NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteins.
Proteomics
; 9(1): 116-25, 2009 Jan.
Article
en En
| MEDLINE
| ID: mdl-19053140
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.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Serina
/
Treonina
/
Bacillus subtilis
/
Proteínas Bacterianas
/
Algoritmos
/
Escherichia coli
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Límite:
Animals
Idioma:
En
Revista:
Proteomics
Asunto de la revista:
BIOQUIMICA
Año:
2009
Tipo del documento:
Article
País de afiliación:
Dinamarca