-- dump date 20140620_034905 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105100000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 1105100000002 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 1105100000003 catalytic residues [active] 1105100000004 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105100000005 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 1105100000006 Walker A/P-loop; other site 1105100000007 ATP binding site [chemical binding]; other site 1105100000008 Q-loop/lid; other site 1105100000009 ABC transporter signature motif; other site 1105100000010 Walker B; other site 1105100000011 D-loop; other site 1105100000012 H-loop/switch region; other site 1105100000013 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 1105100000014 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1105100000015 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105100000016 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105100000017 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 1105100000018 FAD binding pocket [chemical binding]; other site 1105100000019 FAD binding motif [chemical binding]; other site 1105100000020 phosphate binding motif [ion binding]; other site 1105100000021 beta-alpha-beta structure motif; other site 1105100000022 NAD binding pocket [chemical binding]; other site 1105100000023 Iron coordination center [ion binding]; other site 1105100000024 Growth inhibitor [Signal transduction mechanisms]; Region: MazF; COG2337 1105100000025 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 1105100000026 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 1105100000027 active site 1105100000028 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 1105100000029 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105100000030 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105100000031 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 1105100000032 trimer interface [polypeptide binding]; other site 1105100000033 active site 1105100000034 UDP-GlcNAc binding site [chemical binding]; other site 1105100000035 lipid binding site [chemical binding]; lipid-binding site 1105100000036 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105100000037 active site 1105100000038 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105100000039 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 1105100000040 glucose-6-phosphate isomerase; Provisional; Region: PTZ00430 1105100000041 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1105100000042 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 1105100000043 FMN binding site [chemical binding]; other site 1105100000044 active site 1105100000045 catalytic residues [active] 1105100000046 substrate binding site [chemical binding]; other site 1105100000047 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 1105100000048 NodB motif; other site 1105100000049 putative active site [active] 1105100000050 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1105100000051 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 1105100000052 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 1105100000053 intersubunit interface [polypeptide binding]; other site 1105100000054 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105100000055 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105100000056 active site 1105100000057 NTP binding site [chemical binding]; other site 1105100000058 metal binding triad [ion binding]; metal-binding site 1105100000059 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105100000060 Competence protein; Region: Competence; pfam03772 1105100000061 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105100000062 AAA domain; Region: AAA_22; pfam13401 1105100000063 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105100000064 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105100000065 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 1105100000066 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 1105100000067 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105100000068 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 1105100000069 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1105100000070 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 1105100000071 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 1105100000072 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105100000073 Thioredoxin; Region: Thioredoxin_4; pfam13462 1105100000074 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 1105100000075 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105100000076 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 1105100000077 S-adenosylmethionine binding site [chemical binding]; other site 1105100000078 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105100000079 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105100000080 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 1105100000081 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000082 Walker A/P-loop; other site 1105100000083 ATP binding site [chemical binding]; other site 1105100000084 Q-loop/lid; other site 1105100000085 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000086 ABC transporter signature motif; other site 1105100000087 Walker B; other site 1105100000088 D-loop; other site 1105100000089 H-loop/switch region; other site 1105100000090 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 1105100000091 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 1105100000092 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 1105100000093 folate binding site [chemical binding]; other site 1105100000094 NADP+ binding site [chemical binding]; other site 1105100000095 Dihydropteroate synthase and related enzymes [Coenzyme metabolism]; Region: FolP; COG0294 1105100000096 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 1105100000097 inhibitor binding site; inhibition site 1105100000098 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 1105100000099 catalytic center binding site [active] 1105100000100 ATP binding site [chemical binding]; other site 1105100000101 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 1105100000102 substrate binding pocket [chemical binding]; other site 1105100000103 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105100000104 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 1105100000105 Cu(I) binding site [ion binding]; other site 1105100000106 Putative transcriptional regulator [Transcription]; Region: COG1678 1105100000107 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1105100000108 Colicin V production protein; Region: Colicin_V; pfam02674 1105100000109 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105100000110 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105100000111 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105100000112 active site 1105100000113 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105100000114 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105100000115 Clp amino terminal domain; Region: Clp_N; pfam02861 1105100000116 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 1105100000117 Walker A motif; other site 1105100000118 ATP binding site [chemical binding]; other site 1105100000119 Walker B motif; other site 1105100000120 arginine finger; other site 1105100000121 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 1105100000122 Walker A motif; other site 1105100000123 ATP binding site [chemical binding]; other site 1105100000124 Walker B motif; other site 1105100000125 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1105100000126 UGMP family protein; Validated; Region: PRK09604 1105100000127 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1105100000128 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 1105100000129 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105100000130 Di-iron ligands [ion binding]; other site 1105100000131 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 1105100000132 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 1105100000133 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1105100000134 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1105100000135 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105100000136 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105100000137 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105100000138 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1105100000139 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 1105100000140 Ligand Binding Site [chemical binding]; other site 1105100000141 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100000142 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105100000143 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105100000144 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 1105100000145 Walker A motif; other site 1105100000146 ATP binding site [chemical binding]; other site 1105100000147 Walker B motif; other site 1105100000148 arginine finger; other site 1105100000149 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105100000150 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 1105100000151 cofactor binding site; other site 1105100000152 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105100000153 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1105100000154 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105100000155 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100000156 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1105100000157 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1105100000158 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105100000159 membrane protein insertase; Provisional; Region: PRK01318 1105100000160 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1105100000161 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105100000162 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 1105100000163 S-adenosylmethionine binding site [chemical binding]; other site 1105100000164 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105100000165 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 1105100000166 active site 1105100000167 catalytic residues [active] 1105100000168 metal binding site [ion binding]; metal-binding site 1105100000169 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105100000170 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105100000171 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 1105100000172 putative substrate translocation pore; other site 1105100000173 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 1105100000174 active site 1105100000175 multimer interface [polypeptide binding]; other site 1105100000176 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105100000177 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1105100000178 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105100000179 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 1105100000180 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1105100000181 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105100000182 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 1105100000183 P-loop; other site 1105100000184 Magnesium ion binding site [ion binding]; other site 1105100000185 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 1105100000186 Magnesium ion binding site [ion binding]; other site 1105100000187 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 1105100000188 ParB-like nuclease domain; Region: ParB; smart00470 1105100000189 KorB domain; Region: KorB; pfam08535 1105100000190 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105100000191 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105100000192 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105100000193 ABC transporter; Region: ABC_tran_2; pfam12848 1105100000194 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105100000195 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105100000196 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; COG2877 1105100000197 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105100000198 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105100000199 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105100000200 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1105100000201 Zn2+ binding site [ion binding]; other site 1105100000202 Mg2+ binding site [ion binding]; other site 1105100000203 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105100000204 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 1105100000205 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 1105100000206 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105100000207 active site 1105100000208 HIGH motif; other site 1105100000209 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105100000210 KMSK motif region; other site 1105100000211 tRNA binding surface [nucleotide binding]; other site 1105100000212 DALR anticodon binding domain; Region: DALR_1; smart00836 1105100000213 anticodon binding site; other site 1105100000214 Sporulation related domain; Region: SPOR; pfam05036 1105100000215 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105100000216 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 1105100000217 CAP-like domain; other site 1105100000218 active site 1105100000219 primary dimer interface [polypeptide binding]; other site 1105100000220 Gram-negative porin; Region: Porin_4; pfam13609 1105100000221 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105100000222 trimer interface [polypeptide binding]; other site 1105100000223 active site 1105100000224 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 1105100000225 SecA binding site; other site 1105100000226 Preprotein binding site; other site 1105100000227 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105100000228 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 1105100000229 active site 1105100000230 phosphorylation site [posttranslational modification] 1105100000231 intermolecular recognition site; other site 1105100000232 dimerization interface [polypeptide binding]; other site 1105100000233 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 1105100000234 DNA binding site [nucleotide binding] 1105100000235 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 1105100000236 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105100000237 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 1105100000238 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105100000239 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 1105100000240 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105100000241 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 1105100000242 EamA-like transporter family; Region: EamA; pfam00892 1105100000243 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 1105100000244 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 1105100000245 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105100000246 putative substrate translocation pore; other site 1105100000247 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1105100000248 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105100000249 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105100000250 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105100000251 active site 1105100000252 HIGH motif; other site 1105100000253 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105100000254 KMSKS motif; other site 1105100000255 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105100000256 tRNA binding surface [nucleotide binding]; other site 1105100000257 anticodon binding site; other site 1105100000258 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 1105100000259 rRNA interaction site [nucleotide binding]; other site 1105100000260 S8 interaction site; other site 1105100000261 putative laminin-1 binding site; other site 1105100000262 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105100000263 UBA/TS-N domain; Region: UBA; pfam00627 1105100000264 Elongation factor TS; Region: EF_TS; pfam00889 1105100000265 Elongation factor TS; Region: EF_TS; pfam00889 1105100000266 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 1105100000267 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100000268 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105100000269 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 1105100000270 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105100000271 putative acyl-acceptor binding pocket; other site 1105100000272 aspartate aminotransferase; Provisional; Region: PRK05764 1105100000273 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 1105100000274 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105100000275 homodimer interface [polypeptide binding]; other site 1105100000276 catalytic residue [active] 1105100000277 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105100000278 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105100000279 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 1105100000280 binding surface 1105100000281 TPR motif; other site 1105100000282 Methyltransferase domain; Region: Methyltransf_23; pfam13489 1105100000283 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 1105100000284 S-adenosylmethionine binding site [chemical binding]; other site 1105100000285 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 1105100000286 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 1105100000287 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105100000288 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105100000289 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105100000290 active site 1105100000291 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100000292 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 1105100000293 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105100000294 active site 1105100000295 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105100000296 dimer interface [polypeptide binding]; other site 1105100000297 substrate binding site [chemical binding]; other site 1105100000298 catalytic residues [active] 1105100000299 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1105100000300 Permease; Region: Permease; pfam02405 1105100000301 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105100000302 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000303 Walker A/P-loop; other site 1105100000304 ATP binding site [chemical binding]; other site 1105100000305 Q-loop/lid; other site 1105100000306 ABC transporter signature motif; other site 1105100000307 Walker B; other site 1105100000308 D-loop; other site 1105100000309 H-loop/switch region; other site 1105100000310 Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]; Region: RpmB; COG0227 1105100000311 50S ribosomal protein L31; Provisional; Region: PRK01397 1105100000312 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105100000313 G1 box; other site 1105100000314 GTP/Mg2+ binding site [chemical binding]; other site 1105100000315 Switch I region; other site 1105100000316 G2 box; other site 1105100000317 G3 box; other site 1105100000318 Switch II region; other site 1105100000319 G4 box; other site 1105100000320 G5 box; other site 1105100000321 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 1105100000322 nucleotide binding site [chemical binding]; other site 1105100000323 substrate binding site [chemical binding]; other site 1105100000324 type IV secretion system protein VirB3; Provisional; Region: PRK13899 1105100000325 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105100000326 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105100000327 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000328 Walker A/P-loop; other site 1105100000329 ATP binding site [chemical binding]; other site 1105100000330 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105100000331 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105100000332 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105100000333 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105100000334 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 1105100000335 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105100000336 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105100000337 tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmD; COG0336 1105100000338 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1105100000339 hypothetical protein; Provisional; Region: PRK13694 1105100000340 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105100000341 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105100000342 Protein export membrane protein; Region: SecD_SecF; pfam02355 1105100000343 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105100000344 SLBB domain; Region: SLBB; pfam10531 1105100000345 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 1105100000346 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105100000347 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 1105100000348 Catalytic site [active] 1105100000349 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 1105100000350 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105100000351 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 1105100000352 dimerization interface [polypeptide binding]; other site 1105100000353 active site 1105100000354 metal binding site [ion binding]; metal-binding site 1105100000355 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 1105100000356 dsRNA binding site [nucleotide binding]; other site 1105100000357 GTPase Era; Provisional; Region: era; PRK15494 1105100000358 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100000359 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105100000360 G1 box; other site 1105100000361 GTP/Mg2+ binding site [chemical binding]; other site 1105100000362 Switch I region; other site 1105100000363 G2 box; other site 1105100000364 Switch II region; other site 1105100000365 G3 box; other site 1105100000366 G4 box; other site 1105100000367 G5 box; other site 1105100000368 KH domain; Region: KH_2; pfam07650 1105100000369 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 1105100000370 active site 1105100000371 putative DNA-binding cleft [nucleotide binding]; other site 1105100000372 dimer interface [polypeptide binding]; other site 1105100000373 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105100000374 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 1105100000375 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 1105100000376 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl17552 1105100000377 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105100000378 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105100000379 AAA domain; Region: AAA_31; pfam13614 1105100000380 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 1105100000381 Walker A motif; other site 1105100000382 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 1105100000383 HflK protein; Region: hflK; TIGR01933 1105100000384 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105100000385 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 1105100000386 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105100000387 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105100000388 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 1105100000389 protein binding site [polypeptide binding]; other site 1105100000390 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 1105100000391 protein binding site [polypeptide binding]; other site 1105100000392 hypothetical protein; Validated; Region: PRK01415 1105100000393 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105100000394 active site residue [active] 1105100000395 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 1105100000396 Iron-sulfur protein interface; other site 1105100000397 proximal quinone binding site [chemical binding]; other site 1105100000398 SdhD (CybS) interface [polypeptide binding]; other site 1105100000399 proximal heme binding site [chemical binding]; other site 1105100000400 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 1105100000401 putative SdhC subunit interface [polypeptide binding]; other site 1105100000402 putative proximal heme binding site [chemical binding]; other site 1105100000403 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105100000404 putative proximal quinone binding site; other site 1105100000405 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105100000406 L-aspartate oxidase; Provisional; Region: PRK06175 1105100000407 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105100000408 