Computational identification of sequence motifs in phospho-peptides.

A–C. Phospho-peptides containing single phosphorylation at (A) Ser, (B) Thr or (C) Tyr were analyzed for the presence of sequence motifs using the Motif-X algorithm [44] as described in the Materials and Methods section. Sequence logos for Motif-X aligned peptide sequences were generated using weblogo [45] and are shown above for each of the three types of phospho-peptides identified in this study. D–F. Identification of sequence motifs in multiply phosphorylated peptides. Phospho-peptides containing di- and tri-phospho residues were analyzed for the presence of sequence motifs by manual alignment as described in the Materials and Methods section. Sequence logos for the aligned peptide sequences were generated using weblogo [45] and are shown above for the (D) di-phosphopeptides with varying number of residues in between the two phosphor-sites. A composite sequence logo using all of the (E) the di-phosphopeptides and (F) the tri-phosphopeptides shows the relative preference for the second and the third phosphorylation site in these multi-phosphorylated peptides.