Nucleic Acids Research Advance Access originally published online on November 4, 2007
Nucleic Acids Research 2008 36(Database issue):D1015-D1021; doi:10.1093/nar/gkm812
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Nucleic Acids Research, 2008, Vol. 36, Database issue D1015-D1021
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
1ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley 6009, WA, Australia, 2Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm and 3GoFORSYS, University of Potsdam, Institute of Biochemistry and Biology, c/o MPI-MP, Am Mühlenberg 1, 14424 Potsdam, Germany
*To whom correspondence should be addressed. Tel: + 49 331 5678113; Fax: + 49 331 5678403; Email: wschulze{at}mpimp-golm.mpg.de
Received August 14, 2007. Revised September 18, 2007. Accepted September 18, 2007.
The PhosPhAt database provides a resource consolidating our current knowledge of mass spectrometry-based identified phosphorylation sites in Arabidopsis and combines it with phosphorylation site prediction specifically trained on experimentally identified Arabidopsis phosphorylation motifs. The database currently contains 1187 unique tryptic peptide sequences encompassing 1053 Arabidopsis proteins. Among the characterized phosphorylation sites, there are over 1000 with unambiguous site assignments, and nearly 500 for which the precise phosphorylation site could not be determined. The database is searchable by protein accession number, physical peptide characteristics, as well as by experimental conditions (tissue sampled, phosphopeptide enrichment method). For each protein, a phosphorylation site overview is presented in tabular form with detailed information on each identified phosphopeptide. We have utilized a set of 802 experimentally validated serine phosphorylation sites to develop a method for prediction of serine phosphorylation (pSer) in Arabidopsis. An analysis of the current annotated Arabidopsis proteome yielded in 27 782 predicted phosphoserine sites distributed across 17 035 proteins. These prediction results are summarized graphically in the database together with the experimental phosphorylation sites in a whole sequence context. The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt) provides a valuable resource to the plant science community and can be accessed through the following link http://phosphat.mpimp-golm.mpg.de
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