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105100000409 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 1105100000410 dimer interface [polypeptide binding]; other site 1105100000411 conserved gate region; other site 1105100000412 putative PBP binding loops; other site 1105100000413 ABC-ATPase subunit interface; other site 1105100000414 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 1105100000415 S17 interaction site [polypeptide binding]; other site 1105100000416 S8 interaction site; other site 1105100000417 16S rRNA interaction site [nucleotide binding]; other site 1105100000418 streptomycin interaction site [chemical binding]; other site 1105100000419 23S rRNA interaction site [nucleotide binding]; other site 1105100000420 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105100000421 30S ribosomal protein S7; Validated; Region: PRK05302 1105100000422 elongation factor G; Reviewed; Region: PRK00007 1105100000423 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105100000424 G1 box; other site 1105100000425 putative GEF interaction site [polypeptide binding]; other site 1105100000426 GTP/Mg2+ binding site [chemical binding]; other site 1105100000427 Switch I region; other site 1105100000428 G2 box; other site 1105100000429 G3 box; other site 1105100000430 Switch II region; other site 1105100000431 G4 box; other site 1105100000432 G5 box; other site 1105100000433 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 1105100000434 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 1105100000435 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 1105100000436 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 1105100000437 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105100000438 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105100000439 putative homodimer interface [polypeptide binding]; other site 1105100000440 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1105100000441 heterodimer interface [polypeptide binding]; other site 1105100000442 homodimer interface [polypeptide binding]; other site 1105100000443 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105100000444 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 1105100000445 23S rRNA interface [nucleotide binding]; other site 1105100000446 putative thiostrepton binding site; other site 1105100000447 L7/L12 interface [polypeptide binding]; other site 1105100000448 L25 interface [polypeptide binding]; other site 1105100000449 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 1105100000450 mRNA/rRNA interface [nucleotide binding]; other site 1105100000451 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 1105100000452 23S rRNA interface [nucleotide binding]; other site 1105100000453 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105100000454 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 1105100000455 core dimer interface [polypeptide binding]; other site 1105100000456 peripheral dimer interface [polypeptide binding]; other site 1105100000457 L10 interface [polypeptide binding]; other site 1105100000458 L11 interface [polypeptide binding]; other site 1105100000459 putative EF-Tu interaction site [polypeptide binding]; other site 1105100000460 putative EF-G interaction site [polypeptide binding]; other site 1105100000461 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 1105100000462 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 1105100000463 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105100000464 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 1105100000465 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1105100000466 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 1105100000467 RPB3 interaction site [polypeptide binding]; other site 1105100000468 RPB1 interaction site [polypeptide binding]; other site 1105100000469 RPB11 interaction site [polypeptide binding]; other site 1105100000470 RPB10 interaction site [polypeptide binding]; other site 1105100000471 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105100000472 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105100000473 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1105100000474 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105100000475 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105100000476 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105100000477 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105100000478 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105100000479 DNA binding site [nucleotide binding] 1105100000480 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105100000481 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 1105100000482 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100000483 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105100000484 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 1105100000485 interface (dimer of trimers) [polypeptide binding]; other site 1105100000486 Substrate-binding/catalytic site; other site 1105100000487 Zn-binding sites [ion binding]; other site 1105100000488 ATPase MipZ; Region: MipZ; pfam09140 1105100000489 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 1105100000490 P-loop; other site 1105100000491 Magnesium ion binding site [ion binding]; other site 1105100000492 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 1105100000493 Magnesium ion binding site [ion binding]; other site 1105100000494 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105100000495 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 1105100000496 dimer interface [polypeptide binding]; other site 1105100000497 anticodon binding site; other site 1105100000498 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 1105100000499 homodimer interface [polypeptide binding]; other site 1105100000500 motif 1; other site 1105100000501 active site 1105100000502 motif 2; other site 1105100000503 GAD domain; Region: GAD; pfam02938 1105100000504 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 1105100000505 active site 1105100000506 motif 3; other site 1105100000507 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1105100000508 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105100000509 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105100000510 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1105100000511 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105100000512 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 1105100000513 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105100000514 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 1105100000515 substrate binding pocket [chemical binding]; other site 1105100000516 membrane-bound complex binding site; other site 1105100000517 hinge residues; other site 1105100000518 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105100000519 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105100000520 GatB domain; Region: GatB_Yqey; smart00845 1105100000521 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105100000522 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1105100000523 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1105100000524 Uncharacterized conserved protein [Function unknown]; Region: COG4997 1105100000525 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105100000526 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 1105100000527 hinge region; other site 1105100000528 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 1105100000529 putative nucleotide binding site [chemical binding]; other site 1105100000530 uridine monophosphate binding site [chemical binding]; other site 1105100000531 homohexameric interface [polypeptide binding]; other site 1105100000532 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 1105100000533 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105100000534 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 1105100000535 putative substrate translocation pore; other site 1105100000536 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 1105100000537 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105100000538 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1105100000539 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105100000540 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105100000541 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105100000542 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105100000543 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1105100000544 Surface antigen; Region: Bac_surface_Ag; pfam01103 1105100000545 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105100000546 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 1105100000547 active site 1105100000548 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 1105100000549 protein binding site [polypeptide binding]; other site 1105100000550 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 1105100000551 putative substrate binding region [chemical binding]; other site 1105100000552 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1105100000553 putative RNA binding site [nucleotide binding]; other site 1105100000554 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105100000555 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 1105100000556 S-adenosylmethionine binding site [chemical binding]; other site 1105100000557 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105100000558 putative coenzyme Q binding site [chemical binding]; other site 1105100000559 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100000560 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105100000561 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105100000562 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 1105100000563 RNA methyltransferase, RsmE family; Region: TIGR00046 1105100000564 Uncharacterized conserved protein [Function unknown]; Region: COG2155 1105100000565 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105100000566 Protein export membrane protein; Region: SecD_SecF; cl14618 1105100000567 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 1105100000568 IHF dimer interface [polypeptide binding]; other site 1105100000569 IHF - DNA interface [nucleotide binding]; other site 1105100000570 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105100000571 signal recognition particle protein; Provisional; Region: PRK10867 1105100000572 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 1105100000573 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 1105100000574 P loop; other site 1105100000575 GTP binding site [chemical binding]; other site 1105100000576 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105100000577 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105100000578 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105100000579 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105100000580 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105100000581 potential frameshift: common BLAST hit: gi|67459496|ref|YP_247120.1| prolyl endopeptidase 1105100000582 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105100000583 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 1105100000584 FeS/SAM binding site; other site 1105100000585 HemN C-terminal domain; Region: HemN_C; pfam06969 1105100000586 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 1105100000587 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105100000588 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 1105100000589 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105100000590 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 1105100000591 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 1105100000592 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 1105100000593 active site 1105100000594 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105100000595 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 1105100000596 E3 interaction surface; other site 1105100000597 lipoyl attachment site [posttranslational modification]; other site 1105100000598 e3 binding domain; Region: E3_binding; pfam02817 1105100000599 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105100000600 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105100000601 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 1105100000602 TPP-binding site [chemical binding]; other site 1105100000603 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 1105100000604 dimer interface [polypeptide binding]; other site 1105100000605 PYR/PP interface [polypeptide binding]; other site 1105100000606 TPP binding site [chemical binding]; other site 1105100000607 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 1105100000608 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 1105100000609 active site 1105100000610 Zn binding site [ion binding]; other site 1105100000611 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105100000612 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105100000613 Walker A/P-loop; other site 1105100000614 ATP binding site [chemical binding]; other site 1105100000615 Q-loop/lid; other site 1105100000616 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105100000617 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 1105100000618 ABC transporter signature motif; other site 1105100000619 Walker B; other site 1105100000620 D-loop; other site 1105100000621 H-loop/switch region; other site 1105100000622 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105100000623 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105100000624 Putative cation transport regulator [General function prediction only]; Region: ChaB; COG4572 1105100000625 chaperone protein DnaJ; Provisional; Region: PRK14300 1105100000626 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 1105100000627 HSP70 interaction site [polypeptide binding]; other site 1105100000628 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105100000629 substrate binding site [polypeptide binding]; other site 1105100000630 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105100000631 Zn binding sites [ion binding]; other site 1105100000632 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105100000633 dimer interface [polypeptide binding]; other site 1105100000634 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105100000635 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105100000636 nucleotide binding site [chemical binding]; other site 1105100000637 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 1105100000638 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1105100000639 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 1105100000640 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105100000641 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105100000642 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105100000643 diiron binding motif [ion binding]; other site 1105100000644 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 1105100000645 Subunit III/VIIa interface [polypeptide binding]; other site 1105100000646 Phospholipid binding site [chemical binding]; other site 1105100000647 Subunit I/III interface [polypeptide binding]; other site 1105100000648 Subunit III/VIb interface [polypeptide binding]; other site 1105100000649 Subunit III/VIa interface; other site 1105100000650 Subunit III/Vb interface [polypeptide binding]; other site 1105100000651 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 1105100000652 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 1105100000653 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105100000654 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 1105100000655 trimer interface [polypeptide binding]; other site 1105100000656 active site 1105100000657 substrate binding site [chemical binding]; other site 1105100000658 CoA binding site [chemical binding]; other site 1105100000659 potential frameshift: common BLAST hit: gi|15892172|ref|NP_359886.1| bifunctional penicillin-binding protein 1C 1105100000660 potential frameshift: common BLAST hit: gi|350273249|ref|YP_004884562.1| bifunctional penicillin-binding protein 1C 1105100000661 potential frameshift: common BLAST hit: gi|67459460|ref|YP_247084.1| cell surface antigen-like protein Sca8 1105100000662 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 1105100000663 Ligand Binding Site [chemical binding]; other site 1105100000664 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105100000665 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 1105100000666 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 1105100000667 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 1105100000668 catalytic loop [active] 1105100000669 iron binding site [ion binding]; other site 1105100000670 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105100000671 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 1105100000672 nucleotide binding site [chemical binding]; other site 1105100000673 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105100000674 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 1105100000675 HSP70 interaction site [polypeptide binding]; other site 1105100000676 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105100000677 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105100000678 active site 1105100000679 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105100000680 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 1105100000681 ATP binding site [chemical binding]; other site 1105100000682 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 1105100000683 nucleotide binding region [chemical binding]; other site 1105100000684 ATP-binding site [chemical binding]; other site 1105100000685 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105100000686 UvrB/uvrC motif; Region: UVR; pfam02151 1105100000687 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 1105100000688 GSH binding site [chemical binding]; other site 1105100000689 catalytic residues [active] 1105100000690 potential frameshift: common BLAST hit: gi|157964270|ref|YP_001499094.1| multidrug resistance protein Atm1 1105100000691 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105100000692 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000693 Walker A/P-loop; other site 1105100000694 ATP binding site [chemical binding]; other site 1105100000695 Q-loop/lid; other site 1105100000696 Pleckstrin homology-like domain; Region: PH-like; cl17171 1105100000697 DNA gyrase subunit A; Validated; Region: PRK05560 1105100000698 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 1105100000699 CAP-like domain; other site 1105100000700 active site 1105100000701 primary dimer interface [polypeptide binding]; other site 1105100000702 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105100000703 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105100000704 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105100000705 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105100000706 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105100000707 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105100000708 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105100000709 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105100000710 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 1105100000711 active site 1105100000712 catalytic residues [active] 1105100000713 metal binding site [ion binding]; metal-binding site 1105100000714 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105100000715 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105100000716 putative active site [active] 1105100000717 substrate binding site [chemical binding]; other site 1105100000718 putative cosubstrate binding site; other site 1105100000719 catalytic site [active] 1105100000720 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105100000721 substrate binding site [chemical binding]; other site 1105100000722 potential protein location (hypothetical protein RPJ_01570 [Rickettsia rickettsii str. Hino]) that overlaps RNA (23S ribosomal RNA) 1105100000723 Protein of unknown function (DUF563); Region: DUF563; cl15705 1105100000724 Predicted ATPase [General function prediction only]; Region: COG1485 1105100000725 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 1105100000726 Walker A motif; other site 1105100000727 ATP binding site [chemical binding]; other site 1105100000728 Walker B motif; other site 1105100000729 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 1105100000730 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1105100000731 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 1105100000732 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105100000733 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105100000734 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105100000735 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000736 Walker A/P-loop; other site 1105100000737 ATP binding site [chemical binding]; other site 1105100000738 Q-loop/lid; other site 1105100000739 ABC transporter signature motif; other site 1105100000740 Walker B; other site 1105100000741 D-loop; other site 1105100000742 H-loop/switch region; other site 1105100000743 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105100000744 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 1105100000745 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105100000746 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105100000747 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 1105100000748 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 1105100000749 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105100000750 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105100000751 putative metal binding site; other site 1105100000752 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105100000753 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105100000754 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105100000755 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105100000756 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105100000757 ATP binding site [chemical binding]; other site 1105100000758 active site 1105100000759 substrate binding site [chemical binding]; other site 1105100000760 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105100000761 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 1105100000762 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105100000763 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 1105100000764 active site 1105100000765 dimer interface [polypeptide binding]; other site 1105100000766 motif 1; other site 1105100000767 motif 2; other site 1105100000768 motif 3; other site 1105100000769 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 1105100000770 anticodon binding site; other site 1105100000771 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000772 Walker A/P-loop; other site 1105100000773 ATP binding site [chemical binding]; other site 1105100000774 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000775 ABC transporter signature motif; other site 1105100000776 Walker B; other site 1105100000777 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100000778 H-loop/switch region; other site 1105100000779 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 1105100000780 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105100000781 V-type ATP synthase subunit I; Validated; Region: PRK05771 1105100000782 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105100000783 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 1105100000784 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 1105100000785 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105100000786 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105100000787 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 1105100000788 ATP binding site [chemical binding]; other site 1105100000789 Mg2+ binding site [ion binding]; other site 1105100000790 G-X-G motif; other site 1105100000791 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 1105100000792 anchoring element; other site 1105100000793 dimer interface [polypeptide binding]; other site 1105100000794 ATP binding site [chemical binding]; other site 1105100000795 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 1105100000796 active site 1105100000797 metal binding site [ion binding]; metal-binding site 1105100000798 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105100000799 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105100000800 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105100000801 