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Database Commons

a catalog of worldwide biological databases

Database Profile

General information

URL: http://phosphat.uni-hohenheim.de/
Full name: The Arabidopsis Protein Phosphorylation Site Database
Description: The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 4.0) contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide properties, their annotated biological function as well as the experimental and analytical context is given. For a majority of peptides, the actual annotated mass spectrum is displayed in interactive manner.
Year founded: 2008
Last update: 2013-01-01
Version: v4.0
Accessibility:
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Country/Region: Germany

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Contact information

University/Institution: Max Planck Institute for Molecular Plant Physiology
Address: Am Mühlenberg 1, 14476 Golm, Germany
City: Golm
Province/State:
Country/Region: Germany
Contact name (PI/Team): Waltraud X. Schulze
Contact email (PI/Helpdesk): wschulze@mpimp-golm.mpg.de

Publications

23172287
PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt. [PMID: 23172287]
Zulawski M, Braginets R, Schulze WX.

Reversible phosphorylation is a key mechanism for regulating protein function. Thus it is of high interest to know which kinase can phosphorylate which proteins. Comprehensive information about phosphorylation sites in Arabidopsis proteins is hosted within the PhosPhAt database (http://phosphat.mpimp-golm.mpg.de). However, our knowledge of the kinases that phosphorylate those sites is dispersed throughout the literature and very difficult to access, particularly for investigators seeking to interpret large scale and high-throughput experiments. Therefore, we aimed to compile information on kinase-substrate interactions and kinase-specific regulatory information and make this available via a new functionality embedded in PhosPhAt. Our approach involved systematic surveying of the literature for regulatory information on the members of the major kinase families in Arabidopsis thaliana, such as CDPKs, MPK(KK)s, AGC kinases and SnRKs, as well as individual kinases from other families. To date, we have researched more than 4450 kinase-related publications, which collectively contain information on about 289 kinases. Users can now query the PhosPhAt database not only for experimental and predicted phosphorylation sites of individual proteins, but also for known substrates for a given kinase or kinase family. Further developments include addition of new phosphorylation sites and visualization of clustered phosphorylation events, known as phosphorylation hotspots.

Nucleic Acids Res. 2013:41(Database issue) | 73 Citations (from Europe PMC, 2024-06-15)
19880383
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. [PMID: 19880383]
Durek P, Schmidt R, Heazlewood JL, Jones A, MacLean D, Nagel A, Kersten B, Schulze WX.

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.

Nucleic Acids Res. 2010:38(Database issue) | 224 Citations (from Europe PMC, 2024-06-15)
17984086
PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. [PMID: 17984086]
Heazlewood JL, Durek P, Hummel J, Selbig J, Weckwerth W, Walther D, Schulze WX.

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.

Nucleic Acids Res. 2008:36(Database issue) | 192 Citations (from Europe PMC, 2024-06-15)

Ranking

All databases:
371/6000 (93.833%)
Modification:
25/287 (91.638%)
371
Total Rank
486
Citations
30.375
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Record metadata

Created on: 2015-06-20
Curated by:
Shixiang Sun [2016-04-11]
Lina Ma [2016-03-31]
Shixiang Sun [2016-03-25]
Mengwei Li [2016-02-19]
Shixiang Sun [2015-11-21]
Shixiang Sun [2015-06-26]
Jian Sang [2015-06-26]