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SOP031: Finding a Degenerate Peptide Motif in Selected Organisms

This procedure explains how to use the protScan tool (BLAST or Scan in the Search menu) to find a particular sequence in one or more genomes. For complete instructions on how to use both protScan and dnaScan, see Search Patterns.

First, go to the BLAST or Scan search page. This is the search page for using sequence data as the query term for searching the database.

This example uses a degenerate amino acid sequence, so select the protScan tool from the dropdown list.

Type the motif of interest in the sequence box.

• For example, use a collagen-binding motif implicated in acute rheumatic fever (ARF) following streptococcal infection, AXYLXXN ( J Biol Chem 282:18686). The X characters will match any amino acid.

Select the genomes to search in the genome list.

• For example, select all strains of Streptococcus pyogenes from the genomes list quickly by typing pyogenes in the text box after "type to narrow selection" and clicking the "Go" button.

Features with matching sequences are presented in a table with links to respective Annotation Overview pages.

• ProtScan finds AEYLKGLN in the M protein of two M3 strains. Does the motif appear in the ARF isolate MGAS8232? Find the reason at PMID 12813026. The tool also finds AAYLDDLN in the SatD proteins of strains with M-types M1, M2, M4, M12, and M28. What is the role of SatD in pyogenes? Find the answer at PMID 11274114.

Use the form below to try the example, or to attempt your own search. The results will open in a new tab or window.