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 1105100000802 protein binding site [polypeptide binding]; other site 1105100000803 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105100000804 Catalytic dyad [active] 1105100000805 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1105100000806 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 1105100000807 dimer interface [polypeptide binding]; other site 1105100000808 phosphorylation site [posttranslational modification] 1105100000809 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 1105100000810 ATP binding site [chemical binding]; other site 1105100000811 Mg2+ binding site [ion binding]; other site 1105100000812 G-X-G motif; other site 1105100000813 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105100000814 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105100000815 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105100000816 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105100000817 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105100000818 Trp docking motif [polypeptide binding]; other site 1105100000819 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 1105100000820 23S rRNA interface [nucleotide binding]; other site 1105100000821 L3 interface [polypeptide binding]; other site 1105100000822 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1105100000823 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 1105100000824 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105100000825 DCoH tetramer interaction site [polypeptide binding]; other site 1105100000826 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 1105100000827 putative active site [active] 1105100000828 Ap4A binding site [chemical binding]; other site 1105100000829 nudix motif; other site 1105100000830 putative metal binding site [ion binding]; other site 1105100000831 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105100000832 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 1105100000833 active site 1105100000834 phosphorylation site [posttranslational modification] 1105100000835 intermolecular recognition site; other site 1105100000836 dimerization interface [polypeptide binding]; other site 1105100000837 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 1105100000838 active site 1105100000839 phosphorylation site [posttranslational modification] 1105100000840 intermolecular recognition site; other site 1105100000841 dimerization interface [polypeptide binding]; other site 1105100000842 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105100000843 metal binding site [ion binding]; metal-binding site 1105100000844 active site 1105100000845 I-site; other site 1105100000846 elongation factor P; Validated; Region: PRK00529 1105100000847 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105100000848 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 1105100000849 RNA binding site [nucleotide binding]; other site 1105100000850 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 1105100000851 RNA binding site [nucleotide binding]; other site 1105100000852 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105100000853 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 1105100000854 active site 1105100000855 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105100000856 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 1105100000857 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105100000858 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1105100000859 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1105100000860 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105100000861 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105100000862 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100000863 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105100000864 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 1105100000865 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105100000866 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105100000867 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105100000868 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105100000869 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105100000870 FAD binding domain; Region: FAD_binding_4; pfam01565 1105100000871 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105100000872 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105100000873 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105100000874 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1105100000875 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 1105100000876 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105100000877 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105100000878 cell division protein FtsA; Region: ftsA; TIGR01174 1105100000879 Cell division protein FtsA; Region: FtsA; smart00842 1105100000880 Cell division protein FtsA; Region: FtsA; pfam14450 1105100000881 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 1105100000882 Cytochrome c2 [Energy production and conversion]; Region: COG3474 1105100000883 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1105100000884 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105100000885 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 1105100000886 RNA binding site [nucleotide binding]; other site 1105100000887 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 1105100000888 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 1105100000889 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105100000890 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 1105100000891 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105100000892 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 1105100000893 RNA binding surface [nucleotide binding]; other site 1105100000894 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105100000895 active site 1105100000896 potential frameshift: common BLAST hit: gi|238650484|ref|YP_002916336.1| penicillin-binding protein 4* 1105100000897 potential frameshift: common BLAST hit: gi|15892268|ref|NP_359982.1| penicillin-binding protein 4* 1105100000898 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 1105100000899 putative catalytic site [active] 1105100000900 putative phosphate binding site [ion binding]; other site 1105100000901 active site 1105100000902 metal binding site A [ion binding]; metal-binding site 1105100000903 DNA binding site [nucleotide binding] 1105100000904 putative AP binding site [nucleotide binding]; other site 1105100000905 putative metal binding site B [ion binding]; other site 1105100000906 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105100000907 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 1105100000908 tetramer interface [polypeptide binding]; other site 1105100000909 TPP-binding site [chemical binding]; other site 1105100000910 heterodimer interface [polypeptide binding]; other site 1105100000911 phosphorylation loop region [posttranslational modification] 1105100000912 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105100000913 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 1105100000914 alpha subunit interface [polypeptide binding]; other site 1105100000915 TPP binding site [chemical binding]; other site 1105100000916 heterodimer interface [polypeptide binding]; other site 1105100000917 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105100000918 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1105100000919 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105100000920 G1 box; other site 1105100000921 putative GEF interaction site [polypeptide binding]; other site 1105100000922 GTP/Mg2+ binding site [chemical binding]; other site 1105100000923 Switch I region; other site 1105100000924 G2 box; other site 1105100000925 G3 box; other site 1105100000926 Switch II region; other site 1105100000927 G4 box; other site 1105100000928 G5 box; other site 1105100000929 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 1105100000930 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 1105100000931 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 1105100000932 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105100000933 isocitrate dehydrogenase; Validated; Region: PRK09222 1105100000934 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 1105100000935 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 1105100000936 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105100000937 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 1105100000938 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105100000939 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105100000940 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105100000941 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105100000942 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 1105100000943 [2Fe-2S] cluster binding site [ion binding]; other site 1105100000944 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 1105100000945 Qi binding site; other site 1105100000946 cytochrome b; Provisional; Region: CYTB; MTH00191 1105100000947 intrachain domain interface; other site 1105100000948 interchain domain interface [polypeptide binding]; other site 1105100000949 heme bH binding site [chemical binding]; other site 1105100000950 heme bL binding site [chemical binding]; other site 1105100000951 Qo binding site; other site 1105100000952 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 1105100000953 interchain domain interface [polypeptide binding]; other site 1105100000954 intrachain domain interface; other site 1105100000955 Qi binding site; other site 1105100000956 Qo binding site; other site 1105100000957 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105100000958 catalytic site [active] 1105100000959 metal binding site [ion binding]; metal-binding site 1105100000960 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105100000961 Cytochrome c; Region: Cytochrom_C; cl11414 1105100000962 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 1105100000963 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 1105100000964 putative dimer interface [polypeptide binding]; other site 1105100000965 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105100000966 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105100000967 PCRF domain; Region: PCRF; pfam03462 1105100000968 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105100000969 RF-1 domain; Region: RF-1; pfam00472 1105100000970 GTP-binding protein LepA; Provisional; Region: PRK05433 1105100000971 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105100000972 G1 box; other site 1105100000973 putative GEF interaction site [polypeptide binding]; other site 1105100000974 GTP/Mg2+ binding site [chemical binding]; other site 1105100000975 Switch I region; other site 1105100000976 G2 box; other site 1105100000977 G3 box; other site 1105100000978 Switch II region; other site 1105100000979 G4 box; other site 1105100000980 G5 box; other site 1105100000981 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 1105100000982 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 1105100000983 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105100000984 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 1105100000985 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 1105100000986 potential frameshift: common BLAST hit: gi|67458839|ref|YP_246463.1| NACHT domain-containing protein 1105100000987 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105100000988 HD domain; Region: HD_4; pfam13328 1105100000989 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105100000990 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 1105100000991 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105100000992 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105100000993 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105100000994 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105100000995 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105100000996 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 1105100000997 oligomeric interface; other site 1105100000998 putative active site [active] 1105100000999 homodimer interface [polypeptide binding]; other site 1105100001000 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105100001001 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105100001002 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105100001003 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105100001004 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 1105100001005 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105100001006 VirB7 interaction site; other site 1105100001007 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105100001008 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105100001009 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 1105100001010 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1105100001011 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1105100001012 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 1105100001013 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 1105100001014 Walker A motif; other site 1105100001015 hexamer interface [polypeptide binding]; other site 1105100001016 ATP binding site [chemical binding]; other site 1105100001017 Walker B motif; other site 1105100001018 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105100001019 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 1105100001020 Walker A motif; other site 1105100001021 ATP binding site [chemical binding]; other site 1105100001022 Walker B motif; other site 1105100001023 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105100001024 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 1105100001025 Phage-related protein [Function unknown]; Region: COG4695; cl01923 1105100001026 Phage portal protein; Region: Phage_portal; pfam04860 1105100001027 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105100001028 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105100001029 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 1105100001030 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 1105100001031 active site 1105100001032 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105100001033 MutS domain I; Region: MutS_I; pfam01624 1105100001034 MutS domain II; Region: MutS_II; pfam05188 1105100001035 MutS domain III; Region: MutS_III; pfam05192 1105100001036 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 1105100001037 Walker A/P-loop; other site 1105100001038 ATP binding site [chemical binding]; other site 1105100001039 Q-loop/lid; other site 1105100001040 ABC transporter signature motif; other site 1105100001041 Walker B; other site 1105100001042 D-loop; other site 1105100001043 H-loop/switch region; other site 1105100001044 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105100001045 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105100001046 Protein of unknown function DUF45; Region: DUF45; pfam01863 1105100001047 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1105100001048 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105100001049 TolB amino-terminal domain; Region: TolB_N; pfam04052 1105100001050 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105100001051 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105100001052 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105100001053 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105100001054 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105100001055 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105100001056 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 1105100001057 DNA binding residues [nucleotide binding] 1105100001058 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 1105100001059 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1105100001060 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 1105100001061 Ligand Binding Site [chemical binding]; other site 1105100001062 amino acid transporter; Region: 2A0306; TIGR00909 1105100001063 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105100001064 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 1105100001065 dimer interface [polypeptide binding]; other site 1105100001066 motif 1; other site 1105100001067 active site 1105100001068 motif 2; other site 1105100001069 motif 3; other site 1105100001070 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 1105100001071 anticodon binding site; other site 1105100001072 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105100001073 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105100001074 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105100001075 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105100001076 TolQ protein; Region: tolQ; TIGR02796 1105100001077 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1105100001078 TolR protein; Region: tolR; TIGR02801 1105100001079 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1105100001080 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105100001081 HD domain; Region: HD_4; pfam13328 1105100001082 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 1105100001083 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105100001084 putative substrate translocation pore; other site 1105100001085 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105100001086 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 1105100001087 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105100001088 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105100001089 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 1105100001090 Walker A/P-loop; other site 1105100001091 ATP binding site [chemical binding]; other site 1105100001092 Q-loop/lid; other site 1105100001093 ABC transporter signature motif; other site 1105100001094 Walker B; other site 1105100001095 D-loop; other site 1105100001096 H-loop/switch region; other site 1105100001097 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105100001098 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1105100001099 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 1105100001100 nucleotide binding site/active site [active] 1105100001101 HIT family signature motif; other site 1105100001102 catalytic residue [active] 1105100001103 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105100001104 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105100001105 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 1105100001106 active site 1105100001107 HslU subunit interaction site [polypeptide binding]; other site 1105100001108 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105100001109 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 1105100001110 Walker A motif; other site 1105100001111 ATP binding site [chemical binding]; other site 1105100001112 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1105100001113 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105100001114 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 1105100001115 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1105100001116 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 1105100001117 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1105100001118 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 1105100001119 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100001120 Uncharacterized conserved protein [Function unknown]; Region: COG5464 1105100001121 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100001122 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105100001123 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105100001124 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105100001125 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 1105100001126 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105100001127 dimerization interface [polypeptide binding]; other site 1105100001128 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 1105100001129 putative iron binding site [ion binding]; other site 1105100001130 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105100001131 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105100001132 HIGH motif; other site 1105100001133 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105100001134 active site 1105100001135 KMSKS motif; other site 1105100001136 DNA topoisomerase I; Validated; Region: PRK06599 1105100001137 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 1105100001138 active site 1105100001139 interdomain interaction site; other site 1105100001140 putative metal-binding site [ion binding]; other site 1105100001141 nucleotide binding site [chemical binding]; other site 1105100001142 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 1105100001143 domain I; other site 1105100001144 DNA binding groove [nucleotide binding] 1105100001145 phosphate binding site [ion binding]; other site 1105100001146 domain II; other site 1105100001147 domain III; other site 1105100001148 nucleotide binding site [chemical binding]; other site 1105100001149 catalytic site [active] 1105100001150 domain IV; other site 1105100001151 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105100001152 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1105100001153 DNA protecting protein DprA; Region: dprA; TIGR00732 1105100001154 DNA protecting protein DprA; Region: dprA; TIGR00732 1105100001155 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105100001156 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 1105100001157 dimer interface [polypeptide binding]; other site 1105100001158 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105100001159 catalytic triad [active] 1105100001160 peroxidatic and resolving cysteines [active] 1105100001161 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105100001162 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 1105100001163 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105100001164 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105100001165 Sulfatase; Region: Sulfatase; pfam00884 1105100001166 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) [DNA replication, recombination, and repair]; Region: COG0816 1105100001167 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 1105100001168 sequence-specific DNA binding site [nucleotide binding]; other site 1105100001169 salt bridge; other site 1105100001170 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105100001171 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105100001172 NADP binding site [chemical binding]; other site 1105100001173 active site 1105100001174 putative substrate binding site [chemical binding]; other site 1105100001175 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105100001176 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105100001177 NAD(P) binding site [chemical binding]; other site 1105100001178 homodimer interface [polypeptide binding]; other site 1105100001179 substrate binding site [chemical binding]; other site 1105100001180 active site 1105100001181 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105100001182 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105100001183 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 1105100001184 active site 1105100001185 homodimer interface [polypeptide binding]; other site 1105100001186 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105100001187 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 1105100001188 S-adenosylmethionine binding site [chemical binding]; other site 1105100001189 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105100001190 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 1105100001191 active site 1105100001192 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105100001193 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 1105100001194 active site 1105100001195 Membrane-fusion protein [Cell envelope biogenesis, outer membrane]; Region: AcrA; COG0845 1105100001196 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1105100001197 HlyD family secretion protein; Region: HlyD_3; pfam13437 1105100001198 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 1105100001199 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105100001200 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 1105100001201 catalytic site [active] 1105100001202 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105100001203 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 1105100001204 putative ADP-binding pocket [chemical binding]; other site 1105100001205 