-- dump date 20140620_034819 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105102000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 1105102000002 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 1105102000003 catalytic residues [active] 1105102000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105102000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 1105102000006 Walker A/P-loop; other site 1105102000007 ATP binding site [chemical binding]; other site 1105102000008 Q-loop/lid; other site 1105102000009 ABC transporter signature motif; other site 1105102000010 Walker B; other site 1105102000011 D-loop; other site 1105102000012 H-loop/switch region; other site 1105102000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1105102000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1105102000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105102000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105102000017 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 1105102000018 FAD binding pocket [chemical binding]; other site 1105102000019 FAD binding motif [chemical binding]; other site 1105102000020 phosphate binding motif [ion binding]; other site 1105102000021 beta-alpha-beta structure motif; other site 1105102000022 NAD binding pocket [chemical binding]; other site 1105102000023 Iron coordination center [ion binding]; other site 1105102000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 1105102000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 1105102000026 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 1105102000027 active site 1105102000028 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 1105102000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105102000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105102000031 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 1105102000032 trimer interface [polypeptide binding]; other site 1105102000033 active site 1105102000034 UDP-GlcNAc binding site [chemical binding]; other site 1105102000035 lipid binding site [chemical binding]; lipid-binding site 1105102000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105102000037 active site 1105102000038 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105102000039 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 1105102000040 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1105102000041 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 1105102000042 FMN binding site [chemical binding]; other site 1105102000043 active site 1105102000044 catalytic residues [active] 1105102000045 substrate binding site [chemical binding]; other site 1105102000046 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 1105102000047 NodB motif; other site 1105102000048 putative active site [active] 1105102000049 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1105102000050 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 1105102000051 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 1105102000052 intersubunit interface [polypeptide binding]; other site 1105102000053 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105102000054 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105102000055 active site 1105102000056 NTP binding site [chemical binding]; other site 1105102000057 metal binding triad [ion binding]; metal-binding site 1105102000058 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105102000059 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105102000060 AAA domain; Region: AAA_22; pfam13401 1105102000061 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105102000062 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105102000063 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 1105102000064 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 1105102000065 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105102000066 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 1105102000067 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1105102000068 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 1105102000069 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 1105102000070 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105102000071 Thioredoxin; Region: Thioredoxin_4; pfam13462 1105102000072 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 1105102000073 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105102000074 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 1105102000075 S-adenosylmethionine binding site [chemical binding]; other site 1105102000076 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105102000077 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105102000078 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 1105102000079 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000080 Walker A/P-loop; other site 1105102000081 ATP binding site [chemical binding]; other site 1105102000082 Q-loop/lid; other site 1105102000083 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000084 ABC transporter signature motif; other site 1105102000085 Walker B; other site 1105102000086 D-loop; other site 1105102000087 H-loop/switch region; other site 1105102000088 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 1105102000089 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1105102000090 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 1105102000091 folate binding site [chemical binding]; other site 1105102000092 NADP+ binding site [chemical binding]; other site 1105102000093 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 1105102000094 catalytic center binding site [active] 1105102000095 ATP binding site [chemical binding]; other site 1105102000096 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 1105102000097 substrate binding pocket [chemical binding]; other site 1105102000098 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105102000099 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 1105102000100 Cu(I) binding site [ion binding]; other site 1105102000101 Putative transcriptional regulator [Transcription]; Region: COG1678 1105102000102 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1105102000103 Colicin V production protein; Region: Colicin_V; pfam02674 1105102000104 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105102000105 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105102000106 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105102000107 active site 1105102000108 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105102000109 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105102000110 Clp amino terminal domain; Region: Clp_N; pfam02861 1105102000111 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 1105102000112 Walker A motif; other site 1105102000113 ATP binding site [chemical binding]; other site 1105102000114 Walker B motif; other site 1105102000115 arginine finger; other site 1105102000116 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 1105102000117 Walker A motif; other site 1105102000118 ATP binding site [chemical binding]; other site 1105102000119 Walker B motif; other site 1105102000120 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1105102000121 UGMP family protein; Validated; Region: PRK09604 1105102000122 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1105102000123 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 1105102000124 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105102000125 Di-iron ligands [ion binding]; other site 1105102000126 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 1105102000127 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105102000128 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 1105102000129 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1105102000130 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1105102000131 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105102000132 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105102000133 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105102000134 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1105102000135 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 1105102000136 Ligand Binding Site [chemical binding]; other site 1105102000137 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102000138 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105102000139 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105102000140 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 1105102000141 Walker A motif; other site 1105102000142 ATP binding site [chemical binding]; other site 1105102000143 Walker B motif; other site 1105102000144 arginine finger; other site 1105102000145 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105102000146 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 1105102000147 cofactor binding site; other site 1105102000148 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 1105102000149 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105102000150 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1105102000151 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105102000152 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102000153 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1105102000154 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1105102000155 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105102000156 membrane protein insertase; Provisional; Region: PRK01318 1105102000157 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1105102000158 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105102000159 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 1105102000160 S-adenosylmethionine binding site [chemical binding]; other site 1105102000161 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105102000162 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 1105102000163 active site 1105102000164 catalytic residues [active] 1105102000165 metal binding site [ion binding]; metal-binding site 1105102000166 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105102000167 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105102000168 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 1105102000169 putative substrate translocation pore; other site 1105102000170 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 1105102000171 active site 1105102000172 multimer interface [polypeptide binding]; other site 1105102000173 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105102000174 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1105102000175 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105102000176 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1105102000177 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1105102000178 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105102000179 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 1105102000180 P-loop; other site 1105102000181 Magnesium ion binding site [ion binding]; other site 1105102000182 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 1105102000183 Magnesium ion binding site [ion binding]; other site 1105102000184 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 1105102000185 ParB-like nuclease domain; Region: ParB; smart00470 1105102000186 KorB domain; Region: KorB; pfam08535 1105102000187 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105102000188 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105102000189 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105102000190 ABC transporter; Region: ABC_tran_2; pfam12848 1105102000191 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105102000192 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105102000193 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 1105102000194 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105102000195 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105102000196 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105102000197 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1105102000198 Zn2+ binding site [ion binding]; other site 1105102000199 Mg2+ binding site [ion binding]; other site 1105102000200 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105102000201 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1105102000202 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1105102000203 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105102000204 active site 1105102000205 HIGH motif; other site 1105102000206 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105102000207 KMSK motif region; other site 1105102000208 tRNA binding surface [nucleotide binding]; other site 1105102000209 DALR anticodon binding domain; Region: DALR_1; smart00836 1105102000210 anticodon binding site; other site 1105102000211 Sporulation related domain; Region: SPOR; pfam05036 1105102000212 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105102000213 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 1105102000214 CAP-like domain; other site 1105102000215 active site 1105102000216 primary dimer interface [polypeptide binding]; other site 1105102000217 Gram-negative porin; Region: Porin_4; pfam13609 1105102000218 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105102000219 trimer interface [polypeptide binding]; other site 1105102000220 active site 1105102000221 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 1105102000222 SecA binding site; other site 1105102000223 Preprotein binding site; other site 1105102000224 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105102000225 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 1105102000226 active site 1105102000227 phosphorylation site [posttranslational modification] 1105102000228 intermolecular recognition site; other site 1105102000229 dimerization interface [polypeptide binding]; other site 1105102000230 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 1105102000231 DNA binding site [nucleotide binding] 1105102000232 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 1105102000233 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105102000234 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 1105102000235 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105102000236 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 1105102000237 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105102000238 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 1105102000239 EamA-like transporter family; Region: EamA; pfam00892 1105102000240 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1105102000241 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 1105102000242 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105102000243 putative substrate translocation pore; other site 1105102000244 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1105102000245 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105102000246 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105102000247 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105102000248 active site 1105102000249 HIGH motif; other site 1105102000250 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105102000251 KMSKS motif; other site 1105102000252 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105102000253 tRNA binding surface [nucleotide binding]; other site 1105102000254 anticodon binding site; other site 1105102000255 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 1105102000256 rRNA interaction site [nucleotide binding]; other site 1105102000257 S8 interaction site; other site 1105102000258 putative laminin-1 binding site; other site 1105102000259 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105102000260 UBA/TS-N domain; Region: UBA; pfam00627 1105102000261 Elongation factor TS; Region: EF_TS; pfam00889 1105102000262 Elongation factor TS; Region: EF_TS; pfam00889 1105102000263 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 1105102000264 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102000265 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105102000266 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 1105102000267 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105102000268 putative acyl-acceptor binding pocket; other site 1105102000269 aspartate aminotransferase; Provisional; Region: PRK05764 1105102000270 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 1105102000271 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105102000272 homodimer interface [polypeptide binding]; other site 1105102000273 catalytic residue [active] 1105102000274 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105102000275 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105102000276 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 1105102000277 binding surface 1105102000278 TPR motif; other site 1105102000279 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1105102000280 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 1105102000281 S-adenosylmethionine binding site [chemical binding]; other site 1105102000282 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1105102000283 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 1105102000284 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105102000285 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105102000286 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105102000287 active site 1105102000288 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102000289 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1105102000290 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105102000291 active site 1105102000292 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105102000293 dimer interface [polypeptide binding]; other site 1105102000294 substrate binding site [chemical binding]; other site 1105102000295 catalytic residues [active] 1105102000296 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1105102000297 Permease; Region: Permease; pfam02405 1105102000298 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105102000299 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000300 Walker A/P-loop; other site 1105102000301 ATP binding site [chemical binding]; other site 1105102000302 Q-loop/lid; other site 1105102000303 ABC transporter signature motif; other site 1105102000304 Walker B; other site 1105102000305 D-loop; other site 1105102000306 H-loop/switch region; other site 1105102000307 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 1105102000308 50S ribosomal protein L31; Provisional; Region: PRK01397 1105102000309 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105102000310 G1 box; other site 1105102000311 GTP/Mg2+ binding site [chemical binding]; other site 1105102000312 Switch I region; other site 1105102000313 G2 box; other site 1105102000314 G3 box; other site 1105102000315 Switch II region; other site 1105102000316 G4 box; other site 1105102000317 G5 box; other site 1105102000318 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 1105102000319 nucleotide binding site [chemical binding]; other site 1105102000320 substrate binding site [chemical binding]; other site 1105102000321 type IV secretion system protein VirB3; Provisional; Region: PRK13899 1105102000322 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105102000323 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105102000324 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000325 Walker A/P-loop; other site 1105102000326 ATP binding site [chemical binding]; other site 1105102000327 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105102000328 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105102000329 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105102000330 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105102000331 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105102000332 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105102000333 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105102000334 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 1105102000335 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1105102000336 hypothetical protein; Provisional; Region: PRK13694 1105102000337 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105102000338 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105102000339 Protein export membrane protein; Region: SecD_SecF; pfam02355 1105102000340 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105102000341 SLBB domain; Region: SLBB; pfam10531 1105102000342 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 1105102000343 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105102000344 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 1105102000345 Catalytic site [active] 1105102000346 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 1105102000347 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105102000348 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 1105102000349 dimerization interface [polypeptide binding]; other site 1105102000350 active site 1105102000351 metal binding site [ion binding]; metal-binding site 1105102000352 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 1105102000353 dsRNA binding site [nucleotide binding]; other site 1105102000354 GTPase Era; Provisional; Region: era; PRK15494 1105102000355 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102000356 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105102000357 G1 box; other site 1105102000358 GTP/Mg2+ binding site [chemical binding]; other site 1105102000359 Switch I region; other site 1105102000360 G2 box; other site 1105102000361 Switch II region; other site 1105102000362 G3 box; other site 1105102000363 G4 box; other site 1105102000364 G5 box; other site 1105102000365 KH domain; Region: KH_2; pfam07650 1105102000366 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 1105102000367 active site 1105102000368 putative DNA-binding cleft [nucleotide binding]; other site 1105102000369 dimer interface [polypeptide binding]; other site 1105102000370 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105102000371 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1105102000372 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 1105102000373 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 1105102000374 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105102000375 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105102000376 AAA domain; Region: AAA_31; pfam13614 1105102000377 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 1105102000378 Walker A motif; other site 1105102000379 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 1105102000380 HflK protein; Region: hflK; TIGR01933 1105102000381 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105102000382 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 1105102000383 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105102000384 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105102000385 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 1105102000386 protein binding site [polypeptide binding]; other site 1105102000387 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 1105102000388 protein binding site [polypeptide binding]; other site 1105102000389 hypothetical protein; Validated; Region: PRK01415 1105102000390 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105102000391 active site residue [active] 1105102000392 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 1105102000393 Iron-sulfur protein interface; other site 1105102000394 proximal quinone binding site [chemical binding]; other site 1105102000395 SdhD (CybS) interface [polypeptide binding]; other site 1105102000396 proximal heme binding site [chemical binding]; other site 1105102000397 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 1105102000398 putative SdhC subunit interface [polypeptide binding]; other site 1105102000399 putative proximal heme binding site [chemical binding]; other site 1105102000400 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105102000401 putative proximal quinone binding site; other site 1105102000402 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105102000403 L-aspartate oxidase; Provisional; Region: PRK06175 1105102000404 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105102000405 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105102000406 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 1105102000407 dimer interface [polypeptide binding]; other site 1105102000408 conserved gate region; other site 1105102000409 putative