-- dump date 20140620_034611 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105105000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 1105105000002 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 1105105000003 catalytic residues [active] 1105105000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105105000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 1105105000006 Walker A/P-loop; other site 1105105000007 ATP binding site [chemical binding]; other site 1105105000008 Q-loop/lid; other site 1105105000009 ABC transporter signature motif; other site 1105105000010 Walker B; other site 1105105000011 D-loop; other site 1105105000012 H-loop/switch region; other site 1105105000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1105105000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1105105000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105105000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105105000017 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 1105105000018 FAD binding pocket [chemical binding]; other site 1105105000019 FAD binding motif [chemical binding]; other site 1105105000020 phosphate binding motif [ion binding]; other site 1105105000021 beta-alpha-beta structure motif; other site 1105105000022 NAD binding pocket [chemical binding]; other site 1105105000023 Iron coordination center [ion binding]; other site 1105105000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 1105105000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 1105105000026 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 1105105000027 active site 1105105000028 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 1105105000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105105000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105105000031 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 1105105000032 trimer interface [polypeptide binding]; other site 1105105000033 active site 1105105000034 UDP-GlcNAc binding site [chemical binding]; other site 1105105000035 lipid binding site [chemical binding]; lipid-binding site 1105105000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105105000037 active site 1105105000038 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105105000039 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 1105105000040 glucose-6-phosphate isomerase; Provisional; Region: PTZ00430 1105105000041 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1105105000042 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 1105105000043 FMN binding site [chemical binding]; other site 1105105000044 active site 1105105000045 catalytic residues [active] 1105105000046 substrate binding site [chemical binding]; other site 1105105000047 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 1105105000048 NodB motif; other site 1105105000049 putative active site [active] 1105105000050 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1105105000051 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 1105105000052 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 1105105000053 intersubunit interface [polypeptide binding]; other site 1105105000054 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105105000055 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105105000056 active site 1105105000057 NTP binding site [chemical binding]; other site 1105105000058 metal binding triad [ion binding]; metal-binding site 1105105000059 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105105000060 Competence protein; Region: Competence; pfam03772 1105105000061 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105105000062 AAA domain; Region: AAA_22; pfam13401 1105105000063 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105105000064 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105105000065 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 1105105000066 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 1105105000067 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105105000068 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 1105105000069 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1105105000070 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 1105105000071 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 1105105000072 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105105000073 Thioredoxin; Region: Thioredoxin_4; pfam13462 1105105000074 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 1105105000075 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105105000076 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 1105105000077 S-adenosylmethionine binding site [chemical binding]; other site 1105105000078 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105105000079 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105105000080 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 1105105000081 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000082 Walker A/P-loop; other site 1105105000083 ATP binding site [chemical binding]; other site 1105105000084 Q-loop/lid; other site 1105105000085 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000086 ABC transporter signature motif; other site 1105105000087 Walker B; other site 1105105000088 D-loop; other site 1105105000089 H-loop/switch region; other site 1105105000090 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 1105105000091 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1105105000092 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 1105105000093 folate binding site [chemical binding]; other site 1105105000094 NADP+ binding site [chemical binding]; other site 1105105000095 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 1105105000096 catalytic center binding site [active] 1105105000097 ATP binding site [chemical binding]; other site 1105105000098 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 1105105000099 substrate binding pocket [chemical binding]; other site 1105105000100 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105105000101 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 1105105000102 Cu(I) binding site [ion binding]; other site 1105105000103 Putative transcriptional regulator [Transcription]; Region: COG1678 1105105000104 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1105105000105 Colicin V production protein; Region: Colicin_V; pfam02674 1105105000106 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105105000107 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105105000108 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105105000109 active site 1105105000110 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105105000111 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105105000112 Clp amino terminal domain; Region: Clp_N; pfam02861 1105105000113 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 1105105000114 Walker A motif; other site 1105105000115 ATP binding site [chemical binding]; other site 1105105000116 Walker B motif; other site 1105105000117 arginine finger; other site 1105105000118 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 1105105000119 Walker A motif; other site 1105105000120 ATP binding site [chemical binding]; other site 1105105000121 Walker B motif; other site 1105105000122 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1105105000123 UGMP family protein; Validated; Region: PRK09604 1105105000124 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1105105000125 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 1105105000126 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105105000127 Di-iron ligands [ion binding]; other site 1105105000128 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 1105105000129 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 1105105000130 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1105105000131 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1105105000132 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105105000133 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105105000134 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105105000135 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1105105000136 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 1105105000137 Ligand Binding Site [chemical binding]; other site 1105105000138 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105000139 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105105000140 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105105000141 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 1105105000142 Walker A motif; other site 1105105000143 ATP binding site [chemical binding]; other site 1105105000144 Walker B motif; other site 1105105000145 arginine finger; other site 1105105000146 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105105000147 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 1105105000148 cofactor binding site; other site 1105105000149 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 1105105000150 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105105000151 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1105105000152 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105105000153 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105000154 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1105105000155 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1105105000156 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105105000157 membrane protein insertase; Provisional; Region: PRK01318 1105105000158 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1105105000159 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105105000160 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 1105105000161 S-adenosylmethionine binding site [chemical binding]; other site 1105105000162 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105105000163 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 1105105000164 active site 1105105000165 catalytic residues [active] 1105105000166 metal binding site [ion binding]; metal-binding site 1105105000167 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105105000168 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105105000169 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 1105105000170 putative substrate translocation pore; other site 1105105000171 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 1105105000172 active site 1105105000173 multimer interface [polypeptide binding]; other site 1105105000174 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105105000175 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1105105000176 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105105000177 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1105105000178 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1105105000179 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105105000180 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 1105105000181 P-loop; other site 1105105000182 Magnesium ion binding site [ion binding]; other site 1105105000183 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 1105105000184 Magnesium ion binding site [ion binding]; other site 1105105000185 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 1105105000186 ParB-like nuclease domain; Region: ParB; smart00470 1105105000187 KorB domain; Region: KorB; pfam08535 1105105000188 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105105000189 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105105000190 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105105000191 ABC transporter; Region: ABC_tran_2; pfam12848 1105105000192 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105105000193 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105105000194 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 1105105000195 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105105000196 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105105000197 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105105000198 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1105105000199 Zn2+ binding site [ion binding]; other site 1105105000200 Mg2+ binding site [ion binding]; other site 1105105000201 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105105000202 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1105105000203 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1105105000204 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105105000205 active site 1105105000206 HIGH motif; other site 1105105000207 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105105000208 KMSK motif region; other site 1105105000209 tRNA binding surface [nucleotide binding]; other site 1105105000210 DALR anticodon binding domain; Region: DALR_1; smart00836 1105105000211 anticodon binding site; other site 1105105000212 Sporulation related domain; Region: SPOR; pfam05036 1105105000213 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105105000214 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 1105105000215 CAP-like domain; other site 1105105000216 active site 1105105000217 primary dimer interface [polypeptide binding]; other site 1105105000218 Gram-negative porin; Region: Porin_4; pfam13609 1105105000219 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105105000220 trimer interface [polypeptide binding]; other site 1105105000221 active site 1105105000222 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 1105105000223 SecA binding site; other site 1105105000224 Preprotein binding site; other site 1105105000225 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105105000226 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 1105105000227 active site 1105105000228 phosphorylation site [posttranslational modification] 1105105000229 intermolecular recognition site; other site 1105105000230 dimerization interface [polypeptide binding]; other site 1105105000231 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 1105105000232 DNA binding site [nucleotide binding] 1105105000233 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 1105105000234 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105105000235 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 1105105000236 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105105000237 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 1105105000238 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105105000239 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 1105105000240 EamA-like transporter family; Region: EamA; pfam00892 1105105000241 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1105105000242 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 1105105000243 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105105000244 putative substrate translocation pore; other site 1105105000245 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1105105000246 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105105000247 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105105000248 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105105000249 active site 1105105000250 HIGH motif; other site 1105105000251 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105105000252 KMSKS motif; other site 1105105000253 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105105000254 tRNA binding surface [nucleotide binding]; other site 1105105000255 anticodon binding site; other site 1105105000256 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 1105105000257 rRNA interaction site [nucleotide binding]; other site 1105105000258 S8 interaction site; other site 1105105000259 putative laminin-1 binding site; other site 1105105000260 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105105000261 UBA/TS-N domain; Region: UBA; pfam00627 1105105000262 Elongation factor TS; Region: EF_TS; pfam00889 1105105000263 Elongation factor TS; Region: EF_TS; pfam00889 1105105000264 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 1105105000265 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105000266 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105105000267 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 1105105000268 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105105000269 putative acyl-acceptor binding pocket; other site 1105105000270 aspartate aminotransferase; Provisional; Region: PRK05764 1105105000271 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 1105105000272 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105105000273 homodimer interface [polypeptide binding]; other site 1105105000274 catalytic residue [active] 1105105000275 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105105000276 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105105000277 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 1105105000278 binding surface 1105105000279 TPR motif; other site 1105105000280 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1105105000281 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 1105105000282 S-adenosylmethionine binding site [chemical binding]; other site 1105105000283 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1105105000284 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 1105105000285 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105105000286 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105105000287 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105105000288 active site 1105105000289 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105000290 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1105105000291 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105105000292 active site 1105105000293 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105105000294 dimer interface [polypeptide binding]; other site 1105105000295 substrate binding site [chemical binding]; other site 1105105000296 catalytic residues [active] 1105105000297 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1105105000298 Permease; Region: Permease; pfam02405 1105105000299 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105105000300 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000301 Walker A/P-loop; other site 1105105000302 ATP binding site [chemical binding]; other site 1105105000303 Q-loop/lid; other site 1105105000304 ABC transporter signature motif; other site 1105105000305 Walker B; other site 1105105000306 D-loop; other site 1105105000307 H-loop/switch region; other site 1105105000308 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 1105105000309 50S ribosomal protein L31; Provisional; Region: PRK01397 1105105000310 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105105000311 G1 box; other site 1105105000312 GTP/Mg2+ binding site [chemical binding]; other site 1105105000313 Switch I region; other site 1105105000314 G2 box; other site 1105105000315 G3 box; other site 1105105000316 Switch II region; other site 1105105000317 G4 box; other site 1105105000318 G5 box; other site 1105105000319 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 1105105000320 nucleotide binding site [chemical binding]; other site 1105105000321 substrate binding site [chemical binding]; other site 1105105000322 type IV secretion system protein VirB3; Provisional; Region: PRK13899 1105105000323 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105105000324 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105105000325 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000326 Walker A/P-loop; other site 1105105000327 ATP binding site [chemical binding]; other site 1105105000328 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105105000329 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105105000330 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105105000331 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105105000332 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105105000333 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105105000334 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105105000335 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 1105105000336 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1105105000337 hypothetical protein; Provisional; Region: PRK13694 1105105000338 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105105000339 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105105000340 Protein export membrane protein; Region: SecD_SecF; pfam02355 1105105000341 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105105000342 SLBB domain; Region: SLBB; pfam10531 1105105000343 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 1105105000344 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105105000345 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 1105105000346 Catalytic site [active] 1105105000347 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 1105105000348 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105105000349 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 1105105000350 dimerization interface [polypeptide binding]; other site 1105105000351 active site 1105105000352 metal binding site [ion binding]; metal-binding site 1105105000353 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 1105105000354 dsRNA binding site [nucleotide binding]; other site 1105105000355 GTPase Era; Provisional; Region: era; PRK15494 1105105000356 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105000357 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105105000358 G1 box; other site 1105105000359 GTP/Mg2+ binding site [chemical binding]; other site 1105105000360 Switch I region; other site 1105105000361 G2 box; other site 1105105000362 Switch II region; other site 1105105000363 G3 box; other site 1105105000364 G4 box; other site 1105105000365 G5 box; other site 1105105000366 KH domain; Region: KH_2; pfam07650 1105105000367 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 1105105000368 active site 1105105000369 putative DNA-binding cleft [nucleotide binding]; other site 1105105000370 dimer interface [polypeptide binding]; other site 1105105000371 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105105000372 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1105105000373 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 1105105000374 potential frameshift: common BLAST hit: gi|165932732|ref|YP_001649521.1| nucleotidyltransferase 1105105000375 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105105000376 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105105000377 AAA domain; Region: AAA_31; pfam13614 1105105000378 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 1105105000379 Walker A motif; other site 1105105000380 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 1105105000381 HflK protein; Region: hflK; TIGR01933 1105105000382 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105105000383 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 1105105000384 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105105000385 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105105000386 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 1105105000387 protein binding site [polypeptide binding]; other site 1105105000388 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 1105105000389 protein binding site [polypeptide binding]; other site 1105105000390 hypothetical protein; Validated; Region: PRK01415 1105105000391 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105105000392 active site residue [active] 1105105000393 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 1105105000394 Iron-sulfur protein interface; other site 1105105000395 proximal quinone binding site [chemical binding]; other site 1105105000396 SdhD (CybS) interface [polypeptide binding]; other site 1105105000397 proximal heme binding site [chemical binding]; other site 1105105000398 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 1105105000399 putative SdhC subunit interface [polypeptide binding]; other site 1105105000400 putative proximal heme binding site [chemical binding]; other site 1105105000401 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105105000402 putative proximal quinone binding site; other site 1105105000403 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105105000404 L-aspartate oxidase; Provisional; Region: PRK06175 1105105000405 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105105000406 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105105000407 