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100001206 Walker A/P-loop; other site 1105100001207 ATP binding site [chemical binding]; other site 1105100001208 Q-loop/lid; other site 1105100001209 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105100001210 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105100001211 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 1105100001212 RNA binding surface [nucleotide binding]; other site 1105100001213 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 1105100001214 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105100001215 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 1105100001216 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105100001217 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105100001218 TPR repeat; Region: TPR_11; pfam13414 1105100001219 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 1105100001220 TPR motif; other site 1105100001221 binding surface 1105100001222 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105100001223 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105100001224 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105100001225 RimM N-terminal domain; Region: RimM; pfam01782 1105100001226 PRC-barrel domain; Region: PRC; pfam05239 1105100001227 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105100001228 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 1105100001229 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105100001230 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105100001231 active site 1105100001232 DNA binding site [nucleotide binding] 1105100001233 YCII-related domain; Region: YCII; cl00999 1105100001234 hypothetical protein; Provisional; Region: PRK14388 1105100001235 NADH dehydrogenase subunit E; Validated; Region: PRK07539 1105100001236 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 1105100001237 putative dimer interface [polypeptide binding]; other site 1105100001238 [2Fe-2S] cluster binding site [ion binding]; other site 1105100001239 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 1105100001240 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1105100001241 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105100001242 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 1105100001243 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1105100001244 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 1105100001245 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105100001246 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 1105100001247 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105100001248 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105100001249 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 1105100001250 active site 1105100001251 DNA binding site [nucleotide binding] 1105100001252 Int/Topo IB signature motif; other site 1105100001253 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 1105100001254 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105100001255 NAD binding site [chemical binding]; other site 1105100001256 homotetramer interface [polypeptide binding]; other site 1105100001257 homodimer interface [polypeptide binding]; other site 1105100001258 substrate binding site [chemical binding]; other site 1105100001259 active site 1105100001260 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105100001261 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105100001262 putative active site [active] 1105100001263 catalytic triad [active] 1105100001264 putative dimer interface [polypeptide binding]; other site 1105100001265 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105100001266 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 1105100001267 amidase catalytic site [active] 1105100001268 Zn binding residues [ion binding]; other site 1105100001269 substrate binding site [chemical binding]; other site 1105100001270 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105100001271 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 1105100001272 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 1105100001273 TM-ABC transporter signature motif; other site 1105100001274 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1105100001275 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100001276 Walker A/P-loop; other site 1105100001277 ATP binding site [chemical binding]; other site 1105100001278 Q-loop/lid; other site 1105100001279 ABC transporter signature motif; other site 1105100001280 Walker B; other site 1105100001281 D-loop; other site 1105100001282 H-loop/switch region; other site 1105100001283 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 1105100001284 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 1105100001285 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105100001286 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105100001287 active site 1105100001288 HIGH motif; other site 1105100001289 KMSKS motif; other site 1105100001290 Predicted permeases [General function prediction only]; Region: COG0679 1105100001291 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105100001292 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105100001293 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105100001294 putative NAD(P) binding site [chemical binding]; other site 1105100001295 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 1105100001296 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 1105100001297 putative active site [active] 1105100001298 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105100001299 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105100001300 malate dehydrogenase; Reviewed; Region: PRK06223 1105100001301 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105100001302 NAD(P) binding site [chemical binding]; other site 1105100001303 dimer interface [polypeptide binding]; other site 1105100001304 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105100001305 substrate binding site [chemical binding]; other site 1105100001306 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 1105100001307 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105100001308 CTP synthetase; Validated; Region: pyrG; PRK05380 1105100001309 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 1105100001310 Catalytic site [active] 1105100001311 active site 1105100001312 UTP binding site [chemical binding]; other site 1105100001313 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105100001314 active site 1105100001315 putative oxyanion hole; other site 1105100001316 catalytic triad [active] 1105100001317 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1105100001318 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105100001319 Ligand binding site; other site 1105100001320 oligomer interface; other site 1105100001321 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 1105100001322 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 1105100001323 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105100001324 active site 1105100001325 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105100001326 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 1105100001327 dimer interface [polypeptide binding]; other site 1105100001328 motif 1; other site 1105100001329 active site 1105100001330 motif 2; other site 1105100001331 motif 3; other site 1105100001332 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 1105100001333 anticodon binding site; other site 1105100001334 Fic family protein [Function unknown]; Region: COG3177 1105100001335 Fic/DOC family; Region: Fic; pfam02661 1105100001336 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105100001337 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105100001338 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105100001339 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 1105100001340 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 1105100001341 Walker A motif; other site 1105100001342 ATP binding site [chemical binding]; other site 1105100001343 Walker B motif; other site 1105100001344 arginine finger; other site 1105100001345 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105100001346 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105100001347 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105100001348 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100001349 Walker A/P-loop; other site 1105100001350 ATP binding site [chemical binding]; other site 1105100001351 Q-loop/lid; other site 1105100001352 ABC transporter signature motif; other site 1105100001353 Walker B; other site 1105100001354 D-loop; other site 1105100001355 H-loop/switch region; other site 1105100001356 muropeptide transporter; Validated; Region: ampG; cl17669 1105100001357 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105100001358 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 1105100001359 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105100001360 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100001361 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105100001362 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1105100001363 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1105100001364 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105100001365 BON domain; Region: BON; pfam04972 1105100001366 BON domain; Region: BON; pfam04972 1105100001367 Intracellular septation protein A [Cell division and chromosome partitioning]; Region: COG2917 1105100001368 Iron permease FTR1 family; Region: FTR1; cl00475 1105100001369 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 1105100001370 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105100001371 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105100001372 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 1105100001373 active site 1105100001374 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 1105100001375 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1105100001376 catalytic residues [active] 1105100001377 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 1105100001378 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105100001379 tandem repeat interface [polypeptide binding]; other site 1105100001380 oligomer interface [polypeptide binding]; other site 1105100001381 active site residues [active] 1105100001382 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105100001383 trimer interface [polypeptide binding]; other site 1105100001384 active site 1105100001385 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105100001386 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 1105100001387 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105100001388 catalytic residue [active] 1105100001389 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105100001390 dimer interface [polypeptide binding]; other site 1105100001391 catalytic triad [active] 1105100001392 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105100001393 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 1105100001394 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105100001395 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105100001396 catalytic triad [active] 1105100001397 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105100001398 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 1105100001399 Subunit I/III interface [polypeptide binding]; other site 1105100001400 D-pathway; other site 1105100001401 Subunit I/VIIc interface [polypeptide binding]; other site 1105100001402 Subunit I/IV interface [polypeptide binding]; other site 1105100001403 Subunit I/II interface [polypeptide binding]; other site 1105100001404 Low-spin heme (heme a) binding site [chemical binding]; other site 1105100001405 Subunit I/VIIa interface [polypeptide binding]; other site 1105100001406 Subunit I/VIa interface [polypeptide binding]; other site 1105100001407 Dimer interface; other site 1105100001408 Putative water exit pathway; other site 1105100001409 Binuclear center (heme a3/CuB) [ion binding]; other site 1105100001410 K-pathway; other site 1105100001411 Subunit I/Vb interface [polypeptide binding]; other site 1105100001412 Putative proton exit pathway; other site 1105100001413 Subunit I/VIb interface; other site 1105100001414 Subunit I/VIc interface [polypeptide binding]; other site 1105100001415 Electron transfer pathway; other site 1105100001416 Subunit I/VIIIb interface [polypeptide binding]; other site 1105100001417 Subunit I/VIIb interface [polypeptide binding]; other site 1105100001418 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 1105100001419 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 1105100001420 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100001421 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105100001422 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105100001423 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 1105100001424 putative peptidase; Provisional; Region: PRK11649 1105100001425 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105100001426 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1105100001427 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 1105100001428 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105100001429 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105100001430 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105100001431 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105100001432 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105100001433 cell division protein FtsW; Region: ftsW; TIGR02614 1105100001434 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105100001435 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 1105100001436 active site 1105100001437 homodimer interface [polypeptide binding]; other site 1105100001438 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105100001439 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105100001440 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105100001441 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105100001442 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105100001443 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105100001444 potential frameshift: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 1105100001445 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105100001446 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 1105100001447 potential frameshift: common BLAST hit: gi|374319263|ref|YP_005065762.1| Transposase-like protein 1105100001448 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100001449 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100001450 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100001451 diaminopimelate epimerase; Region: DapF; TIGR00652 1105100001452 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105100001453 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105100001454 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105100001455 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105100001456 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 1105100001457 FeS/SAM binding site; other site 1105100001458 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105100001459 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105100001460 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 1105100001461 dimer interface [polypeptide binding]; other site 1105100001462 motif 1; other site 1105100001463 active site 1105100001464 motif 2; other site 1105100001465 motif 3; other site 1105100001466 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105100001467 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 1105100001468 putative tRNA-binding site [nucleotide binding]; other site 1105100001469 B3/4 domain; Region: B3_4; pfam03483 1105100001470 tRNA synthetase B5 domain; Region: B5; smart00874 1105100001471 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 1105100001472 dimer interface [polypeptide binding]; other site 1105100001473 motif 1; other site 1105100001474 motif 3; other site 1105100001475 motif 2; other site 1105100001476 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 1105100001477 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 1105100001478 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105100001479 putative DNA binding surface [nucleotide binding]; other site 1105100001480 dimer interface [polypeptide binding]; other site 1105100001481 beta-clamp/clamp loader binding surface; other site 1105100001482 beta-clamp/translesion DNA polymerase binding surface; other site 1105100001483 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105100001484 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105100001485 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105100001486 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105100001487 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105100001488 HIGH motif; other site 1105100001489 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105100001490 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105100001491 active site 1105100001492 KMSKS motif; other site 1105100001493 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105100001494 tRNA binding surface [nucleotide binding]; other site 1105100001495 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105100001496 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105100001497 catalytic site [active] 1105100001498 putative active site [active] 1105100001499 putative substrate binding site [chemical binding]; other site 1105100001500 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 1105100001501 Septum formation initiator; Region: DivIC; pfam04977 1105100001502 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1105100001503 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1105100001504 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 1105100001505 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105100001506 catalytic residue [active] 1105100001507 putative FPP diphosphate binding site; other site 1105100001508 putative FPP binding hydrophobic cleft; other site 1105100001509 dimer interface [polypeptide binding]; other site 1105100001510 putative IPP diphosphate binding site; other site 1105100001511 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105100001512 HAMP domain; Region: HAMP; pfam00672 1105100001513 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 1105100001514 dimer interface [polypeptide binding]; other site 1105100001515 phosphorylation site [posttranslational modification] 1105100001516 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 1105100001517 ATP binding site [chemical binding]; other site 1105100001518 Mg2+ binding site [ion binding]; other site 1105100001519 G-X-G motif; other site 1105100001520 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105100001521 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 1105100001522 active site 1105100001523 phosphorylation site [posttranslational modification] 1105100001524 intermolecular recognition site; other site 1105100001525 dimerization interface [polypeptide binding]; other site 1105100001526 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 1105100001527 DNA binding site [nucleotide binding] 1105100001528 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1105100001529 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 1105100001530 homodimer interface [polypeptide binding]; other site 1105100001531 substrate-cofactor binding pocket; other site 1105100001532 catalytic residue [active] 1105100001533 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105100001534 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105100001535 dimer interface [polypeptide binding]; other site 1105100001536 active site 1105100001537 catalytic residue [active] 1105100001538 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 1105100001539 SmpB-tmRNA interface; other site 1105100001540 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 1105100001541 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105100001542 catalytic residues [active] 1105100001543 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105100001544 CoA binding domain; Region: CoA_binding; pfam02629 1105100001545 CoA-ligase; Region: Ligase_CoA; pfam00549 1105100001546 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105100001547 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 1105100001548 CoA-ligase; Region: Ligase_CoA; pfam00549 1105100001549 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 1105100001550 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 1105100001551 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 1105100001552 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105100001553 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105100001554 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 1105100001555 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105100001556 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1105100001557 Predicted membrane protein [Function unknown]; Region: COG1238 1105100001558 Predicted membrane protein/domain [Function unknown]; Region: COG1714 1105100001559 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 1105100001560 RecR protein; Region: RecR; pfam02132 1105100001561 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 1105100001562 putative active site [active] 1105100001563 putative metal-binding site [ion binding]; other site 1105100001564 tetramer interface [polypeptide binding]; other site 1105100001565 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 1105100001566 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105100001567 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 1105100001568 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105100001569 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105100001570 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1105100001571 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105100001572 Predicted permeases [General function prediction only]; Region: COG0679 1105100001573 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 1105100001574 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105100001575 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105100001576 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105100001577 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1105100001578 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 1105100001579 tetramerization interface [polypeptide binding]; other site 1105100001580 NAD(P) binding site [chemical binding]; other site 1105100001581 catalytic residues [active] 1105100001582 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1105100001583 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 1105100001584 active site 1105100001585 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1105100001586 Part of AAA domain; Region: AAA_19; pfam13245 1105100001587 Family description; Region: UvrD_C_2; pfam13538 1105100001588 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 1105100001589 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105100001590 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 1105100001591 tetramer interface [polypeptide binding]; other site 1105100001592 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105100001593 catalytic residue [active] 1105100001594 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105100001595 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105100001596 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 1105100001597 Walker A motif; other site 1105100001598 ATP binding site [chemical binding]; other site 1105100001599 Walker B motif; other site 1105100001600 arginine finger; other site 1105100001601 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1105100001602 potential frameshift: common BLAST hit: gi|67459085|ref|YP_246709.1| cell surface antigen Sca3 1105100001603 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 1105100001604 30S subunit binding site; other site 1105100001605 potential frameshift: common BLAST hit: gi|238650270|ref|YP_002916122.1| carbonic anhydrase 1105100001606 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105100001607 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105100001608 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105100001609 homodimer interface [polypeptide binding]; other site 1105100001610 NADP binding site [chemical binding]; other site 1105100001611 substrate binding site [chemical binding]; other site 1105100001612 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105100001613 