Heazlewood Joshua L, Durek Pawel, Hummel Jan, Selbig Joachim, Weckwerth Wolfram, Walther Dirk, Schulze Waltraud X
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley 6009, WA, Australia.
Nucleic Acids Res. 2008 Jan;36(Database issue):D1015-21. doi: 10.1093/nar/gkm812. Epub 2007 Nov 4.
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.
磷酸化数据库（PhosPhAt）整合了目前我们对基于质谱鉴定的拟南芥磷酸化位点的认识，并将其与专门针对通过实验鉴定的拟南芥磷酸化基序进行训练的磷酸化位点预测相结合。该数据库目前包含1187个独特的胰蛋白酶肽序列，涵盖1053种拟南芥蛋白质。在已鉴定的磷酸化位点中，有1000多个位点分配明确，近500个位点的精确磷酸化位点无法确定。该数据库可通过蛋白质登录号、物理肽特征以及实验条件（取样组织、磷酸肽富集方法）进行搜索。对于每种蛋白质，以表格形式呈现磷酸化位点概述，并提供每个鉴定出的磷酸肽的详细信息。我们利用一组802个经过实验验证的丝氨酸磷酸化位点开发了一种预测拟南芥中丝氨酸磷酸化（pSer）的方法。对当前注释的拟南芥蛋白质组进行分析，得到了分布在17035种蛋白质中的27782个预测的磷酸丝氨酸位点。这些预测结果在数据库中以图形方式汇总，并与整个序列背景下的实验磷酸化位点一起呈现。拟南芥蛋白质磷酸化位点数据库（PhosPhAt）为植物科学界提供了宝贵的资源，可通过以下链接http://phosphat.mpimp-golm.mpg.de访问。
