Locate approximate protein matches using PAM or BLOSUM scoring matrices with adjustable gap penalties.
Raw or FASTA-formatted protein sequence to search (limit 2,000 characters). Non-protein symbols are removed.
Protein motif to search for (limit 30 characters).
Positive labels soften gap penalties; negative labels reward gaps (matching legacy behaviour).
Paste your target protein sequence (up to 2,000 characters) and a query motif (up to 30 characters). Non-protein characters are automatically filtered out.
Select PAM30 or PAM70 for closely related sequences, BLOSUM62 for general use, or BLOSUM45/BLOSUM80 for distant or closely related proteins respectively.
Configure the gap penalty to control how insertions and deletions are scored. Select the number of top hits (1-40) to retrieve from the target sequence.
Each hit shows aligned query and target segments with start/end positions and alignment scores. Higher scores indicate better matches.
Choose PAM matrices for short evolutionary distances (e.g. PAM30) or BLOSUM matrices for broader homology searches (e.g. BLOSUM62).
Positive labels penalise gaps, whereas negative labels reward them, matching the behaviour of the legacy SMS tool.
The search iteratively reports up to the configured number of highest-scoring alignments, clearing matched regions between passes.