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1105100001614 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105100001615 Uncharacterized secreted protein [Function unknown]; Region: COG5430 1105100001616 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105100001617 potential frameshift: common BLAST hit: gi|91205792|ref|YP_538147.1| P pilus assembly, fimbrial usher protein 1105100001618 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105100001619 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105100001620 Spore Coat Protein U domain; Region: SCPU; pfam05229 1105100001621 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105100001622 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105100001623 active site 1105100001624 dimer interface [polypeptide binding]; other site 1105100001625 catalytic residues [active] 1105100001626 effector binding site; other site 1105100001627 R2 peptide binding site; other site 1105100001628 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105100001629 dimer interface [polypeptide binding]; other site 1105100001630 putative radical transfer pathway; other site 1105100001631 diiron center [ion binding]; other site 1105100001632 tyrosyl radical; other site 1105100001633 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105100001634 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 1105100001635 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105100001636 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105100001637 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 1105100001638 active site 1105100001639 substrate binding site [chemical binding]; other site 1105100001640 metal binding site [ion binding]; metal-binding site 1105100001641 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105100001642 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100001643 Walker A/P-loop; other site 1105100001644 ATP binding site [chemical binding]; other site 1105100001645 Q-loop/lid; other site 1105100001646 ABC transporter signature motif; other site 1105100001647 Walker B; other site 1105100001648 D-loop; other site 1105100001649 H-loop/switch region; other site 1105100001650 OstA-like protein; Region: OstA; pfam03968 1105100001651 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105100001652 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 1105100001653 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 1105100001654 putative active site [active] 1105100001655 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 1105100001656 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105100001657 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105100001658 RNase E interface [polypeptide binding]; other site 1105100001659 trimer interface [polypeptide binding]; other site 1105100001660 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105100001661 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105100001662 RNase E interface [polypeptide binding]; other site 1105100001663 trimer interface [polypeptide binding]; other site 1105100001664 active site 1105100001665 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 1105100001666 putative nucleic acid binding region [nucleotide binding]; other site 1105100001667 G-X-X-G motif; other site 1105100001668 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 1105100001669 RNA binding site [nucleotide binding]; other site 1105100001670 domain interface; other site 1105100001671 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 1105100001672 16S/18S rRNA binding site [nucleotide binding]; other site 1105100001673 S13e-L30e interaction site [polypeptide binding]; other site 1105100001674 25S rRNA binding site [nucleotide binding]; other site 1105100001675 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105100001676 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105100001677 RNA binding site [nucleotide binding]; other site 1105100001678 active site 1105100001679 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100001680 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105100001681 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105100001682 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 1105100001683 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 1105100001684 non-specific DNA binding site [nucleotide binding]; other site 1105100001685 salt bridge; other site 1105100001686 sequence-specific DNA binding site [nucleotide binding]; other site 1105100001687 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 1105100001688 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 1105100001689 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105100001690 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105100001691 uncharacterized protein, YfiH family; Region: TIGR00726 1105100001692 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 1105100001693 catalytic residues [active] 1105100001694 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100001695 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105100001696 putative active site [active] 1105100001697 homotetrameric interface [polypeptide binding]; other site 1105100001698 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105100001699 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105100001700 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 1105100001701 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1105100001702 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105100001703 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 1105100001704 GSH binding site (G-site) [chemical binding]; other site 1105100001705 C-terminal domain interface [polypeptide binding]; other site 1105100001706 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105100001707 N-terminal domain interface [polypeptide binding]; other site 1105100001708 dimer interface [polypeptide binding]; other site 1105100001709 substrate binding pocket (H-site) [chemical binding]; other site 1105100001710 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105100001711 conserved cys residue [active] 1105100001712 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 1105100001713 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1105100001714 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105100001715 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105100001716 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105100001717 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105100001718 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105100001719 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105100001720 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105100001721 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 1105100001722 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105100001723 Uncharacterized conserved protein [Function unknown]; Region: COG5448 1105100001724 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1105100001725 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105100001726 Predicted membrane protein [Function unknown]; Region: COG5346 1105100001727 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1105100001728 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105100001729 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105100001730 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 1105100001731 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105100001732 E3 interaction surface; other site 1105100001733 lipoyl attachment site [posttranslational modification]; other site 1105100001734 e3 binding domain; Region: E3_binding; pfam02817 1105100001735 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 1105100001736 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105100001737 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1105100001738 RF-1 domain; Region: RF-1; pfam00472 1105100001739 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105100001740 DHH family; Region: DHH; pfam01368 1105100001741 DHHA1 domain; Region: DHHA1; pfam02272 1105100001742 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 1105100001743 S-adenosylmethionine binding site [chemical binding]; other site 1105100001744 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105100001745 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105100001746 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1105100001747 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 1105100001748 RNA binding site [nucleotide binding]; other site 1105100001749 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 1105100001750 multimer interface [polypeptide binding]; other site 1105100001751 Walker A motif; other site 1105100001752 ATP binding site [chemical binding]; other site 1105100001753 Walker B motif; other site 1105100001754 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1105100001755 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105100001756 tandem repeat interface [polypeptide binding]; other site 1105100001757 oligomer interface [polypeptide binding]; other site 1105100001758 active site residues [active] 1105100001759 Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]; Region: HimA; COG0776 1105100001760 IHF - DNA interface [nucleotide binding]; other site 1105100001761 IHF dimer interface [polypeptide binding]; other site 1105100001762 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3022 1105100001763 hypothetical protein; Region: PHA00670 1105100001764 hypothetical protein; Region: PHA00670 1105100001765 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105100001766 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105100001767 active site 1105100001768 HIGH motif; other site 1105100001769 dimer interface [polypeptide binding]; other site 1105100001770 KMSKS motif; other site 1105100001771 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1105100001772 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105100001773 putative acyl-acceptor binding pocket; other site 1105100001774 Protein required for attachment to host cells [Cell motility and secretion]; Region: COG5622 1105100001775 RelB antitoxin; Region: RelB; cl01171 1105100001776 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105100001777 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1105100001778 HemY protein N-terminus; Region: HemY_N; pfam07219 1105100001779 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105100001780 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105100001781 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 1105100001782 active site 1105100001783 Lysine efflux permease [General function prediction only]; Region: COG1279 1105100001784 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105100001785 AmpG-like permease; Region: 2A0125; TIGR00901 1105100001786 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 1105100001787 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 1105100001788 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105100001789 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105100001790 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105100001791 substrate binding pocket [chemical binding]; other site 1105100001792 chain length determination region; other site 1105100001793 substrate-Mg2+ binding site; other site 1105100001794 catalytic residues [active] 1105100001795 aspartate-rich region 1; other site 1105100001796 active site lid residues [active] 1105100001797 aspartate-rich region 2; other site 1105100001798 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105100001799 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105100001800 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 1105100001801 active site 1105100001802 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105100001803 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1105100001804 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 1105100001805 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105100001806 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105100001807 trimerization site [polypeptide binding]; other site 1105100001808 active site 1105100001809 cysteine desulfurase; Provisional; Region: PRK14012 1105100001810 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105100001811 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105100001812 catalytic residue [active] 1105100001813 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 1105100001814 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1105100001815 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105100001816 catalytic residue [active] 1105100001817 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105100001818 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 1105100001819 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105100001820 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105100001821 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 1105100001822 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105100001823 Coenzyme A binding pocket [chemical binding]; other site 1105100001824 Predicted acetyltransferase [General function prediction only]; Region: COG5628 1105100001825 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105100001826 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 1105100001827 homotetramer interface [polypeptide binding]; other site 1105100001828 FMN binding site [chemical binding]; other site 1105100001829 homodimer contacts [polypeptide binding]; other site 1105100001830 putative active site [active] 1105100001831 putative substrate binding site [chemical binding]; other site 1105100001832 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 1105100001833 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105100001834 oligomer interface [polypeptide binding]; other site 1105100001835 active site residues [active] 1105100001836 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105100001837 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 1105100001838 RNA binding site [nucleotide binding]; other site 1105100001839 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 1105100001840 RNA binding site [nucleotide binding]; other site 1105100001841 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 1105100001842 RNA binding site [nucleotide binding]; other site 1105100001843 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 1105100001844 RNA binding site [nucleotide binding]; other site 1105100001845 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 1105100001846 RNA binding site [nucleotide binding]; other site 1105100001847 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 1105100001848 RNA binding site [nucleotide binding]; other site 1105100001849 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 1105100001850 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 1105100001851 CMP-binding site; other site 1105100001852 The sites determining sugar specificity; other site 1105100001853 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 1105100001854 non-specific DNA binding site [nucleotide binding]; other site 1105100001855 salt bridge; other site 1105100001856 sequence-specific DNA binding site [nucleotide binding]; other site 1105100001857 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 1105100001858 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 1105100001859 hypothetical protein; Region: PHA00670 1105100001860 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105100001861 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105100001862 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105100001863 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 1105100001864 domain interfaces; other site 1105100001865 active site 1105100001866 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105100001867 dimer interface [polypeptide binding]; other site 1105100001868 catalytic triad [active] 1105100001869 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 1105100001870 G-X-G motif; other site 1105100001871 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 1105100001872 dimer interface [polypeptide binding]; other site 1105100001873 phosphorylation site [posttranslational modification] 1105100001874 potential frameshift: common BLAST hit: gi|15892625|ref|NP_360339.1| sodium/pantothenate symporter 1105100001875 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 1105100001876 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105100001877 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105100001878 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105100001879 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105100001880 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105100001881 Uncharacterized conserved protein [Function unknown]; Region: COG1723 1105100001882 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 1105100001883 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105100001884 catalytic site [active] 1105100001885 putative active site [active] 1105100001886 putative substrate binding site [chemical binding]; other site 1105100001887 Helicase and RNase D C-terminal; Region: HRDC; smart00341 1105100001888 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 1105100001889 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 1105100001890 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105100001891 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 1105100001892 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105100001893 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105100001894 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1105100001895 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 1105100001896 S-adenosylmethionine binding site [chemical binding]; other site 1105100001897 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1105100001898 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 1105100001899 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105100001900 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105100001901 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 1105100001902 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105100001903 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 1105100001904 hypothetical protein; Validated; Region: PRK00110 1105100001905 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105100001906 Substrate binding site; other site 1105100001907 Mg++ binding site; other site 1105100001908 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 1105100001909 metal binding site [ion binding]; metal-binding site 1105100001910 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 1105100001911 Coenzyme A binding pocket [chemical binding]; other site 1105100001912 AAA domain; Region: AAA_17; pfam13207 1105100001913 AAA domain; Region: AAA_18; pfam13238 1105100001914 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105100001915 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105100001916 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 1105100001917 dimer interface [polypeptide binding]; other site 1105100001918 allosteric magnesium binding site [ion binding]; other site 1105100001919 active site 1105100001920 aspartate-rich active site metal binding site; other site 1105100001921 Schiff base residues; other site 1105100001922 primosome assembly protein PriA; Validated; Region: PRK05580 1105100001923 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 1105100001924 ATP binding site [chemical binding]; other site 1105100001925 putative Mg++ binding site [ion binding]; other site 1105100001926 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1105100001927 aromatic acid decarboxylase; Validated; Region: PRK05920 1105100001928 Flavoprotein; Region: Flavoprotein; pfam02441 1105100001929 SacI restriction endonuclease; Region: RE_SacI; pfam09566 1105100001930 replicative DNA helicase; Provisional; Region: PRK09165 1105100001931 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105100001932 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 1105100001933 Walker A motif; other site 1105100001934 ATP binding site [chemical binding]; other site 1105100001935 Walker B motif; other site 1105100001936 DNA binding loops [nucleotide binding] 1105100001937 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105100001938 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105100001939 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 1105100001940 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105100001941 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 1105100001942 RNA binding surface [nucleotide binding]; other site 1105100001943 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105100001944 active site 1105100001945 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105100001946 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105100001947 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105100001948 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105100001949 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105100001950 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1105100001951 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 1105100001952 S-adenosylmethionine binding site [chemical binding]; other site 1105100001953 DNA repair protein RadA; Provisional; Region: PRK11823 1105100001954 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 1105100001955 Walker A motif/ATP binding site; other site 1105100001956 ATP binding site [chemical binding]; other site 1105100001957 Walker B motif; other site 1105100001958 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1105100001959 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105100001960 Recombination protein O N terminal; Region: RecO_N; pfam11967 1105100001961 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105100001962 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 1105100001963 Glycoprotease family; Region: Peptidase_M22; pfam00814 1105100001964 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105100001965 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 1105100001966 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105100001967 G1 box; other site 1105100001968 putative GEF interaction site [polypeptide binding]; other site 1105100001969 GTP/Mg2+ binding site [chemical binding]; other site 1105100001970 Switch I region; other site 1105100001971 G2 box; other site 1105100001972 G3 box; other site 1105100001973 Switch II region; other site 1105100001974 G4 box; other site 1105100001975 G5 box; other site 1105100001976 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 1105100001977 Translation-initiation factor 2; Region: IF-2; pfam11987 1105100001978 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 1105100001979 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105100001980 NusA N-terminal domain; Region: NusA_N; pfam08529 1105100001981 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 1105100001982 RNA binding site [nucleotide binding]; other site 1105100001983 homodimer interface [polypeptide binding]; other site 1105100001984 NusA-like KH domain; Region: KH_5; pfam13184 1105100001985 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 1105100001986 G-X-X-G motif; other site 1105100001987 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105100001988 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 1105100001989 Sm and related proteins; Region: Sm_like; cl00259 1105100001990 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1105100001991 putative oligomer interface [polypeptide binding]; other site 1105100001992 putative RNA binding site [nucleotide binding]; other site 1105100001993 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 1105100001994 NAD binding pocket [chemical binding]; other site 1105100001995 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105100001996 Transcriptional regulator; Region: Rrf2; cl17282 1105100001997 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105100001998 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 1105100001999 RNA binding surface [nucleotide binding]; other site 1105100002000 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 1105100002001 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105100002002 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105100002003 active site 1105100002004 HIGH motif; other site 1105100002005 dimer interface [polypeptide binding]; other site 1105100002006 KMSKS motif; other site 1105100002007 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 1105100002008 RNA