Phospho.BLAST Search Help

Phospho.BLAST reports peptides in submitted sequences that match to phosphopeptides in the Phospho.ELM database. The database entries are experimentally demonstrated to contain phosphorylated residues as published in the scientific literature.

It is important to note that Phospho.BLAST does NOT PREDICT phosphorylation motifs in the query protein. Short peptide matches found by BLAST do not have meaningful significance values.

Retrieval by sequence similarity is complementary to retrieval by keyword. It is likely to be useful for retrieving phosphorylation sites in a protein of interest (e.g. when keywords may be poorly defined) or for retrieving phosphorylation sites that are conserved in related proteins (whether orthologues or paralogues). Occasionally, phosphorylation sites in Phospho.ELM are also matched by unrelated query proteins: these are likely to be found interesting by the user. It is up to the user to consider carefully whether there is any meaning (e.g. shared kinase and/or phosphopeptide binding domain specificities) to the match. Since the match is not significant per se, the biological context should be reviewed to help the user decide whether experimental verification is worth attempting.

To submit a Phospho.BLAST search against the Phospho.ELM data set of known phosphorylated peptides, enter an UniProt ID or ACC or the raw protein sequence.

The Graphic Output:

The graphic output of the query sequence shows a summary of the results: the detected SMART domains and phosphopeptide matches. Clicking on the matches bar (in black), one will go directly to the alignment details.

The Results Table:

The results table shows the phosphopeptide alignments that have been detected. The sorting of the alignments is according to the position on the query sequence and NOT according to e-value. It is not possible to show the e-value given that these are not significant for small peptides. Full length matches are 11 amino acids centered on the phosphopeptide. Shorter matches are either N- and C-terminal sites or truncated by the BLAST algorithm.
Phospho.BLAST uses settings for BLAST, optimised for short peptide matches.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410