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. 2014 Dec 22;2014:bau121.
doi: 10.1093/database/bau121. Print 2014.

dbPPT: A Comprehensive Database of Protein Phosphorylation in Plants

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Free PMC article

dbPPT: A Comprehensive Database of Protein Phosphorylation in Plants

Han Cheng et al. Database (Oxford). .
Free PMC article

Abstract

As one of the most important protein post-translational modifications, the reversible phosphorylation is critical for plants in regulating a variety of biological processes such as cellular metabolism, signal transduction and responses to environmental stress. Numerous efforts especially large-scale phosphoproteome profiling studies have been contributed to dissect the phosphorylation signaling in various plants, while a large number of phosphorylation events were identified. To provide an integrated data resource for further investigations, here we present a comprehensive database of dbPPT (database of Phosphorylation site in PlanTs, at http://dbppt.biocuckoo.org), which contains experimentally identified phosphorylation sites in proteins from plants. The phosphorylation sites in dbPPT were manually curated from the literatures, whereas datasets in other public databases were also integrated. In total, there were 82,175 phosphorylation sites in 31,012 proteins from 20 plant organisms in dbPPT, presenting a larger quantity of phosphorylation sites and a higher coverage of plant species in comparison with other databases. The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively. All the phosphoproteins and phosphorylation sites in the database were critically annotated. Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community. Database URL: http://dbppt.biocuckoo.or

Figures

Figure 1.
Figure 1.
The heatmap for the distribution of site numbers and percentages for phosphoserine (pS), phosphothreonine (pT) and phosphotyrosine (pY) in different species.
Figure 2.
Figure 2.
The browse option developed for browsing by plant species in the dbPPT database. (A) The 20 plant species which contain identified phosphorylation sites. (B) The list of identified phosphoprotein in T. aestivum. (C) The detailed information of T. aestivum SNF1-type serine–threonine protein kinase.
Figure 3.
Figure 3.
The search options in the dbPPT database. (A) dbPPT can be queried with a simple keyword. (B) The results of simple search for ‘snrk2’ in the area ‘Protein Name’. (C) Advanced search allows users to perform a complex search using multiple keywords in several areas and three operators including ‘and’, ‘or’ and ‘exclude’. (D) Advanced search result of ‘SnRK2’ in wheat while its full-length sequence was retrieved from UniProt. (E) Multiple search allows user to search multiple keywords in one query event. (F) The results of searching ‘C8CBK4’ and ‘SnRK’ in any field. (G) BLAST search was implemented for search similar phosphoproteins with FASTA format protein sequence. (H) BLAST search for SNF1-type serine–threonine protein kinase in wheat.
Figure 4.
Figure 4.
The top four most representative motifs discovered by Motif-x for phosphoserine, phosphothreonine and phosphotyrosine in Arabidopsis. (A) Motifs for phosphoserine. (B) Motifs for phosphothreonine. (C) Motifs for phosphotyrosine. The position 0 represents the modified residues.

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