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 1105105000408 dimer interface [polypeptide binding]; other site 1105105000409 conserved gate region; other site 1105105000410 putative PBP binding loops; other site 1105105000411 ABC-ATPase subunit interface; other site 1105105000412 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 1105105000413 S17 interaction site [polypeptide binding]; other site 1105105000414 S8 interaction site; other site 1105105000415 16S rRNA interaction site [nucleotide binding]; other site 1105105000416 streptomycin interaction site [chemical binding]; other site 1105105000417 23S rRNA interaction site [nucleotide binding]; other site 1105105000418 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105105000419 30S ribosomal protein S7; Validated; Region: PRK05302 1105105000420 elongation factor G; Reviewed; Region: PRK00007 1105105000421 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105105000422 G1 box; other site 1105105000423 putative GEF interaction site [polypeptide binding]; other site 1105105000424 GTP/Mg2+ binding site [chemical binding]; other site 1105105000425 Switch I region; other site 1105105000426 G2 box; other site 1105105000427 G3 box; other site 1105105000428 Switch II region; other site 1105105000429 G4 box; other site 1105105000430 G5 box; other site 1105105000431 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 1105105000432 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 1105105000433 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 1105105000434 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 1105105000435 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105105000436 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105105000437 putative homodimer interface [polypeptide binding]; other site 1105105000438 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1105105000439 heterodimer interface [polypeptide binding]; other site 1105105000440 homodimer interface [polypeptide binding]; other site 1105105000441 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105105000442 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 1105105000443 23S rRNA interface [nucleotide binding]; other site 1105105000444 putative thiostrepton binding site; other site 1105105000445 L7/L12 interface [polypeptide binding]; other site 1105105000446 L25 interface [polypeptide binding]; other site 1105105000447 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 1105105000448 mRNA/rRNA interface [nucleotide binding]; other site 1105105000449 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 1105105000450 23S rRNA interface [nucleotide binding]; other site 1105105000451 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105105000452 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 1105105000453 core dimer interface [polypeptide binding]; other site 1105105000454 peripheral dimer interface [polypeptide binding]; other site 1105105000455 L10 interface [polypeptide binding]; other site 1105105000456 L11 interface [polypeptide binding]; other site 1105105000457 putative EF-Tu interaction site [polypeptide binding]; other site 1105105000458 putative EF-G interaction site [polypeptide binding]; other site 1105105000459 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1105105000460 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 1105105000461 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105105000462 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 1105105000463 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1105105000464 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 1105105000465 RPB3 interaction site [polypeptide binding]; other site 1105105000466 RPB1 interaction site [polypeptide binding]; other site 1105105000467 RPB11 interaction site [polypeptide binding]; other site 1105105000468 RPB10 interaction site [polypeptide binding]; other site 1105105000469 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105105000470 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105105000471 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1105105000472 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105105000473 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105105000474 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105105000475 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105105000476 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105105000477 DNA binding site [nucleotide binding] 1105105000478 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105105000479 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 1105105000480 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105000481 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105105000482 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 1105105000483 interface (dimer of trimers) [polypeptide binding]; other site 1105105000484 Substrate-binding/catalytic site; other site 1105105000485 Zn-binding sites [ion binding]; other site 1105105000486 ATPase MipZ; Region: MipZ; pfam09140 1105105000487 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 1105105000488 P-loop; other site 1105105000489 Magnesium ion binding site [ion binding]; other site 1105105000490 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 1105105000491 Magnesium ion binding site [ion binding]; other site 1105105000492 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105105000493 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 1105105000494 dimer interface [polypeptide binding]; other site 1105105000495 anticodon binding site; other site 1105105000496 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 1105105000497 homodimer interface [polypeptide binding]; other site 1105105000498 motif 1; other site 1105105000499 active site 1105105000500 motif 2; other site 1105105000501 GAD domain; Region: GAD; pfam02938 1105105000502 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 1105105000503 active site 1105105000504 motif 3; other site 1105105000505 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1105105000506 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105105000507 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105105000508 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1105105000509 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105105000510 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 1105105000511 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105105000512 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 1105105000513 substrate binding pocket [chemical binding]; other site 1105105000514 membrane-bound complex binding site; other site 1105105000515 hinge residues; other site 1105105000516 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105105000517 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105105000518 GatB domain; Region: GatB_Yqey; smart00845 1105105000519 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105105000520 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1105105000521 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1105105000522 Uncharacterized conserved protein [Function unknown]; Region: COG4997 1105105000523 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105105000524 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 1105105000525 hinge region; other site 1105105000526 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 1105105000527 putative nucleotide binding site [chemical binding]; other site 1105105000528 uridine monophosphate binding site [chemical binding]; other site 1105105000529 homohexameric interface [polypeptide binding]; other site 1105105000530 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 1105105000531 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105105000532 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 1105105000533 putative substrate translocation pore; other site 1105105000534 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 1105105000535 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105105000536 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1105105000537 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105105000538 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105105000539 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105105000540 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105105000541 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105105000542 Surface antigen; Region: Bac_surface_Ag; pfam01103 1105105000543 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105105000544 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 1105105000545 active site 1105105000546 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 1105105000547 protein binding site [polypeptide binding]; other site 1105105000548 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 1105105000549 putative substrate binding region [chemical binding]; other site 1105105000550 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1105105000551 putative RNA binding site [nucleotide binding]; other site 1105105000552 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105105000553 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 1105105000554 S-adenosylmethionine binding site [chemical binding]; other site 1105105000555 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105105000556 putative coenzyme Q binding site [chemical binding]; other site 1105105000557 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105000558 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105105000559 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105105000560 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 1105105000561 RNA methyltransferase, RsmE family; Region: TIGR00046 1105105000562 Uncharacterized conserved protein [Function unknown]; Region: COG2155 1105105000563 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105105000564 Protein export membrane protein; Region: SecD_SecF; cl14618 1105105000565 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 1105105000566 IHF dimer interface [polypeptide binding]; other site 1105105000567 IHF - DNA interface [nucleotide binding]; other site 1105105000568 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105105000569 signal recognition particle protein; Provisional; Region: PRK10867 1105105000570 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1105105000571 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 1105105000572 P loop; other site 1105105000573 GTP binding site [chemical binding]; other site 1105105000574 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105105000575 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105105000576 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105105000577 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105105000578 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105105000579 potential frameshift: common BLAST hit: gi|67459496|ref|YP_247120.1| prolyl endopeptidase 1105105000580 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105105000581 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 1105105000582 FeS/SAM binding site; other site 1105105000583 HemN C-terminal domain; Region: HemN_C; pfam06969 1105105000584 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 1105105000585 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105105000586 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 1105105000587 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105105000588 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1105105000589 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 1105105000590 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 1105105000591 active site 1105105000592 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105105000593 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 1105105000594 E3 interaction surface; other site 1105105000595 lipoyl attachment site [posttranslational modification]; other site 1105105000596 e3 binding domain; Region: E3_binding; pfam02817 1105105000597 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105105000598 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105105000599 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 1105105000600 TPP-binding site [chemical binding]; other site 1105105000601 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1105105000602 dimer interface [polypeptide binding]; other site 1105105000603 PYR/PP interface [polypeptide binding]; other site 1105105000604 TPP binding site [chemical binding]; other site 1105105000605 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 1105105000606 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 1105105000607 active site 1105105000608 Zn binding site [ion binding]; other site 1105105000609 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105105000610 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105105000611 Walker A/P-loop; other site 1105105000612 ATP binding site [chemical binding]; other site 1105105000613 Q-loop/lid; other site 1105105000614 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105105000615 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105105000616 ABC transporter signature motif; other site 1105105000617 Walker B; other site 1105105000618 D-loop; other site 1105105000619 H-loop/switch region; other site 1105105000620 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105105000621 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105105000622 Putative cation transport regulator [General function prediction only]; Region: ChaB; COG4572 1105105000623 chaperone protein DnaJ; Provisional; Region: PRK14300 1105105000624 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 1105105000625 HSP70 interaction site [polypeptide binding]; other site 1105105000626 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105105000627 substrate binding site [polypeptide binding]; other site 1105105000628 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105105000629 Zn binding sites [ion binding]; other site 1105105000630 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105105000631 dimer interface [polypeptide binding]; other site 1105105000632 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105105000633 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105105000634 nucleotide binding site [chemical binding]; other site 1105105000635 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 1105105000636 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105105000637 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 1105105000638 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105105000639 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105105000640 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105105000641 diiron binding motif [ion binding]; other site 1105105000642 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 1105105000643 Subunit III/VIIa interface [polypeptide binding]; other site 1105105000644 Phospholipid binding site [chemical binding]; other site 1105105000645 Subunit I/III interface [polypeptide binding]; other site 1105105000646 Subunit III/VIb interface [polypeptide binding]; other site 1105105000647 Subunit III/VIa interface; other site 1105105000648 Subunit III/Vb interface [polypeptide binding]; other site 1105105000649 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1105105000650 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 1105105000651 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105105000652 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 1105105000653 trimer interface [polypeptide binding]; other site 1105105000654 active site 1105105000655 substrate binding site [chemical binding]; other site 1105105000656 CoA binding site [chemical binding]; other site 1105105000657 potential frameshift: common BLAST hit: gi|15892172|ref|NP_359886.1| bifunctional penicillin-binding protein 1C 1105105000658 potential frameshift: common BLAST hit: gi|350273249|ref|YP_004884562.1| bifunctional penicillin-binding protein 1C 1105105000659 potential frameshift: common BLAST hit: gi|67459460|ref|YP_247084.1| cell surface antigen-like protein Sca8 1105105000660 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 1105105000661 Ligand Binding Site [chemical binding]; other site 1105105000662 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105105000663 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1105105000664 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1105105000665 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 1105105000666 catalytic loop [active] 1105105000667 iron binding site [ion binding]; other site 1105105000668 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105105000669 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105105000670 nucleotide binding site [chemical binding]; other site 1105105000671 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105105000672 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 1105105000673 HSP70 interaction site [polypeptide binding]; other site 1105105000674 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105105000675 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105105000676 active site 1105105000677 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105105000678 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 1105105000679 ATP binding site [chemical binding]; other site 1105105000680 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 1105105000681 nucleotide binding region [chemical binding]; other site 1105105000682 ATP-binding site [chemical binding]; other site 1105105000683 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105105000684 UvrB/uvrC motif; Region: UVR; pfam02151 1105105000685 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 1105105000686 GSH binding site [chemical binding]; other site 1105105000687 catalytic residues [active] 1105105000688 potential frameshift: common BLAST hit: gi|157964270|ref|YP_001499094.1| multidrug resistance protein Atm1 1105105000689 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105105000690 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000691 Walker A/P-loop; other site 1105105000692 ATP binding site [chemical binding]; other site 1105105000693 Q-loop/lid; other site 1105105000694 Pleckstrin homology-like domain; Region: PH-like; cl17171 1105105000695 DNA gyrase subunit A; Validated; Region: PRK05560 1105105000696 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 1105105000697 CAP-like domain; other site 1105105000698 active site 1105105000699 primary dimer interface [polypeptide binding]; other site 1105105000700 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105105000701 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105105000702 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105105000703 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105105000704 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105105000705 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105105000706 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105105000707 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105105000708 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 1105105000709 active site 1105105000710 catalytic residues [active] 1105105000711 metal binding site [ion binding]; metal-binding site 1105105000712 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105105000713 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105105000714 putative active site [active] 1105105000715 substrate binding site [chemical binding]; other site 1105105000716 putative cosubstrate binding site; other site 1105105000717 catalytic site [active] 1105105000718 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105105000719 substrate binding site [chemical binding]; other site 1105105000720 Protein of unknown function (DUF563); Region: DUF563; cl15705 1105105000721 Predicted ATPase [General function prediction only]; Region: COG1485 1105105000722 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 1105105000723 Walker A motif; other site 1105105000724 ATP binding site [chemical binding]; other site 1105105000725 Walker B motif; other site 1105105000726 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 1105105000727 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1105105000728 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 1105105000729 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105105000730 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105105000731 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105105000732 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000733 Walker A/P-loop; other site 1105105000734 ATP binding site [chemical binding]; other site 1105105000735 Q-loop/lid; other site 1105105000736 ABC transporter signature motif; other site 1105105000737 Walker B; other site 1105105000738 D-loop; other site 1105105000739 H-loop/switch region; other site 1105105000740 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105105000741 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 1105105000742 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105105000743 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105105000744 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105105000745 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 1105105000746 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105105000747 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105105000748 putative metal binding site; other site 1105105000749 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105105000750 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105105000751 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105105000752 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105105000753 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105105000754 ATP binding site [chemical binding]; other site 1105105000755 active site 1105105000756 substrate binding site [chemical binding]; other site 1105105000757 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105105000758 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 1105105000759 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105105000760 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 1105105000761 active site 1105105000762 dimer interface [polypeptide binding]; other site 1105105000763 motif 1; other site 1105105000764 motif 2; other site 1105105000765 motif 3; other site 1105105000766 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 1105105000767 anticodon binding site; other site 1105105000768 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000769 Walker A/P-loop; other site 1105105000770 ATP binding site [chemical binding]; other site 1105105000771 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000772 ABC transporter signature motif; other site 1105105000773 Walker B; other site 1105105000774 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105000775 H-loop/switch region; other site 1105105000776 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 1105105000777 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105105000778 V-type ATP synthase subunit I; Validated; Region: PRK05771 1105105000779 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105105000780 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 1105105000781 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 1105105000782 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105105000783 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105105000784 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 1105105000785 ATP binding site [chemical binding]; other site 1105105000786 Mg2+ binding site [ion binding]; other site 1105105000787 G-X-G motif; other site 1105105000788 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 1105105000789 anchoring element; other site 1105105000790 dimer interface [polypeptide binding]; other site 1105105000791 ATP binding site [chemical binding]; other site 1105105000792 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 1105105000793 active site 1105105000794 metal binding site [ion binding]; metal-binding site 1105105000795 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105105000796 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105105000797 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105105000798 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 