dbPSP

dbPSP catalogs experimentally identified phosphorylation sites (p-sites) in prokaryotic proteins to support analyses of protein phosphorylation in bacteria and archaea.

Key Features:

• Comprehensive dataset: dbPSP 2.0 contains 19,296 experimentally identified p-sites in 8,586 proteins from 200 prokaryotic organisms spanning 12 phyla within bacteria and archaea, with dbPSP 2.0 sized at ~9 GB versus ~30 MB in version 1.0.
• Integration with public databases: Integrates knowledge from 88 publicly available resources and provides annotations across nine dimensions: taxonomy, genome annotation, function, transcriptional regulation, sequence and structure information, family and domain annotation, interaction networks, orthologous relationships, and biological pathways.
• Phosphorylation site annotation: Annotates phosphorylation on seven amino acid residue types—serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine (H), and cysteine (C)—to support analyses of sequence preferences and functional roles and comparisons between bacteria, archaea, and eukaryotes.
• Literature-backed entries: Each phosphorylation site entry includes original literature references and detailed descriptions of the experimentally validated p-sites.

Scientific Applications:

• Signal transduction and cellular regulation: Supports investigation of signal transduction pathways and other cellular processes regulated by protein phosphorylation in prokaryotes.
• Comparative and evolutionary analyses: Enables comparative studies of phosphorylation across bacteria, archaea, and eukaryotes to examine evolutionary conservation and divergence of post-translational modifications.
• Functional and mechanistic studies: Facilitates exploration of the temporal, spatial, and functional impacts of phosphorylation on prokaryotic proteins.

Methodology:

dbPSP was compiled through meticulous literature curation and integration with existing public databases to assemble experimentally validated phosphorylation site annotations.