105101002958 dimer interface [polypeptide binding]; other site 1105101002959 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 1105101002960 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105101002961 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 1105101002962 active site 1105101002963 DNA binding site [nucleotide binding] 1105101002964 Int/Topo IB signature motif; other site 1105101002965 Phasin protein; Region: Phasin_2; pfam09361 1105101002966 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105101002967 PLD-like domain; Region: PLDc_2; pfam13091 1105101002968 putative active site [active] 1105101002969 catalytic site [active] 1105101002970 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105101002971 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105101002972 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 1105101002973 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1105101002974 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1105101002975 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105101002976 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105101002977 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105101002978 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1105101002979 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1105101002980 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105101002981 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 1105101002982 active site 1105101002983 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105101002984 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105101002985 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105101002986 MPN+ (JAMM) motif; other site 1105101002987 Zinc-binding site [ion binding]; other site 1105101002988 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105101002989 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 1105101002990 Mg++ binding site [ion binding]; other site 1105101002991 putative catalytic motif [active] 1105101002992 putative substrate binding site [chemical binding]; other site 1105101002993 Protein of unknown function (DUF721); Region: DUF721; pfam05258 1105101002994 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105101002995 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105101002996 Ferredoxin [Energy production and conversion]; Region: COG1146 1105101002997 4Fe-4S binding domain; Region: Fer4; cl02805 1105101002998 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105101002999 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 1105101003000 nucleoside/Zn binding site; other site 1105101003001 dimer interface [polypeptide binding]; other site 1105101003002 catalytic motif [active] 1105101003003 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105101003004 Cation efflux family; Region: Cation_efflux; cl00316 1105101003005 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105101003006 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105101003007 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105101003008 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 1105101003009 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105101003010 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105101003011 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105101003012 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1105101003013 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105101003014 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 1105101003015 dimer interface [polypeptide binding]; other site 1105101003016 ssDNA binding site [nucleotide binding]; other site 1105101003017 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105101003018 hypothetical protein; Reviewed; Region: PRK01530 1105101003019 heat shock protein 90; Provisional; Region: PRK05218 1105101003020 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 1105101003021 ATP binding site [chemical binding]; other site 1105101003022 Mg2+ binding site [ion binding]; other site 1105101003023 G-X-G motif; other site 1105101003024 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1105101003025 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 1105101003026 substrate-cofactor binding pocket; other site 1105101003027 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105101003028 catalytic residue [active] 1105101003029 trigger factor; Provisional; Region: tig; PRK01490 1105101003030 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105101003031 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105101003032 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105101003033 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105101003034 Obg GTPase; Region: Obg; cd01898 1105101003035 G1 box; other site 1105101003036 GTP/Mg2+ binding site [chemical binding]; other site 1105101003037 Switch I region; other site 1105101003038 G2 box; other site 1105101003039 G3 box; other site 1105101003040 Switch II region; other site 1105101003041 G4 box; other site 1105101003042 G5 box; other site 1105101003043 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 1105101003044 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1105101003045 dimer interface [polypeptide binding]; other site 1105101003046 active site 1105101003047 citrylCoA binding site [chemical binding]; other site 1105101003048 NADH binding [chemical binding]; other site 1105101003049 cationic pore residues; other site 1105101003050 oxalacetate/citrate binding site [chemical binding]; other site 1105101003051 coenzyme A binding site [chemical binding]; other site 1105101003052 catalytic triad [active] 1105101003053 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 1105101003054 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105101003055 Fe-S cluster binding site [ion binding]; other site 1105101003056 active site 1105101003057 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105101003058 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 1105101003059 RNA binding surface [nucleotide binding]; other site 1105101003060 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105101003061 active site 1105101003062 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105101003063 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 1105101003064 S-adenosylmethionine binding site [chemical binding]; other site 1105101003065 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 1105101003066 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1105101003067 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105101003068 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 1105101003069 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105101003070 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 1105101003071 motif 1; other site 1105101003072 dimer interface [polypeptide binding]; other site 1105101003073 active site 1105101003074 motif 2; other site 1105101003075 motif 3; other site 1105101003076 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 1105101003077 oligomeric interface; other site 1105101003078 putative active site [active] 1105101003079 homodimer interface [polypeptide binding]; other site 1105101003080 prevent-host-death family protein; Region: phd_fam; TIGR01552 1105101003081 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 1105101003082 potential frameshift: common BLAST hit: gi|350273988|ref|YP_004885301.1| proline/betaine transporter 1105101003083 ADP-specific Phosphofructokinase/Glucokinase conserved region; Region: ADP_PFK_GK; cl14060 1105101003084 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105101003085 