1105105000799 protein binding site [polypeptide binding]; other site 1105105000800 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105105000801 Catalytic dyad [active] 1105105000802 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1105105000803 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 1105105000804 dimer interface [polypeptide binding]; other site 1105105000805 phosphorylation site [posttranslational modification] 1105105000806 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 1105105000807 ATP binding site [chemical binding]; other site 1105105000808 Mg2+ binding site [ion binding]; other site 1105105000809 G-X-G motif; other site 1105105000810 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105105000811 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105105000812 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105105000813 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105105000814 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105105000815 Trp docking motif [polypeptide binding]; other site 1105105000816 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 1105105000817 23S rRNA interface [nucleotide binding]; other site 1105105000818 L3 interface [polypeptide binding]; other site 1105105000819 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1105105000820 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 1105105000821 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105105000822 DCoH tetramer interaction site [polypeptide binding]; other site 1105105000823 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 1105105000824 putative active site [active] 1105105000825 Ap4A binding site [chemical binding]; other site 1105105000826 nudix motif; other site 1105105000827 putative metal binding site [ion binding]; other site 1105105000828 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105105000829 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 1105105000830 active site 1105105000831 phosphorylation site [posttranslational modification] 1105105000832 intermolecular recognition site; other site 1105105000833 dimerization interface [polypeptide binding]; other site 1105105000834 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 1105105000835 active site 1105105000836 phosphorylation site [posttranslational modification] 1105105000837 intermolecular recognition site; other site 1105105000838 dimerization interface [polypeptide binding]; other site 1105105000839 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105105000840 metal binding site [ion binding]; metal-binding site 1105105000841 active site 1105105000842 I-site; other site 1105105000843 elongation factor P; Validated; Region: PRK00529 1105105000844 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105105000845 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 1105105000846 RNA binding site [nucleotide binding]; other site 1105105000847 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 1105105000848 RNA binding site [nucleotide binding]; other site 1105105000849 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105105000850 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 1105105000851 active site 1105105000852 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105105000853 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 1105105000854 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105105000855 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1105105000856 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1105105000857 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105105000858 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105105000859 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105000860 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105105000861 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 1105105000862 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105105000863 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105105000864 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105105000865 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105105000866 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105105000867 FAD binding domain; Region: FAD_binding_4; pfam01565 1105105000868 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105105000869 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105105000870 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105105000871 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1105105000872 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1105105000873 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105105000874 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105105000875 cell division protein FtsA; Region: ftsA; TIGR01174 1105105000876 Cell division protein FtsA; Region: FtsA; smart00842 1105105000877 Cell division protein FtsA; Region: FtsA; pfam14450 1105105000878 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1105105000879 Cytochrome c2 [Energy production and conversion]; Region: COG3474 1105105000880 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1105105000881 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105105000882 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 1105105000883 RNA binding site [nucleotide binding]; other site 1105105000884 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 1105105000885 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 1105105000886 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105105000887 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 1105105000888 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105105000889 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 1105105000890 RNA binding surface [nucleotide binding]; other site 1105105000891 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105105000892 active site 1105105000893 potential frameshift: common BLAST hit: gi|238650484|ref|YP_002916336.1| penicillin-binding protein 4* 1105105000894 potential frameshift: common BLAST hit: gi|15892268|ref|NP_359982.1| penicillin-binding protein 4* 1105105000895 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 1105105000896 putative catalytic site [active] 1105105000897 putative phosphate binding site [ion binding]; other site 1105105000898 active site 1105105000899 metal binding site A [ion binding]; metal-binding site 1105105000900 DNA binding site [nucleotide binding] 1105105000901 putative AP binding site [nucleotide binding]; other site 1105105000902 putative metal binding site B [ion binding]; other site 1105105000903 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105105000904 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 1105105000905 tetramer interface [polypeptide binding]; other site 1105105000906 TPP-binding site [chemical binding]; other site 1105105000907 heterodimer interface [polypeptide binding]; other site 1105105000908 phosphorylation loop region [posttranslational modification] 1105105000909 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105105000910 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 1105105000911 alpha subunit interface [polypeptide binding]; other site 1105105000912 TPP binding site [chemical binding]; other site 1105105000913 heterodimer interface [polypeptide binding]; other site 1105105000914 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105105000915 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1105105000916 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105105000917 G1 box; other site 1105105000918 putative GEF interaction site [polypeptide binding]; other site 1105105000919 GTP/Mg2+ binding site [chemical binding]; other site 1105105000920 Switch I region; other site 1105105000921 G2 box; other site 1105105000922 G3 box; other site 1105105000923 Switch II region; other site 1105105000924 G4 box; other site 1105105000925 G5 box; other site 1105105000926 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 1105105000927 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 1105105000928 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 1105105000929 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105105000930 isocitrate dehydrogenase; Validated; Region: PRK09222 1105105000931 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 1105105000932 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 1105105000933 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105105000934 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 1105105000935 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105105000936 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105105000937 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105105000938 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105105000939 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 1105105000940 [2Fe-2S] cluster binding site [ion binding]; other site 1105105000941 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 1105105000942 Qi binding site; other site 1105105000943 cytochrome b; Provisional; Region: CYTB; MTH00191 1105105000944 intrachain domain interface; other site 1105105000945 interchain domain interface [polypeptide binding]; other site 1105105000946 heme bH binding site [chemical binding]; other site 1105105000947 heme bL binding site [chemical binding]; other site 1105105000948 Qo binding site; other site 1105105000949 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 1105105000950 interchain domain interface [polypeptide binding]; other site 1105105000951 intrachain domain interface; other site 1105105000952 Qi binding site; other site 1105105000953 Qo binding site; other site 1105105000954 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105105000955 catalytic site [active] 1105105000956 metal binding site [ion binding]; metal-binding site 1105105000957 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105105000958 Cytochrome c; Region: Cytochrom_C; cl11414 1105105000959 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1105105000960 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 1105105000961 putative dimer interface [polypeptide binding]; other site 1105105000962 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105105000963 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105105000964 PCRF domain; Region: PCRF; pfam03462 1105105000965 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105105000966 RF-1 domain; Region: RF-1; pfam00472 1105105000967 GTP-binding protein LepA; Provisional; Region: PRK05433 1105105000968 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105105000969 G1 box; other site 1105105000970 putative GEF interaction site [polypeptide binding]; other site 1105105000971 GTP/Mg2+ binding site [chemical binding]; other site 1105105000972 Switch I region; other site 1105105000973 G2 box; other site 1105105000974 G3 box; other site 1105105000975 Switch II region; other site 1105105000976 G4 box; other site 1105105000977 G5 box; other site 1105105000978 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 1105105000979 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 1105105000980 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105105000981 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 1105105000982 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 1105105000983 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105105000984 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105105000985 HD domain; Region: HD_4; pfam13328 1105105000986 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105105000987 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1105105000988 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105105000989 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105105000990 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105105000991 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105105000992 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105105000993 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 1105105000994 oligomeric interface; other site 1105105000995 putative active site [active] 1105105000996 homodimer interface [polypeptide binding]; other site 1105105000997 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105105000998 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105105000999 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105105001000 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105105001001 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 1105105001002 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105105001003 VirB7 interaction site; other site 1105105001004 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105105001005 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105105001006 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105105001007 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1105105001008 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1105105001009 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 1105105001010 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 1105105001011 Walker A motif; other site 1105105001012 hexamer interface [polypeptide binding]; other site 1105105001013 ATP binding site [chemical binding]; other site 1105105001014 Walker B motif; other site 1105105001015 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105105001016 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 1105105001017 Walker A motif; other site 1105105001018 ATP binding site [chemical binding]; other site 1105105001019 Walker B motif; other site 1105105001020 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105105001021 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1105105001022 Phage-related protein [Function unknown]; Region: COG4695; cl01923 1105105001023 Phage portal protein; Region: Phage_portal; pfam04860 1105105001024 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105105001025 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105105001026 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105105001027 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 1105105001028 active site 1105105001029 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105105001030 MutS domain I; Region: MutS_I; pfam01624 1105105001031 MutS domain II; Region: MutS_II; pfam05188 1105105001032 MutS domain III; Region: MutS_III; pfam05192 1105105001033 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1105105001034 Walker A/P-loop; other site 1105105001035 ATP binding site [chemical binding]; other site 1105105001036 Q-loop/lid; other site 1105105001037 ABC transporter signature motif; other site 1105105001038 Walker B; other site 1105105001039 D-loop; other site 1105105001040 H-loop/switch region; other site 1105105001041 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105105001042 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105105001043 Protein of unknown function DUF45; Region: DUF45; pfam01863 1105105001044 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1105105001045 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105105001046 TolB amino-terminal domain; Region: TolB_N; pfam04052 1105105001047 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105105001048 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105105001049 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105105001050 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105105001051 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105105001052 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105105001053 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 1105105001054 DNA binding residues [nucleotide binding] 1105105001055 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 1105105001056 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1105105001057 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 1105105001058 Ligand Binding Site [chemical binding]; other site 1105105001059 amino acid transporter; Region: 2A0306; TIGR00909 1105105001060 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105105001061 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 1105105001062 dimer interface [polypeptide binding]; other site 1105105001063 motif 1; other site 1105105001064 active site 1105105001065 motif 2; other site 1105105001066 motif 3; other site 1105105001067 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 1105105001068 anticodon binding site; other site 1105105001069 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105105001070 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105105001071 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105105001072 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105105001073 TolQ protein; Region: tolQ; TIGR02796 1105105001074 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1105105001075 TolR protein; Region: tolR; TIGR02801 1105105001076 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1105105001077 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105105001078 HD domain; Region: HD_4; pfam13328 1105105001079 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 1105105001080 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105105001081 putative substrate translocation pore; other site 1105105001082 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105105001083 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 1105105001084 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105105001085 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105105001086 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1105105001087 Walker A/P-loop; other site 1105105001088 ATP binding site [chemical binding]; other site 1105105001089 Q-loop/lid; other site 1105105001090 ABC transporter signature motif; other site 1105105001091 Walker B; other site 1105105001092 D-loop; other site 1105105001093 H-loop/switch region; other site 1105105001094 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105105001095 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1105105001096 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 1105105001097 nucleotide binding site/active site [active] 1105105001098 HIT family signature motif; other site 1105105001099 catalytic residue [active] 1105105001100 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105105001101 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105105001102 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 1105105001103 active site 1105105001104 HslU subunit interaction site [polypeptide binding]; other site 1105105001105 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105105001106 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 1105105001107 Walker A motif; other site 1105105001108 ATP binding site [chemical binding]; other site 1105105001109 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1105105001110 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105105001111 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 1105105001112 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1105105001113 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 1105105001114 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1105105001115 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 1105105001116 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105001117 Uncharacterized conserved protein [Function unknown]; Region: COG5464 1105105001118 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105001119 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105105001120 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105105001121 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105105001122 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1105105001123 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105105001124 dimerization interface [polypeptide binding]; other site 1105105001125 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 1105105001126 putative iron binding site [ion binding]; other site 1105105001127 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105105001128 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105105001129 HIGH motif; other site 1105105001130 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105105001131 active site 1105105001132 KMSKS motif; other site 1105105001133 DNA topoisomerase I; Validated; Region: PRK06599 1105105001134 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 1105105001135 active site 1105105001136 interdomain interaction site; other site 1105105001137 putative metal-binding site [ion binding]; other site 1105105001138 nucleotide binding site [chemical binding]; other site 1105105001139 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 1105105001140 domain I; other site 1105105001141 DNA binding groove [nucleotide binding] 1105105001142 phosphate binding site [ion binding]; other site 1105105001143 domain II; other site 1105105001144 domain III; other site 1105105001145 nucleotide binding site [chemical binding]; other site 1105105001146 catalytic site [active] 1105105001147 domain IV; other site 1105105001148 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105105001149 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1105105001150 DNA protecting protein DprA; Region: dprA; TIGR00732 1105105001151 DNA protecting protein DprA; Region: dprA; TIGR00732 1105105001152 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105105001153 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 1105105001154 dimer interface [polypeptide binding]; other site 1105105001155 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105105001156 catalytic triad [active] 1105105001157 peroxidatic and resolving cysteines [active] 1105105001158 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105105001159 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 1105105001160 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105105001161 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105105001162 Sulfatase; Region: Sulfatase; pfam00884 1105105001163 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 1105105001164 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 1105105001165 sequence-specific DNA binding site [nucleotide binding]; other site 1105105001166 salt bridge; other site 1105105001167 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105105001168 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105105001169 NADP binding site [chemical binding]; other site 1105105001170 active site 1105105001171 putative substrate binding site [chemical binding]; other site 1105105001172 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105105001173 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105105001174 NAD(P) binding site [chemical binding]; other site 1105105001175 homodimer interface [polypeptide binding]; other site 1105105001176 substrate binding site [chemical binding]; other site 1105105001177 active site 1105105001178 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105105001179 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105105001180 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 1105105001181 active site 1105105001182 homodimer interface [polypeptide binding]; other site 1105105001183 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105105001184 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 1105105001185 S-adenosylmethionine binding site [chemical binding]; other site 1105105001186 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105105001187 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 1105105001188 active site 1105105001189 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105105001190 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 1105105001191 active site 1105105001192 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 1105105001193 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105105001194 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105105001195 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105105001196 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105105001197 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 1105105001198 catalytic site [active] 1105105001199 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105105001200 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 1105105001201 putative ADP-binding pocket [chemical binding]; other site 1105105001202 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105001203 