PBP binding loops; other site 1105102000410 ABC-ATPase subunit interface; other site 1105102000411 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 1105102000412 S17 interaction site [polypeptide binding]; other site 1105102000413 S8 interaction site; other site 1105102000414 16S rRNA interaction site [nucleotide binding]; other site 1105102000415 streptomycin interaction site [chemical binding]; other site 1105102000416 23S rRNA interaction site [nucleotide binding]; other site 1105102000417 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105102000418 30S ribosomal protein S7; Validated; Region: PRK05302 1105102000419 elongation factor G; Reviewed; Region: PRK00007 1105102000420 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105102000421 G1 box; other site 1105102000422 putative GEF interaction site [polypeptide binding]; other site 1105102000423 GTP/Mg2+ binding site [chemical binding]; other site 1105102000424 Switch I region; other site 1105102000425 G2 box; other site 1105102000426 G3 box; other site 1105102000427 Switch II region; other site 1105102000428 G4 box; other site 1105102000429 G5 box; other site 1105102000430 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 1105102000431 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 1105102000432 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 1105102000433 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 1105102000434 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105102000435 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105102000436 putative homodimer interface [polypeptide binding]; other site 1105102000437 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1105102000438 heterodimer interface [polypeptide binding]; other site 1105102000439 homodimer interface [polypeptide binding]; other site 1105102000440 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105102000441 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 1105102000442 23S rRNA interface [nucleotide binding]; other site 1105102000443 putative thiostrepton binding site; other site 1105102000444 L7/L12 interface [polypeptide binding]; other site 1105102000445 L25 interface [polypeptide binding]; other site 1105102000446 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 1105102000447 mRNA/rRNA interface [nucleotide binding]; other site 1105102000448 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 1105102000449 23S rRNA interface [nucleotide binding]; other site 1105102000450 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105102000451 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 1105102000452 core dimer interface [polypeptide binding]; other site 1105102000453 peripheral dimer interface [polypeptide binding]; other site 1105102000454 L10 interface [polypeptide binding]; other site 1105102000455 L11 interface [polypeptide binding]; other site 1105102000456 putative EF-Tu interaction site [polypeptide binding]; other site 1105102000457 putative EF-G interaction site [polypeptide binding]; other site 1105102000458 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1105102000459 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 1105102000460 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105102000461 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 1105102000462 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1105102000463 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 1105102000464 RPB3 interaction site [polypeptide binding]; other site 1105102000465 RPB1 interaction site [polypeptide binding]; other site 1105102000466 RPB11 interaction site [polypeptide binding]; other site 1105102000467 RPB10 interaction site [polypeptide binding]; other site 1105102000468 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105102000469 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105102000470 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1105102000471 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105102000472 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105102000473 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105102000474 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105102000475 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105102000476 DNA binding site [nucleotide binding] 1105102000477 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105102000478 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 1105102000479 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102000480 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105102000481 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 1105102000482 interface (dimer of trimers) [polypeptide binding]; other site 1105102000483 Substrate-binding/catalytic site; other site 1105102000484 Zn-binding sites [ion binding]; other site 1105102000485 ATPase MipZ; Region: MipZ; pfam09140 1105102000486 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 1105102000487 P-loop; other site 1105102000488 Magnesium ion binding site [ion binding]; other site 1105102000489 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 1105102000490 Magnesium ion binding site [ion binding]; other site 1105102000491 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105102000492 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 1105102000493 dimer interface [polypeptide binding]; other site 1105102000494 anticodon binding site; other site 1105102000495 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 1105102000496 homodimer interface [polypeptide binding]; other site 1105102000497 motif 1; other site 1105102000498 active site 1105102000499 motif 2; other site 1105102000500 GAD domain; Region: GAD; pfam02938 1105102000501 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 1105102000502 active site 1105102000503 motif 3; other site 1105102000504 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1105102000505 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105102000506 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105102000507 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1105102000508 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105102000509 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 1105102000510 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105102000511 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 1105102000512 substrate binding pocket [chemical binding]; other site 1105102000513 membrane-bound complex binding site; other site 1105102000514 hinge residues; other site 1105102000515 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105102000516 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105102000517 GatB domain; Region: GatB_Yqey; smart00845 1105102000518 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105102000519 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1105102000520 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1105102000521 Uncharacterized conserved protein [Function unknown]; Region: COG4997 1105102000522 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105102000523 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 1105102000524 hinge region; other site 1105102000525 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 1105102000526 putative nucleotide binding site [chemical binding]; other site 1105102000527 uridine monophosphate binding site [chemical binding]; other site 1105102000528 homohexameric interface [polypeptide binding]; other site 1105102000529 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 1105102000530 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105102000531 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 1105102000532 putative substrate translocation pore; other site 1105102000533 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 1105102000534 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105102000535 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1105102000536 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105102000537 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105102000538 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105102000539 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105102000540 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105102000541 Surface antigen; Region: Bac_surface_Ag; pfam01103 1105102000542 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105102000543 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 1105102000544 active site 1105102000545 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 1105102000546 protein binding site [polypeptide binding]; other site 1105102000547 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 1105102000548 putative substrate binding region [chemical binding]; other site 1105102000549 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1105102000550 putative RNA binding site [nucleotide binding]; other site 1105102000551 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105102000552 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 1105102000553 S-adenosylmethionine binding site [chemical binding]; other site 1105102000554 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105102000555 putative coenzyme Q binding site [chemical binding]; other site 1105102000556 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102000557 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105102000558 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105102000559 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 1105102000560 RNA methyltransferase, RsmE family; Region: TIGR00046 1105102000561 Uncharacterized conserved protein [Function unknown]; Region: COG2155 1105102000562 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105102000563 Protein export membrane protein; Region: SecD_SecF; cl14618 1105102000564 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 1105102000565 IHF dimer interface [polypeptide binding]; other site 1105102000566 IHF - DNA interface [nucleotide binding]; other site 1105102000567 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105102000568 signal recognition particle protein; Provisional; Region: PRK10867 1105102000569 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1105102000570 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 1105102000571 P loop; other site 1105102000572 GTP binding site [chemical binding]; other site 1105102000573 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105102000574 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105102000575 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105102000576 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105102000577 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105102000578 potential frameshift: common BLAST hit: gi|67459496|ref|YP_247120.1| prolyl endopeptidase 1105102000579 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105102000580 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 1105102000581 FeS/SAM binding site; other site 1105102000582 HemN C-terminal domain; Region: HemN_C; pfam06969 1105102000583 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 1105102000584 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105102000585 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 1105102000586 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105102000587 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1105102000588 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 1105102000589 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 1105102000590 active site 1105102000591 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105102000592 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 1105102000593 E3 interaction surface; other site 1105102000594 lipoyl attachment site [posttranslational modification]; other site 1105102000595 e3 binding domain; Region: E3_binding; pfam02817 1105102000596 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105102000597 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105102000598 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 1105102000599 TPP-binding site [chemical binding]; other site 1105102000600 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1105102000601 dimer interface [polypeptide binding]; other site 1105102000602 PYR/PP interface [polypeptide binding]; other site 1105102000603 TPP binding site [chemical binding]; other site 1105102000604 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 1105102000605 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 1105102000606 active site 1105102000607 Zn binding site [ion binding]; other site 1105102000608 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105102000609 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105102000610 Walker A/P-loop; other site 1105102000611 ATP binding site [chemical binding]; other site 1105102000612 Q-loop/lid; other site 1105102000613 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105102000614 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105102000615 ABC transporter signature motif; other site 1105102000616 Walker B; other site 1105102000617 D-loop; other site 1105102000618 H-loop/switch region; other site 1105102000619 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105102000620 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105102000621 ChaB; Region: ChaB; cl01887 1105102000622 ChaB; Region: ChaB; cl01887 1105102000623 chaperone protein DnaJ; Provisional; Region: PRK14300 1105102000624 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 1105102000625 HSP70 interaction site [polypeptide binding]; other site 1105102000626 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105102000627 substrate binding site [polypeptide binding]; other site 1105102000628 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105102000629 Zn binding sites [ion binding]; other site 1105102000630 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105102000631 dimer interface [polypeptide binding]; other site 1105102000632 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105102000633 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105102000634 nucleotide binding site [chemical binding]; other site 1105102000635 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 1105102000636 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105102000637 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 1105102000638 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105102000639 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105102000640 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105102000641 diiron binding motif [ion binding]; other site 1105102000642 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 1105102000643 Subunit III/VIIa interface [polypeptide binding]; other site 1105102000644 Phospholipid binding site [chemical binding]; other site 1105102000645 Subunit I/III interface [polypeptide binding]; other site 1105102000646 Subunit III/VIb interface [polypeptide binding]; other site 1105102000647 Subunit III/VIa interface; other site 1105102000648 Subunit III/Vb interface [polypeptide binding]; other site 1105102000649 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1105102000650 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 1105102000651 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105102000652 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 1105102000653 trimer interface [polypeptide binding]; other site 1105102000654 active site 1105102000655 substrate binding site [chemical binding]; other site 1105102000656 CoA binding site [chemical binding]; other site 1105102000657 potential frameshift: common BLAST hit: gi|15892172|ref|NP_359886.1| bifunctional penicillin-binding protein 1C 1105102000658 potential frameshift: common BLAST hit: gi|350273249|ref|YP_004884562.1| bifunctional penicillin-binding protein 1C 1105102000659 potential frameshift: common BLAST hit: gi|67459460|ref|YP_247084.1| cell surface antigen-like protein Sca8 1105102000660 potential frameshift: common BLAST hit: gi|67459460|ref|YP_247084.1| cell surface antigen-like protein Sca8 1105102000661 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 1105102000662 Ligand Binding Site [chemical binding]; other site 1105102000663 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105102000664 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1105102000665 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1105102000666 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 1105102000667 catalytic loop [active] 1105102000668 iron binding site [ion binding]; other site 1105102000669 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105102000670 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105102000671 nucleotide binding site [chemical binding]; other site 1105102000672 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105102000673 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 1105102000674 HSP70 interaction site [polypeptide binding]; other site 1105102000675 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105102000676 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105102000677 active site 1105102000678 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105102000679 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 1105102000680 ATP binding site [chemical binding]; other site 1105102000681 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 1105102000682 nucleotide binding region [chemical binding]; other site 1105102000683 ATP-binding site [chemical binding]; other site 1105102000684 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105102000685 UvrB/uvrC motif; Region: UVR; pfam02151 1105102000686 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 1105102000687 GSH binding site [chemical binding]; other site 1105102000688 catalytic residues [active] 1105102000689 potential frameshift: common BLAST hit: gi|157964270|ref|YP_001499094.1| multidrug resistance protein Atm1 1105102000690 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105102000691 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000692 Walker A/P-loop; other site 1105102000693 ATP binding site [chemical binding]; other site 1105102000694 Q-loop/lid; other site 1105102000695 Pleckstrin homology-like domain; Region: PH-like; cl17171 1105102000696 DNA gyrase subunit A; Validated; Region: PRK05560 1105102000697 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 1105102000698 CAP-like domain; other site 1105102000699 active site 1105102000700 primary dimer interface [polypeptide binding]; other site 1105102000701 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105102000702 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105102000703 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105102000704 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105102000705 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105102000706 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105102000707 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105102000708 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105102000709 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 1105102000710 active site 1105102000711 catalytic residues [active] 1105102000712 metal binding site [ion binding]; metal-binding site 1105102000713 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105102000714 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105102000715 putative active site [active] 1105102000716 substrate binding site [chemical binding]; other site 1105102000717 putative cosubstrate binding site; other site 1105102000718 catalytic site [active] 1105102000719 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105102000720 substrate binding site [chemical binding]; other site 1105102000721 Protein of unknown function (DUF563); Region: DUF563; cl15705 1105102000722 Predicted ATPase [General function prediction only]; Region: COG1485 1105102000723 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 1105102000724 Walker A motif; other site 1105102000725 ATP binding site [chemical binding]; other site 1105102000726 Walker B motif; other site 1105102000727 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 1105102000728 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1105102000729 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 1105102000730 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105102000731 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105102000732 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105102000733 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000734 Walker A/P-loop; other site 1105102000735 ATP binding site [chemical binding]; other site 1105102000736 Q-loop/lid; other site 1105102000737 ABC transporter signature motif; other site 1105102000738 Walker B; other site 1105102000739 D-loop; other site 1105102000740 H-loop/switch region; other site 1105102000741 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105102000742 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 1105102000743 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105102000744 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105102000745 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105102000746 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 1105102000747 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105102000748 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105102000749 putative metal binding site; other site 1105102000750 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105102000751 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105102000752 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105102000753 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105102000754 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105102000755 ATP binding site [chemical binding]; other site 1105102000756 active site 1105102000757 substrate binding site [chemical binding]; other site 1105102000758 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105102000759 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 1105102000760 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105102000761 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 1105102000762 active site 1105102000763 dimer interface [polypeptide binding]; other site 1105102000764 motif 1; other site 1105102000765 motif 2; other site 1105102000766 motif 3; other site 1105102000767 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 1105102000768 anticodon binding site; other site 1105102000769 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000770 Walker A/P-loop; other site 1105102000771 ATP binding site [chemical binding]; other site 1105102000772 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000773 ABC transporter signature motif; other site 1105102000774 Walker B; other site 1105102000775 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102000776 H-loop/switch region; other site 1105102000777 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 1105102000778 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105102000779 V-type ATP synthase subunit I; Validated; Region: PRK05771 1105102000780 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105102000781 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 1105102000782 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 1105102000783 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105102000784 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105102000785 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 1105102000786 ATP binding site [chemical binding]; other site 1105102000787 Mg2+ binding site [ion binding]; other site 1105102000788 G-X-G motif; other site 1105102000789 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 1105102000790 anchoring element; other site 1105102000791 dimer interface [polypeptide binding]; other site 1105102000792 ATP binding site [chemical binding]; other site 1105102000793 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 1105102000794 active site 1105102000795 metal binding site [ion binding]; metal-binding site 1105102000796 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105102000797 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105102000798 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105102000799 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 1105102000800 protein binding site [polypeptide binding]; other site 1105102000801 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105102000802 