P3DB (Plant Protein Phosphorylation) and Soybean Knowledge Base (SoyKB) Web Resources

Protein phosphorylation is widely recognized as the most widespread, enzyme-catalyzed post-translational modification in eukaryotes. Plants have particularly appropriated this signaling mechanism as evidenced by their two-fold higher frequency of protein kinases compared to animals. While all aspects of plant protein phosphorylation research have grown in the past ten years, phosphorylation site mapping using high-resolution mass spectrometry has grown exponentially. To manage these data in a user-intuitive format, we have developed P³DB, the Plant Protein Phosphorylation Database (http://p3db.org/). This database is a repository for plant protein phosphorylation sites, currently hosting information on 33,252 non-redundant sites from 26 experimental studies of eight plant species. Data can also be queried using an integrated BLAST module to search similar sequences with known phosphorylation sites from other plants. P³DB applies a general framework extendable to other protein modifications and can be easily linked to our in house prediction tool Musite (http://musite.net/) as well as Soybean Knowledge Base (SoyKB; http://soykb.org), which utilizes the information of PTMs in the biological context.

SoyKB is a comprehensive all-inclusive web resource targeted towards hypothesis generation, translational genomics and breeding in soybean. It handles the management and integration of soybean genomics and multi-omics data, gene function annotations, PTMs such as phosphorylation, biological pathway and trait information. It has many innovative and useful tools including Protein BioViewer, multiple gene/metabolite analysis, motif prediction, protein 3D structure viewer, genome browser and Missouri Breeding Program integrating QTLs, traits, markers and SNPs.