Walker A/P-loop; other site 1105105001204 ATP binding site [chemical binding]; other site 1105105001205 Q-loop/lid; other site 1105105001206 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105105001207 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105105001208 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 1105105001209 RNA binding surface [nucleotide binding]; other site 1105105001210 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 1105105001211 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105105001212 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 1105105001213 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105105001214 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105105001215 TPR repeat; Region: TPR_11; pfam13414 1105105001216 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 1105105001217 TPR motif; other site 1105105001218 binding surface 1105105001219 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105105001220 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105105001221 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105105001222 RimM N-terminal domain; Region: RimM; pfam01782 1105105001223 PRC-barrel domain; Region: PRC; pfam05239 1105105001224 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105105001225 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1105105001226 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105105001227 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105105001228 active site 1105105001229 DNA binding site [nucleotide binding] 1105105001230 YCII-related domain; Region: YCII; cl00999 1105105001231 hypothetical protein; Provisional; Region: PRK14388 1105105001232 NADH dehydrogenase subunit E; Validated; Region: PRK07539 1105105001233 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 1105105001234 putative dimer interface [polypeptide binding]; other site 1105105001235 [2Fe-2S] cluster binding site [ion binding]; other site 1105105001236 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 1105105001237 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1105105001238 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105105001239 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1105105001240 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1105105001241 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1105105001242 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105105001243 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 1105105001244 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105105001245 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105105001246 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 1105105001247 active site 1105105001248 DNA binding site [nucleotide binding] 1105105001249 Int/Topo IB signature motif; other site 1105105001250 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 1105105001251 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105105001252 NAD binding site [chemical binding]; other site 1105105001253 homotetramer interface [polypeptide binding]; other site 1105105001254 homodimer interface [polypeptide binding]; other site 1105105001255 substrate binding site [chemical binding]; other site 1105105001256 active site 1105105001257 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105105001258 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105105001259 putative active site [active] 1105105001260 catalytic triad [active] 1105105001261 putative dimer interface [polypeptide binding]; other site 1105105001262 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105105001263 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 1105105001264 amidase catalytic site [active] 1105105001265 Zn binding residues [ion binding]; other site 1105105001266 substrate binding site [chemical binding]; other site 1105105001267 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105105001268 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 1105105001269 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 1105105001270 TM-ABC transporter signature motif; other site 1105105001271 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1105105001272 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105001273 Walker A/P-loop; other site 1105105001274 ATP binding site [chemical binding]; other site 1105105001275 Q-loop/lid; other site 1105105001276 ABC transporter signature motif; other site 1105105001277 Walker B; other site 1105105001278 D-loop; other site 1105105001279 H-loop/switch region; other site 1105105001280 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 1105105001281 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 1105105001282 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105105001283 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105105001284 active site 1105105001285 HIGH motif; other site 1105105001286 KMSKS motif; other site 1105105001287 Predicted permeases [General function prediction only]; Region: COG0679 1105105001288 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105105001289 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105105001290 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105105001291 putative NAD(P) binding site [chemical binding]; other site 1105105001292 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 1105105001293 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 1105105001294 putative active site [active] 1105105001295 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105105001296 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105105001297 malate dehydrogenase; Reviewed; Region: PRK06223 1105105001298 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105105001299 NAD(P) binding site [chemical binding]; other site 1105105001300 dimer interface [polypeptide binding]; other site 1105105001301 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105105001302 substrate binding site [chemical binding]; other site 1105105001303 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 1105105001304 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105105001305 CTP synthetase; Validated; Region: pyrG; PRK05380 1105105001306 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 1105105001307 Catalytic site [active] 1105105001308 active site 1105105001309 UTP binding site [chemical binding]; other site 1105105001310 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105105001311 active site 1105105001312 putative oxyanion hole; other site 1105105001313 catalytic triad [active] 1105105001314 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1105105001315 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105105001316 Ligand binding site; other site 1105105001317 oligomer interface; other site 1105105001318 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 1105105001319 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 1105105001320 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105105001321 active site 1105105001322 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105105001323 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 1105105001324 dimer interface [polypeptide binding]; other site 1105105001325 motif 1; other site 1105105001326 active site 1105105001327 motif 2; other site 1105105001328 motif 3; other site 1105105001329 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 1105105001330 anticodon binding site; other site 1105105001331 Fic family protein [Function unknown]; Region: COG3177 1105105001332 Fic/DOC family; Region: Fic; pfam02661 1105105001333 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105105001334 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105105001335 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105105001336 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 1105105001337 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 1105105001338 Walker A motif; other site 1105105001339 ATP binding site [chemical binding]; other site 1105105001340 Walker B motif; other site 1105105001341 arginine finger; other site 1105105001342 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105105001343 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105105001344 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105105001345 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105001346 Walker A/P-loop; other site 1105105001347 ATP binding site [chemical binding]; other site 1105105001348 Q-loop/lid; other site 1105105001349 ABC transporter signature motif; other site 1105105001350 Walker B; other site 1105105001351 D-loop; other site 1105105001352 H-loop/switch region; other site 1105105001353 muropeptide transporter; Validated; Region: ampG; cl17669 1105105001354 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105105001355 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1105105001356 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105105001357 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105001358 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105105001359 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1105105001360 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1105105001361 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105105001362 BON domain; Region: BON; pfam04972 1105105001363 BON domain; Region: BON; pfam04972 1105105001364 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 1105105001365 Iron permease FTR1 family; Region: FTR1; cl00475 1105105001366 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 1105105001367 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105105001368 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105105001369 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 1105105001370 active site 1105105001371 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 1105105001372 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1105105001373 catalytic residues [active] 1105105001374 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 1105105001375 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105105001376 tandem repeat interface [polypeptide binding]; other site 1105105001377 oligomer interface [polypeptide binding]; other site 1105105001378 active site residues [active] 1105105001379 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105105001380 trimer interface [polypeptide binding]; other site 1105105001381 active site 1105105001382 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105105001383 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 1105105001384 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105105001385 catalytic residue [active] 1105105001386 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105105001387 dimer interface [polypeptide binding]; other site 1105105001388 catalytic triad [active] 1105105001389 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105105001390 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 1105105001391 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105105001392 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105105001393 catalytic triad [active] 1105105001394 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105105001395 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 1105105001396 Subunit I/III interface [polypeptide binding]; other site 1105105001397 D-pathway; other site 1105105001398 Subunit I/VIIc interface [polypeptide binding]; other site 1105105001399 Subunit I/IV interface [polypeptide binding]; other site 1105105001400 Subunit I/II interface [polypeptide binding]; other site 1105105001401 Low-spin heme (heme a) binding site [chemical binding]; other site 1105105001402 Subunit I/VIIa interface [polypeptide binding]; other site 1105105001403 Subunit I/VIa interface [polypeptide binding]; other site 1105105001404 Dimer interface; other site 1105105001405 Putative water exit pathway; other site 1105105001406 Binuclear center (heme a3/CuB) [ion binding]; other site 1105105001407 K-pathway; other site 1105105001408 Subunit I/Vb interface [polypeptide binding]; other site 1105105001409 Putative proton exit pathway; other site 1105105001410 Subunit I/VIb interface; other site 1105105001411 Subunit I/VIc interface [polypeptide binding]; other site 1105105001412 Electron transfer pathway; other site 1105105001413 Subunit I/VIIIb interface [polypeptide binding]; other site 1105105001414 Subunit I/VIIb interface [polypeptide binding]; other site 1105105001415 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 1105105001416 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 1105105001417 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105001418 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105105001419 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105105001420 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1105105001421 putative peptidase; Provisional; Region: PRK11649 1105105001422 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105105001423 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1105105001424 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1105105001425 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105105001426 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105105001427 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105105001428 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105105001429 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105105001430 cell division protein FtsW; Region: ftsW; TIGR02614 1105105001431 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105105001432 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 1105105001433 active site 1105105001434 homodimer interface [polypeptide binding]; other site 1105105001435 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105105001436 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105105001437 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105105001438 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105105001439 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 1105105001440 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105105001441 potential frameshift: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 1105105001442 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105105001443 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 1105105001444 potential frameshift: common BLAST hit: gi|374319263|ref|YP_005065762.1| Transposase-like protein 1105105001445 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105001446 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105001447 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105001448 diaminopimelate epimerase; Region: DapF; TIGR00652 1105105001449 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105105001450 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105105001451 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105105001452 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105105001453 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 1105105001454 FeS/SAM binding site; other site 1105105001455 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105105001456 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105105001457 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 1105105001458 dimer interface [polypeptide binding]; other site 1105105001459 motif 1; other site 1105105001460 active site 1105105001461 motif 2; other site 1105105001462 motif 3; other site 1105105001463 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105105001464 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 1105105001465 putative tRNA-binding site [nucleotide binding]; other site 1105105001466 B3/4 domain; Region: B3_4; pfam03483 1105105001467 tRNA synthetase B5 domain; Region: B5; smart00874 1105105001468 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 1105105001469 dimer interface [polypeptide binding]; other site 1105105001470 motif 1; other site 1105105001471 motif 3; other site 1105105001472 motif 2; other site 1105105001473 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1105105001474 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 1105105001475 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105105001476 putative DNA binding surface [nucleotide binding]; other site 1105105001477 dimer interface [polypeptide binding]; other site 1105105001478 beta-clamp/clamp loader binding surface; other site 1105105001479 beta-clamp/translesion DNA polymerase binding surface; other site 1105105001480 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105105001481 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105105001482 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105105001483 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105105001484 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105105001485 HIGH motif; other site 1105105001486 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105105001487 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105105001488 active site 1105105001489 KMSKS motif; other site 1105105001490 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105105001491 tRNA binding surface [nucleotide binding]; other site 1105105001492 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105105001493 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105105001494 catalytic site [active] 1105105001495 putative active site [active] 1105105001496 putative substrate binding site [chemical binding]; other site 1105105001497 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 1105105001498 Septum formation initiator; Region: DivIC; pfam04977 1105105001499 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1105105001500 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1105105001501 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 1105105001502 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105105001503 catalytic residue [active] 1105105001504 putative FPP diphosphate binding site; other site 1105105001505 putative FPP binding hydrophobic cleft; other site 1105105001506 dimer interface [polypeptide binding]; other site 1105105001507 putative IPP diphosphate binding site; other site 1105105001508 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105105001509 HAMP domain; Region: HAMP; pfam00672 1105105001510 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 1105105001511 dimer interface [polypeptide binding]; other site 1105105001512 phosphorylation site [posttranslational modification] 1105105001513 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 1105105001514 ATP binding site [chemical binding]; other site 1105105001515 Mg2+ binding site [ion binding]; other site 1105105001516 G-X-G motif; other site 1105105001517 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105105001518 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 1105105001519 active site 1105105001520 phosphorylation site [posttranslational modification] 1105105001521 intermolecular recognition site; other site 1105105001522 dimerization interface [polypeptide binding]; other site 1105105001523 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 1105105001524 DNA binding site [nucleotide binding] 1105105001525 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1105105001526 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 1105105001527 homodimer interface [polypeptide binding]; other site 1105105001528 substrate-cofactor binding pocket; other site 1105105001529 catalytic residue [active] 1105105001530 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105105001531 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105105001532 dimer interface [polypeptide binding]; other site 1105105001533 active site 1105105001534 catalytic residue [active] 1105105001535 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 1105105001536 SmpB-tmRNA interface; other site 1105105001537 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 1105105001538 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105105001539 catalytic residues [active] 1105105001540 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105105001541 CoA binding domain; Region: CoA_binding; pfam02629 1105105001542 CoA-ligase; Region: Ligase_CoA; pfam00549 1105105001543 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105105001544 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1105105001545 CoA-ligase; Region: Ligase_CoA; pfam00549 1105105001546 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 1105105001547 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105105001548 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 1105105001549 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105105001550 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105105001551 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 1105105001552 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105105001553 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1105105001554 Predicted membrane protein [Function unknown]; Region: COG1238 1105105001555 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1105105001556 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 1105105001557 RecR protein; Region: RecR; pfam02132 1105105001558 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 1105105001559 putative active site [active] 1105105001560 putative metal-binding site [ion binding]; other site 1105105001561 tetramer interface [polypeptide binding]; other site 1105105001562 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 1105105001563 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105105001564 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1105105001565 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105105001566 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105105001567 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1105105001568 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105105001569 Predicted permeases [General function prediction only]; Region: COG0679 1105105001570 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105105001571 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105105001572 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105105001573 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105105001574 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1105105001575 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 1105105001576 tetramerization interface [polypeptide binding]; other site 1105105001577 NAD(P) binding site [chemical binding]; other site 1105105001578 catalytic residues [active] 1105105001579 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105105001580 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 1105105001581 active site 1105105001582 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1105105001583 Part of AAA domain; Region: AAA_19; pfam13245 1105105001584 Family description; Region: UvrD_C_2; pfam13538 1105105001585 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 1105105001586 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105105001587 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 1105105001588 tetramer interface [polypeptide binding]; other site 1105105001589 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105105001590 catalytic residue [active] 1105105001591 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105105001592 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105105001593 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 1105105001594 Walker A motif; other site 1105105001595 ATP binding site [chemical binding]; other site 1105105001596 Walker B motif; other site 1105105001597 arginine finger; other site 1105105001598 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1105105001599 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 1105105001600 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 1105105001601 30S subunit binding site; other site 1105105001602 potential frameshift: common BLAST hit: gi|238650270|ref|YP_002916122.1| carbonic anhydrase 1105105001603 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105105001604 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105105001605 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105105001606 homodimer interface [polypeptide binding]; other site 1105105001607 NADP binding site [chemical binding]; other site 1105105001608 substrate binding site [chemical binding]; other site 1105105001609 