PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
By J. Heazlewood, P. Durek, Jan Hummel, Joachim Selbig, Wolfram Weckwerth, Dirk Walther, Waltraud X. Schulze. Nucleic Acids Res., 2007
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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
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/a28ed67d1c530631c2e65d3e9a67f04defb51ec7
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Citations in the corpus
- PPDB, the Plant Proteomics Database at Cornell (2008, background): “PPDB is a unique resource for the plant community and complements other plant proteomics resources, such as the plant mass spectral reference database Promex (4), SUBA for Arabidopsis protein localization (5), as well as databases specialized in other organelles, such as peroxisomes (6) or phosphope”
- PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update (2009, methodology): “Furthermore, these data were also used to develop a serine phosphorylation prediction algorithm, which was also made available through PhosPhAt (16).”