NetPhosBac - A predictor for Ser/Thr phosphorylation sites in bacterial proteins. in bacteria.
Martin Lee Miller1,4, Boumediene Soufi2,4, Carsten Jers2, Nikolaj Blom1 Boris Macek3 and Ivan Majakovic2.
Proteomics. 2008 Dec 3. PUBMED

1Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
2Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
3Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, DE-82152 Martinsried, Germany

4These authors contributed equally to this work.


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.