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105105001610 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105105001611 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105105001612 Uncharacterized secreted protein [Function unknown]; Region: COG5430 1105105001613 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105105001614 potential frameshift: common BLAST hit: gi|91205792|ref|YP_538147.1| P pilus assembly, fimbrial usher protein 1105105001615 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105105001616 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105105001617 Spore Coat Protein U domain; Region: SCPU; pfam05229 1105105001618 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105105001619 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105105001620 active site 1105105001621 dimer interface [polypeptide binding]; other site 1105105001622 catalytic residues [active] 1105105001623 effector binding site; other site 1105105001624 R2 peptide binding site; other site 1105105001625 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105105001626 dimer interface [polypeptide binding]; other site 1105105001627 putative radical transfer pathway; other site 1105105001628 diiron center [ion binding]; other site 1105105001629 tyrosyl radical; other site 1105105001630 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105105001631 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1105105001632 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105105001633 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105105001634 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 1105105001635 active site 1105105001636 substrate binding site [chemical binding]; other site 1105105001637 metal binding site [ion binding]; metal-binding site 1105105001638 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105105001639 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105001640 Walker A/P-loop; other site 1105105001641 ATP binding site [chemical binding]; other site 1105105001642 Q-loop/lid; other site 1105105001643 ABC transporter signature motif; other site 1105105001644 Walker B; other site 1105105001645 D-loop; other site 1105105001646 H-loop/switch region; other site 1105105001647 OstA-like protein; Region: OstA; pfam03968 1105105001648 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105105001649 KpsF/GutQ family protein; Region: kpsF; TIGR00393 1105105001650 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 1105105001651 putative active site [active] 1105105001652 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 1105105001653 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105105001654 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105105001655 RNase E interface [polypeptide binding]; other site 1105105001656 trimer interface [polypeptide binding]; other site 1105105001657 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105105001658 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105105001659 RNase E interface [polypeptide binding]; other site 1105105001660 trimer interface [polypeptide binding]; other site 1105105001661 active site 1105105001662 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 1105105001663 putative nucleic acid binding region [nucleotide binding]; other site 1105105001664 G-X-X-G motif; other site 1105105001665 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 1105105001666 RNA binding site [nucleotide binding]; other site 1105105001667 domain interface; other site 1105105001668 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 1105105001669 16S/18S rRNA binding site [nucleotide binding]; other site 1105105001670 S13e-L30e interaction site [polypeptide binding]; other site 1105105001671 25S rRNA binding site [nucleotide binding]; other site 1105105001672 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105105001673 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105105001674 RNA binding site [nucleotide binding]; other site 1105105001675 active site 1105105001676 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105001677 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105105001678 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105105001679 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1105105001680 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 1105105001681 non-specific DNA binding site [nucleotide binding]; other site 1105105001682 salt bridge; other site 1105105001683 sequence-specific DNA binding site [nucleotide binding]; other site 1105105001684 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 1105105001685 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1105105001686 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105105001687 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105105001688 uncharacterized protein, YfiH family; Region: TIGR00726 1105105001689 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 1105105001690 catalytic residues [active] 1105105001691 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105001692 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105105001693 putative active site [active] 1105105001694 homotetrameric interface [polypeptide binding]; other site 1105105001695 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105105001696 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105105001697 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1105105001698 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1105105001699 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105105001700 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 1105105001701 GSH binding site (G-site) [chemical binding]; other site 1105105001702 C-terminal domain interface [polypeptide binding]; other site 1105105001703 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105105001704 N-terminal domain interface [polypeptide binding]; other site 1105105001705 dimer interface [polypeptide binding]; other site 1105105001706 substrate binding pocket (H-site) [chemical binding]; other site 1105105001707 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105105001708 conserved cys residue [active] 1105105001709 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 1105105001710 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1105105001711 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105105001712 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105105001713 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105105001714 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105105001715 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105105001716 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105105001717 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105105001718 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1105105001719 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105105001720 Uncharacterized conserved protein [Function unknown]; Region: COG5448 1105105001721 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1105105001722 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105105001723 Predicted membrane protein [Function unknown]; Region: COG5346 1105105001724 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1105105001725 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105105001726 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105105001727 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 1105105001728 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105105001729 E3 interaction surface; other site 1105105001730 lipoyl attachment site [posttranslational modification]; other site 1105105001731 e3 binding domain; Region: E3_binding; pfam02817 1105105001732 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105105001733 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105105001734 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1105105001735 RF-1 domain; Region: RF-1; pfam00472 1105105001736 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105105001737 DHH family; Region: DHH; pfam01368 1105105001738 DHHA1 domain; Region: DHHA1; pfam02272 1105105001739 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 1105105001740 S-adenosylmethionine binding site [chemical binding]; other site 1105105001741 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105105001742 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105105001743 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1105105001744 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 1105105001745 RNA binding site [nucleotide binding]; other site 1105105001746 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 1105105001747 multimer interface [polypeptide binding]; other site 1105105001748 Walker A motif; other site 1105105001749 ATP binding site [chemical binding]; other site 1105105001750 Walker B motif; other site 1105105001751 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1105105001752 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105105001753 tandem repeat interface [polypeptide binding]; other site 1105105001754 oligomer interface [polypeptide binding]; other site 1105105001755 active site residues [active] 1105105001756 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 1105105001757 IHF - DNA interface [nucleotide binding]; other site 1105105001758 IHF dimer interface [polypeptide binding]; other site 1105105001759 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 1105105001760 hypothetical protein; Region: PHA00670 1105105001761 hypothetical protein; Region: PHA00670 1105105001762 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105105001763 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105105001764 active site 1105105001765 HIGH motif; other site 1105105001766 dimer interface [polypeptide binding]; other site 1105105001767 KMSKS motif; other site 1105105001768 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1105105001769 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105105001770 putative acyl-acceptor binding pocket; other site 1105105001771 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 1105105001772 RelB antitoxin; Region: RelB; cl01171 1105105001773 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105105001774 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105105001775 HemY protein N-terminus; Region: HemY_N; pfam07219 1105105001776 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105105001777 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105105001778 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 1105105001779 active site 1105105001780 Lysine efflux permease [General function prediction only]; Region: COG1279 1105105001781 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105105001782 AmpG-like permease; Region: 2A0125; TIGR00901 1105105001783 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1105105001784 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 1105105001785 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105105001786 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105105001787 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105105001788 substrate binding pocket [chemical binding]; other site 1105105001789 chain length determination region; other site 1105105001790 substrate-Mg2+ binding site; other site 1105105001791 catalytic residues [active] 1105105001792 aspartate-rich region 1; other site 1105105001793 active site lid residues [active] 1105105001794 aspartate-rich region 2; other site 1105105001795 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105105001796 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105105001797 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 1105105001798 active site 1105105001799 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105105001800 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1105105001801 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105105001802 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105105001803 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105105001804 trimerization site [polypeptide binding]; other site 1105105001805 active site 1105105001806 cysteine desulfurase; Provisional; Region: PRK14012 1105105001807 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105105001808 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105105001809 catalytic residue [active] 1105105001810 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1105105001811 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105105001812 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105105001813 catalytic residue [active] 1105105001814 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105105001815 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 1105105001816 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105105001817 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105105001818 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1105105001819 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105105001820 Coenzyme A binding pocket [chemical binding]; other site 1105105001821 Predicted acetyltransferase [General function prediction only]; Region: COG5628 1105105001822 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105105001823 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 1105105001824 homotetramer interface [polypeptide binding]; other site 1105105001825 FMN binding site [chemical binding]; other site 1105105001826 homodimer contacts [polypeptide binding]; other site 1105105001827 putative active site [active] 1105105001828 putative substrate binding site [chemical binding]; other site 1105105001829 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1105105001830 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105105001831 oligomer interface [polypeptide binding]; other site 1105105001832 active site residues [active] 1105105001833 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105105001834 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 1105105001835 RNA binding site [nucleotide binding]; other site 1105105001836 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 1105105001837 RNA binding site [nucleotide binding]; other site 1105105001838 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 1105105001839 RNA binding site [nucleotide binding]; other site 1105105001840 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 1105105001841 RNA binding site [nucleotide binding]; other site 1105105001842 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 1105105001843 RNA binding site [nucleotide binding]; other site 1105105001844 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 1105105001845 RNA binding site [nucleotide binding]; other site 1105105001846 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 1105105001847 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 1105105001848 CMP-binding site; other site 1105105001849 The sites determining sugar specificity; other site 1105105001850 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 1105105001851 non-specific DNA binding site [nucleotide binding]; other site 1105105001852 salt bridge; other site 1105105001853 sequence-specific DNA binding site [nucleotide binding]; other site 1105105001854 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 1105105001855 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 1105105001856 hypothetical protein; Region: PHA00670 1105105001857 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105105001858 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105105001859 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105105001860 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 1105105001861 domain interfaces; other site 1105105001862 active site 1105105001863 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105105001864 dimer interface [polypeptide binding]; other site 1105105001865 catalytic triad [active] 1105105001866 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 1105105001867 G-X-G motif; other site 1105105001868 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 1105105001869 dimer interface [polypeptide binding]; other site 1105105001870 phosphorylation site [posttranslational modification] 1105105001871 potential frameshift: common BLAST hit: gi|15892625|ref|NP_360339.1| sodium/pantothenate symporter 1105105001872 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 1105105001873 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105105001874 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105105001875 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105105001876 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105105001877 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105105001878 Uncharacterized conserved protein [Function unknown]; Region: COG1723 1105105001879 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105105001880 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105105001881 catalytic site [active] 1105105001882 putative active site [active] 1105105001883 putative substrate binding site [chemical binding]; other site 1105105001884 Helicase and RNase D C-terminal; Region: HRDC; smart00341 1105105001885 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1105105001886 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1105105001887 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105105001888 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1105105001889 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105105001890 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105105001891 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1105105001892 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 1105105001893 S-adenosylmethionine binding site [chemical binding]; other site 1105105001894 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1105105001895 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 1105105001896 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105105001897 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105105001898 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 1105105001899 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105105001900 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 1105105001901 hypothetical protein; Validated; Region: PRK00110 1105105001902 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105105001903 Substrate binding site; other site 1105105001904 Mg++ binding site; other site 1105105001905 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 1105105001906 metal binding site [ion binding]; metal-binding site 1105105001907 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 1105105001908 Coenzyme A binding pocket [chemical binding]; other site 1105105001909 AAA domain; Region: AAA_17; pfam13207 1105105001910 AAA domain; Region: AAA_18; pfam13238 1105105001911 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105105001912 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105105001913 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 1105105001914 dimer interface [polypeptide binding]; other site 1105105001915 allosteric magnesium binding site [ion binding]; other site 1105105001916 active site 1105105001917 aspartate-rich active site metal binding site; other site 1105105001918 Schiff base residues; other site 1105105001919 primosome assembly protein PriA; Validated; Region: PRK05580 1105105001920 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 1105105001921 ATP binding site [chemical binding]; other site 1105105001922 putative Mg++ binding site [ion binding]; other site 1105105001923 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1105105001924 aromatic acid decarboxylase; Validated; Region: PRK05920 1105105001925 Flavoprotein; Region: Flavoprotein; pfam02441 1105105001926 SacI restriction endonuclease; Region: RE_SacI; pfam09566 1105105001927 replicative DNA helicase; Provisional; Region: PRK09165 1105105001928 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105105001929 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 1105105001930 Walker A motif; other site 1105105001931 ATP binding site [chemical binding]; other site 1105105001932 Walker B motif; other site 1105105001933 DNA binding loops [nucleotide binding] 1105105001934 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105105001935 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105105001936 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105105001937 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105105001938 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 1105105001939 RNA binding surface [nucleotide binding]; other site 1105105001940 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105105001941 active site 1105105001942 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105105001943 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105105001944 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105105001945 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105105001946 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105105001947 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1105105001948 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 1105105001949 S-adenosylmethionine binding site [chemical binding]; other site 1105105001950 DNA repair protein RadA; Provisional; Region: PRK11823 1105105001951 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 1105105001952 Walker A motif/ATP binding site; other site 1105105001953 ATP binding site [chemical binding]; other site 1105105001954 Walker B motif; other site 1105105001955 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1105105001956 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105105001957 Recombination protein O N terminal; Region: RecO_N; pfam11967 1105105001958 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105105001959 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 1105105001960 Glycoprotease family; Region: Peptidase_M22; pfam00814 1105105001961 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105105001962 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 1105105001963 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105105001964 G1 box; other site 1105105001965 putative GEF interaction site [polypeptide binding]; other site 1105105001966 GTP/Mg2+ binding site [chemical binding]; other site 1105105001967 Switch I region; other site 1105105001968 G2 box; other site 1105105001969 G3 box; other site 1105105001970 Switch II region; other site 1105105001971 G4 box; other site 1105105001972 G5 box; other site 1105105001973 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 1105105001974 Translation-initiation factor 2; Region: IF-2; pfam11987 1105105001975 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 1105105001976 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105105001977 NusA N-terminal domain; Region: NusA_N; pfam08529 1105105001978 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 1105105001979 RNA binding site [nucleotide binding]; other site 1105105001980 homodimer interface [polypeptide binding]; other site 1105105001981 NusA-like KH domain; Region: KH_5; pfam13184 1105105001982 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 1105105001983 G-X-X-G motif; other site 1105105001984 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105105001985 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 1105105001986 Sm and related proteins; Region: Sm_like; cl00259 1105105001987 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1105105001988 putative oligomer interface [polypeptide binding]; other site 1105105001989 putative RNA binding site [nucleotide binding]; other site 1105105001990 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 1105105001991 NAD binding pocket [chemical binding]; other site 1105105001992 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105105001993 Transcriptional regulator; Region: Rrf2; cl17282 1105105001994 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105105001995 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 1105105001996 RNA binding surface [nucleotide binding]; other site 1105105001997 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1105105001998 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105105001999 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105105002000 active site 1105105002001 HIGH motif; other site 1105105002002 dimer interface [polypeptide