Catalytic dyad [active] 1105102000803 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1105102000804 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 1105102000805 dimer interface [polypeptide binding]; other site 1105102000806 phosphorylation site [posttranslational modification] 1105102000807 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 1105102000808 ATP binding site [chemical binding]; other site 1105102000809 Mg2+ binding site [ion binding]; other site 1105102000810 G-X-G motif; other site 1105102000811 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105102000812 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105102000813 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105102000814 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105102000815 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105102000816 Trp docking motif [polypeptide binding]; other site 1105102000817 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 1105102000818 23S rRNA interface [nucleotide binding]; other site 1105102000819 L3 interface [polypeptide binding]; other site 1105102000820 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1105102000821 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cl00942 1105102000822 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105102000823 DCoH tetramer interaction site [polypeptide binding]; other site 1105102000824 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 1105102000825 putative active site [active] 1105102000826 Ap4A binding site [chemical binding]; other site 1105102000827 nudix motif; other site 1105102000828 putative metal binding site [ion binding]; other site 1105102000829 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105102000830 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 1105102000831 active site 1105102000832 phosphorylation site [posttranslational modification] 1105102000833 intermolecular recognition site; other site 1105102000834 dimerization interface [polypeptide binding]; other site 1105102000835 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 1105102000836 active site 1105102000837 phosphorylation site [posttranslational modification] 1105102000838 intermolecular recognition site; other site 1105102000839 dimerization interface [polypeptide binding]; other site 1105102000840 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105102000841 metal binding site [ion binding]; metal-binding site 1105102000842 active site 1105102000843 I-site; other site 1105102000844 elongation factor P; Validated; Region: PRK00529 1105102000845 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105102000846 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 1105102000847 RNA binding site [nucleotide binding]; other site 1105102000848 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 1105102000849 RNA binding site [nucleotide binding]; other site 1105102000850 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105102000851 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 1105102000852 active site 1105102000853 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105102000854 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 1105102000855 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105102000856 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1105102000857 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1105102000858 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105102000859 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105102000860 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102000861 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105102000862 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 1105102000863 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105102000864 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105102000865 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105102000866 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105102000867 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105102000868 FAD binding domain; Region: FAD_binding_4; pfam01565 1105102000869 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105102000870 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105102000871 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105102000872 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1105102000873 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1105102000874 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105102000875 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105102000876 cell division protein FtsA; Region: ftsA; TIGR01174 1105102000877 Cell division protein FtsA; Region: FtsA; smart00842 1105102000878 Cell division protein FtsA; Region: FtsA; pfam14450 1105102000879 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1105102000880 Cytochrome c2 [Energy production and conversion]; Region: COG3474 1105102000881 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1105102000882 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105102000883 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 1105102000884 RNA binding site [nucleotide binding]; other site 1105102000885 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 1105102000886 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 1105102000887 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105102000888 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 1105102000889 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105102000890 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 1105102000891 RNA binding surface [nucleotide binding]; other site 1105102000892 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105102000893 active site 1105102000894 potential frameshift: common BLAST hit: gi|238650484|ref|YP_002916336.1| penicillin-binding protein 4* 1105102000895 potential frameshift: common BLAST hit: gi|15892268|ref|NP_359982.1| penicillin-binding protein 4* 1105102000896 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 1105102000897 putative catalytic site [active] 1105102000898 putative phosphate binding site [ion binding]; other site 1105102000899 active site 1105102000900 metal binding site A [ion binding]; metal-binding site 1105102000901 DNA binding site [nucleotide binding] 1105102000902 putative AP binding site [nucleotide binding]; other site 1105102000903 putative metal binding site B [ion binding]; other site 1105102000904 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105102000905 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 1105102000906 tetramer interface [polypeptide binding]; other site 1105102000907 TPP-binding site [chemical binding]; other site 1105102000908 heterodimer interface [polypeptide binding]; other site 1105102000909 phosphorylation loop region [posttranslational modification] 1105102000910 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105102000911 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 1105102000912 alpha subunit interface [polypeptide binding]; other site 1105102000913 TPP binding site [chemical binding]; other site 1105102000914 heterodimer interface [polypeptide binding]; other site 1105102000915 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105102000916 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1105102000917 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105102000918 G1 box; other site 1105102000919 putative GEF interaction site [polypeptide binding]; other site 1105102000920 GTP/Mg2+ binding site [chemical binding]; other site 1105102000921 Switch I region; other site 1105102000922 G2 box; other site 1105102000923 G3 box; other site 1105102000924 Switch II region; other site 1105102000925 G4 box; other site 1105102000926 G5 box; other site 1105102000927 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 1105102000928 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 1105102000929 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 1105102000930 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105102000931 isocitrate dehydrogenase; Validated; Region: PRK09222 1105102000932 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 1105102000933 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 1105102000934 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105102000935 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 1105102000936 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105102000937 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105102000938 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105102000939 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105102000940 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 1105102000941 [2Fe-2S] cluster binding site [ion binding]; other site 1105102000942 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 1105102000943 Qi binding site; other site 1105102000944 cytochrome b; Provisional; Region: CYTB; MTH00191 1105102000945 intrachain domain interface; other site 1105102000946 interchain domain interface [polypeptide binding]; other site 1105102000947 heme bH binding site [chemical binding]; other site 1105102000948 heme bL binding site [chemical binding]; other site 1105102000949 Qo binding site; other site 1105102000950 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 1105102000951 interchain domain interface [polypeptide binding]; other site 1105102000952 intrachain domain interface; other site 1105102000953 Qi binding site; other site 1105102000954 Qo binding site; other site 1105102000955 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105102000956 catalytic site [active] 1105102000957 metal binding site [ion binding]; metal-binding site 1105102000958 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105102000959 Cytochrome c; Region: Cytochrom_C; cl11414 1105102000960 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1105102000961 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 1105102000962 putative dimer interface [polypeptide binding]; other site 1105102000963 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105102000964 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105102000965 PCRF domain; Region: PCRF; pfam03462 1105102000966 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105102000967 RF-1 domain; Region: RF-1; pfam00472 1105102000968 GTP-binding protein LepA; Provisional; Region: PRK05433 1105102000969 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105102000970 G1 box; other site 1105102000971 putative GEF interaction site [polypeptide binding]; other site 1105102000972 GTP/Mg2+ binding site [chemical binding]; other site 1105102000973 Switch I region; other site 1105102000974 G2 box; other site 1105102000975 G3 box; other site 1105102000976 Switch II region; other site 1105102000977 G4 box; other site 1105102000978 G5 box; other site 1105102000979 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 1105102000980 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 1105102000981 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105102000982 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 1105102000983 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 1105102000984 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105102000985 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105102000986 HD domain; Region: HD_4; pfam13328 1105102000987 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105102000988 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1105102000989 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105102000990 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105102000991 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105102000992 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105102000993 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105102000994 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 1105102000995 oligomeric interface; other site 1105102000996 putative active site [active] 1105102000997 homodimer interface [polypeptide binding]; other site 1105102000998 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105102000999 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105102001000 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105102001001 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105102001002 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 1105102001003 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105102001004 VirB7 interaction site; other site 1105102001005 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105102001006 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105102001007 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105102001008 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1105102001009 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1105102001010 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 1105102001011 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 1105102001012 Walker A motif; other site 1105102001013 hexamer interface [polypeptide binding]; other site 1105102001014 ATP binding site [chemical binding]; other site 1105102001015 Walker B motif; other site 1105102001016 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105102001017 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 1105102001018 Walker A motif; other site 1105102001019 ATP binding site [chemical binding]; other site 1105102001020 Walker B motif; other site 1105102001021 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105102001022 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1105102001023 Phage-related protein [Function unknown]; Region: COG4695; cl01923 1105102001024 Phage portal protein; Region: Phage_portal; pfam04860 1105102001025 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105102001026 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105102001027 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105102001028 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 1105102001029 active site 1105102001030 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105102001031 MutS domain I; Region: MutS_I; pfam01624 1105102001032 MutS domain II; Region: MutS_II; pfam05188 1105102001033 MutS domain III; Region: MutS_III; pfam05192 1105102001034 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1105102001035 Walker A/P-loop; other site 1105102001036 ATP binding site [chemical binding]; other site 1105102001037 Q-loop/lid; other site 1105102001038 ABC transporter signature motif; other site 1105102001039 Walker B; other site 1105102001040 D-loop; other site 1105102001041 H-loop/switch region; other site 1105102001042 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105102001043 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105102001044 Protein of unknown function DUF45; Region: DUF45; pfam01863 1105102001045 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1105102001046 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105102001047 TolB amino-terminal domain; Region: TolB_N; pfam04052 1105102001048 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105102001049 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105102001050 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105102001051 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105102001052 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105102001053 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 1105102001054 DNA binding residues [nucleotide binding] 1105102001055 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 1105102001056 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1105102001057 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 1105102001058 Ligand Binding Site [chemical binding]; other site 1105102001059 amino acid transporter; Region: 2A0306; TIGR00909 1105102001060 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105102001061 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 1105102001062 dimer interface [polypeptide binding]; other site 1105102001063 motif 1; other site 1105102001064 active site 1105102001065 motif 2; other site 1105102001066 motif 3; other site 1105102001067 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 1105102001068 anticodon binding site; other site 1105102001069 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105102001070 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105102001071 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105102001072 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105102001073 TolQ protein; Region: tolQ; TIGR02796 1105102001074 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1105102001075 TolR protein; Region: tolR; TIGR02801 1105102001076 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1105102001077 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105102001078 HD domain; Region: HD_4; pfam13328 1105102001079 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 1105102001080 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105102001081 putative substrate translocation pore; other site 1105102001082 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105102001083 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 1105102001084 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105102001085 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105102001086 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1105102001087 Walker A/P-loop; other site 1105102001088 ATP binding site [chemical binding]; other site 1105102001089 Q-loop/lid; other site 1105102001090 ABC transporter signature motif; other site 1105102001091 Walker B; other site 1105102001092 D-loop; other site 1105102001093 H-loop/switch region; other site 1105102001094 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105102001095 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1105102001096 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 1105102001097 nucleotide binding site/active site [active] 1105102001098 HIT family signature motif; other site 1105102001099 catalytic residue [active] 1105102001100 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105102001101 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105102001102 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 1105102001103 active site 1105102001104 HslU subunit interaction site [polypeptide binding]; other site 1105102001105 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105102001106 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 1105102001107 Walker A motif; other site 1105102001108 ATP binding site [chemical binding]; other site 1105102001109 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1105102001110 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105102001111 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 1105102001112 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1105102001113 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 1105102001114 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1105102001115 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 1105102001116 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102001117 Uncharacterized conserved protein [Function unknown]; Region: COG5464 1105102001118 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102001119 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105102001120 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105102001121 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105102001122 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1105102001123 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105102001124 dimerization interface [polypeptide binding]; other site 1105102001125 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 1105102001126 putative iron binding site [ion binding]; other site 1105102001127 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105102001128 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105102001129 HIGH motif; other site 1105102001130 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105102001131 active site 1105102001132 KMSKS motif; other site 1105102001133 DNA topoisomerase I; Validated; Region: PRK06599 1105102001134 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 1105102001135 active site 1105102001136 interdomain interaction site; other site 1105102001137 putative metal-binding site [ion binding]; other site 1105102001138 nucleotide binding site [chemical binding]; other site 1105102001139 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 1105102001140 domain I; other site 1105102001141 DNA binding groove [nucleotide binding] 1105102001142 phosphate binding site [ion binding]; other site 1105102001143 domain II; other site 1105102001144 domain III; other site 1105102001145 nucleotide binding site [chemical binding]; other site 1105102001146 catalytic site [active] 1105102001147 domain IV; other site 1105102001148 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105102001149 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1105102001150 DNA protecting protein DprA; Region: dprA; TIGR00732 1105102001151 DNA protecting protein DprA; Region: dprA; TIGR00732 1105102001152 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105102001153 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 1105102001154 dimer interface [polypeptide binding]; other site 1105102001155 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105102001156 catalytic triad [active] 1105102001157 peroxidatic and resolving cysteines [active] 1105102001158 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105102001159 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 1105102001160 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105102001161 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105102001162 Sulfatase; Region: Sulfatase; pfam00884 1105102001163 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 1105102001164 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 1105102001165 sequence-specific DNA binding site [nucleotide binding]; other site 1105102001166 salt bridge; other site 1105102001167 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105102001168 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105102001169 NADP binding site [chemical binding]; other site 1105102001170 active site 1105102001171 putative substrate binding site [chemical binding]; other site 1105102001172 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105102001173 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105102001174 NAD(P) binding site [chemical binding]; other site 1105102001175 homodimer interface [polypeptide binding]; other site 1105102001176 substrate binding site [chemical binding]; other site 1105102001177 active site 1105102001178 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105102001179 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105102001180 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 1105102001181 active site 1105102001182 homodimer interface [polypeptide binding]; other site 1105102001183 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105102001184 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 1105102001185 S-adenosylmethionine binding site [chemical binding]; other site 1105102001186 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105102001187 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 1105102001188 active site 1105102001189 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105102001190 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 1105102001191 active site 1105102001192 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 1105102001193 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105102001194 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105102001195 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105102001196 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105102001197 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 1105102001198 catalytic site [active] 1105102001199 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105102001200 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 1105102001201 putative ADP-binding pocket [chemical binding]; other site 1105102001202 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 1105102001203 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105102001204 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105102001205 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 1105102001206 RNA binding surface [nucleotide binding]; other site 