binding surface [nucleotide binding]; other site 1105100002009 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 1105100002010 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 1105100002011 proline/glycine betaine transporter; Provisional; Region: PRK10642 1105100002012 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105100002013 potential frameshift: common BLAST hit: gi|157964695|ref|YP_001499519.1| large extracellular alpha-helical protein 1105100002014 potential frameshift: common BLAST hit: gi|350273648|ref|YP_004884961.1| large extracellular alpha-helical protein 1105100002015 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105100002016 potential frameshift: common BLAST hit: gi|229586888|ref|YP_002845389.1| Large extracellular alpha-helical protein 1105100002017 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105100002018 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105100002019 potential frameshift: common BLAST hit: gi|67459282|ref|YP_246906.1| 3-hydroxyacyl-CoA dehydrogenase 1105100002020 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 1105100002021 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 1105100002022 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002023 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105100002024 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 1105100002025 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 1105100002026 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105100002027 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 1105100002028 active site 1105100002029 phosphorylation site [posttranslational modification] 1105100002030 intermolecular recognition site; other site 1105100002031 dimerization interface [polypeptide binding]; other site 1105100002032 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 1105100002033 Walker A motif; other site 1105100002034 ATP binding site [chemical binding]; other site 1105100002035 Walker B motif; other site 1105100002036 arginine finger; other site 1105100002037 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 1105100002038 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105100002039 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105100002040 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105100002041 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105100002042 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105100002043 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105100002044 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105100002045 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105100002046 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105100002047 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1105100002048 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105100002049 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1105100002050 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 1105100002051 S-adenosylmethionine binding site [chemical binding]; other site 1105100002052 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105100002053 MraZ protein; Region: MraZ; pfam02381 1105100002054 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105100002055 Na binding site [ion binding]; other site 1105100002056 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105100002057 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105100002058 GIY-YIG motif/motif A; other site 1105100002059 active site 1105100002060 catalytic site [active] 1105100002061 putative DNA binding site [nucleotide binding]; other site 1105100002062 metal binding site [ion binding]; metal-binding site 1105100002063 UvrB/uvrC motif; Region: UVR; pfam02151 1105100002064 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105100002065 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 1105100002066 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 1105100002067 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105100002068 active site 1105100002069 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 1105100002070 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105100002071 active site 1105100002072 DNA binding site [nucleotide binding] 1105100002073 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 1105100002074 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1105100002075 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105100002076 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 1105100002077 DNA binding site [nucleotide binding] 1105100002078 active site 1105100002079 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 1105100002080 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105100002081 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105100002082 DEAD/DEAH box helicase; Region: DEAD; pfam00270 1105100002083 ATP binding site [chemical binding]; other site 1105100002084 putative Mg++ binding site [ion binding]; other site 1105100002085 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1105100002086 SEC-C motif; Region: SEC-C; pfam02810 1105100002087 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 1105100002088 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1105100002089 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1105100002090 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 1105100002091 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105100002092 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 1105100002093 hinge; other site 1105100002094 active site 1105100002095 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105100002096 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 1105100002097 ATP binding site [chemical binding]; other site 1105100002098 Mg2+ binding site [ion binding]; other site 1105100002099 G-X-G motif; other site 1105100002100 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 1105100002101 anchoring element; other site 1105100002102 dimer interface [polypeptide binding]; other site 1105100002103 ATP binding site [chemical binding]; other site 1105100002104 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 1105100002105 active site 1105100002106 putative metal-binding site [ion binding]; other site 1105100002107 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105100002108 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105100002109 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 1105100002110 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 1105100002111 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105100002112 MgtE intracellular N domain; Region: MgtE_N; pfam03448 1105100002113 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 1105100002114 Divalent cation transporter; Region: MgtE; pfam01769 1105100002115 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105100002116 HD domain; Region: HD_4; pfam13328 1105100002117 Protein of unknown function (DUF969); Region: DUF969; cl01573 1105100002118 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 1105100002119 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105100002120 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1105100002121 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105100002122 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1105100002123 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105100002124 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 1105100002125 Cu(I) binding site [ion binding]; other site 1105100002126 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 1105100002127 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 1105100002128 dimer interface [polypeptide binding]; other site 1105100002129 substrate binding site [chemical binding]; other site 1105100002130 metal binding sites [ion binding]; metal-binding site 1105100002131 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002132 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1105100002133 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1105100002134 TraX protein; Region: TraX; pfam05857 1105100002135 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105100002136 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 1105100002137 ssDNA binding site; other site 1105100002138 generic binding surface II; other site 1105100002139 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 1105100002140 ATP binding site [chemical binding]; other site 1105100002141 putative Mg++ binding site [ion binding]; other site 1105100002142 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 1105100002143 nucleotide binding region [chemical binding]; other site 1105100002144 ATP-binding site [chemical binding]; other site 1105100002145 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1105100002146 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1105100002147 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 1105100002148 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105100002149 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 1105100002150 Mg++ binding site [ion binding]; other site 1105100002151 putative catalytic motif [active] 1105100002152 putative substrate binding site [chemical binding]; other site 1105100002153 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 1105100002154 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105100002155 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105100002156 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105100002157 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105100002158 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105100002159 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105100002160 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105100002161 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105100002162 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1105100002163 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 1105100002164 ATP binding site [chemical binding]; other site 1105100002165 putative Mg++ binding site [ion binding]; other site 1105100002166 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 1105100002167 nucleotide binding region [chemical binding]; other site 1105100002168 ATP-binding site [chemical binding]; other site 1105100002169 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1105100002170 Uncharacterized conserved protein [Function unknown]; Region: COG2938 1105100002171 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 1105100002172 active site residue [active] 1105100002173 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105100002174 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105100002175 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 1105100002176 Walker A motif; other site 1105100002177 ATP binding site [chemical binding]; other site 1105100002178 Walker B motif; other site 1105100002179 arginine finger; other site 1105100002180 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 1105100002181 DnaA box-binding interface [nucleotide binding]; other site 1105100002182 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 1105100002183 Patatin [General function prediction only]; Region: COG3621 1105100002184 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105100002185 active site 1105100002186 nucleophile elbow; other site 1105100002187 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105100002188 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105100002189 HEPN domain; Region: HEPN; cl00824 1105100002190 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1105100002191 metal binding triad [ion binding]; metal-binding site 1105100002192 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105100002193 YchF GTPase; Region: YchF; cd01900 1105100002194 G1 box; other site 1105100002195 GTP/Mg2+ binding site [chemical binding]; other site 1105100002196 Switch I region; other site 1105100002197 G2 box; other site 1105100002198 Switch II region; other site 1105100002199 G3 box; other site 1105100002200 G4 box; other site 1105100002201 G5 box; other site 1105100002202 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 1105100002203 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105100002204 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 1105100002205 putative active site [active] 1105100002206 catalytic residue [active] 1105100002207 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105100002208 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105100002209 5S rRNA interface [nucleotide binding]; other site 1105100002210 CTC domain interface [polypeptide binding]; other site 1105100002211 L16 interface [polypeptide binding]; other site 1105100002212 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105100002213 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 1105100002214 FeS/SAM binding site; other site 1105100002215 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1105100002216 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105100002217 23S rRNA binding site [nucleotide binding]; other site 1105100002218 L21 binding site [polypeptide binding]; other site 1105100002219 L13 binding site [polypeptide binding]; other site 1105100002220 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1105100002221 ribonuclease P; Reviewed; Region: rnpA; PRK01492 1105100002222 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105100002223 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105100002224 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 1105100002225 Cl binding site [ion binding]; other site 1105100002226 oligomer interface [polypeptide binding]; other site 1105100002227 potential frameshift: common BLAST hit: gi|157828799|ref|YP_001495041.1| acetyltransferase 1105100002228 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 1105100002229 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105100002230 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 1105100002231 dimerization interface [polypeptide binding]; other site 1105100002232 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 1105100002233 dimer interface [polypeptide binding]; other site 1105100002234 phosphorylation site [posttranslational modification] 1105100002235 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 1105100002236 ATP binding site [chemical binding]; other site 1105100002237 Mg2+ binding site [ion binding]; other site 1105100002238 G-X-G motif; other site 1105100002239 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 1105100002240 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105100002241 COQ9; Region: COQ9; pfam08511 1105100002242 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105100002243 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105100002244 HIGH motif; other site 1105100002245 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105100002246 active site 1105100002247 KMSKS motif; other site 1105100002248 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105100002249 tRNA binding surface [nucleotide binding]; other site 1105100002250 anticodon binding site; other site 1105100002251 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 1105100002252 TPR motif; other site 1105100002253 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105100002254 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105100002255 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1105100002256 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1105100002257 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 1105100002258 carboxyltransferase (CT) interaction site; other site 1105100002259 biotinylation site [posttranslational modification]; other site 1105100002260 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 1105100002261 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1105100002262 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 1105100002263 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105100002264 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 1105100002265 putative substrate translocation pore; other site 1105100002266 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105100002267 putative acyl-acceptor binding pocket; other site 1105100002268 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 1105100002269 acyl-activating enzyme (AAE) consensus motif; other site 1105100002270 putative AMP binding site [chemical binding]; other site 1105100002271 TfoX N-terminal domain; Region: TfoX_N; pfam04993 1105100002272 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 1105100002273 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 1105100002274 ABC-ATPase subunit interface; other site 1105100002275 dimer interface [polypeptide binding]; other site 1105100002276 putative PBP binding regions; other site 1105100002277 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105100002278 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002279 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 1105100002280 S-adenosylmethionine binding site [chemical binding]; other site 1105100002281 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105100002282 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105100002283 HIGH motif; other site 1105100002284 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105100002285 active site 1105100002286 KMSKS motif; other site 1105100002287 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002288 Invasion protein B, involved in pathogenesis [General function prediction only]; Region: COG5342 1105100002289 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105100002290 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 1105100002291 ring oligomerisation interface [polypeptide binding]; other site 1105100002292 ATP/Mg binding site [chemical binding]; other site 1105100002293 stacking interactions; other site 1105100002294 hinge regions; other site 1105100002295 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 1105100002296 oligomerisation interface [polypeptide binding]; other site 1105100002297 mobile loop; other site 1105100002298 roof hairpin; other site 1105100002299 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105100002300 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 1105100002301 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105100002302 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105100002303 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105100002304 hexamer interface [polypeptide binding]; other site 1105100002305 active site 1105100002306 GrpE; Region: GrpE; pfam01025 1105100002307 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 1105100002308 dimer interface [polypeptide binding]; other site 1105100002309 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105100002310 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1105100002311 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105100002312 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 1105100002313 hypothetical protein; Validated; Region: PRK06620 1105100002314 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105100002315 potential frameshift: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 1105100002316 HD domain; Region: HD_4; pfam13328 1105100002317 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1105100002318 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 1105100002319 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105100002320 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105100002321 alphaNTD - beta interaction site [polypeptide binding]; other site 1105100002322 alphaNTD homodimer interface [polypeptide binding]; other site 1105100002323 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105100002324 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1105100002325 30S ribosomal protein S11; Validated; Region: PRK05309 1105100002326 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105100002327 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1105100002328 adenylate kinase; Reviewed; Region: adk; PRK00279 1105100002329 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 1105100002330 AMP-binding site [chemical binding]; other site 1105100002331 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105100002332 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105100002333 SecY translocase; Region: SecY; pfam00344 1105100002334 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1105100002335 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 1105100002336 23S rRNA binding site [nucleotide binding]; other site 1105100002337 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105100002338 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105100002339 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105100002340 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 1105100002341 5S rRNA interface [nucleotide binding]; other site 1105100002342 23S rRNA interface [nucleotide binding]; other site 1105100002343 L5 interface [polypeptide binding]; other site 1105100002344 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105100002345 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105100002346 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105100002347 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1105100002348 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 1105100002349 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105100002350 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105100002351 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105100002352 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105100002353 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1105100002354 RNA binding site [nucleotide binding]; other site 1105100002355 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1105100002356 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1105100002357 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 1105100002358 L23 interface [polypeptide binding]; other site 1105100002359 trigger factor interaction site; other site 1105100002360 23S rRNA interface [nucleotide binding]; other site 1105100002361 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 1105100002362 23S rRNA interface [nucleotide binding]; other site 1105100002363 5S rRNA interface [nucleotide binding]; other site 1105100002364 putative antibiotic binding site [chemical binding]; other site 1105100002365 L25 interface [polypeptide binding]; other site 1105100002366 L27 interface [polypeptide binding]; other site 1105100002367 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105100002368 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 1105100002369 G-X-X-G motif; other site 1105100002370 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105100002371 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 1105100002372 putative translocon binding site; other site 1105100002373 protein-rRNA interface [nucleotide binding]; other site 1105100002374 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1105100002375 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105100002376 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105100002377 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105100002378 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1105100002379 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 1105100002380 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 1105100002381 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1105100002382 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002383 elongation factor Tu; Reviewed; Region: PRK00049 1105100002384 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105100002385 G1 box; other site 1105100002386 GEF interaction site [polypeptide binding]; other site 1105100002387 GTP/Mg2+ binding site [chemical binding]; other site 1105100002388 Switch I region; other site 1105100002389 G2 box; other site 1105100002390 G3 box; other site 1105100002391 Switch II region; other site 1105100002392 G4 box; other site 1105100002393 G5 box; other site 1105100002394 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 1105100002395 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 1105100002396 Antibiotic Binding Site [chemical binding]; other site 1105100002397 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105100002398 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1105100002399 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1105100002400 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105100002401 Class II fumarases; Region: Fumarase_classII; cd01362 1105100002402 active site 1105100002403 tetramer interface [polypeptide binding]; other site 