binding]; other site 1105105002003 KMSKS motif; other site 1105105002004 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 1105105002005 RNA binding surface [nucleotide binding]; other site 1105105002006 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105105002007 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 1105105002008 proline/glycine betaine transporter; Provisional; Region: PRK10642 1105105002009 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105105002010 potential frameshift: common BLAST hit: gi|157964695|ref|YP_001499519.1| large extracellular alpha-helical protein 1105105002011 potential frameshift: common BLAST hit: gi|350273648|ref|YP_004884961.1| large extracellular alpha-helical protein 1105105002012 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105105002013 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105105002014 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105105002015 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105105002016 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105105002017 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 1105105002018 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1105105002019 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002020 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105105002021 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1105105002022 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 1105105002023 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105105002024 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 1105105002025 active site 1105105002026 phosphorylation site [posttranslational modification] 1105105002027 intermolecular recognition site; other site 1105105002028 dimerization interface [polypeptide binding]; other site 1105105002029 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 1105105002030 Walker A motif; other site 1105105002031 ATP binding site [chemical binding]; other site 1105105002032 Walker B motif; other site 1105105002033 arginine finger; other site 1105105002034 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1105105002035 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105105002036 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105105002037 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105105002038 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105105002039 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105105002040 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105105002041 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105105002042 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105105002043 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105105002044 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105105002045 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105105002046 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1105105002047 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 1105105002048 S-adenosylmethionine binding site [chemical binding]; other site 1105105002049 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105105002050 MraZ protein; Region: MraZ; pfam02381 1105105002051 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105105002052 Na binding site [ion binding]; other site 1105105002053 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105105002054 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105105002055 GIY-YIG motif/motif A; other site 1105105002056 active site 1105105002057 catalytic site [active] 1105105002058 putative DNA binding site [nucleotide binding]; other site 1105105002059 metal binding site [ion binding]; metal-binding site 1105105002060 UvrB/uvrC motif; Region: UVR; pfam02151 1105105002061 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105105002062 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 1105105002063 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 1105105002064 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105105002065 active site 1105105002066 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 1105105002067 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105105002068 active site 1105105002069 DNA binding site [nucleotide binding] 1105105002070 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1105105002071 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1105105002072 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105105002073 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 1105105002074 DNA binding site [nucleotide binding] 1105105002075 active site 1105105002076 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 1105105002077 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105105002078 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105105002079 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1105105002080 ATP binding site [chemical binding]; other site 1105105002081 putative Mg++ binding site [ion binding]; other site 1105105002082 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1105105002083 SEC-C motif; Region: SEC-C; pfam02810 1105105002084 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 1105105002085 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1105105002086 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1105105002087 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 1105105002088 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105105002089 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 1105105002090 hinge; other site 1105105002091 active site 1105105002092 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105105002093 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 1105105002094 ATP binding site [chemical binding]; other site 1105105002095 Mg2+ binding site [ion binding]; other site 1105105002096 G-X-G motif; other site 1105105002097 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 1105105002098 anchoring element; other site 1105105002099 dimer interface [polypeptide binding]; other site 1105105002100 ATP binding site [chemical binding]; other site 1105105002101 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 1105105002102 active site 1105105002103 putative metal-binding site [ion binding]; other site 1105105002104 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105105002105 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105105002106 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 1105105002107 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 1105105002108 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105105002109 MgtE intracellular N domain; Region: MgtE_N; pfam03448 1105105002110 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 1105105002111 Divalent cation transporter; Region: MgtE; pfam01769 1105105002112 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105105002113 HD domain; Region: HD_4; pfam13328 1105105002114 Protein of unknown function (DUF969); Region: DUF969; cl01573 1105105002115 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 1105105002116 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105105002117 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1105105002118 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105105002119 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1105105002120 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105105002121 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 1105105002122 Cu(I) binding site [ion binding]; other site 1105105002123 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 1105105002124 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 1105105002125 dimer interface [polypeptide binding]; other site 1105105002126 substrate binding site [chemical binding]; other site 1105105002127 metal binding sites [ion binding]; metal-binding site 1105105002128 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002129 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1105105002130 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1105105002131 TraX protein; Region: TraX; pfam05857 1105105002132 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105105002133 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 1105105002134 ssDNA binding site; other site 1105105002135 generic binding surface II; other site 1105105002136 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 1105105002137 ATP binding site [chemical binding]; other site 1105105002138 putative Mg++ binding site [ion binding]; other site 1105105002139 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 1105105002140 nucleotide binding region [chemical binding]; other site 1105105002141 ATP-binding site [chemical binding]; other site 1105105002142 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1105105002143 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1105105002144 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 1105105002145 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105105002146 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 1105105002147 Mg++ binding site [ion binding]; other site 1105105002148 putative catalytic motif [active] 1105105002149 putative substrate binding site [chemical binding]; other site 1105105002150 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1105105002151 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105105002152 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105105002153 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105105002154 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105105002155 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105105002156 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105105002157 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105105002158 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105105002159 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1105105002160 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 1105105002161 ATP binding site [chemical binding]; other site 1105105002162 putative Mg++ binding site [ion binding]; other site 1105105002163 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 1105105002164 nucleotide binding region [chemical binding]; other site 1105105002165 ATP-binding site [chemical binding]; other site 1105105002166 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1105105002167 Uncharacterized conserved protein [Function unknown]; Region: COG2938 1105105002168 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 1105105002169 active site residue [active] 1105105002170 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105105002171 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105105002172 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 1105105002173 Walker A motif; other site 1105105002174 ATP binding site [chemical binding]; other site 1105105002175 Walker B motif; other site 1105105002176 arginine finger; other site 1105105002177 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 1105105002178 DnaA box-binding interface [nucleotide binding]; other site 1105105002179 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 1105105002180 Patatin [General function prediction only]; Region: COG3621 1105105002181 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105105002182 active site 1105105002183 nucleophile elbow; other site 1105105002184 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105105002185 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105105002186 HEPN domain; Region: HEPN; cl00824 1105105002187 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1105105002188 metal binding triad [ion binding]; metal-binding site 1105105002189 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105105002190 YchF GTPase; Region: YchF; cd01900 1105105002191 G1 box; other site 1105105002192 GTP/Mg2+ binding site [chemical binding]; other site 1105105002193 Switch I region; other site 1105105002194 G2 box; other site 1105105002195 Switch II region; other site 1105105002196 G3 box; other site 1105105002197 G4 box; other site 1105105002198 G5 box; other site 1105105002199 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 1105105002200 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105105002201 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 1105105002202 putative active site [active] 1105105002203 catalytic residue [active] 1105105002204 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105105002205 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105105002206 5S rRNA interface [nucleotide binding]; other site 1105105002207 CTC domain interface [polypeptide binding]; other site 1105105002208 L16 interface [polypeptide binding]; other site 1105105002209 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105105002210 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 1105105002211 FeS/SAM binding site; other site 1105105002212 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1105105002213 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105105002214 23S rRNA binding site [nucleotide binding]; other site 1105105002215 L21 binding site [polypeptide binding]; other site 1105105002216 L13 binding site [polypeptide binding]; other site 1105105002217 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1105105002218 ribonuclease P; Reviewed; Region: rnpA; PRK01492 1105105002219 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105105002220 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105105002221 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 1105105002222 Cl binding site [ion binding]; other site 1105105002223 oligomer interface [polypeptide binding]; other site 1105105002224 potential frameshift: common BLAST hit: gi|157828799|ref|YP_001495041.1| acetyltransferase 1105105002225 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 1105105002226 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105105002227 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 1105105002228 dimerization interface [polypeptide binding]; other site 1105105002229 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 1105105002230 dimer interface [polypeptide binding]; other site 1105105002231 phosphorylation site [posttranslational modification] 1105105002232 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 1105105002233 ATP binding site [chemical binding]; other site 1105105002234 Mg2+ binding site [ion binding]; other site 1105105002235 G-X-G motif; other site 1105105002236 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 1105105002237 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105105002238 COQ9; Region: COQ9; pfam08511 1105105002239 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105105002240 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105105002241 HIGH motif; other site 1105105002242 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105105002243 active site 1105105002244 KMSKS motif; other site 1105105002245 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105105002246 tRNA binding surface [nucleotide binding]; other site 1105105002247 anticodon binding site; other site 1105105002248 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 1105105002249 TPR motif; other site 1105105002250 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105105002251 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105105002252 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1105105002253 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1105105002254 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 1105105002255 carboxyltransferase (CT) interaction site; other site 1105105002256 biotinylation site [posttranslational modification]; other site 1105105002257 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1105105002258 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1105105002259 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1105105002260 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105105002261 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 1105105002262 putative substrate translocation pore; other site 1105105002263 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105105002264 putative acyl-acceptor binding pocket; other site 1105105002265 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 1105105002266 acyl-activating enzyme (AAE) consensus motif; other site 1105105002267 putative AMP binding site [chemical binding]; other site 1105105002268 TfoX N-terminal domain; Region: TfoX_N; pfam04993 1105105002269 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1105105002270 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 1105105002271 ABC-ATPase subunit interface; other site 1105105002272 dimer interface [polypeptide binding]; other site 1105105002273 putative PBP binding regions; other site 1105105002274 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105105002275 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002276 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 1105105002277 S-adenosylmethionine binding site [chemical binding]; other site 1105105002278 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105105002279 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105105002280 HIGH motif; other site 1105105002281 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105105002282 active site 1105105002283 KMSKS motif; other site 1105105002284 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002285 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 1105105002286 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105105002287 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 1105105002288 ring oligomerisation interface [polypeptide binding]; other site 1105105002289 ATP/Mg binding site [chemical binding]; other site 1105105002290 stacking interactions; other site 1105105002291 hinge regions; other site 1105105002292 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 1105105002293 oligomerisation interface [polypeptide binding]; other site 1105105002294 mobile loop; other site 1105105002295 roof hairpin; other site 1105105002296 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105105002297 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 1105105002298 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105105002299 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105105002300 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105105002301 hexamer interface [polypeptide binding]; other site 1105105002302 active site 1105105002303 GrpE; Region: GrpE; pfam01025 1105105002304 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 1105105002305 dimer interface [polypeptide binding]; other site 1105105002306 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105105002307 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1105105002308 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105105002309 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 1105105002310 hypothetical protein; Validated; Region: PRK06620 1105105002311 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105105002312 potential frameshift: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 1105105002313 HD domain; Region: HD_4; pfam13328 1105105002314 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1105105002315 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 1105105002316 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105105002317 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105105002318 alphaNTD - beta interaction site [polypeptide binding]; other site 1105105002319 alphaNTD homodimer interface [polypeptide binding]; other site 1105105002320 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105105002321 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1105105002322 30S ribosomal protein S11; Validated; Region: PRK05309 1105105002323 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105105002324 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1105105002325 adenylate kinase; Reviewed; Region: adk; PRK00279 1105105002326 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 1105105002327 AMP-binding site [chemical binding]; other site 1105105002328 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105105002329 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105105002330 SecY translocase; Region: SecY; pfam00344 1105105002331 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1105105002332 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 1105105002333 23S rRNA binding site [nucleotide binding]; other site 1105105002334 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105105002335 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105105002336 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105105002337 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 1105105002338 5S rRNA interface [nucleotide binding]; other site 1105105002339 23S rRNA interface [nucleotide binding]; other site 1105105002340 L5 interface [polypeptide binding]; other site 1105105002341 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105105002342 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105105002343 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105105002344 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1105105002345 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1105105002346 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105105002347 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105105002348 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105105002349 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105105002350 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1105105002351 RNA binding site [nucleotide binding]; other site 1105105002352 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1105105002353 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1105105002354 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 1105105002355 L23 interface [polypeptide binding]; other site 1105105002356 trigger factor interaction site; other site 1105105002357 23S rRNA interface [nucleotide binding]; other site 1105105002358 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 1105105002359 23S rRNA interface [nucleotide binding]; other site 1105105002360 5S rRNA interface [nucleotide binding]; other site 1105105002361 putative antibiotic binding site [chemical binding]; other site 1105105002362 L25 interface [polypeptide binding]; other site 1105105002363 L27 interface [polypeptide binding]; other site 1105105002364 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105105002365 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 1105105002366 G-X-X-G motif; other site 1105105002367 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105105002368 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 1105105002369 putative translocon binding site; other site 1105105002370 protein-rRNA interface [nucleotide binding]; other site 1105105002371 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1105105002372 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105105002373 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105105002374 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105105002375 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1105105002376 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1105105002377 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1105105002378 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1105105002379 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002380 elongation factor Tu; Reviewed; Region: PRK00049 1105105002381 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105105002382 G1 box; other site 1105105002383 GEF interaction site [polypeptide binding]; other site 1105105002384 GTP/Mg2+ binding site [chemical binding]; other site 1105105002385 Switch I region; other site 1105105002386 G2 box; other site 1105105002387 G3 box; other site 1105105002388 Switch II region; other site 1105105002389 G4 box; other site 1105105002390 G5 box; other site 1105105002391 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 1105105002392 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 1105105002393 Antibiotic Binding Site [chemical binding]; other site 1105105002394 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105105002395 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1105105002396 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1105105002397 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105105002398 