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Nucleic Acids Research Advance Access published online on October 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp810
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

Pawel Durek1, Robert Schmidt1, Joshua L. Heazlewood2, Alexandra Jones3, Daniel MacLean3, Axel Nagel1, Birgit Kersten1 and Waltraud X. Schulze1,*

1Max Planck Institut für molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany 2Joint BioEnergy Institute, Lawrence Berkley National Laboratory, Berkeley, CA 94720, USA and 3The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK

*To whom correspondence should be addressed. Fax: +49 331 5678134; Email: wschulze{at}mpimp-golm.mpg.de

Received August 21, 2009. Revised September 10, 2009. Accepted September 14, 2009.

The PhosPhAt database of Arabidopsis phosphorylation sites was initially launched in August 2007. Since then, along with 10-fold increase in database entries, functionality of PhosPhAt (phosphat.mpimp-golm.mpg.de) has been considerably upgraded and re-designed. PhosPhAt is now more of a web application with the inclusion of advanced search functions allowing combinatorial searches by Boolean terms. The results output now includes interactive visualization of annotated fragmentation spectra and the ability to export spectra and peptide sequences as text files for use in other applications. We have also implemented dynamic links to other web resources thus augmenting PhosPhAt-specific information with external protein-related data. For experimental phosphorylation sites with information about dynamic behavior in response to external stimuli, we display simple time-resolved diagrams. We have included predictions for pT and pY sites and updated pS predictions. Access to prediction algorithm now allows ‘on-the-fly’ prediction of phosphorylation of any user-uploaded protein sequence. Protein Pfam domain structures are now mapped onto the protein sequence display next to experimental and predicted phosphorylation sites. Finally, we have implemented functional annotation of proteins using MAPMAN ontology. These new developments make the PhosPhAt resource a useful and powerful tool for the scientific community as a whole beyond the plant sciences.

Present address: Pawel Durek, Institute of Pathology, Universitätsmedizin Charite, Chariteplatz 1, D-10117 Berlin, Germany.


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