Evolutionary Analysis
We determined homologous proteins to all identified phosphoproteins across 70 species from E.coli to human via BLASTP. We defined proteins to homologous when the resulting E-values were lower than 10-5. For homologous proteins, we used a bidirectional BLASTP approach to distinguish between paralogs and orthologs.
PHOSIDA displays the results of the homology searches and illustrates the approximate phylogeny of all investigated species. Taxonomic divisions are displayed, when pointing the computer mouse to the phylogenetic tree.
If the selected phosphoprotein is not homologous to any protein of a certain organism, that organism is highlighted in red. If the similarity between the sequence of the phosphoprotein and its homologous protein is the significantly best one in both directions, the given organism is highlighted in green. A higher similarity between the sequence of the homologous protein and another protein of the organism of the selected phosphoprotein suggests paralogy, which is indicated in blue.
In addition, we created global alignments between each phosphoprotein and its corresponding interspecific homolog via the Needleman-Wunsch algorithm. If you click on any green or blue 'species' button, the corresponding global alignment appears at the bottom of the page.
If you click on a phosphorylation site of interest, the conservation status of the selected phosphorylation site is indicated in red or green. Green points to conservation. For conserved phosphosites, the alignment of the surrounding sequence is displayed.
The following paper describes the results of the evolutionary analysis from a global point of view:
'PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites',
Florian Gnad, Shubin Ren, Juergen Cox, Jesper V Olsen, Boris Macek, Mario Oroshi, Matthias Mann (2007). Genome Biology, 8:R250.