Class II fumarases; Region: Fumarase_classII; cd01362 1105105002399 active site 1105105002400 tetramer interface [polypeptide binding]; other site 1105105002401 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105105002402 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105105002403 putative active site [active] 1105105002404 homotetrameric interface [polypeptide binding]; other site 1105105002405 cell division protein FtsZ; Validated; Region: PRK09330 1105105002406 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 1105105002407 nucleotide binding site [chemical binding]; other site 1105105002408 SulA interaction site; other site 1105105002409 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 1105105002410 secondary substrate binding site; other site 1105105002411 primary substrate binding site; other site 1105105002412 inhibition loop; other site 1105105002413 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 1105105002414 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1105105002415 muropeptide transporter; Validated; Region: ampG; cl17669 1105105002416 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 1105105002417 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105105002418 ATP binding site [chemical binding]; other site 1105105002419 Mg++ binding site [ion binding]; other site 1105105002420 motif III; other site 1105105002421 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 1105105002422 nucleotide binding region [chemical binding]; other site 1105105002423 ATP-binding site [chemical binding]; other site 1105105002424 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 1105105002425 DNA-binding site [nucleotide binding]; DNA binding site 1105105002426 RNA-binding motif; other site 1105105002427 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1105105002428 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 1105105002429 S-adenosylmethionine binding site [chemical binding]; other site 1105105002430 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105105002431 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105105002432 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105105002433 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 1105105002434 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 1105105002435 generic binding surface II; other site 1105105002436 generic binding surface I; other site 1105105002437 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105105002438 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 1105105002439 putative catalytic site [active] 1105105002440 putative phosphate binding site [ion binding]; other site 1105105002441 active site 1105105002442 metal binding site A [ion binding]; metal-binding site 1105105002443 DNA binding site [nucleotide binding] 1105105002444 putative AP binding site [nucleotide binding]; other site 1105105002445 putative metal binding site B [ion binding]; other site 1105105002446 Uncharacterized conserved protein [Function unknown]; Region: COG4095 1105105002447 GTP-binding protein Der; Reviewed; Region: PRK00093 1105105002448 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105105002449 G1 box; other site 1105105002450 GTP/Mg2+ binding site [chemical binding]; other site 1105105002451 Switch I region; other site 1105105002452 G2 box; other site 1105105002453 Switch II region; other site 1105105002454 G3 box; other site 1105105002455 G4 box; other site 1105105002456 G5 box; other site 1105105002457 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105105002458 G1 box; other site 1105105002459 GTP/Mg2+ binding site [chemical binding]; other site 1105105002460 Switch I region; other site 1105105002461 G2 box; other site 1105105002462 G3 box; other site 1105105002463 Switch II region; other site 1105105002464 G4 box; other site 1105105002465 G5 box; other site 1105105002466 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105105002467 AAA domain; Region: AAA_14; pfam13173 1105105002468 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 1105105002469 ABC1 family; Region: ABC1; pfam03109 1105105002470 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 1105105002471 active site 1105105002472 ATP binding site [chemical binding]; other site 1105105002473 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105105002474 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 1105105002475 S-adenosylmethionine binding site [chemical binding]; other site 1105105002476 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105105002477 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105105002478 DNA binding site [nucleotide binding] 1105105002479 catalytic residue [active] 1105105002480 H2TH interface [polypeptide binding]; other site 1105105002481 putative catalytic residues [active] 1105105002482 turnover-facilitating residue; other site 1105105002483 intercalation triad [nucleotide binding]; other site 1105105002484 8OG recognition residue [nucleotide binding]; other site 1105105002485 putative reading head residues; other site 1105105002486 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105105002487 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105105002488 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002489 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105105002490 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 1105105002491 active site 1105105002492 potential frameshift: common BLAST hit: gi|15892963|ref|NP_360677.1| mannose-1-phosphate guanylyltransferase 1105105002493 potential frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 1105105002494 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105105002495 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105105002496 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105105002497 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105105002498 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 1105105002499 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105105002500 active site 1105105002501 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105105002502 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105105002503 HIGH motif; other site 1105105002504 active site 1105105002505 KMSKS motif; other site 1105105002506 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105105002507 tRNA binding surface [nucleotide binding]; other site 1105105002508 anticodon binding site; other site 1105105002509 thymidylate kinase; Validated; Region: tmk; PRK00698 1105105002510 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 1105105002511 TMP-binding site; other site 1105105002512 ATP-binding site [chemical binding]; other site 1105105002513 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105105002514 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 1105105002515 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105105002516 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105105002517 potential frameshift: common BLAST hit: gi|67458622|ref|YP_246246.1| transposase 1105105002518 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105105002519 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105105002520 active site 1105105002521 HIGH motif; other site 1105105002522 nucleotide binding site [chemical binding]; other site 1105105002523 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105105002524 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105105002525 active site 1105105002526 KMSKS motif; other site 1105105002527 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105105002528 tRNA binding surface [nucleotide binding]; other site 1105105002529 anticodon binding site; other site 1105105002530 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105105002531 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105105002532 potential frameshift: common BLAST hit: gi|157804076|ref|YP_001492625.1| ATPase 1105105002533 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 1105105002534 RmuC family; Region: RmuC; pfam02646 1105105002535 potential frameshift: common BLAST hit: gi|341584242|ref|YP_004764733.1| Alpha-(1,3)-fucosyltransferase 1105105002536 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 1105105002537 DoxX-like family; Region: DoxX_3; pfam13781 1105105002538 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105105002539 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1105105002540 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 1105105002541 Walker A motif; other site 1105105002542 ATP binding site [chemical binding]; other site 1105105002543 Walker B motif; other site 1105105002544 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105105002545 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105105002546 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105105002547 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 1105105002548 Ligand Binding Site [chemical binding]; other site 1105105002549 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 1105105002550 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 1105105002551 HicB family; Region: HicB; pfam05534 1105105002552 YcfA-like protein; Region: YcfA; cl00752 1105105002553 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105105002554 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105105002555 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105002556 Walker A/P-loop; other site 1105105002557 ATP binding site [chemical binding]; other site 1105105002558 Q-loop/lid; other site 1105105002559 ABC transporter signature motif; other site 1105105002560 Walker B; other site 1105105002561 D-loop; other site 1105105002562 H-loop/switch region; other site 1105105002563 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105105002564 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105105002565 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 1105105002566 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105105002567 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105105002568 FtsX-like permease family; Region: FtsX; pfam02687 1105105002569 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105105002570 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1105105002571 Walker A/P-loop; other site 1105105002572 ATP binding site [chemical binding]; other site 1105105002573 Q-loop/lid; other site 1105105002574 ABC transporter signature motif; other site 1105105002575 Walker B; other site 1105105002576 D-loop; other site 1105105002577 H-loop/switch region; other site 1105105002578 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105105002579 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105105002580 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 1105105002581 Transporter associated domain; Region: CorC_HlyC; smart01091 1105105002582 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 1105105002583 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 1105105002584 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105105002585 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105105002586 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105105002587 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105105002588 synthetase active site [active] 1105105002589 NTP binding site [chemical binding]; other site 1105105002590 metal binding site [ion binding]; metal-binding site 1105105002591 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1105105002592 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105105002593 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1105105002594 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105105002595 DNA binding residues [nucleotide binding] 1105105002596 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 1105105002597 IHF dimer interface [polypeptide binding]; other site 1105105002598 IHF - DNA interface [nucleotide binding]; other site 1105105002599 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105105002600 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 1105105002601 catalytic triad [active] 1105105002602 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105105002603 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105105002604 putative acyl-acceptor binding pocket; other site 1105105002605 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1105105002606 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1105105002607 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1105105002608 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105105002609 Protein of unknown function (DUF519); Region: DUF519; pfam04378 1105105002610 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105105002611 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 1105105002612 nucleotide binding pocket [chemical binding]; other site 1105105002613 K-X-D-G motif; other site 1105105002614 catalytic site [active] 1105105002615 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105105002616 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105105002617 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 1105105002618 Dimer interface [polypeptide binding]; other site 1105105002619 BRCT sequence motif; other site 1105105002620 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1105105002621 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105105002622 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105105002623 HD domain; Region: HD_4; pfam13328 1105105002624 potential frameshift: common BLAST hit: gi|67458578|ref|YP_246202.1| proline/betaine transporter 1105105002625 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1105105002626 mce related protein; Region: MCE; pfam02470 1105105002627 hypothetical protein; Provisional; Region: PRK06630 1105105002628 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105105002629 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105105002630 active site 1105105002631 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 1105105002632 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 1105105002633 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105105002634 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 1105105002635 CoA-binding site [chemical binding]; other site 1105105002636 ATP-binding [chemical binding]; other site 1105105002637 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105105002638 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 1105105002639 active site 1105105002640 catalytic site [active] 1105105002641 substrate binding site [chemical binding]; other site 1105105002642 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 1105105002643 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105105002644 Part of AAA domain; Region: AAA_19; pfam13245 1105105002645 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105105002646 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 1105105002647 Family description; Region: UvrD_C_2; pfam13538 1105105002648 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1105105002649 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105105002650 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105105002651 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105105002652 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105105002653 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105105002654 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105105002655 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 1105105002656 nudix motif; other site 1105105002657 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1105105002658 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 1105105002659 Transporter associated domain; Region: CorC_HlyC; smart01091 1105105002660 metal-binding heat shock protein; Provisional; Region: PRK00016 1105105002661 PemK-like protein; Region: PemK; cl00995 1105105002662 lipoyl synthase; Provisional; Region: PRK05481 1105105002663 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 1105105002664 FeS/SAM binding site; other site 1105105002665 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105105002666 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 1105105002667 dimer interface [polypeptide binding]; other site 1105105002668 active site 1105105002669 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105105002670 folate binding site [chemical binding]; other site 1105105002671 Predicted esterase [General function prediction only]; Region: COG0400 1105105002672 putative hydrolase; Provisional; Region: PRK11460 1105105002673 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 1105105002674 putative GSH binding site [chemical binding]; other site 1105105002675 catalytic residues [active] 1105105002676 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105105002677 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105105002678 minor groove reading motif; other site 1105105002679 helix-hairpin-helix signature motif; other site 1105105002680 substrate binding pocket [chemical binding]; other site 1105105002681 active site 1105105002682 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1105105002683 Predicted small secreted protein [Function unknown]; Region: COG5510 1105105002684 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105002685 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105002686 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105105002687 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1105105002688 putative SAM binding site [chemical binding]; other site 1105105002689 putative homodimer interface [polypeptide binding]; other site 1105105002690 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105105002691 putative ligand binding site [chemical binding]; other site 1105105002692 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 1105105002693 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105105002694 tetramer interfaces [polypeptide binding]; other site 1105105002695 binuclear metal-binding site [ion binding]; other site 1105105002696 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 1105105002697 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1105105002698 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1105105002699 aspartate kinase; Reviewed; Region: PRK06635 1105105002700 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 1105105002701 putative nucleotide binding site [chemical binding]; other site 1105105002702 putative catalytic residues [active] 1105105002703 putative Mg ion binding site [ion binding]; other site 1105105002704 putative aspartate binding site [chemical binding]; other site 1105105002705 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 1105105002706 putative allosteric regulatory residue; other site 1105105002707 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 1105105002708 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105105002709 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1105105002710 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1105105002711 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105105002712 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 1105105002713 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105105002714 putative substrate translocation pore; other site 1105105002715 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 1105105002716 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002717 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 1105105002718 Helix-turn-helix domain; Region: HTH_25; pfam13413 1105105002719 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105105002720 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 1105105002721 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 1105105002722 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105105002723 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105105002724 G1 box; other site 1105105002725 GTP/Mg2+ binding site [chemical binding]; other site 1105105002726 Switch I region; other site 1105105002727 G2 box; other site 1105105002728 Switch II region; other site 1105105002729 G3 box; other site 1105105002730 G4 box; other site 1105105002731 G5 box; other site 1105105002732 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105105002733 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105105002734 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 1105105002735 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 1105105002736 hexamer interface [polypeptide binding]; other site 1105105002737 Walker A motif; other site 1105105002738 ATP binding site [chemical binding]; other site 1105105002739 Walker B motif; other site 1105105002740 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105105002741 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105105002742 NAD(P) binding site [chemical binding]; other site 1105105002743 active site 1105105002744 acyl carrier protein; Provisional; Region: acpP; PRK00982 1105105002745 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105105002746 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 1105105002747 dimer interface [polypeptide binding]; other site 1105105002748 active site 1105105002749 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105105002750 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105105002751 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105105002752 endonuclease subunit; Provisional; Region: 46; PHA02562 1105105002753 AAA domain; Region: AAA_14; pfam13173 1105105002754 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105105002755 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002756 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105105002757 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 1105105002758 catalytic site [active] 1105105002759 G-X2-G-X-G-K; other site 1105105002760 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 1105105002761 sequence-specific DNA binding site [nucleotide binding]; other site 1105105002762 salt bridge; other site 1105105002763 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 1105105002764 rod shape-determining protein MreC; Region: MreC; pfam04085 1105105002765 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105105002766 MreB and similar proteins; Region: MreB_like; cd10225 1105105002767 nucleotide binding site [chemical binding]; other site 1105105002768 Mg binding site [ion binding]; other site 1105105002769 putative protofilament interaction site [polypeptide binding]; other site 1105105002770 RodZ interaction site [polypeptide binding]; other site 1105105002771 Predicted permeases [General function prediction only]; Region: COG0795 1105105002772 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105105002773 putative outer membrane lipoprotein; Provisional; Region: PRK09967 1105105002774 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105105002775 ligand binding site [chemical binding]; other site 1105105002776 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105105002777 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105105002778 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 1105105002779 dimer interface [polypeptide binding]; other site 1105105002780 active site 1105105002781 CoA binding pocket [chemical binding]; other site 1105105002782 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 1105105002783 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 1105105002784 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 1105105002785 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105105002786 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1105105002787 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 1105105002788 P loop; other site 1105105002789 GTP binding site [chemical binding]; other site 1105105002790 DNA polymerase I; Provisional; Region: PRK05755 1105105002791 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105105002792 active site 1105105002793 metal binding site 1 [ion binding]; metal-binding site 1105105002794 putative 5' ssDNA interaction site; other site 1105105002795 metal binding site 3; metal-binding site 1105105002796 metal binding site 2 [ion binding]; metal-binding site 1105105002797 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105105002798 putative DNA binding site [nucleotide binding]; other site 1105105002799 putative metal binding site [ion binding]; other site 1105105002800 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105105002801 active site 1105105002802 substrate