1105102001207 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 1105102001208 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105102001209 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 1105102001210 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105102001211 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105102001212 TPR repeat; Region: TPR_11; pfam13414 1105102001213 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 1105102001214 TPR motif; other site 1105102001215 binding surface 1105102001216 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105102001217 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105102001218 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105102001219 RimM N-terminal domain; Region: RimM; pfam01782 1105102001220 PRC-barrel domain; Region: PRC; pfam05239 1105102001221 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105102001222 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1105102001223 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105102001224 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 1105102001225 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 1105102001226 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105102001227 active site 1105102001228 DNA binding site [nucleotide binding] 1105102001229 YCII-related domain; Region: YCII; cl00999 1105102001230 hypothetical protein; Provisional; Region: PRK14388 1105102001231 NADH dehydrogenase subunit E; Validated; Region: PRK07539 1105102001232 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 1105102001233 putative dimer interface [polypeptide binding]; other site 1105102001234 [2Fe-2S] cluster binding site [ion binding]; other site 1105102001235 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 1105102001236 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1105102001237 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105102001238 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1105102001239 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1105102001240 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1105102001241 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105102001242 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 1105102001243 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105102001244 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105102001245 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 1105102001246 active site 1105102001247 DNA binding site [nucleotide binding] 1105102001248 Int/Topo IB signature motif; other site 1105102001249 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 1105102001250 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105102001251 NAD binding site [chemical binding]; other site 1105102001252 homotetramer interface [polypeptide binding]; other site 1105102001253 homodimer interface [polypeptide binding]; other site 1105102001254 substrate binding site [chemical binding]; other site 1105102001255 active site 1105102001256 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105102001257 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105102001258 putative active site [active] 1105102001259 catalytic triad [active] 1105102001260 putative dimer interface [polypeptide binding]; other site 1105102001261 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105102001262 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 1105102001263 amidase catalytic site [active] 1105102001264 Zn binding residues [ion binding]; other site 1105102001265 substrate binding site [chemical binding]; other site 1105102001266 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105102001267 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 1105102001268 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 1105102001269 TM-ABC transporter signature motif; other site 1105102001270 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1105102001271 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102001272 Walker A/P-loop; other site 1105102001273 ATP binding site [chemical binding]; other site 1105102001274 Q-loop/lid; other site 1105102001275 ABC transporter signature motif; other site 1105102001276 Walker B; other site 1105102001277 D-loop; other site 1105102001278 H-loop/switch region; other site 1105102001279 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 1105102001280 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 1105102001281 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105102001282 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105102001283 active site 1105102001284 HIGH motif; other site 1105102001285 KMSKS motif; other site 1105102001286 Predicted permeases [General function prediction only]; Region: COG0679 1105102001287 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105102001288 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105102001289 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105102001290 putative NAD(P) binding site [chemical binding]; other site 1105102001291 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 1105102001292 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 1105102001293 putative active site [active] 1105102001294 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105102001295 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105102001296 malate dehydrogenase; Reviewed; Region: PRK06223 1105102001297 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105102001298 NAD(P) binding site [chemical binding]; other site 1105102001299 dimer interface [polypeptide binding]; other site 1105102001300 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105102001301 substrate binding site [chemical binding]; other site 1105102001302 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 1105102001303 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105102001304 CTP synthetase; Validated; Region: pyrG; PRK05380 1105102001305 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 1105102001306 Catalytic site [active] 1105102001307 active site 1105102001308 UTP binding site [chemical binding]; other site 1105102001309 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105102001310 active site 1105102001311 putative oxyanion hole; other site 1105102001312 catalytic triad [active] 1105102001313 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1105102001314 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105102001315 Ligand binding site; other site 1105102001316 oligomer interface; other site 1105102001317 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 1105102001318 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 1105102001319 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105102001320 active site 1105102001321 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105102001322 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 1105102001323 dimer interface [polypeptide binding]; other site 1105102001324 motif 1; other site 1105102001325 active site 1105102001326 motif 2; other site 1105102001327 motif 3; other site 1105102001328 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 1105102001329 anticodon binding site; other site 1105102001330 Fic family protein [Function unknown]; Region: COG3177 1105102001331 Fic/DOC family; Region: Fic; pfam02661 1105102001332 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105102001333 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105102001334 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105102001335 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 1105102001336 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 1105102001337 Walker A motif; other site 1105102001338 ATP binding site [chemical binding]; other site 1105102001339 Walker B motif; other site 1105102001340 arginine finger; other site 1105102001341 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105102001342 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105102001343 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105102001344 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102001345 Walker A/P-loop; other site 1105102001346 ATP binding site [chemical binding]; other site 1105102001347 Q-loop/lid; other site 1105102001348 ABC transporter signature motif; other site 1105102001349 Walker B; other site 1105102001350 D-loop; other site 1105102001351 H-loop/switch region; other site 1105102001352 muropeptide transporter; Validated; Region: ampG; cl17669 1105102001353 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105102001354 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1105102001355 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105102001356 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102001357 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105102001358 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1105102001359 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1105102001360 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105102001361 BON domain; Region: BON; pfam04972 1105102001362 BON domain; Region: BON; pfam04972 1105102001363 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 1105102001364 Iron permease FTR1 family; Region: FTR1; cl00475 1105102001365 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 1105102001366 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105102001367 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105102001368 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 1105102001369 active site 1105102001370 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 1105102001371 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1105102001372 catalytic residues [active] 1105102001373 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 1105102001374 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105102001375 tandem repeat interface [polypeptide binding]; other site 1105102001376 oligomer interface [polypeptide binding]; other site 1105102001377 active site residues [active] 1105102001378 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105102001379 trimer interface [polypeptide binding]; other site 1105102001380 active site 1105102001381 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105102001382 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 1105102001383 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105102001384 catalytic residue [active] 1105102001385 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105102001386 dimer interface [polypeptide binding]; other site 1105102001387 catalytic triad [active] 1105102001388 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105102001389 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 1105102001390 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105102001391 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105102001392 catalytic triad [active] 1105102001393 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105102001394 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 1105102001395 Subunit I/III interface [polypeptide binding]; other site 1105102001396 D-pathway; other site 1105102001397 Subunit I/VIIc interface [polypeptide binding]; other site 1105102001398 Subunit I/IV interface [polypeptide binding]; other site 1105102001399 Subunit I/II interface [polypeptide binding]; other site 1105102001400 Low-spin heme (heme a) binding site [chemical binding]; other site 1105102001401 Subunit I/VIIa interface [polypeptide binding]; other site 1105102001402 Subunit I/VIa interface [polypeptide binding]; other site 1105102001403 Dimer interface; other site 1105102001404 Putative water exit pathway; other site 1105102001405 Binuclear center (heme a3/CuB) [ion binding]; other site 1105102001406 K-pathway; other site 1105102001407 Subunit I/Vb interface [polypeptide binding]; other site 1105102001408 Putative proton exit pathway; other site 1105102001409 Subunit I/VIb interface; other site 1105102001410 Subunit I/VIc interface [polypeptide binding]; other site 1105102001411 Electron transfer pathway; other site 1105102001412 Subunit I/VIIIb interface [polypeptide binding]; other site 1105102001413 Subunit I/VIIb interface [polypeptide binding]; other site 1105102001414 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 1105102001415 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 1105102001416 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102001417 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105102001418 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105102001419 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1105102001420 putative peptidase; Provisional; Region: PRK11649 1105102001421 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105102001422 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1105102001423 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1105102001424 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105102001425 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105102001426 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105102001427 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105102001428 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105102001429 cell division protein FtsW; Region: ftsW; TIGR02614 1105102001430 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105102001431 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 1105102001432 active site 1105102001433 homodimer interface [polypeptide binding]; other site 1105102001434 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105102001435 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105102001436 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105102001437 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105102001438 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105102001439 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 1105102001440 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105102001441 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105102001442 potential frameshift: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 1105102001443 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105102001444 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 1105102001445 potential frameshift: common BLAST hit: gi|374319263|ref|YP_005065762.1| Transposase-like protein 1105102001446 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102001447 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102001448 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102001449 diaminopimelate epimerase; Region: DapF; TIGR00652 1105102001450 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105102001451 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105102001452 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105102001453 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105102001454 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 1105102001455 FeS/SAM binding site; other site 1105102001456 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105102001457 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105102001458 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 1105102001459 dimer interface [polypeptide binding]; other site 1105102001460 motif 1; other site 1105102001461 active site 1105102001462 motif 2; other site 1105102001463 motif 3; other site 1105102001464 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105102001465 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 1105102001466 putative tRNA-binding site [nucleotide binding]; other site 1105102001467 B3/4 domain; Region: B3_4; pfam03483 1105102001468 tRNA synthetase B5 domain; Region: B5; smart00874 1105102001469 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 1105102001470 dimer interface [polypeptide binding]; other site 1105102001471 motif 1; other site 1105102001472 motif 3; other site 1105102001473 motif 2; other site 1105102001474 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1105102001475 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 1105102001476 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105102001477 putative DNA binding surface [nucleotide binding]; other site 1105102001478 dimer interface [polypeptide binding]; other site 1105102001479 beta-clamp/clamp loader binding surface; other site 1105102001480 beta-clamp/translesion DNA polymerase binding surface; other site 1105102001481 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105102001482 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105102001483 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105102001484 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105102001485 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105102001486 HIGH motif; other site 1105102001487 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105102001488 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105102001489 active site 1105102001490 KMSKS motif; other site 1105102001491 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105102001492 tRNA binding surface [nucleotide binding]; other site 1105102001493 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105102001494 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105102001495 catalytic site [active] 1105102001496 putative active site [active] 1105102001497 putative substrate binding site [chemical binding]; other site 1105102001498 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 1105102001499 Septum formation initiator; Region: DivIC; pfam04977 1105102001500 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1105102001501 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1105102001502 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 1105102001503 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105102001504 catalytic residue [active] 1105102001505 putative FPP diphosphate binding site; other site 1105102001506 putative FPP binding hydrophobic cleft; other site 1105102001507 dimer interface [polypeptide binding]; other site 1105102001508 putative IPP diphosphate binding site; other site 1105102001509 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105102001510 HAMP domain; Region: HAMP; pfam00672 1105102001511 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 1105102001512 dimer interface [polypeptide binding]; other site 1105102001513 phosphorylation site [posttranslational modification] 1105102001514 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 1105102001515 ATP binding site [chemical binding]; other site 1105102001516 Mg2+ binding site [ion binding]; other site 1105102001517 G-X-G motif; other site 1105102001518 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105102001519 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 1105102001520 active site 1105102001521 phosphorylation site [posttranslational modification] 1105102001522 intermolecular recognition site; other site 1105102001523 dimerization interface [polypeptide binding]; other site 1105102001524 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 1105102001525 DNA binding site [nucleotide binding] 1105102001526 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1105102001527 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 1105102001528 homodimer interface [polypeptide binding]; other site 1105102001529 substrate-cofactor binding pocket; other site 1105102001530 catalytic residue [active] 1105102001531 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105102001532 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105102001533 dimer interface [polypeptide binding]; other site 1105102001534 active site 1105102001535 catalytic residue [active] 1105102001536 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 1105102001537 SmpB-tmRNA interface; other site 1105102001538 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 1105102001539 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105102001540 catalytic residues [active] 1105102001541 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105102001542 CoA binding domain; Region: CoA_binding; pfam02629 1105102001543 CoA-ligase; Region: Ligase_CoA; pfam00549 1105102001544 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105102001545 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1105102001546 CoA-ligase; Region: Ligase_CoA; pfam00549 1105102001547 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 1105102001548 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105102001549 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 1105102001550 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105102001551 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105102001552 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 1105102001553 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105102001554 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1105102001555 Predicted membrane protein [Function unknown]; Region: COG1238 1105102001556 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1105102001557 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 1105102001558 RecR protein; Region: RecR; pfam02132 1105102001559 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 1105102001560 putative active site [active] 1105102001561 putative metal-binding site [ion binding]; other site 1105102001562 tetramer interface [polypeptide binding]; other site 1105102001563 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 1105102001564 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105102001565 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1105102001566 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105102001567 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105102001568 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1105102001569 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105102001570 Predicted permeases [General function prediction only]; Region: COG0679 1105102001571 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105102001572 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105102001573 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105102001574 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105102001575 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1105102001576 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 1105102001577 tetramerization interface [polypeptide binding]; other site 1105102001578 NAD(P) binding site [chemical binding]; other site 1105102001579 catalytic residues [active] 1105102001580 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105102001581 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 1105102001582 active site 1105102001583 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1105102001584 Part of AAA domain; Region: AAA_19; pfam13245 1105102001585 Family description; Region: UvrD_C_2; pfam13538 1105102001586 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 1105102001587 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105102001588 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 1105102001589 tetramer interface [polypeptide binding]; other site 1105102001590 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105102001591 catalytic residue [active] 1105102001592 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105102001593 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105102001594 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 1105102001595 Walker A motif; other site 1105102001596 ATP binding site [chemical binding]; other site 1105102001597 Walker B motif; other site 1105102001598 arginine finger; other site 1105102001599 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1105102001600 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 1105102001601 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 1105102001602 30S subunit binding site; other site 1105102001603 potential frameshift: common BLAST hit: gi|238650270|ref|YP_002916122.1| carbonic anhydrase 1105102001604 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105102001605 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105102001606 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105102001607 homodimer interface [polypeptide binding]; other site 1105102001608 NADP binding site [chemical binding]; other site 1105102001609 substrate binding site [chemical binding]; other site 1105102001610 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105102001611 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105102001612 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105102001613 potential