Nucleic Acids Research Advance Access published online on November 4, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm812
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Database Issue |
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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. Durek, R. Schmidt, J. L. Heazlewood, A. Jones, D. MacLean, A. Nagel, B. Kersten, and W. X. Schulze PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update Nucleic Acids Res., October 30, 2009; (2009) gkp810v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. D. Dennis and K. S. Browning Differential Phosphorylation of Plant Translation Initiation Factors by Arabidopsis thaliana CK2 Holoenzymes J. Biol. Chem., July 31, 2009; 284(31): 20602 - 20614. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. D. Dennis, M. D. Person, and K. S. Browning Phosphorylation of Plant Translation Initiation Factors by CK2 Enhances the in Vitro Interaction of Multifactor Complex Components J. Biol. Chem., July 31, 2009; 284(31): 20615 - 20628. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X.-N. Zhang and S. M. Mount Two Alternatively Spliced Isoforms of the Arabidopsis SR45 Protein Have Distinct Roles during Normal Plant Development Plant Physiology, July 1, 2009; 150(3): 1450 - 1458. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Brady and N. J. Provart Web-Queryable Large-Scale Data Sets for Hypothesis Generation in Plant Biology PLANT CELL, April 1, 2009; 21(4): 1034 - 1051. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M. Riano-Pachon, A. Nagel, J. Neigenfind, R. Wagner, R. Basekow, E. Weber, B. Mueller-Roeber, S. Diehl, and B. Kersten GabiPD: the GABI primary database--a plant integrative 'omics' database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D954 - D959. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Sun, B. Zybailov, W. Majeran, G. Friso, P. D. B. Olinares, and K. J. van Wijk PPDB, the Plant Proteomics Database at Cornell Nucleic Acids Res., January 1, 2009; 37(suppl_1): D969 - D974. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gao, G. K. Agrawal, J. J. Thelen, and D. Xu P3DB: a plant protein phosphorylation database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D960 - D962. [Abstract] [Full Text] [PDF]
|
|