binding site [chemical binding]; other site 1105105002803 catalytic site [active] 1105105002804 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105105002805 active site 1105105002806 DNA binding site [nucleotide binding] 1105105002807 catalytic site [active] 1105105002808 potential frameshift: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 1105105002809 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1105105002810 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105105002811 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105105002812 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 1105105002813 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105105002814 putative active site [active] 1105105002815 putative PHP Thumb interface [polypeptide binding]; other site 1105105002816 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 1105105002817 generic binding surface I; other site 1105105002818 generic binding surface II; other site 1105105002819 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105105002820 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105105002821 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 1105105002822 Protein of unknown function; Region: DUF3971; pfam13116 1105105002823 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105105002824 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 1105105002825 putative substrate translocation pore; other site 1105105002826 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1105105002827 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105105002828 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105105002829 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 1105105002830 dimer interface [polypeptide binding]; other site 1105105002831 active site 1105105002832 motif 1; other site 1105105002833 motif 2; other site 1105105002834 motif 3; other site 1105105002835 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105105002836 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105105002837 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105105002838 Integral membrane protein TerC family; Region: TerC; cl10468 1105105002839 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105105002840 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105105002841 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 1105105002842 S-adenosylmethionine binding site [chemical binding]; other site 1105105002843 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105105002844 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105105002845 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 1105105002846 salt bridge; other site 1105105002847 non-specific DNA binding site [nucleotide binding]; other site 1105105002848 sequence-specific DNA binding site [nucleotide binding]; other site 1105105002849 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105105002850 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1105105002851 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1105105002852 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105105002853 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105105002854 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105105002855 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105105002856 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105105002857 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105105002858 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105002859 Walker A/P-loop; other site 1105105002860 ATP binding site [chemical binding]; other site 1105105002861 Q-loop/lid; other site 1105105002862 ABC transporter signature motif; other site 1105105002863 Walker B; other site 1105105002864 D-loop; other site 1105105002865 H-loop/switch region; other site 1105105002866 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105105002867 4Fe-4S binding domain; Region: Fer4; cl02805 1105105002868 4Fe-4S binding domain; Region: Fer4; pfam00037 1105105002869 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1105105002870 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1105105002871 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105105002872 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 1105105002873 catalytic loop [active] 1105105002874 iron binding site [ion binding]; other site 1105105002875 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1105105002876 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 1105105002877 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105105002878 Predicted membrane protein [Function unknown]; Region: COG3671 1105105002879 aconitate hydratase; Validated; Region: PRK09277 1105105002880 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105105002881 substrate binding site [chemical binding]; other site 1105105002882 ligand binding site [chemical binding]; other site 1105105002883 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 1105105002884 substrate binding site [chemical binding]; other site 1105105002885 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105105002886 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1105105002887 gamma subunit interface [polypeptide binding]; other site 1105105002888 epsilon subunit interface [polypeptide binding]; other site 1105105002889 LBP interface [polypeptide binding]; other site 1105105002890 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105105002891 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105105002892 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 1105105002893 alpha subunit interaction interface [polypeptide binding]; other site 1105105002894 Walker A motif; other site 1105105002895 ATP binding site [chemical binding]; other site 1105105002896 Walker B motif; other site 1105105002897 inhibitor binding site; inhibition site 1105105002898 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105105002899 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1105105002900 core domain interface [polypeptide binding]; other site 1105105002901 delta subunit interface [polypeptide binding]; other site 1105105002902 epsilon subunit interface [polypeptide binding]; other site 1105105002903 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105105002904 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105105002905 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 1105105002906 beta subunit interaction interface [polypeptide binding]; other site 1105105002907 Walker A motif; other site 1105105002908 ATP binding site [chemical binding]; other site 1105105002909 Walker B motif; other site 1105105002910 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105105002911 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 1105105002912 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105105002913 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105105002914 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1105105002915 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105105002916 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105105002917 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1105105002918 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1105105002919 dimerization interface [polypeptide binding]; other site 1105105002920 DPS ferroxidase diiron center [ion binding]; other site 1105105002921 ion pore; other site 1105105002922 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105105002923 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 1105105002924 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105105002925 Transglycosylase; Region: Transgly; pfam00912 1105105002926 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105105002927 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105105002928 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105105002929 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 1105105002930 FeS/SAM binding site; other site 1105105002931 TRAM domain; Region: TRAM; pfam01938 1105105002932 HEPN domain; Region: HEPN; cl00824 1105105002933 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105105002934 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105002935 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105105002936 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 1105105002937 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105105002938 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105105002939 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105105002940 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1105105002941 TrkA-N domain; Region: TrkA_N; pfam02254 1105105002942 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 1105105002943 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105105002944 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105105002945 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105105002946 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105105002947 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 1105105002948 rRNA binding site [nucleotide binding]; other site 1105105002949 predicted 30S ribosome binding site; other site 1105105002950 Maf-like protein; Region: Maf; pfam02545 1105105002951 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 1105105002952 active site 1105105002953 dimer interface [polypeptide binding]; other site 1105105002954 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 1105105002955 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105105002956 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 1105105002957 active site 1105105002958 DNA binding site [nucleotide binding] 1105105002959 Int/Topo IB signature motif; other site 1105105002960 Phasin protein; Region: Phasin_2; cl11491 1105105002961 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105105002962 PLD-like domain; Region: PLDc_2; pfam13091 1105105002963 putative active site [active] 1105105002964 catalytic site [active] 1105105002965 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105105002966 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105105002967 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 1105105002968 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1105105002969 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1105105002970 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105105002971 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105105002972 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105105002973 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1105105002974 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1105105002975 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105105002976 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 1105105002977 active site 1105105002978 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105105002979 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105105002980 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105105002981 MPN+ (JAMM) motif; other site 1105105002982 Zinc-binding site [ion binding]; other site 1105105002983 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105105002984 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 1105105002985 Mg++ binding site [ion binding]; other site 1105105002986 putative catalytic motif [active] 1105105002987 putative substrate binding site [chemical binding]; other site 1105105002988 Protein of unknown function (DUF721); Region: DUF721; pfam05258 1105105002989 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105105002990 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105105002991 Ferredoxin [Energy production and conversion]; Region: COG1146 1105105002992 4Fe-4S binding domain; Region: Fer4; cl02805 1105105002993 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105105002994 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 1105105002995 nucleoside/Zn binding site; other site 1105105002996 dimer interface [polypeptide binding]; other site 1105105002997 catalytic motif [active] 1105105002998 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105105002999 Cation efflux family; Region: Cation_efflux; cl00316 1105105003000 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105105003001 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105105003002 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105105003003 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 1105105003004 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105105003005 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105105003006 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105105003007 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1105105003008 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105105003009 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 1105105003010 dimer interface [polypeptide binding]; other site 1105105003011 ssDNA binding site [nucleotide binding]; other site 1105105003012 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105105003013 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 1105105003014 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 1105105003015 hypothetical protein; Reviewed; Region: PRK01530 1105105003016 heat shock protein 90; Provisional; Region: PRK05218 1105105003017 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 1105105003018 ATP binding site [chemical binding]; other site 1105105003019 Mg2+ binding site [ion binding]; other site 1105105003020 G-X-G motif; other site 1105105003021 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1105105003022 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 1105105003023 substrate-cofactor binding pocket; other site 1105105003024 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105105003025 catalytic residue [active] 1105105003026 trigger factor; Provisional; Region: tig; PRK01490 1105105003027 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105105003028 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105105003029 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105105003030 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105105003031 Obg GTPase; Region: Obg; cd01898 1105105003032 G1 box; other site 1105105003033 GTP/Mg2+ binding site [chemical binding]; other site 1105105003034 Switch I region; other site 1105105003035 G2 box; other site 1105105003036 G3 box; other site 1105105003037 Switch II region; other site 1105105003038 G4 box; other site 1105105003039 G5 box; other site 1105105003040 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 1105105003041 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1105105003042 dimer interface [polypeptide binding]; other site 1105105003043 active site 1105105003044 citrylCoA binding site [chemical binding]; other site 1105105003045 NADH binding [chemical binding]; other site 1105105003046 cationic pore residues; other site 1105105003047 oxalacetate/citrate binding site [chemical binding]; other site 1105105003048 coenzyme A binding site [chemical binding]; other site 1105105003049 catalytic triad [active] 1105105003050 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 1105105003051 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105105003052 Fe-S cluster binding site [ion binding]; other site 1105105003053 active site 1105105003054 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105105003055 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 1105105003056 RNA binding surface [nucleotide binding]; other site 1105105003057 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105105003058 active site 1105105003059 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105105003060 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 1105105003061 S-adenosylmethionine binding site [chemical binding]; other site 1105105003062 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 1105105003063 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1105105003064 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105105003065 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 1105105003066 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105105003067 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 1105105003068 motif 1; other site 1105105003069 dimer interface [polypeptide binding]; other site 1105105003070 active site 1105105003071 motif 2; other site 1105105003072 motif 3; other site 1105105003073 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 1105105003074 oligomeric interface; other site 1105105003075 putative active site [active] 1105105003076 homodimer interface [polypeptide binding]; other site 1105105003077 prevent-host-death family protein; Region: phd_fam; TIGR01552 1105105003078 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 1105105003079 potential frameshift: common BLAST hit: gi|350273988|ref|YP_004885301.1| proline/betaine transporter 1105105003080 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105105003081 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 1105105003082 motif 1; other site 1105105003083 active site 1105105003084 motif 2; other site 1105105003085 motif 3; other site 1105105003086 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105105003087 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105105003088 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105105003089 dimerization interface 3.5A [polypeptide binding]; other site 1105105003090 active site 1105105003091 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105105003092 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105105003093 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105105003094 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105105003095 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105105003096 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 1105105003097 DNA binding residues [nucleotide binding] 1105105003098 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105105003099 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1105105003100 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105105003101 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 1105105003102 active site 1105105003103 metal binding site [ion binding]; metal-binding site 1105105003104 interdomain interaction site; other site 1105105003105 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 1105105003106 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105105003107 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105105003108 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105105003109 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105105003110 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105105003111 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 1105105003112 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105105003113 ligand binding site [chemical binding]; other site 1105105003114 homodimer interface [polypeptide binding]; other site 1105105003115 NAD(P) binding site [chemical binding]; other site 1105105003116 trimer interface B [polypeptide binding]; other site 1105105003117 trimer interface A [polypeptide binding]; other site 1105105003118 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105105003119 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 1105105003120 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 1105105003121 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 1105105003122 Walker A motif; other site 1105105003123 ATP binding site [chemical binding]; other site 1105105003124 Walker B motif; other site 1105105003125 arginine finger; other site 1105105003126 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1105105003127 hypothetical protein; Validated; Region: PRK00153 1105105003128 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105105003129 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105105003130 catalytic motif [active] 1105105003131 Catalytic residue [active] 1105105003132 Beta-lactamase; Region: Beta-lactamase; cl17358 1105105003133 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 1105105003134 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105105003135 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105105003136 Walker A/P-loop; other site 1105105003137 ATP binding site [chemical binding]; other site 1105105003138 Q-loop/lid; other site 1105105003139 ABC transporter signature motif; other site 1105105003140 Walker B; other site 1105105003141 D-loop; other site 1105105003142 H-loop/switch region; other site 1105105003143 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1105105003144 putative hydrolase; Provisional; Region: PRK02113 1105105003145 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 1105105003146 active site 1105105003147 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 1105105003148 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 1105105003149 Predicted permeases [General function prediction only]; Region: COG0795 1105105003150 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105105003151 DNA polymerase III subunit chi; Provisional; Region: PRK06646 1105105003152 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105105003153 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105105003154 metal binding site [ion binding]; metal-binding site 1105105003155 dimer interface [polypeptide binding]; other site 1105105003156 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1105105003157 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1105105003158 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 1105105003159 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 1105105003160 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1105105003161 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 1105105003162 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1105105003163 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 1105105003164 putative active site [active] 1105105003165 lipoate-protein ligase B; Provisional; Region: PRK14347 1105105003166 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105105003167 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 1105105003168 amidase catalytic site [active] 1105105003169 Zn binding residues [ion binding]; other site 1105105003170 substrate binding site [chemical binding]; other site 1105105003171 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105105003172 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1105105003173 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 1105105003174 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105105003175 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 1105105003176 ATP binding site [chemical binding]; other site 1105105003177 Mg2+ binding site [ion binding]; other site 1105105003178 G-X-G motif; other site 1105105003179 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 1105105003180 ATP binding site [chemical binding]; other site 1105105003181 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1105105003182 Zinc-finger domain; Region: zf-CHCC; cl01821 1105105003183 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105105003184 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105105003185 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 1105105003186 TPR motif; other site 1105105003187 TPR repeat; Region: TPR_11; pfam13414 1105105003188 binding surface 1105105003189 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 1105105003190 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105105003191 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 1105105003192 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 1105105003193 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 1105105003194 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105105003195 TIGR00701 family protein; Region: TIGR00701 1105105003196 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105105003197 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 1105105003198 C-terminal domain interface [polypeptide binding]; other site 1105105003199 active site 1105105003200 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 1105105003201 active site 1105105003202 N-terminal domain interface [polypeptide binding]; other site 1105105003203 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 1105105003204 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 1105105003205 substrate binding site [chemical binding]; other site 1105105003206 active site