frameshift: common BLAST hit: gi|165933233|ref|YP_001650022.1| protein U 1105102001614 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105102001615 potential frameshift: common BLAST hit: gi|91205792|ref|YP_538147.1| P pilus assembly, fimbrial usher protein 1105102001616 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105102001617 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105102001618 Spore Coat Protein U domain; Region: SCPU; pfam05229 1105102001619 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105102001620 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105102001621 active site 1105102001622 dimer interface [polypeptide binding]; other site 1105102001623 catalytic residues [active] 1105102001624 effector binding site; other site 1105102001625 R2 peptide binding site; other site 1105102001626 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105102001627 dimer interface [polypeptide binding]; other site 1105102001628 putative radical transfer pathway; other site 1105102001629 diiron center [ion binding]; other site 1105102001630 tyrosyl radical; other site 1105102001631 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105102001632 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1105102001633 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105102001634 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105102001635 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 1105102001636 active site 1105102001637 substrate binding site [chemical binding]; other site 1105102001638 metal binding site [ion binding]; metal-binding site 1105102001639 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105102001640 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102001641 Walker A/P-loop; other site 1105102001642 ATP binding site [chemical binding]; other site 1105102001643 Q-loop/lid; other site 1105102001644 ABC transporter signature motif; other site 1105102001645 Walker B; other site 1105102001646 D-loop; other site 1105102001647 H-loop/switch region; other site 1105102001648 OstA-like protein; Region: OstA; pfam03968 1105102001649 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105102001650 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 1105102001651 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 1105102001652 putative active site [active] 1105102001653 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 1105102001654 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105102001655 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105102001656 RNase E interface [polypeptide binding]; other site 1105102001657 trimer interface [polypeptide binding]; other site 1105102001658 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105102001659 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105102001660 RNase E interface [polypeptide binding]; other site 1105102001661 trimer interface [polypeptide binding]; other site 1105102001662 active site 1105102001663 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 1105102001664 putative nucleic acid binding region [nucleotide binding]; other site 1105102001665 G-X-X-G motif; other site 1105102001666 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 1105102001667 RNA binding site [nucleotide binding]; other site 1105102001668 domain interface; other site 1105102001669 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 1105102001670 16S/18S rRNA binding site [nucleotide binding]; other site 1105102001671 S13e-L30e interaction site [polypeptide binding]; other site 1105102001672 25S rRNA binding site [nucleotide binding]; other site 1105102001673 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105102001674 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105102001675 RNA binding site [nucleotide binding]; other site 1105102001676 active site 1105102001677 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102001678 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105102001679 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105102001680 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1105102001681 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 1105102001682 non-specific DNA binding site [nucleotide binding]; other site 1105102001683 salt bridge; other site 1105102001684 sequence-specific DNA binding site [nucleotide binding]; other site 1105102001685 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 1105102001686 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1105102001687 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105102001688 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105102001689 uncharacterized protein, YfiH family; Region: TIGR00726 1105102001690 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 1105102001691 catalytic residues [active] 1105102001692 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102001693 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105102001694 putative active site [active] 1105102001695 homotetrameric interface [polypeptide binding]; other site 1105102001696 hypothetical protein; Provisional; Region: PRK06661 1105102001697 intersubunit interface [polypeptide binding]; other site 1105102001698 active site 1105102001699 Zn2+ binding site [ion binding]; other site 1105102001700 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105102001701 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105102001702 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1105102001703 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1105102001704 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105102001705 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 1105102001706 GSH binding site (G-site) [chemical binding]; other site 1105102001707 C-terminal domain interface [polypeptide binding]; other site 1105102001708 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105102001709 N-terminal domain interface [polypeptide binding]; other site 1105102001710 dimer interface [polypeptide binding]; other site 1105102001711 substrate binding pocket (H-site) [chemical binding]; other site 1105102001712 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105102001713 conserved cys residue [active] 1105102001714 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 1105102001715 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1105102001716 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105102001717 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105102001718 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105102001719 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105102001720 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105102001721 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105102001722 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105102001723 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1105102001724 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105102001725 Uncharacterized conserved protein [Function unknown]; Region: COG5448 1105102001726 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1105102001727 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105102001728 Predicted membrane protein [Function unknown]; Region: COG5346 1105102001729 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1105102001730 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105102001731 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105102001732 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 1105102001733 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105102001734 E3 interaction surface; other site 1105102001735 lipoyl attachment site [posttranslational modification]; other site 1105102001736 e3 binding domain; Region: E3_binding; pfam02817 1105102001737 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105102001738 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105102001739 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1105102001740 RF-1 domain; Region: RF-1; pfam00472 1105102001741 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105102001742 DHH family; Region: DHH; pfam01368 1105102001743 DHHA1 domain; Region: DHHA1; pfam02272 1105102001744 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 1105102001745 S-adenosylmethionine binding site [chemical binding]; other site 1105102001746 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105102001747 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105102001748 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1105102001749 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 1105102001750 RNA binding site [nucleotide binding]; other site 1105102001751 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 1105102001752 multimer interface [polypeptide binding]; other site 1105102001753 Walker A motif; other site 1105102001754 ATP binding site [chemical binding]; other site 1105102001755 Walker B motif; other site 1105102001756 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1105102001757 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105102001758 tandem repeat interface [polypeptide binding]; other site 1105102001759 oligomer interface [polypeptide binding]; other site 1105102001760 active site residues [active] 1105102001761 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 1105102001762 IHF - DNA interface [nucleotide binding]; other site 1105102001763 IHF dimer interface [polypeptide binding]; other site 1105102001764 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 1105102001765 hypothetical protein; Region: PHA00670 1105102001766 hypothetical protein; Region: PHA00670 1105102001767 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105102001768 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105102001769 active site 1105102001770 HIGH motif; other site 1105102001771 dimer interface [polypeptide binding]; other site 1105102001772 KMSKS motif; other site 1105102001773 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1105102001774 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105102001775 putative acyl-acceptor binding pocket; other site 1105102001776 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 1105102001777 RelB antitoxin; Region: RelB; cl01171 1105102001778 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105102001779 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105102001780 HemY protein N-terminus; Region: HemY_N; pfam07219 1105102001781 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105102001782 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105102001783 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 1105102001784 active site 1105102001785 Lysine efflux permease [General function prediction only]; Region: COG1279 1105102001786 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105102001787 AmpG-like permease; Region: 2A0125; TIGR00901 1105102001788 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105102001789 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1105102001790 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 1105102001791 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105102001792 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105102001793 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105102001794 substrate binding pocket [chemical binding]; other site 1105102001795 chain length determination region; other site 1105102001796 substrate-Mg2+ binding site; other site 1105102001797 catalytic residues [active] 1105102001798 aspartate-rich region 1; other site 1105102001799 active site lid residues [active] 1105102001800 aspartate-rich region 2; other site 1105102001801 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105102001802 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105102001803 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 1105102001804 active site 1105102001805 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105102001806 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105102001807 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105102001808 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105102001809 trimerization site [polypeptide binding]; other site 1105102001810 active site 1105102001811 cysteine desulfurase; Provisional; Region: PRK14012 1105102001812 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105102001813 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105102001814 catalytic residue [active] 1105102001815 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1105102001816 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105102001817 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105102001818 catalytic residue [active] 1105102001819 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105102001820 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 1105102001821 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105102001822 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1105102001823 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105102001824 Coenzyme A binding pocket [chemical binding]; other site 1105102001825 Predicted acetyltransferase [General function prediction only]; Region: COG5628 1105102001826 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105102001827 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 1105102001828 homotetramer interface [polypeptide binding]; other site 1105102001829 FMN binding site [chemical binding]; other site 1105102001830 homodimer contacts [polypeptide binding]; other site 1105102001831 putative active site [active] 1105102001832 putative substrate binding site [chemical binding]; other site 1105102001833 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1105102001834 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105102001835 oligomer interface [polypeptide binding]; other site 1105102001836 active site residues [active] 1105102001837 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105102001838 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 1105102001839 RNA binding site [nucleotide binding]; other site 1105102001840 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 1105102001841 RNA binding site [nucleotide binding]; other site 1105102001842 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 1105102001843 RNA binding site [nucleotide binding]; other site 1105102001844 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 1105102001845 RNA binding site [nucleotide binding]; other site 1105102001846 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 1105102001847 RNA binding site [nucleotide binding]; other site 1105102001848 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 1105102001849 RNA binding site [nucleotide binding]; other site 1105102001850 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 1105102001851 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 1105102001852 CMP-binding site; other site 1105102001853 The sites determining sugar specificity; other site 1105102001854 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 1105102001855 non-specific DNA binding site [nucleotide binding]; other site 1105102001856 salt bridge; other site 1105102001857 sequence-specific DNA binding site [nucleotide binding]; other site 1105102001858 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 1105102001859 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 1105102001860 hypothetical protein; Region: PHA00670 1105102001861 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105102001862 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105102001863 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105102001864 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 1105102001865 domain interfaces; other site 1105102001866 active site 1105102001867 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105102001868 dimer interface [polypeptide binding]; other site 1105102001869 catalytic triad [active] 1105102001870 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 1105102001871 G-X-G motif; other site 1105102001872 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 1105102001873 dimer interface [polypeptide binding]; other site 1105102001874 phosphorylation site [posttranslational modification] 1105102001875 potential frameshift: common BLAST hit: gi|15892625|ref|NP_360339.1| sodium/pantothenate symporter 1105102001876 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 1105102001877 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105102001878 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105102001879 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105102001880 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105102001881 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105102001882 Uncharacterized conserved protein [Function unknown]; Region: COG1723 1105102001883 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105102001884 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105102001885 catalytic site [active] 1105102001886 putative active site [active] 1105102001887 putative substrate binding site [chemical binding]; other site 1105102001888 Helicase and RNase D C-terminal; Region: HRDC; smart00341 1105102001889 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1105102001890 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1105102001891 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105102001892 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1105102001893 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105102001894 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105102001895 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1105102001896 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 1105102001897 S-adenosylmethionine binding site [chemical binding]; other site 1105102001898 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1105102001899 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 1105102001900 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105102001901 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105102001902 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 1105102001903 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105102001904 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 1105102001905 hypothetical protein; Validated; Region: PRK00110 1105102001906 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105102001907 Substrate binding site; other site 1105102001908 Mg++ binding site; other site 1105102001909 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 1105102001910 active site 1105102001911 homodimer interface [polypeptide binding]; other site 1105102001912 putative chemical substrate binding site [chemical binding]; other site 1105102001913 metal binding site [ion binding]; metal-binding site 1105102001914 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 1105102001915 Coenzyme A binding pocket [chemical binding]; other site 1105102001916 AAA domain; Region: AAA_17; pfam13207 1105102001917 AAA domain; Region: AAA_18; pfam13238 1105102001918 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105102001919 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105102001920 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 1105102001921 dimer interface [polypeptide binding]; other site 1105102001922 allosteric magnesium binding site [ion binding]; other site 1105102001923 active site 1105102001924 aspartate-rich active site metal binding site; other site 1105102001925 Schiff base residues; other site 1105102001926 primosome assembly protein PriA; Validated; Region: PRK05580 1105102001927 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 1105102001928 ATP binding site [chemical binding]; other site 1105102001929 putative Mg++ binding site [ion binding]; other site 1105102001930 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1105102001931 aromatic acid decarboxylase; Validated; Region: PRK05920 1105102001932 Flavoprotein; Region: Flavoprotein; pfam02441 1105102001933 SacI restriction endonuclease; Region: RE_SacI; pfam09566 1105102001934 replicative DNA helicase; Provisional; Region: PRK09165 1105102001935 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105102001936 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 1105102001937 Walker A motif; other site 1105102001938 ATP binding site [chemical binding]; other site 1105102001939 Walker B motif; other site 1105102001940 DNA binding loops [nucleotide binding] 1105102001941 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105102001942 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105102001943 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105102001944 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105102001945 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 1105102001946 RNA binding surface [nucleotide binding]; other site 1105102001947 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105102001948 active site 1105102001949 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105102001950 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105102001951 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105102001952 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105102001953 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105102001954 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1105102001955 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 1105102001956 S-adenosylmethionine binding site [chemical binding]; other site 1105102001957 DNA repair protein RadA; Provisional; Region: PRK11823 1105102001958 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 1105102001959 Walker A motif/ATP binding site; other site 1105102001960 ATP binding site [chemical binding]; other site 1105102001961 Walker B motif; other site 1105102001962 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1105102001963 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105102001964 Recombination protein O N terminal; Region: RecO_N; pfam11967 1105102001965 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105102001966 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 1105102001967 Glycoprotease family; Region: Peptidase_M22; pfam00814 1105102001968 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105102001969 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 1105102001970 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105102001971 G1 box; other site 1105102001972 putative GEF interaction site [polypeptide binding]; other site 1105102001973 GTP/Mg2+ binding site [chemical binding]; other site 1105102001974 Switch I region; other site 1105102001975 G2 box; other site 1105102001976 G3 box; other site 1105102001977 Switch II region; other site 1105102001978 G4 box; other site 1105102001979 G5 box; other site 1105102001980 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 1105102001981 Translation-initiation factor 2; Region: IF-2; pfam11987 1105102001982 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 1105102001983 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105102001984 NusA N-terminal domain; Region: NusA_N; pfam08529 1105102001985 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 1105102001986 RNA binding site [nucleotide binding]; other site 1105102001987 homodimer interface [polypeptide binding]; other site 1105102001988 NusA-like KH domain; Region: KH_5; pfam13184 1105102001989 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 1105102001990 G-X-X-G motif; other site 1105102001991 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105102001992 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 1105102001993 Sm and related proteins; Region: Sm_like; cl00259 1105102001994 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1105102001995 putative oligomer interface [polypeptide binding]; other site 1105102001996 putative RNA binding site [nucleotide binding]; other site 1105102001997 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 1105102001998 NAD binding pocket [chemical binding]; other site 1105102001999 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105102002000 Transcriptional regulator; Region: Rrf2; cl17282 1105102002001 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105102002002 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 1105102002003 RNA binding surface [nucleotide binding]; other site 1105102002004 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1105102002005 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105102002006 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105102002007 active site 