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 1105101003086 motif 1; other site 1105101003087 active site 1105101003088 motif 2; other site 1105101003089 motif 3; other site 1105101003090 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105101003091 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105101003092 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105101003093 dimerization interface 3.5A [polypeptide binding]; other site 1105101003094 active site 1105101003095 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105101003096 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105101003097 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105101003098 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105101003099 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105101003100 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 1105101003101 DNA binding residues [nucleotide binding] 1105101003102 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105101003103 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1105101003104 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105101003105 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 1105101003106 active site 1105101003107 metal binding site [ion binding]; metal-binding site 1105101003108 interdomain interaction site; other site 1105101003109 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 1105101003110 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105101003111 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105101003112 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105101003113 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105101003114 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105101003115 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 1105101003116 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105101003117 ligand binding site [chemical binding]; other site 1105101003118 homodimer interface [polypeptide binding]; other site 1105101003119 NAD(P) binding site [chemical binding]; other site 1105101003120 trimer interface B [polypeptide binding]; other site 1105101003121 trimer interface A [polypeptide binding]; other site 1105101003122 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105101003123 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 1105101003124 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 1105101003125 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 1105101003126 Walker A motif; other site 1105101003127 ATP binding site [chemical binding]; other site 1105101003128 Walker B motif; other site 1105101003129 arginine finger; other site 1105101003130 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1105101003131 hypothetical protein; Validated; Region: PRK00153 1105101003132 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105101003133 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105101003134 catalytic motif [active] 1105101003135 Catalytic residue [active] 1105101003136 Beta-lactamase; Region: Beta-lactamase; cl17358 1105101003137 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 1105101003138 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105101003139 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105101003140 Walker A/P-loop; other site 1105101003141 ATP binding site [chemical binding]; other site 1105101003142 Q-loop/lid; other site 1105101003143 ABC transporter signature motif; other site 1105101003144 Walker B; other site 1105101003145 D-loop; other site 1105101003146 H-loop/switch region; other site 1105101003147 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1105101003148 putative hydrolase; Provisional; Region: PRK02113 1105101003149 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 1105101003150 active site 1105101003151 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 1105101003152 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 1105101003153 Predicted permeases [General function prediction only]; Region: COG0795 1105101003154 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105101003155 DNA polymerase III subunit chi; Provisional; Region: PRK06646 1105101003156 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105101003157 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105101003158 metal binding site [ion binding]; metal-binding site 1105101003159 dimer interface [polypeptide binding]; other site 1105101003160 potential frameshift: common BLAST hit: gi|341584500|ref|YP_004764991.1| putative type I restriction enzyme S subunit 1105101003161 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105101003162 potential frameshift: common BLAST hit: gi|157827849|ref|YP_001496913.1| Type I restriction-modification system methyltransferase subunit 1105101003163 potential frameshift: common BLAST hit: gi|157965011|ref|YP_001499835.1| Na+/H+ antiporter NhaA 1105101003164 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1105101003165 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 1105101003166 putative active site [active] 1105101003167 lipoate-protein ligase B; Provisional; Region: PRK14347 1105101003168 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105101003169 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 1105101003170 amidase catalytic site [active] 1105101003171 Zn binding residues [ion binding]; other site 1105101003172 substrate binding site [chemical binding]; other site 1105101003173 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105101003174 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1105101003175 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 1105101003176 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105101003177 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 1105101003178 ATP binding site [chemical binding]; other site 1105101003179 Mg2+ binding site [ion binding]; other site 1105101003180 G-X-G motif; other site 1105101003181 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 1105101003182 ATP binding site [chemical binding]; other site 1105101003183 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1105101003184 Zinc-finger domain; Region: zf-CHCC; cl01821 1105101003185 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105101003186 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105101003187 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 1105101003188 TPR motif; other site 1105101003189 TPR repeat; Region: TPR_11; pfam13414 1105101003190 binding surface 1105101003191 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 1105101003192 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105101003193 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 1105101003194 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 1105101003195 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 1105101003196 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105101003197 TIGR00701 family protein; Region: TIGR00701 1105101003198 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105101003199 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 1105101003200 C-terminal domain interface [polypeptide binding]; other site 1105101003201 active site 1105101003202 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 1105101003203 active site 1105101003204 N-terminal domain interface [polypeptide binding]; other site 1105101003205 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 1105101003206 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 1105101003207 substrate binding site [chemical binding]; other site 1105101003208 active site