Tutorial 3/2: ClustalW

1) Retrieve the sequence of the following proteins from Streptococcus pyogenes: SpeA (Streptococcal pyrogenic exotoxin A), SpeC, SpeG, SpeJ, and SmeZ (Streptococcal mitogenic exotoxin Z). All these proteins are streptococcal toxins with superantigenic properties.

2) Put all sequences in FASTA format (in a Word file). Modify the FASTA identifier line (i.e., the line starting with >) so that it only contains the protein symbol (This will make the following steps easier).

3) Use either NPS@ or EBI ClustalW (Both sites are linked in the side bar under “Blogroll”) to align all the five toxins.

4) Discuss with your colleague whether you can guess the active site of these superantigenic toxins from the multiple sequence alignment. To verify your answer or support your claim, search Pubmed and find whether anybody has worked on conserved residues in superantigens.

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