title: NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteins.
abstract: There is ample evidence for the involvement of protein phosphorylation on serine/threonine/tyrosine in bacterial signaling and regulation, but very few exact phosphorylation sites have been experimentally determined. Recently, gel-free high accuracy MS studies reported over 150 phosphorylation sites in two bacterial model organisms Bacillus subtilis and Escherichia coli. Interestingly, the analysis of these phosphorylation sites revealed that most of them are not characteristic for eukaryotic-type protein kinases, which explains the poor performance of eukaryotic data-trained phosphorylation predictors on bacterial systems. We used these large bacterial datasets and neural network algorithms to create the first bacteria-specific protein phosphorylation predictor: NetPhosBac. With respect to predicting bacterial phosphorylation sites, NetPhosBac significantly outperformed all benchmark predictors. Moreover, NetPhosBac predictions of phosphorylation sites in E. coli proteins were experimentally verified on protein and site-specific levels. In conclusion, NetPhosBac clearly illustrates the advantage of taxa-specific predictors and we hope it will provide a useful asset to the microbiological community.
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Martin Lee
authors.initials: ML
authors.lastname: Miller
authors.forename: Boumediene
authors.initials: B
authors.lastname: Soufi
authors.forename: Carsten
authors.initials: C
authors.lastname: Jers
authors.forename: Nikolaj
authors.initials: N
authors.lastname: Blom
authors.forename: Boris
authors.initials: B
authors.lastname: Macek
authors.forename: Ivan
authors.initials: I
authors.lastname: Mijakovic
mesh_terms: D000465:Algorithms; D000818:Animals; D001412:Bacillus subtilis / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D030562:Databases, Protein; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry; D008956:Models, Chemical; D016571:Neural Networks, Computer; D010766:Phosphorylation; D010770:Phosphotransferases / Q000737:chemistry; D012694:Serine / Q000032:analysis*; D013912:Threonine / Q000032:analysis*
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D013912:Threonine; D012694:Serine; D010770:Phosphotransferases