1105102002008 HIGH motif; other site 1105102002009 dimer interface [polypeptide binding]; other site 1105102002010 KMSKS motif; other site 1105102002011 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 1105102002012 RNA binding surface [nucleotide binding]; other site 1105102002013 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105102002014 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 1105102002015 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 1105102002016 Substrate binding site [chemical binding]; other site 1105102002017 proline/glycine betaine transporter; Provisional; Region: PRK10642 1105102002018 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105102002019 potential frameshift: common BLAST hit: gi|157964695|ref|YP_001499519.1| large extracellular alpha-helical protein 1105102002020 potential frameshift: common BLAST hit: gi|350273648|ref|YP_004884961.1| large extracellular alpha-helical protein 1105102002021 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105102002022 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105102002023 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105102002024 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105102002025 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105102002026 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105102002027 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 1105102002028 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1105102002029 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002030 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105102002031 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1105102002032 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 1105102002033 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105102002034 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 1105102002035 active site 1105102002036 phosphorylation site [posttranslational modification] 1105102002037 intermolecular recognition site; other site 1105102002038 dimerization interface [polypeptide binding]; other site 1105102002039 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 1105102002040 Walker A motif; other site 1105102002041 ATP binding site [chemical binding]; other site 1105102002042 Walker B motif; other site 1105102002043 arginine finger; other site 1105102002044 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1105102002045 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105102002046 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105102002047 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105102002048 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105102002049 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105102002050 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105102002051 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105102002052 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105102002053 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105102002054 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105102002055 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105102002056 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1105102002057 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 1105102002058 S-adenosylmethionine binding site [chemical binding]; other site 1105102002059 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105102002060 MraZ protein; Region: MraZ; pfam02381 1105102002061 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105102002062 Na binding site [ion binding]; other site 1105102002063 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105102002064 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105102002065 GIY-YIG motif/motif A; other site 1105102002066 active site 1105102002067 catalytic site [active] 1105102002068 putative DNA binding site [nucleotide binding]; other site 1105102002069 metal binding site [ion binding]; metal-binding site 1105102002070 UvrB/uvrC motif; Region: UVR; pfam02151 1105102002071 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105102002072 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 1105102002073 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 1105102002074 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105102002075 active site 1105102002076 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 1105102002077 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105102002078 active site 1105102002079 DNA binding site [nucleotide binding] 1105102002080 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1105102002081 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1105102002082 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105102002083 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 1105102002084 DNA binding site [nucleotide binding] 1105102002085 active site 1105102002086 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 1105102002087 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105102002088 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105102002089 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1105102002090 ATP binding site [chemical binding]; other site 1105102002091 putative Mg++ binding site [ion binding]; other site 1105102002092 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1105102002093 SEC-C motif; Region: SEC-C; pfam02810 1105102002094 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 1105102002095 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1105102002096 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1105102002097 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 1105102002098 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105102002099 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 1105102002100 hinge; other site 1105102002101 active site 1105102002102 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105102002103 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 1105102002104 ATP binding site [chemical binding]; other site 1105102002105 Mg2+ binding site [ion binding]; other site 1105102002106 G-X-G motif; other site 1105102002107 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 1105102002108 anchoring element; other site 1105102002109 dimer interface [polypeptide binding]; other site 1105102002110 ATP binding site [chemical binding]; other site 1105102002111 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 1105102002112 active site 1105102002113 putative metal-binding site [ion binding]; other site 1105102002114 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105102002115 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105102002116 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 1105102002117 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 1105102002118 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105102002119 MgtE intracellular N domain; Region: MgtE_N; pfam03448 1105102002120 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 1105102002121 Divalent cation transporter; Region: MgtE; pfam01769 1105102002122 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105102002123 HD domain; Region: HD_4; pfam13328 1105102002124 Protein of unknown function (DUF969); Region: DUF969; cl01573 1105102002125 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 1105102002126 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105102002127 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1105102002128 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105102002129 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1105102002130 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105102002131 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 1105102002132 Cu(I) binding site [ion binding]; other site 1105102002133 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 1105102002134 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 1105102002135 dimer interface [polypeptide binding]; other site 1105102002136 substrate binding site [chemical binding]; other site 1105102002137 metal binding sites [ion binding]; metal-binding site 1105102002138 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002139 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1105102002140 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1105102002141 TraX protein; Region: TraX; pfam05857 1105102002142 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105102002143 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 1105102002144 ssDNA binding site; other site 1105102002145 generic binding surface II; other site 1105102002146 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 1105102002147 ATP binding site [chemical binding]; other site 1105102002148 putative Mg++ binding site [ion binding]; other site 1105102002149 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 1105102002150 nucleotide binding region [chemical binding]; other site 1105102002151 ATP-binding site [chemical binding]; other site 1105102002152 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1105102002153 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1105102002154 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 1105102002155 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105102002156 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 1105102002157 Mg++ binding site [ion binding]; other site 1105102002158 putative catalytic motif [active] 1105102002159 putative substrate binding site [chemical binding]; other site 1105102002160 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1105102002161 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105102002162 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105102002163 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105102002164 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105102002165 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105102002166 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105102002167 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105102002168 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105102002169 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1105102002170 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 1105102002171 ATP binding site [chemical binding]; other site 1105102002172 putative Mg++ binding site [ion binding]; other site 1105102002173 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 1105102002174 nucleotide binding region [chemical binding]; other site 1105102002175 ATP-binding site [chemical binding]; other site 1105102002176 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1105102002177 Uncharacterized conserved protein [Function unknown]; Region: COG2938 1105102002178 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 1105102002179 active site residue [active] 1105102002180 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105102002181 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105102002182 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 1105102002183 Walker A motif; other site 1105102002184 ATP binding site [chemical binding]; other site 1105102002185 Walker B motif; other site 1105102002186 arginine finger; other site 1105102002187 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 1105102002188 DnaA box-binding interface [nucleotide binding]; other site 1105102002189 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 1105102002190 Patatin [General function prediction only]; Region: COG3621 1105102002191 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105102002192 active site 1105102002193 nucleophile elbow; other site 1105102002194 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105102002195 HEPN domain; Region: HEPN; cl00824 1105102002196 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1105102002197 metal binding triad [ion binding]; metal-binding site 1105102002198 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105102002199 YchF GTPase; Region: YchF; cd01900 1105102002200 G1 box; other site 1105102002201 GTP/Mg2+ binding site [chemical binding]; other site 1105102002202 Switch I region; other site 1105102002203 G2 box; other site 1105102002204 Switch II region; other site 1105102002205 G3 box; other site 1105102002206 G4 box; other site 1105102002207 G5 box; other site 1105102002208 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 1105102002209 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105102002210 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 1105102002211 putative active site [active] 1105102002212 catalytic residue [active] 1105102002213 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105102002214 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105102002215 5S rRNA interface [nucleotide binding]; other site 1105102002216 CTC domain interface [polypeptide binding]; other site 1105102002217 L16 interface [polypeptide binding]; other site 1105102002218 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105102002219 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 1105102002220 FeS/SAM binding site; other site 1105102002221 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1105102002222 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105102002223 23S rRNA binding site [nucleotide binding]; other site 1105102002224 L21 binding site [polypeptide binding]; other site 1105102002225 L13 binding site [polypeptide binding]; other site 1105102002226 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1105102002227 ribonuclease P; Reviewed; Region: rnpA; PRK01492 1105102002228 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105102002229 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105102002230 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 1105102002231 Cl binding site [ion binding]; other site 1105102002232 oligomer interface [polypeptide binding]; other site 1105102002233 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 1105102002234 Phosphotransferase enzyme family; Region: APH; pfam01636 1105102002235 active site 1105102002236 ATP binding site [chemical binding]; other site 1105102002237 substrate binding site [chemical binding]; other site 1105102002238 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 1105102002239 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105102002240 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 1105102002241 dimerization interface [polypeptide binding]; other site 1105102002242 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 1105102002243 dimer interface [polypeptide binding]; other site 1105102002244 phosphorylation site [posttranslational modification] 1105102002245 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 1105102002246 ATP binding site [chemical binding]; other site 1105102002247 Mg2+ binding site [ion binding]; other site 1105102002248 G-X-G motif; other site 1105102002249 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 1105102002250 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105102002251 COQ9; Region: COQ9; pfam08511 1105102002252 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105102002253 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105102002254 HIGH motif; other site 1105102002255 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105102002256 active site 1105102002257 KMSKS motif; other site 1105102002258 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105102002259 tRNA binding surface [nucleotide binding]; other site 1105102002260 anticodon binding site; other site 1105102002261 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 1105102002262 TPR motif; other site 1105102002263 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105102002264 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105102002265 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1105102002266 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1105102002267 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 1105102002268 carboxyltransferase (CT) interaction site; other site 1105102002269 biotinylation site [posttranslational modification]; other site 1105102002270 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1105102002271 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1105102002272 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1105102002273 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105102002274 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 1105102002275 putative substrate translocation pore; other site 1105102002276 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105102002277 putative acyl-acceptor binding pocket; other site 1105102002278 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 1105102002279 acyl-activating enzyme (AAE) consensus motif; other site 1105102002280 putative AMP binding site [chemical binding]; other site 1105102002281 TfoX N-terminal domain; Region: TfoX_N; pfam04993 1105102002282 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1105102002283 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 1105102002284 ABC-ATPase subunit interface; other site 1105102002285 dimer interface [polypeptide binding]; other site 1105102002286 putative PBP binding regions; other site 1105102002287 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105102002288 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002289 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 1105102002290 S-adenosylmethionine binding site [chemical binding]; other site 1105102002291 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105102002292 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105102002293 HIGH motif; other site 1105102002294 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105102002295 active site 1105102002296 KMSKS motif; other site 1105102002297 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002298 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 1105102002299 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105102002300 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 1105102002301 ring oligomerisation interface [polypeptide binding]; other site 1105102002302 ATP/Mg binding site [chemical binding]; other site 1105102002303 stacking interactions; other site 1105102002304 hinge regions; other site 1105102002305 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 1105102002306 oligomerisation interface [polypeptide binding]; other site 1105102002307 mobile loop; other site 1105102002308 roof hairpin; other site 1105102002309 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105102002310 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 1105102002311 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105102002312 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105102002313 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105102002314 hexamer interface [polypeptide binding]; other site 1105102002315 active site 1105102002316 GrpE; Region: GrpE; pfam01025 1105102002317 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 1105102002318 dimer interface [polypeptide binding]; other site 1105102002319 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105102002320 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1105102002321 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105102002322 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 1105102002323 hypothetical protein; Validated; Region: PRK06620 1105102002324 potential frameshift: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 1105102002325 HD domain; Region: HD_4; pfam13328 1105102002326 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1105102002327 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 1105102002328 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105102002329 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105102002330 alphaNTD - beta interaction site [polypeptide binding]; other site 1105102002331 alphaNTD homodimer interface [polypeptide binding]; other site 1105102002332 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105102002333 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1105102002334 30S ribosomal protein S11; Validated; Region: PRK05309 1105102002335 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105102002336 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1105102002337 adenylate kinase; Reviewed; Region: adk; PRK00279 1105102002338 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 1105102002339 AMP-binding site [chemical binding]; other site 1105102002340 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105102002341 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105102002342 SecY translocase; Region: SecY; pfam00344 1105102002343 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1105102002344 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 1105102002345 23S rRNA binding site [nucleotide binding]; other site 1105102002346 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105102002347 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105102002348 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105102002349 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 1105102002350 5S rRNA interface [nucleotide binding]; other site 1105102002351 23S rRNA interface [nucleotide binding]; other site 1105102002352 L5 interface [polypeptide binding]; other site 1105102002353 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105102002354 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105102002355 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105102002356 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1105102002357 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1105102002358 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105102002359 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105102002360 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105102002361 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105102002362 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1105102002363 RNA binding site [nucleotide binding]; other site 1105102002364 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1105102002365 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1105102002366 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 1105102002367 L23 interface [polypeptide binding]; other site 1105102002368 trigger factor interaction site; other site 1105102002369 23S rRNA interface [nucleotide binding]; other site 1105102002370 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 1105102002371 23S rRNA interface [nucleotide binding]; other site 1105102002372 5S rRNA interface [nucleotide binding]; other site 1105102002373 putative antibiotic binding site [chemical binding]; other site 1105102002374 L25 interface [polypeptide binding]; other site 1105102002375 L27 interface [polypeptide binding]; other site 1105102002376 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105102002377 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 1105102002378 G-X-X-G motif; other site 1105102002379 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105102002380 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 1105102002381 putative translocon binding site; other site 1105102002382 protein-rRNA interface [nucleotide binding]; other site 1105102002383 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1105102002384 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105102002385 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105102002386 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105102002387 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1105102002388 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1105102002389 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1105102002390 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1105102002391 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002392 elongation factor Tu; Reviewed; Region: PRK00049 1105102002393 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105102002394 G1 box; other site 1105102002395 GEF interaction site [polypeptide binding]; other site 1105102002396 GTP/Mg2+ binding site [chemical binding]; other site 1105102002397 Switch I region; other site 1105102002398 G2 box; other site 1105102002399 G3 box; other site 1105102002400 Switch II region; other site 1105102002401 G4 box; other site 1105102002402 G5 box; other site 1105102002403 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 1105102002404 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 1105102002405 Antibiotic Binding Site [chemical binding]; other