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  PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor

Heazlewood, J. L., Durek, P., Hummel, J., Selbig, J., Weckwerth, W., Walther, D., et al. (2008). PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Research, 36(Database issue), D1015-D1021. doi:10.1093/nar/gkm812.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2783-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2784-D
Genre: Journal Article

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Heazlewood-2008-PhosPhAt_ a database.pdf (Any fulltext), 608KB
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 Creators:
Heazlewood, J. L.1, Author
Durek, P.2, Author              
Hummel, J.2, 3, Author              
Selbig, J.3, Author              
Weckwerth, W.4, Author              
Walther, D.2, Author              
Schulze, W. X.5, Author              
Affiliations:
1External Organizations, escidoc:persistent22              
2BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, escidoc:1753303              
3BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, escidoc:1753315              
4Integrative Proteomics and Metabolomics, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, escidoc:1753334              
5Signalling Proteomics, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, escidoc:1753330              

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Free keywords: in-vivo phosphorylation mass-spectrometry plasma-membrane signal-transduction receptor kinase 14-3-3 proteins identification phosphoproteomics chromatography information
 Abstract: 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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Language(s): eng - English
 Dates: 2007-11-042008
 Publication Status: Published in print
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 Identifiers: ISI: ISI:000252545400177
DOI: 10.1093/nar/gkm812
ISSN: 1362-4962 (Electronic) 0305-1048 (Linking)
URI: ://000252545400177 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238998/pdf/gkm812.pdf?tool=pmcentrez
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Title: Nucleic Acids Research
Source Genre: Journal
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Pages: - Volume / Issue: 36 (Database issue) Sequence Number: - Start / End Page: D1015 - D1021 Identifier: -