1105100002404 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 1105100002405 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105100002406 putative active site [active] 1105100002407 homotetrameric interface [polypeptide binding]; other site 1105100002408 cell division protein FtsZ; Validated; Region: PRK09330 1105100002409 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 1105100002410 nucleotide binding site [chemical binding]; other site 1105100002411 SulA interaction site; other site 1105100002412 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 1105100002413 secondary substrate binding site; other site 1105100002414 primary substrate binding site; other site 1105100002415 inhibition loop; other site 1105100002416 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 1105100002417 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1105100002418 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 1105100002419 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105100002420 putative substrate translocation pore; other site 1105100002421 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 1105100002422 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105100002423 ATP binding site [chemical binding]; other site 1105100002424 Mg++ binding site [ion binding]; other site 1105100002425 motif III; other site 1105100002426 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 1105100002427 nucleotide binding region [chemical binding]; other site 1105100002428 ATP-binding site [chemical binding]; other site 1105100002429 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 1105100002430 DNA-binding site [nucleotide binding]; DNA binding site 1105100002431 RNA-binding motif; other site 1105100002432 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1105100002433 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 1105100002434 S-adenosylmethionine binding site [chemical binding]; other site 1105100002435 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105100002436 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105100002437 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105100002438 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 1105100002439 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 1105100002440 generic binding surface II; other site 1105100002441 generic binding surface I; other site 1105100002442 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105100002443 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 1105100002444 putative catalytic site [active] 1105100002445 putative phosphate binding site [ion binding]; other site 1105100002446 active site 1105100002447 metal binding site A [ion binding]; metal-binding site 1105100002448 DNA binding site [nucleotide binding] 1105100002449 putative AP binding site [nucleotide binding]; other site 1105100002450 putative metal binding site B [ion binding]; other site 1105100002451 Uncharacterized conserved protein [Function unknown]; Region: COG4095 1105100002452 GTP-binding protein Der; Reviewed; Region: PRK00093 1105100002453 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105100002454 G1 box; other site 1105100002455 GTP/Mg2+ binding site [chemical binding]; other site 1105100002456 Switch I region; other site 1105100002457 G2 box; other site 1105100002458 Switch II region; other site 1105100002459 G3 box; other site 1105100002460 G4 box; other site 1105100002461 G5 box; other site 1105100002462 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105100002463 G1 box; other site 1105100002464 GTP/Mg2+ binding site [chemical binding]; other site 1105100002465 Switch I region; other site 1105100002466 G2 box; other site 1105100002467 G3 box; other site 1105100002468 Switch II region; other site 1105100002469 G4 box; other site 1105100002470 G5 box; other site 1105100002471 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105100002472 AAA domain; Region: AAA_14; pfam13173 1105100002473 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 1105100002474 ABC1 family; Region: ABC1; pfam03109 1105100002475 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 1105100002476 active site 1105100002477 ATP binding site [chemical binding]; other site 1105100002478 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105100002479 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 1105100002480 S-adenosylmethionine binding site [chemical binding]; other site 1105100002481 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105100002482 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105100002483 DNA binding site [nucleotide binding] 1105100002484 catalytic residue [active] 1105100002485 H2TH interface [polypeptide binding]; other site 1105100002486 putative catalytic residues [active] 1105100002487 turnover-facilitating residue; other site 1105100002488 intercalation triad [nucleotide binding]; other site 1105100002489 8OG recognition residue [nucleotide binding]; other site 1105100002490 putative reading head residues; other site 1105100002491 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105100002492 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105100002493 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002494 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105100002495 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 1105100002496 active site 1105100002497 potential frameshift: common BLAST hit: gi|15892963|ref|NP_360677.1| mannose-1-phosphate guanylyltransferase 1105100002498 potential frameshift: common BLAST hit: gi|67458630|ref|YP_246254.1| Poly-beta-hydroxyalkanoate depolymerase 1105100002499 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105100002500 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105100002501 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105100002502 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105100002503 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 1105100002504 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105100002505 active site 1105100002506 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105100002507 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105100002508 HIGH motif; other site 1105100002509 active site 1105100002510 KMSKS motif; other site 1105100002511 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105100002512 tRNA binding surface [nucleotide binding]; other site 1105100002513 anticodon binding site; other site 1105100002514 thymidylate kinase; Validated; Region: tmk; PRK00698 1105100002515 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 1105100002516 TMP-binding site; other site 1105100002517 ATP-binding site [chemical binding]; other site 1105100002518 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105100002519 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 1105100002520 UbiA prenyltransferase family; Region: UbiA; pfam01040 1105100002521 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105100002522 potential frameshift: common BLAST hit: gi|67458622|ref|YP_246246.1| transposase 1105100002523 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105100002524 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105100002525 active site 1105100002526 HIGH motif; other site 1105100002527 nucleotide binding site [chemical binding]; other site 1105100002528 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105100002529 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105100002530 active site 1105100002531 KMSKS motif; other site 1105100002532 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105100002533 tRNA binding surface [nucleotide binding]; other site 1105100002534 anticodon binding site; other site 1105100002535 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105100002536 LPS biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3475 1105100002537 potential frameshift: common BLAST hit: gi|157804076|ref|YP_001492625.1| ATPase 1105100002538 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 1105100002539 RmuC family; Region: RmuC; pfam02646 1105100002540 potential frameshift: common BLAST hit: gi|341584242|ref|YP_004764733.1| Alpha-(1,3)-fucosyltransferase 1105100002541 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 1105100002542 DoxX-like family; Region: DoxX_3; pfam13781 1105100002543 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105100002544 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 1105100002545 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 1105100002546 Walker A motif; other site 1105100002547 ATP binding site [chemical binding]; other site 1105100002548 Walker B motif; other site 1105100002549 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1105100002550 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105100002551 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1105100002552 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 1105100002553 Ligand Binding Site [chemical binding]; other site 1105100002554 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 1105100002555 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 1105100002556 HicB family; Region: HicB; pfam05534 1105100002557 YcfA-like protein; Region: YcfA; cl00752 1105100002558 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105100002559 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1105100002560 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100002561 Walker A/P-loop; other site 1105100002562 ATP binding site [chemical binding]; other site 1105100002563 Q-loop/lid; other site 1105100002564 ABC transporter signature motif; other site 1105100002565 Walker B; other site 1105100002566 D-loop; other site 1105100002567 H-loop/switch region; other site 1105100002568 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105100002569 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105100002570 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 1105100002571 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105100002572 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105100002573 FtsX-like permease family; Region: FtsX; pfam02687 1105100002574 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105100002575 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 1105100002576 Walker A/P-loop; other site 1105100002577 ATP binding site [chemical binding]; other site 1105100002578 Q-loop/lid; other site 1105100002579 ABC transporter signature motif; other site 1105100002580 Walker B; other site 1105100002581 D-loop; other site 1105100002582 H-loop/switch region; other site 1105100002583 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105100002584 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105100002585 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 1105100002586 Transporter associated domain; Region: CorC_HlyC; smart01091 1105100002587 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 1105100002588 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 1105100002589 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105100002590 Autotransporter beta-domain; Region: Autotransporter; smart00869 1105100002591 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105100002592 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105100002593 synthetase active site [active] 1105100002594 NTP binding site [chemical binding]; other site 1105100002595 metal binding site [ion binding]; metal-binding site 1105100002596 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 1105100002597 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105100002598 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1105100002599 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105100002600 DNA binding residues [nucleotide binding] 1105100002601 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 1105100002602 IHF dimer interface [polypeptide binding]; other site 1105100002603 IHF - DNA interface [nucleotide binding]; other site 1105100002604 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105100002605 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 1105100002606 catalytic triad [active] 1105100002607 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105100002608 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105100002609 putative acyl-acceptor binding pocket; other site 1105100002610 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 1105100002611 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1105100002612 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1105100002613 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105100002614 Protein of unknown function (DUF519); Region: DUF519; pfam04378 1105100002615 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105100002616 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 1105100002617 nucleotide binding pocket [chemical binding]; other site 1105100002618 K-X-D-G motif; other site 1105100002619 catalytic site [active] 1105100002620 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105100002621 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105100002622 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 1105100002623 Dimer interface [polypeptide binding]; other site 1105100002624 BRCT sequence motif; other site 1105100002625 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1105100002626 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105100002627 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 1105100002628 HD domain; Region: HD_4; pfam13328 1105100002629 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 1105100002630 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1105100002631 mce related protein; Region: MCE; pfam02470 1105100002632 hypothetical protein; Provisional; Region: PRK06630 1105100002633 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105100002634 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105100002635 active site 1105100002636 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 1105100002637 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 1105100002638 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105100002639 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 1105100002640 CoA-binding site [chemical binding]; other site 1105100002641 ATP-binding [chemical binding]; other site 1105100002642 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105100002643 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 1105100002644 active site 1105100002645 catalytic site [active] 1105100002646 substrate binding site [chemical binding]; other site 1105100002647 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 1105100002648 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105100002649 Part of AAA domain; Region: AAA_19; pfam13245 1105100002650 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 1105100002651 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 1105100002652 Family description; Region: UvrD_C_2; pfam13538 1105100002653 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1105100002654 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105100002655 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105100002656 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105100002657 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105100002658 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105100002659 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105100002660 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 1105100002661 nudix motif; other site 1105100002662 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1105100002663 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 1105100002664 Transporter associated domain; Region: CorC_HlyC; smart01091 1105100002665 metal-binding heat shock protein; Provisional; Region: PRK00016 1105100002666 PemK-like protein; Region: PemK; cl00995 1105100002667 lipoyl synthase; Provisional; Region: PRK05481 1105100002668 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 1105100002669 FeS/SAM binding site; other site 1105100002670 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105100002671 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 1105100002672 dimer interface [polypeptide binding]; other site 1105100002673 active site 1105100002674 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105100002675 folate binding site [chemical binding]; other site 1105100002676 Predicted esterase [General function prediction only]; Region: COG0400 1105100002677 putative hydrolase; Provisional; Region: PRK11460 1105100002678 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 1105100002679 putative GSH binding site [chemical binding]; other site 1105100002680 catalytic residues [active] 1105100002681 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105100002682 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105100002683 minor groove reading motif; other site 1105100002684 helix-hairpin-helix signature motif; other site 1105100002685 substrate binding pocket [chemical binding]; other site 1105100002686 active site 1105100002687 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1105100002688 Predicted small secreted protein [Function unknown]; Region: COG5510 1105100002689 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100002690 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100002691 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105100002692 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1105100002693 putative SAM binding site [chemical binding]; other site 1105100002694 putative homodimer interface [polypeptide binding]; other site 1105100002695 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105100002696 putative ligand binding site [chemical binding]; other site 1105100002697 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 1105100002698 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105100002699 tetramer interfaces [polypeptide binding]; other site 1105100002700 binuclear metal-binding site [ion binding]; other site 1105100002701 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 1105100002702 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1105100002703 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1105100002704 aspartate kinase; Reviewed; Region: PRK06635 1105100002705 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 1105100002706 putative nucleotide binding site [chemical binding]; other site 1105100002707 putative catalytic residues [active] 1105100002708 putative Mg ion binding site [ion binding]; other site 1105100002709 putative aspartate binding site [chemical binding]; other site 1105100002710 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 1105100002711 putative allosteric regulatory residue; other site 1105100002712 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 1105100002713 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105100002714 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 1105100002715 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1105100002716 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105100002717 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 1105100002718 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105100002719 putative substrate translocation pore; other site 1105100002720 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 1105100002721 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002722 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 1105100002723 Helix-turn-helix domain; Region: HTH_25; pfam13413 1105100002724 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105100002725 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 1105100002726 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 1105100002727 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105100002728 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105100002729 G1 box; other site 1105100002730 GTP/Mg2+ binding site [chemical binding]; other site 1105100002731 Switch I region; other site 1105100002732 G2 box; other site 1105100002733 Switch II region; other site 1105100002734 G3 box; other site 1105100002735 G4 box; other site 1105100002736 G5 box; other site 1105100002737 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105100002738 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105100002739 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 1105100002740 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 1105100002741 hexamer interface [polypeptide binding]; other site 1105100002742 Walker A motif; other site 1105100002743 ATP binding site [chemical binding]; other site 1105100002744 Walker B motif; other site 1105100002745 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105100002746 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105100002747 NAD(P) binding site [chemical binding]; other site 1105100002748 active site 1105100002749 acyl carrier protein; Provisional; Region: acpP; PRK00982 1105100002750 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105100002751 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 1105100002752 dimer interface [polypeptide binding]; other site 1105100002753 active site 1105100002754 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 1105100002755 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105100002756 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1105100002757 endonuclease subunit; Provisional; Region: 46; PHA02562 1105100002758 AAA domain; Region: AAA_14; pfam13173 1105100002759 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105100002760 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002761 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105100002762 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 1105100002763 catalytic site [active] 1105100002764 G-X2-G-X-G-K; other site 1105100002765 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 1105100002766 sequence-specific DNA binding site [nucleotide binding]; other site 1105100002767 salt bridge; other site 1105100002768 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 1105100002769 rod shape-determining protein MreC; Region: MreC; pfam04085 1105100002770 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105100002771 MreB and similar proteins; Region: MreB_like; cd10225 1105100002772 nucleotide binding site [chemical binding]; other site 1105100002773 Mg binding site [ion binding]; other site 1105100002774 putative protofilament interaction site [polypeptide binding]; other site 1105100002775 RodZ interaction site [polypeptide binding]; other site 1105100002776 Predicted permeases [General function prediction only]; Region: COG0795 1105100002777 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105100002778 putative outer membrane lipoprotein; Provisional; Region: PRK09967 1105100002779 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105100002780 ligand binding site [chemical binding]; other site 1105100002781 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105100002782 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105100002783 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 1105100002784 dimer interface [polypeptide binding]; other site 1105100002785 active site 1105100002786 CoA binding pocket [chemical binding]; other site 1105100002787 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 1105100002788 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 1105100002789 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 1105100002790 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105100002791 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 1105100002792 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 1105100002793 P loop; other site 1105100002794 GTP binding site [chemical binding]; other site 1105100002795 DNA polymerase I; Provisional; Region: PRK05755 1105100002796 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105100002797 active site 1105100002798 metal binding site 1 [ion binding]; metal-binding site 1105100002799 putative 5' ssDNA interaction site; other site 1105100002800 metal binding site 3; metal-binding site 1105100002801 metal binding site 2 [ion binding]; metal-binding site 1105100002802 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105100002803 putative DNA binding site [nucleotide binding]; other site 1105100002804 putative metal binding site [ion binding]; other site 1105100002805 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105100002806 active site 1105100002807 substrate binding site [chemical binding]; other site 1105100002808 catalytic site [active] 1105100002809 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105100002810 active site 