file - BioMed Central
advertisement
1 Additional file 1: Table, listing of the reanalyzed putative proteins __________________________________________________________________________________ assignment1 Bfl protein Gene Number name functional category molecular function Bfl012 yidC Intracellular trafficking and secretion signal transduction; Component:membrane good Bfl024 pitA Inorganic ion transport and metabolism phosphate transport; Component:membrane good Bfl029 yjcE Inorganic ion transport and metabolism hydrogen antiporter activity; regulation of pH; integral to membrane good Bfl031 yjgF Translation Inhibits protein synthesis by cleavage of mRNA good Bfl036 yjgP inner membrane protein Predicted permeases putative Bfl037 yjgQ inner membrane protein Predicted permeases putative Bfl038 yidZ Transcription regulation of transcription, DNAdependent good Bfl040 Bfl040 Inorganic ion transport and metabolism ABC transporter good Bfl041 Bfl041 Inorganic ion transport and metabolism ABC transporter good Bfl054 yqjA inner membrane protein inner membrane protein putative Bfl060 ygiH inner membrane protein inner membrane protein putative Bfl073 yjeP Cell wall/membrane Mechanosensitive ion channel; protection against hypo-osmotic shock good Bfl077 yjeE Predicted ATPase or kinase hydrolase putative Bfl080 hflX GTPases GTPases putative Bfl090 ytfN Uncharacterized BCR Uncharacterized BCR unknown Bfl134 yabC Cell envelope biogenesis, outer membrane methyltransferase activity fair Bfl180 yfiO DNA uptake lipoprotein DNA uptake lipoprotein good 2 Bfl240 yajR Carbohydrate transport and metabolism; Amino acid transport and metabolism; Inorganic ion transport and metabolism transporter activity integral to membrane good Bfl250 yqgF Replication, recombination Predicted endonuclease involved and repair in recombination fair Bfl251 yqgE Transcription Uncharacterized ACR putative Bfl257 ygfA Coenzyme metabolism 5-formyltetrahydrofolate cycloligase family; catalytic activity good Bfl260 ygfZ Predicted aminomethylGlycine cleavage T-protein; transferase related to GcvT aminomethyltransferase activity good Bfl278 yaeL Cell envelope biogenesis, outer membrane metalloendopeptidase activity membrane-associated good Bfl298 pmbA Zn-dependent proteases Predicted modulator of DNA gyrase; may be involved in secretion; fair Bfl307 ytfF Carbohydrate transport and Permeases of the drug/metabolite metabolism; Amino acid transporter (DMT) superfamily transport and metabolism; good Bfl318 ubiF Coenzyme transport and metabolism, Energy production and conversion Monooxygenase fair Bfl340 ybgF predicted lipoprotein predicted lipoprotein putative Bfl343 ybhL inner membrane protein Integral membrane protein, interacts with FtsH good Bfl344 ychF Translation Predicted GTPase, probable translation factor fair Bfl349 hemK Translation Methylase of polypeptide chain release factors good Bfl358 sufA HesB-like domain; may be involved in nitrogen fixation HesB-like domain; unknown exact molecular function unknown Bfl359 sufB Posttranslational ABC-type transport system good modification, involved in Fe-S cluster assembly, protein turnover, chaperones permease component 3 Bfl374 eaeH putative adhesin putative adhesion Bfl397 ycfM General function prediction Collagen-binding surface adhesin Only SpaP (antigen I/II family) good Bfl398 ycfF Nucleotide transport and metabolism; Carbohydrate transport and metabolism; good Bfl399 ycfH Replication, recombination TatD related Dnase; DNase and repair enzyme; good Bfl418 yccK Inorganic ion transport and metabolism Dissimilatory sulfite reductase (desulfoviridin), gamma subunit good Bfl444 yoaE Inorganic ion transport and metabolism involved in efflux of tellurium ions; integral to membrane; fair Bfl455 yceL Carbohydrate transport and metabolism Arabinose efflux permease good Bfl459 gutQ Cell wall/membrane biogenesis Predicted sugar phosphate isomerase involved in capsule formation good Bfl480 yfaE Energy production and conversion Ferredoxin good Bfl521 ureG Posttranslational modification, protein turnover, chaperones; Transcription Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase good Bfl522 ureF Posttranslational modification, protein turnover, chaperones UreF; nickel ion binding; nitrogen; good metabolism; Complex bilding with UreG and UreD Bfl523 ureC Amino acid transport and metabolism Urease alpha-subunit, N-terminal good domain; nickel ion binding; nitrogen metabolism; Amidohydrolase family; hydrolase activity Bfl524 ureB Amino acid transport and metabolism Urease beta subunit; nickel ion; binding; nitrogen metabolism good Bfl525 ureA Amino acid transport and metabolism Urease gamma subunit; nickel ion binding; nitrogen metabolism good Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases putative 4 Bfl526 ureD Posttranslational modification, protein turnover, chaperones UreD; nickel ion binding; nitrog good metabolism; Complex bilding with UreG and UreF; Bfl530 engA General function prediction only GTPase of unknown function putative Bfl534 nifS Amino acid transport and metabolism Aminotransferase class-V; transaminase activity; metabolism good Bfl535 suhB Carbohydrate transport and metabolism inositol/phosphatidylinositol phosphatase activity good Bfl537 yfhC Nucleotide transport and metabolism; Translation Cytidine and deoxycytidylate deaminase zinc-binding region; hydrolase activity good Bfl539 pdxJ Coenzyme metabolism; Pyridoxal phosphate biosynthesis protein PdxJ; pyridoxine biosynthesis; cytoplasm good Bfl548 smpB Posttranslational modification, protein turnover, chaperones SmpB protein; RNA binding; protein biosynthesis good Bfl575 yhgN Intracellular trafficking and secretion MarC family integral membrane protein good Bfl576 yigL General function prediction only Predicted hydrolases of the HAD superfamily putative Bfl578 yigB General function prediction only Predicted hydrolases of the HAD superfamily putative Bfl606 yibN Inorganic ion transport and metabolism Rhodanese-related sulfurtransferases fair Bfl614 yicC Function unknown YicC-like family, N-terminal fair region; play a role in stationary phase survival; not essential during stationary phase Bfl615 bfl615 Transcription MarR family; transcription factor activity; regulation of transcription, repressor good Bfl620 yigC Coenzyme transport and metabolism 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; This enzyme good 5 catalyses the third reaction in ubiquinone biosynthesis; Bfl623 rumC Bfl628 yhhF DNA recombination RmuC family fair DNA replication, N6-adenine-specific methylase good recombination and repair _______________________________________________________________________________ 1 Blochmannia protein number (the same numbers as the Blochmannia gene number) and gene name is followed by function assignment: For 39 proteins an informative assignment (categorized as “good”; right column) on the molecular function could be made with a high confidence (blast expected e-value below 10-6), for 9 proteins there remain only minor uncertainties (“fair”). For 15 proteins there is still only a putative function assignment possible and for one protein no (“unknown”) prediction is possible.