site 1105102002406 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105102002407 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1105102002408 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1105102002409 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105102002410 Class II fumarases; Region: Fumarase_classII; cd01362 1105102002411 active site 1105102002412 tetramer interface [polypeptide binding]; other site 1105102002413 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105102002414 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105102002415 putative active site [active] 1105102002416 homotetrameric interface [polypeptide binding]; other site 1105102002417 cell division protein FtsZ; Validated; Region: PRK09330 1105102002418 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 1105102002419 nucleotide binding site [chemical binding]; other site 1105102002420 SulA interaction site; other site 1105102002421 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 1105102002422 secondary substrate binding site; other site 1105102002423 primary substrate binding site; other site 1105102002424 inhibition loop; other site 1105102002425 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 1105102002426 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1105102002427 muropeptide transporter; Validated; Region: ampG; cl17669 1105102002428 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 1105102002429 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105102002430 ATP binding site [chemical binding]; other site 1105102002431 Mg++ binding site [ion binding]; other site 1105102002432 motif III; other site 1105102002433 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 1105102002434 nucleotide binding region [chemical binding]; other site 1105102002435 ATP-binding site [chemical binding]; other site 1105102002436 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 1105102002437 DNA-binding site [nucleotide binding]; DNA binding site 1105102002438 RNA-binding motif; other site 1105102002439 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1105102002440 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 1105102002441 S-adenosylmethionine binding site [chemical binding]; other site 1105102002442 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105102002443 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105102002444 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105102002445 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 1105102002446 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 1105102002447 generic binding surface II; other site 1105102002448 generic binding surface I; other site 1105102002449 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 1105102002450 putative catalytic site [active] 1105102002451 putative phosphate binding site [ion binding]; other site 1105102002452 active site 1105102002453 metal binding site A [ion binding]; metal-binding site 1105102002454 DNA binding site [nucleotide binding] 1105102002455 putative AP binding site [nucleotide binding]; other site 1105102002456 putative metal binding site B [ion binding]; other site 1105102002457 Uncharacterized conserved protein [Function unknown]; Region: COG4095 1105102002458 GTP-binding protein Der; Reviewed; Region: PRK00093 1105102002459 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105102002460 G1 box; other site 1105102002461 GTP/Mg2+ binding site [chemical binding]; other site 1105102002462 Switch I region; other site 1105102002463 G2 box; other site 1105102002464 Switch II region; other site 1105102002465 G3 box; other site 1105102002466 G4 box; other site 1105102002467 G5 box; other site 1105102002468 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105102002469 G1 box; other site 1105102002470 GTP/Mg2+ binding site [chemical binding]; other site 1105102002471 Switch I region; other site 1105102002472 G2 box; other site 1105102002473 G3 box; other site 1105102002474 Switch II region; other site 1105102002475 G4 box; other site 1105102002476 G5 box; other site 1105102002477 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105102002478 AAA domain; Region: AAA_14; pfam13173 1105102002479 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 1105102002480 ABC1 family; Region: ABC1; pfam03109 1105102002481 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 1105102002482 active site 1105102002483 ATP binding site [chemical binding]; other site 1105102002484 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105102002485 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 1105102002486 S-adenosylmethionine binding site [chemical binding]; other site 1105102002487 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105102002488 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105102002489 DNA binding site [nucleotide binding] 1105102002490 catalytic residue [active] 1105102002491 H2TH interface [polypeptide binding]; other site 1105102002492 putative catalytic residues [active] 1105102002493 turnover-facilitating residue; other site 1105102002494 intercalation triad [nucleotide binding]; other site 1105102002495 8OG recognition residue [nucleotide binding]; other site 1105102002496 putative reading head residues; other site 1105102002497 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105102002498 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105102002499 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002500 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105102002501 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 1105102002502 active site 1105102002503 potential frameshift: common BLAST hit: gi|15892963|ref|NP_360677.1| mannose-1-phosphate guanylyltransferase 1105102002504 potential frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 1105102002505 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105102002506 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105102002507 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105102002508 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105102002509 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 1105102002510 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105102002511 active site 1105102002512 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105102002513 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105102002514 HIGH motif; other site 1105102002515 active site 1105102002516 KMSKS motif; other site 1105102002517 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105102002518 tRNA binding surface [nucleotide binding]; other site 1105102002519 anticodon binding site; other site 1105102002520 thymidylate kinase; Validated; Region: tmk; PRK00698 1105102002521 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 1105102002522 TMP-binding site; other site 1105102002523 ATP-binding site [chemical binding]; other site 1105102002524 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105102002525 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 1105102002526 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105102002527 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105102002528 potential frameshift: common BLAST hit: gi|67458622|ref|YP_246246.1| transposase 1105102002529 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105102002530 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105102002531 active site 1105102002532 HIGH motif; other site 1105102002533 nucleotide binding site [chemical binding]; other site 1105102002534 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105102002535 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105102002536 active site 1105102002537 KMSKS motif; other site 1105102002538 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105102002539 tRNA binding surface [nucleotide binding]; other site 1105102002540 anticodon binding site; other site 1105102002541 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105102002542 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105102002543 potential frameshift: common BLAST hit: gi|157804076|ref|YP_001492625.1| ATPase 1105102002544 potential frameshift: common BLAST hit: gi|67458618|ref|YP_246242.1| ATPase 1105102002545 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 1105102002546 RmuC family; Region: RmuC; pfam02646 1105102002547 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cl01298 1105102002548 DoxX-like family; Region: DoxX_3; pfam13781 1105102002549 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105102002550 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1105102002551 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 1105102002552 Walker A motif; other site 1105102002553 ATP binding site [chemical binding]; other site 1105102002554 Walker B motif; other site 1105102002555 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105102002556 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105102002557 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105102002558 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 1105102002559 Ligand Binding Site [chemical binding]; other site 1105102002560 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 1105102002561 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 1105102002562 HicB family; Region: HicB; pfam05534 1105102002563 YcfA-like protein; Region: YcfA; cl00752 1105102002564 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105102002565 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105102002566 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102002567 Walker A/P-loop; other site 1105102002568 ATP binding site [chemical binding]; other site 1105102002569 Q-loop/lid; other site 1105102002570 ABC transporter signature motif; other site 1105102002571 Walker B; other site 1105102002572 D-loop; other site 1105102002573 H-loop/switch region; other site 1105102002574 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105102002575 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105102002576 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 1105102002577 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105102002578 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105102002579 FtsX-like permease family; Region: FtsX; pfam02687 1105102002580 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105102002581 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1105102002582 Walker A/P-loop; other site 1105102002583 ATP binding site [chemical binding]; other site 1105102002584 Q-loop/lid; other site 1105102002585 ABC transporter signature motif; other site 1105102002586 Walker B; other site 1105102002587 D-loop; other site 1105102002588 H-loop/switch region; other site 1105102002589 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105102002590 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105102002591 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 1105102002592 Transporter associated domain; Region: CorC_HlyC; smart01091 1105102002593 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 1105102002594 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 1105102002595 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105102002596 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105102002597 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105102002598 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105102002599 synthetase active site [active] 1105102002600 NTP binding site [chemical binding]; other site 1105102002601 metal binding site [ion binding]; metal-binding site 1105102002602 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1105102002603 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105102002604 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1105102002605 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105102002606 DNA binding residues [nucleotide binding] 1105102002607 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 1105102002608 IHF dimer interface [polypeptide binding]; other site 1105102002609 IHF - DNA interface [nucleotide binding]; other site 1105102002610 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105102002611 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 1105102002612 catalytic triad [active] 1105102002613 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105102002614 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105102002615 putative acyl-acceptor binding pocket; other site 1105102002616 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1105102002617 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1105102002618 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1105102002619 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105102002620 Protein of unknown function (DUF519); Region: DUF519; pfam04378 1105102002621 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105102002622 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 1105102002623 nucleotide binding pocket [chemical binding]; other site 1105102002624 K-X-D-G motif; other site 1105102002625 catalytic site [active] 1105102002626 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105102002627 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105102002628 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 1105102002629 Dimer interface [polypeptide binding]; other site 1105102002630 BRCT sequence motif; other site 1105102002631 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1105102002632 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105102002633 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105102002634 HD domain; Region: HD_4; pfam13328 1105102002635 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1105102002636 mce related protein; Region: MCE; pfam02470 1105102002637 hypothetical protein; Provisional; Region: PRK06630 1105102002638 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105102002639 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105102002640 active site 1105102002641 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 1105102002642 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 1105102002643 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105102002644 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 1105102002645 CoA-binding site [chemical binding]; other site 1105102002646 ATP-binding [chemical binding]; other site 1105102002647 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105102002648 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 1105102002649 active site 1105102002650 catalytic site [active] 1105102002651 substrate binding site [chemical binding]; other site 1105102002652 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 1105102002653 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105102002654 Part of AAA domain; Region: AAA_19; pfam13245 1105102002655 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105102002656 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 1105102002657 Family description; Region: UvrD_C_2; pfam13538 1105102002658 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1105102002659 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105102002660 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105102002661 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105102002662 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105102002663 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105102002664 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105102002665 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 1105102002666 nudix motif; other site 1105102002667 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1105102002668 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 1105102002669 Transporter associated domain; Region: CorC_HlyC; smart01091 1105102002670 metal-binding heat shock protein; Provisional; Region: PRK00016 1105102002671 PemK-like protein; Region: PemK; cl00995 1105102002672 lipoyl synthase; Provisional; Region: PRK05481 1105102002673 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 1105102002674 FeS/SAM binding site; other site 1105102002675 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105102002676 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 1105102002677 dimer interface [polypeptide binding]; other site 1105102002678 active site 1105102002679 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105102002680 folate binding site [chemical binding]; other site 1105102002681 Predicted esterase [General function prediction only]; Region: COG0400 1105102002682 putative hydrolase; Provisional; Region: PRK11460 1105102002683 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 1105102002684 putative GSH binding site [chemical binding]; other site 1105102002685 catalytic residues [active] 1105102002686 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105102002687 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105102002688 minor groove reading motif; other site 1105102002689 helix-hairpin-helix signature motif; other site 1105102002690 substrate binding pocket [chemical binding]; other site 1105102002691 active site 1105102002692 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1105102002693 Predicted small secreted protein [Function unknown]; Region: COG5510 1105102002694 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102002695 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102002696 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105102002697 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1105102002698 putative SAM binding site [chemical binding]; other site 1105102002699 putative homodimer interface [polypeptide binding]; other site 1105102002700 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105102002701 putative ligand binding site [chemical binding]; other site 1105102002702 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 1105102002703 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105102002704 tetramer interfaces [polypeptide binding]; other site 1105102002705 binuclear metal-binding site [ion binding]; other site 1105102002706 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 1105102002707 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1105102002708 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1105102002709 aspartate kinase; Reviewed; Region: PRK06635 1105102002710 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 1105102002711 putative nucleotide binding site [chemical binding]; other site 1105102002712 putative catalytic residues [active] 1105102002713 putative Mg ion binding site [ion binding]; other site 1105102002714 putative aspartate binding site [chemical binding]; other site 1105102002715 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 1105102002716 putative allosteric regulatory residue; other site 1105102002717 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 1105102002718 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105102002719 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1105102002720 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1105102002721 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105102002722 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 1105102002723 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105102002724 putative substrate translocation pore; other site 1105102002725 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 1105102002726 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002727 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 1105102002728 Helix-turn-helix domain; Region: HTH_25; pfam13413 1105102002729 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105102002730 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 1105102002731 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 1105102002732 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105102002733 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105102002734 G1 box; other site 1105102002735 GTP/Mg2+ binding site [chemical binding]; other site 1105102002736 Switch I region; other site 1105102002737 G2 box; other site 1105102002738 Switch II region; other site 1105102002739 G3 box; other site 1105102002740 G4 box; other site 1105102002741 G5 box; other site 1105102002742 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105102002743 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105102002744 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 1105102002745 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 1105102002746 hexamer interface [polypeptide binding]; other site 1105102002747 Walker A motif; other site 1105102002748 ATP binding site [chemical binding]; other site 1105102002749 Walker B motif; other site 1105102002750 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105102002751 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105102002752 NAD(P) binding site [chemical binding]; other site 1105102002753 active site 1105102002754 acyl carrier protein; Provisional; Region: acpP; PRK00982 1105102002755 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105102002756 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 1105102002757 dimer interface [polypeptide binding]; other site 1105102002758 active site 1105102002759 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105102002760 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105102002761 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105102002762 endonuclease subunit; Provisional; Region: 46; PHA02562 1105102002763 AAA domain; Region: AAA_14; pfam13173 1105102002764 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105102002765 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002766 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105102002767 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 1105102002768 catalytic site [active] 1105102002769 G-X2-G-X-G-K; other site 1105102002770 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 1105102002771 sequence-specific DNA binding site [nucleotide binding]; other site 1105102002772 salt bridge; other site 1105102002773 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 1105102002774 rod shape-determining protein MreC; Region: MreC; pfam04085 1105102002775 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105102002776 MreB and similar proteins; Region: MreB_like; cd10225 1105102002777 nucleotide binding site [chemical binding]; other site 1105102002778 Mg binding site [ion binding]; other site 1105102002779 putative protofilament interaction site [polypeptide binding]; other site 1105102002780 RodZ interaction site [polypeptide binding]; other site 1105102002781 Predicted permeases [General function prediction only]; Region: COG0795 1105102002782 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105102002783 putative outer membrane lipoprotein; Provisional; Region: PRK09967 1105102002784 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105102002785 ligand binding site [chemical binding]; other site 1105102002786 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105102002787 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105102002788 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 1105102002789 dimer interface [polypeptide binding]; other site 1105102002790 active site 1105102002791 CoA binding pocket [chemical binding]; other site 1105102002792 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 1105102002793 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 1105102002794 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 1105102002795 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105102002796 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1105102002797 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 1105102002798 P loop; other site 1105102002799 GTP binding site [chemical binding]; other site 1105102002800 DNA polymerase I; Provisional; Region: PRK05755 1105102002801 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105102002802 active site 1105102002803 metal binding site 1 [ion binding]; metal-binding site 1105102002804 putative 5' ssDNA interaction site; other site 1105102002805 metal binding site 3; metal-binding site 1105102002806 metal binding site 2 [ion binding]; metal-binding site 1105102002807 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105102002808 putative DNA binding site [nucleotide binding]; other site 1105102002809 putative metal binding site [ion binding]; other site 1105102002810 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105102002811 active site 1105102002812 