Multipe Sequence Alignments:
Identifying catalytic residues in an enzyme
Fetch the sequence.
Make a Blast against SwissProt to try to find homologues. Request the maximum number of matches to be reported. In order to produce an informative alignment, do not pick up the best matches, but those with a lower sequence identity and an unquestionable protease activity.
Align these sequences using ClustalW or T-Coffee and identify fully conserved positions. Increase the number of sequences in order to have as few as possible conserved positions, but avoid introducing false positives.
In the BLAST output, identify a reasonnable match (conserved where it matters as indicated by the multiple alignment) without any protease activity.
Questions should be sent to C.Notredame