1105100002811 DNA binding site [nucleotide binding] 1105100002812 catalytic site [active] 1105100002813 potential frameshift: common BLAST hit: gi|157826229|ref|YP_001493949.1| S-adenosylmethionine synthetase 1105100002814 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1105100002815 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105100002816 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105100002817 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 1105100002818 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105100002819 putative active site [active] 1105100002820 putative PHP Thumb interface [polypeptide binding]; other site 1105100002821 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 1105100002822 generic binding surface I; other site 1105100002823 generic binding surface II; other site 1105100002824 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105100002825 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105100002826 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 1105100002827 Protein of unknown function; Region: DUF3971; pfam13116 1105100002828 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 1105100002829 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 1105100002830 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 1105100002831 putative substrate translocation pore; other site 1105100002832 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1105100002833 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105100002834 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105100002835 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 1105100002836 dimer interface [polypeptide binding]; other site 1105100002837 active site 1105100002838 motif 1; other site 1105100002839 motif 2; other site 1105100002840 motif 3; other site 1105100002841 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105100002842 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105100002843 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105100002844 Integral membrane protein TerC family; Region: TerC; cl10468 1105100002845 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105100002846 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1105100002847 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 1105100002848 S-adenosylmethionine binding site [chemical binding]; other site 1105100002849 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105100002850 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105100002851 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 1105100002852 salt bridge; other site 1105100002853 non-specific DNA binding site [nucleotide binding]; other site 1105100002854 sequence-specific DNA binding site [nucleotide binding]; other site 1105100002855 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105100002856 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1105100002857 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1105100002858 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105100002859 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105100002860 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105100002861 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105100002862 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1105100002863 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105100002864 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100002865 Walker A/P-loop; other site 1105100002866 ATP binding site [chemical binding]; other site 1105100002867 Q-loop/lid; other site 1105100002868 ABC transporter signature motif; other site 1105100002869 Walker B; other site 1105100002870 D-loop; other site 1105100002871 H-loop/switch region; other site 1105100002872 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105100002873 4Fe-4S binding domain; Region: Fer4; cl02805 1105100002874 4Fe-4S binding domain; Region: Fer4; pfam00037 1105100002875 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1105100002876 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1105100002877 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105100002878 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 1105100002879 catalytic loop [active] 1105100002880 iron binding site [ion binding]; other site 1105100002881 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1105100002882 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 1105100002883 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105100002884 Predicted membrane protein [Function unknown]; Region: COG3671 1105100002885 aconitate hydratase; Validated; Region: PRK09277 1105100002886 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105100002887 substrate binding site [chemical binding]; other site 1105100002888 ligand binding site [chemical binding]; other site 1105100002889 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 1105100002890 substrate binding site [chemical binding]; other site 1105100002891 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105100002892 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1105100002893 gamma subunit interface [polypeptide binding]; other site 1105100002894 epsilon subunit interface [polypeptide binding]; other site 1105100002895 LBP interface [polypeptide binding]; other site 1105100002896 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105100002897 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105100002898 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 1105100002899 alpha subunit interaction interface [polypeptide binding]; other site 1105100002900 Walker A motif; other site 1105100002901 ATP binding site [chemical binding]; other site 1105100002902 Walker B motif; other site 1105100002903 inhibitor binding site; inhibition site 1105100002904 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105100002905 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1105100002906 core domain interface [polypeptide binding]; other site 1105100002907 delta subunit interface [polypeptide binding]; other site 1105100002908 epsilon subunit interface [polypeptide binding]; other site 1105100002909 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105100002910 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1105100002911 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 1105100002912 beta subunit interaction interface [polypeptide binding]; other site 1105100002913 Walker A motif; other site 1105100002914 ATP binding site [chemical binding]; other site 1105100002915 Walker B motif; other site 1105100002916 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105100002917 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 1105100002918 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105100002919 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105100002920 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1105100002921 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105100002922 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105100002923 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1105100002924 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1105100002925 dimerization interface [polypeptide binding]; other site 1105100002926 DPS ferroxidase diiron center [ion binding]; other site 1105100002927 ion pore; other site 1105100002928 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105100002929 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 1105100002930 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105100002931 Transglycosylase; Region: Transgly; pfam00912 1105100002932 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 1105100002933 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105100002934 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105100002935 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 1105100002936 FeS/SAM binding site; other site 1105100002937 TRAM domain; Region: TRAM; pfam01938 1105100002938 HEPN domain; Region: HEPN; cl00824 1105100002939 potential frameshift: common BLAST hit: gi|67459332|ref|YP_246956.1| nucleotidyltransferase/HEPN domain-containing protein 1105100002940 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100002941 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105100002942 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 1105100002943 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105100002944 Bacterial SH3 domain; Region: SH3_4; pfam06347 1105100002945 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105100002946 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1105100002947 TrkA-N domain; Region: TrkA_N; pfam02254 1105100002948 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 1105100002949 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 1105100002950 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105100002951 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105100002952 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105100002953 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 1105100002954 rRNA binding site [nucleotide binding]; other site 1105100002955 predicted 30S ribosome binding site; other site 1105100002956 Maf-like protein; Region: Maf; pfam02545 1105100002957 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 1105100002958 active site 1105100002959 dimer interface [polypeptide binding]; other site 1105100002960 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 1105100002961 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105100002962 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 1105100002963 active site 1105100002964 DNA binding site [nucleotide binding] 1105100002965 Int/Topo IB signature motif; other site 1105100002966 Phasin protein; Region: Phasin_2; cl11491 1105100002967 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105100002968 PLD-like domain; Region: PLDc_2; pfam13091 1105100002969 putative active site [active] 1105100002970 catalytic site [active] 1105100002971 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105100002972 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105100002973 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 1105100002974 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 1105100002975 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1105100002976 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105100002977 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1105100002978 potential frameshift: common BLAST hit: gi|157964970|ref|YP_001499794.1| ankyrin repeat-containing protein 1105100002979 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105100002980 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1105100002981 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 1105100002982 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 1105100002983 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 1105100002984 active site 1105100002985 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105100002986 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105100002987 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105100002988 MPN+ (JAMM) motif; other site 1105100002989 Zinc-binding site [ion binding]; other site 1105100002990 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105100002991 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 1105100002992 Mg++ binding site [ion binding]; other site 1105100002993 putative catalytic motif [active] 1105100002994 putative substrate binding site [chemical binding]; other site 1105100002995 Protein of unknown function (DUF721); Region: DUF721; pfam05258 1105100002996 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105100002997 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 1105100002998 Ferredoxin [Energy production and conversion]; Region: COG1146 1105100002999 4Fe-4S binding domain; Region: Fer4; cl02805 1105100003000 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105100003001 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 1105100003002 nucleoside/Zn binding site; other site 1105100003003 dimer interface [polypeptide binding]; other site 1105100003004 catalytic motif [active] 1105100003005 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105100003006 Cation efflux family; Region: Cation_efflux; cl00316 1105100003007 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105100003008 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105100003009 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105100003010 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 1105100003011 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105100003012 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105100003013 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 1105100003014 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 1105100003015 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105100003016 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 1105100003017 dimer interface [polypeptide binding]; other site 1105100003018 ssDNA binding site [nucleotide binding]; other site 1105100003019 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105100003020 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 1105100003021 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 1105100003022 hypothetical protein; Reviewed; Region: PRK01530 1105100003023 heat shock protein 90; Provisional; Region: PRK05218 1105100003024 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 1105100003025 ATP binding site [chemical binding]; other site 1105100003026 Mg2+ binding site [ion binding]; other site 1105100003027 G-X-G motif; other site 1105100003028 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1105100003029 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 1105100003030 substrate-cofactor binding pocket; other site 1105100003031 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105100003032 catalytic residue [active] 1105100003033 trigger factor; Provisional; Region: tig; PRK01490 1105100003034 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1105100003035 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105100003036 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105100003037 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105100003038 Obg GTPase; Region: Obg; cd01898 1105100003039 G1 box; other site 1105100003040 GTP/Mg2+ binding site [chemical binding]; other site 1105100003041 Switch I region; other site 1105100003042 G2 box; other site 1105100003043 G3 box; other site 1105100003044 Switch II region; other site 1105100003045 G4 box; other site 1105100003046 G5 box; other site 1105100003047 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 1105100003048 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 1105100003049 dimer interface [polypeptide binding]; other site 1105100003050 active site 1105100003051 citrylCoA binding site [chemical binding]; other site 1105100003052 NADH binding [chemical binding]; other site 1105100003053 cationic pore residues; other site 1105100003054 oxalacetate/citrate binding site [chemical binding]; other site 1105100003055 coenzyme A binding site [chemical binding]; other site 1105100003056 catalytic triad [active] 1105100003057 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 1105100003058 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105100003059 Fe-S cluster binding site [ion binding]; other site 1105100003060 active site 1105100003061 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105100003062 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 1105100003063 RNA binding surface [nucleotide binding]; other site 1105100003064 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105100003065 active site 1105100003066 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105100003067 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 1105100003068 S-adenosylmethionine binding site [chemical binding]; other site 1105100003069 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 1105100003070 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 1105100003071 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105100003072 Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]; Region: GlyS; COG0751 1105100003073 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105100003074 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 1105100003075 motif 1; other site 1105100003076 dimer interface [polypeptide binding]; other site 1105100003077 active site 1105100003078 motif 2; other site 1105100003079 motif 3; other site 1105100003080 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 1105100003081 oligomeric interface; other site 1105100003082 putative active site [active] 1105100003083 homodimer interface [polypeptide binding]; other site 1105100003084 prevent-host-death family protein; Region: phd_fam; TIGR01552 1105100003085 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 1105100003086 potential frameshift: common BLAST hit: gi|350273988|ref|YP_004885301.1| proline/betaine transporter 1105100003087 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105100003088 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 1105100003089 motif 1; other site 1105100003090 active site 1105100003091 motif 2; other site 1105100003092 motif 3; other site 1105100003093 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1105100003094 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105100003095 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105100003096 dimerization interface 3.5A [polypeptide binding]; other site 1105100003097 active site 1105100003098 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105100003099 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105100003100 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105100003101 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105100003102 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105100003103 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 1105100003104 DNA binding residues [nucleotide binding] 1105100003105 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105100003106 CHC2 zinc finger; Region: zf-CHC2; pfam01807 1105100003107 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105100003108 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 1105100003109 active site 1105100003110 metal binding site [ion binding]; metal-binding site 1105100003111 interdomain interaction site; other site 1105100003112 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 1105100003113 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105100003114 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105100003115 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105100003116 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105100003117 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105100003118 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 1105100003119 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105100003120 ligand binding site [chemical binding]; other site 1105100003121 homodimer interface [polypeptide binding]; other site 1105100003122 NAD(P) binding site [chemical binding]; other site 1105100003123 trimer interface B [polypeptide binding]; other site 1105100003124 trimer interface A [polypeptide binding]; other site 1105100003125 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105100003126 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 1105100003127 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 1105100003128 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 1105100003129 Walker A motif; other site 1105100003130 ATP binding site [chemical binding]; other site 1105100003131 Walker B motif; other site 1105100003132 arginine finger; other site 1105100003133 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1105100003134 hypothetical protein; Validated; Region: PRK00153 1105100003135 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105100003136 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105100003137 catalytic motif [active] 1105100003138 Catalytic residue [active] 1105100003139 Beta-lactamase; Region: Beta-lactamase; cl17358 1105100003140 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 1105100003141 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105100003142 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1105100003143 Walker A/P-loop; other site 1105100003144 ATP binding site [chemical binding]; other site 1105100003145 Q-loop/lid; other site 1105100003146 ABC transporter signature motif; other site 1105100003147 Walker B; other site 1105100003148 D-loop; other site 1105100003149 H-loop/switch region; other site 1105100003150 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 1105100003151 putative hydrolase; Provisional; Region: PRK02113 1105100003152 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 1105100003153 active site 1105100003154 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 1105100003155 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 1105100003156 Predicted permeases [General function prediction only]; Region: COG0795 1105100003157 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105100003158 DNA polymerase III subunit chi; Provisional; Region: PRK06646 1105100003159 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105100003160 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105100003161 metal binding site [ion binding]; metal-binding site 1105100003162 dimer interface [polypeptide binding]; other site 1105100003163 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1105100003164 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1105100003165 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 1105100003166 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 1105100003167 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1105100003168 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 1105100003169 Uncharacterized conserved protein [Function unknown]; Region: COG1434 1105100003170 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 1105100003171 putative active site [active] 1105100003172 lipoate-protein ligase B; Provisional; Region: PRK14347 1105100003173 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105100003174 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 1105100003175 amidase catalytic site [active] 1105100003176 Zn binding residues [ion binding]; other site 1105100003177 substrate binding site [chemical binding]; other site 1105100003178 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 1105100003179 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1105100003180 ribosomal protein L33, bacterial type; Region: rpmG_bact; TIGR01023 1105100003181 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105100003182 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 1105100003183 ATP binding site [chemical binding]; other site 1105100003184 Mg2+ binding site [ion binding]; other site 1105100003185 G-X-G motif; other site 1105100003186 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 1105100003187 ATP binding site [chemical binding]; other site 1105100003188 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 1105100003189 Zinc-finger domain; Region: zf-CHCC; cl01821 1105100003190 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105100003191 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105100003192 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 1105100003193 TPR motif; other site 1105100003194 TPR repeat; Region: TPR_11; pfam13414 1105100003195 binding surface 1105100003196 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 1105100003197 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105100003198 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 1105100003199 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 1105100003200 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 1105100003201 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105100003202 TIGR00701 family protein; Region: TIGR00701 1105100003203 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105100003204 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 1105100003205 C-terminal domain interface [polypeptide binding]; other site 1105100003206 active site 1105100003207 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 1105100003208 active site 1105100003209 N-terminal domain interface [polypeptide binding]; other site 1105100003210 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 1105100003211 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 1105100003212 substrate binding site [chemical binding]; other site 1105100003213 active site