substrate binding site [chemical binding]; other site 1105102002813 catalytic site [active] 1105102002814 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105102002815 active site 1105102002816 DNA binding site [nucleotide binding] 1105102002817 catalytic site [active] 1105102002818 potential frameshift: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 1105102002819 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1105102002820 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105102002821 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105102002822 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 1105102002823 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105102002824 putative active site [active] 1105102002825 putative PHP Thumb interface [polypeptide binding]; other site 1105102002826 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 1105102002827 generic binding surface I; other site 1105102002828 generic binding surface II; other site 1105102002829 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105102002830 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105102002831 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 1105102002832 Protein of unknown function; Region: DUF3971; pfam13116 1105102002833 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105102002834 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 1105102002835 putative substrate translocation pore; other site 1105102002836 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1105102002837 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105102002838 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105102002839 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 1105102002840 dimer interface [polypeptide binding]; other site 1105102002841 active site 1105102002842 motif 1; other site 1105102002843 motif 2; other site 1105102002844 motif 3; other site 1105102002845 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105102002846 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105102002847 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105102002848 Integral membrane protein TerC family; Region: TerC; cl10468 1105102002849 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105102002850 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105102002851 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 1105102002852 S-adenosylmethionine binding site [chemical binding]; other site 1105102002853 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105102002854 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105102002855 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 1105102002856 salt bridge; other site 1105102002857 non-specific DNA binding site [nucleotide binding]; other site 1105102002858 sequence-specific DNA binding site [nucleotide binding]; other site 1105102002859 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105102002860 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1105102002861 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1105102002862 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105102002863 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105102002864 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105102002865 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105102002866 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105102002867 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105102002868 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102002869 Walker A/P-loop; other site 1105102002870 ATP binding site [chemical binding]; other site 1105102002871 Q-loop/lid; other site 1105102002872 ABC transporter signature motif; other site 1105102002873 Walker B; other site 1105102002874 D-loop; other site 1105102002875 H-loop/switch region; other site 1105102002876 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105102002877 4Fe-4S binding domain; Region: Fer4; cl02805 1105102002878 4Fe-4S binding domain; Region: Fer4; pfam00037 1105102002879 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1105102002880 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1105102002881 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105102002882 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 1105102002883 catalytic loop [active] 1105102002884 iron binding site [ion binding]; other site 1105102002885 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1105102002886 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 1105102002887 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105102002888 Predicted membrane protein [Function unknown]; Region: COG3671 1105102002889 aconitate hydratase; Validated; Region: PRK09277 1105102002890 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105102002891 substrate binding site [chemical binding]; other site 1105102002892 ligand binding site [chemical binding]; other site 1105102002893 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 1105102002894 substrate binding site [chemical binding]; other site 1105102002895 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105102002896 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1105102002897 gamma subunit interface [polypeptide binding]; other site 1105102002898 epsilon subunit interface [polypeptide binding]; other site 1105102002899 LBP interface [polypeptide binding]; other site 1105102002900 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105102002901 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105102002902 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 1105102002903 alpha subunit interaction interface [polypeptide binding]; other site 1105102002904 Walker A motif; other site 1105102002905 ATP binding site [chemical binding]; other site 1105102002906 Walker B motif; other site 1105102002907 inhibitor binding site; inhibition site 1105102002908 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105102002909 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1105102002910 core domain interface [polypeptide binding]; other site 1105102002911 delta subunit interface [polypeptide binding]; other site 1105102002912 epsilon subunit interface [polypeptide binding]; other site 1105102002913 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105102002914 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105102002915 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 1105102002916 beta subunit interaction interface [polypeptide binding]; other site 1105102002917 Walker A motif; other site 1105102002918 ATP binding site [chemical binding]; other site 1105102002919 Walker B motif; other site 1105102002920 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105102002921 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 1105102002922 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105102002923 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105102002924 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1105102002925 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105102002926 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105102002927 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1105102002928 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1105102002929 dimerization interface [polypeptide binding]; other site 1105102002930 DPS ferroxidase diiron center [ion binding]; other site 1105102002931 ion pore; other site 1105102002932 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105102002933 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 1105102002934 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105102002935 Transglycosylase; Region: Transgly; pfam00912 1105102002936 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105102002937 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105102002938 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105102002939 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 1105102002940 FeS/SAM binding site; other site 1105102002941 TRAM domain; Region: TRAM; pfam01938 1105102002942 HEPN domain; Region: HEPN; cl00824 1105102002943 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105102002944 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102002945 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105102002946 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 1105102002947 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105102002948 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105102002949 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105102002950 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1105102002951 TrkA-N domain; Region: TrkA_N; pfam02254 1105102002952 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 1105102002953 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105102002954 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105102002955 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105102002956 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105102002957 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 1105102002958 rRNA binding site [nucleotide binding]; other site 1105102002959 predicted 30S ribosome binding site; other site 1105102002960 Maf-like protein; Region: Maf; pfam02545 1105102002961 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 1105102002962 active site 1105102002963 dimer interface [polypeptide binding]; other site 1105102002964 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 1105102002965 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105102002966 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 1105102002967 active site 1105102002968 DNA binding site [nucleotide binding] 1105102002969 Int/Topo IB signature motif; other site 1105102002970 Phasin protein; Region: Phasin_2; cl11491 1105102002971 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105102002972 PLD-like domain; Region: PLDc_2; pfam13091 1105102002973 putative active site [active] 1105102002974 catalytic site [active] 1105102002975 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105102002976 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105102002977 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 1105102002978 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1105102002979 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1105102002980 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105102002981 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105102002982 potential frameshift: common BLAST hit: gi|157964970|ref|YP_001499794.1| ankyrin repeat-containing protein 1105102002983 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105102002984 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1105102002985 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1105102002986 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105102002987 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 1105102002988 active site 1105102002989 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105102002990 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105102002991 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105102002992 MPN+ (JAMM) motif; other site 1105102002993 Zinc-binding site [ion binding]; other site 1105102002994 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105102002995 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 1105102002996 Mg++ binding site [ion binding]; other site 1105102002997 putative catalytic motif [active] 1105102002998 putative substrate binding site [chemical binding]; other site 1105102002999 Protein of unknown function (DUF721); Region: DUF721; pfam05258 1105102003000 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105102003001 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105102003002 Ferredoxin [Energy production and conversion]; Region: COG1146 1105102003003 4Fe-4S binding domain; Region: Fer4; cl02805 1105102003004 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105102003005 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 1105102003006 nucleoside/Zn binding site; other site 1105102003007 dimer interface [polypeptide binding]; other site 1105102003008 catalytic motif [active] 1105102003009 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105102003010 Cation efflux family; Region: Cation_efflux; cl00316 1105102003011 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105102003012 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105102003013 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105102003014 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 1105102003015 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105102003016 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105102003017 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105102003018 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1105102003019 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105102003020 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 1105102003021 dimer interface [polypeptide binding]; other site 1105102003022 ssDNA binding site [nucleotide binding]; other site 1105102003023 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105102003024 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 1105102003025 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 1105102003026 hypothetical protein; Reviewed; Region: PRK01530 1105102003027 heat shock protein 90; Provisional; Region: PRK05218 1105102003028 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 1105102003029 ATP binding site [chemical binding]; other site 1105102003030 Mg2+ binding site [ion binding]; other site 1105102003031 G-X-G motif; other site 1105102003032 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1105102003033 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 1105102003034 substrate-cofactor binding pocket; other site 1105102003035 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105102003036 catalytic residue [active] 1105102003037 trigger factor; Provisional; Region: tig; PRK01490 1105102003038 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105102003039 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105102003040 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105102003041 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105102003042 Obg GTPase; Region: Obg; cd01898 1105102003043 G1 box; other site 1105102003044 GTP/Mg2+ binding site [chemical binding]; other site 1105102003045 Switch I region; other site 1105102003046 G2 box; other site 1105102003047 G3 box; other site 1105102003048 Switch II region; other site 1105102003049 G4 box; other site 1105102003050 G5 box; other site 1105102003051 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 1105102003052 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1105102003053 dimer interface [polypeptide binding]; other site 1105102003054 active site 1105102003055 citrylCoA binding site [chemical binding]; other site 1105102003056 NADH binding [chemical binding]; other site 1105102003057 cationic pore residues; other site 1105102003058 oxalacetate/citrate binding site [chemical binding]; other site 1105102003059 coenzyme A binding site [chemical binding]; other site 1105102003060 catalytic triad [active] 1105102003061 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 1105102003062 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105102003063 Fe-S cluster binding site [ion binding]; other site 1105102003064 active site 1105102003065 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105102003066 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 1105102003067 RNA binding surface [nucleotide binding]; other site 1105102003068 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105102003069 active site 1105102003070 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105102003071 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 1105102003072 S-adenosylmethionine binding site [chemical binding]; other site 1105102003073 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 1105102003074 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1105102003075 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105102003076 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 1105102003077 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105102003078 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 1105102003079 motif 1; other site 1105102003080 dimer interface [polypeptide binding]; other site 1105102003081 active site 1105102003082 motif 2; other site 1105102003083 motif 3; other site 1105102003084 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 1105102003085 oligomeric interface; other site 1105102003086 putative active site [active] 1105102003087 homodimer interface [polypeptide binding]; other site 1105102003088 prevent-host-death family protein; Region: phd_fam; TIGR01552 1105102003089 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 1105102003090 potential frameshift: common BLAST hit: gi|350273988|ref|YP_004885301.1| proline/betaine transporter 1105102003091 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105102003092 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 1105102003093 motif 1; other site 1105102003094 active site 1105102003095 motif 2; other site 1105102003096 motif 3; other site 1105102003097 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105102003098 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105102003099 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105102003100 dimerization interface 3.5A [polypeptide binding]; other site 1105102003101 active site 1105102003102 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105102003103 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105102003104 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105102003105 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105102003106 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105102003107 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 1105102003108 DNA binding residues [nucleotide binding] 1105102003109 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105102003110 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1105102003111 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105102003112 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 1105102003113 active site 1105102003114 metal binding site [ion binding]; metal-binding site 1105102003115 interdomain interaction site; other site 1105102003116 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 1105102003117 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105102003118 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105102003119 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105102003120 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105102003121 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105102003122 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 1105102003123 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105102003124 ligand binding site [chemical binding]; other site 1105102003125 homodimer interface [polypeptide binding]; other site 1105102003126 NAD(P) binding site [chemical binding]; other site 1105102003127 trimer interface B [polypeptide binding]; other site 1105102003128 trimer interface A [polypeptide binding]; other site 1105102003129 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105102003130 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 1105102003131 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 1105102003132 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 1105102003133 Walker A motif; other site 1105102003134 ATP binding site [chemical binding]; other site 1105102003135 Walker B motif; other site 1105102003136 arginine finger; other site 1105102003137 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1105102003138 hypothetical protein; Validated; Region: PRK00153 1105102003139 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105102003140 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105102003141 catalytic motif [active] 1105102003142 Catalytic residue [active] 1105102003143 Beta-lactamase; Region: Beta-lactamase; cl17358 1105102003144 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 1105102003145 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105102003146 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105102003147 Walker A/P-loop; other site 1105102003148 ATP binding site [chemical binding]; other site 1105102003149 Q-loop/lid; other site 1105102003150 ABC transporter signature motif; other site 1105102003151 Walker B; other site 1105102003152 D-loop; other site 1105102003153 H-loop/switch region; other site 1105102003154 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1105102003155 putative hydrolase; Provisional; Region: PRK02113 1105102003156 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 1105102003157 active site 1105102003158 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 1105102003159 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 1105102003160 Predicted permeases [General function prediction only]; Region: COG0795 1105102003161 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105102003162 DNA polymerase III subunit chi; Provisional; Region: PRK06646 1105102003163 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105102003164 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105102003165 metal binding site [ion binding]; metal-binding site 1105102003166 dimer interface [polypeptide binding]; other site 1105102003167 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1105102003168 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1105102003169 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 1105102003170 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1105102003171 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 1105102003172 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1105102003173 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 1105102003174 putative active site [active] 1105102003175 lipoate-protein ligase B; Provisional; Region: PRK14347 1105102003176 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105102003177 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 1105102003178 amidase catalytic site [active] 1105102003179 Zn binding residues [ion binding]; other site 1105102003180 substrate binding site [chemical binding]; other site 1105102003181 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105102003182 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1105102003183 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 1105102003184 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105102003185 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 1105102003186 ATP binding site [chemical binding]; other site 1105102003187 Mg2+ binding site [ion binding]; other site 1105102003188 G-X-G motif; other site 1105102003189 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 1105102003190 ATP binding site [chemical binding]; other site 1105102003191 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1105102003192 Zinc-finger domain; Region: zf-CHCC; cl01821 1105102003193 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105102003194 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105102003195 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 1105102003196 TPR motif; other site 1105102003197 TPR repeat; Region: TPR_11; pfam13414 1105102003198 binding surface 1105102003199 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 1105102003200 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105102003201 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 1105102003202 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 1105102003203 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 1105102003204 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105102003205 TIGR00701 family protein; Region: TIGR00701 1105102003206 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105102003207 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 1105102003208 C-terminal domain interface [polypeptide binding]; other site 1105102003209 active site 1105102003210 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 1105102003211 active site 1105102003212 N-terminal domain interface [polypeptide binding]; other site 1105102003213 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 1105102003214 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 1105102003215 substrate binding site [chemical binding]; other site 1105102003216 active site