Identify the various components using blast. Treat each domain separately. Scan each domain for repeats. Build a multiple alignment of the repeats to identify conserved residues. Use prosite to predict the activity of the various elements.
- Prosite patterns usually include the active site as an invariant residue.
- If the active site is mutated, the pattern will not be detected...
- The only way around is to align the prospective motif with an active homologue...
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