mutations not found

[gry-613]

Hello, I used the mutation search module, and although the results show mutations, such as one or two mutations, I could not find the specific mutation sites when comparing matched_motif and similar_motif_found. What is the reason for this?

[gciaberi]

Hi, could you explain a bit more in detail what you are trying to do ? I'm not sure I understand where the problem is with the output file.

Note that for hits with mutations, the matched_motif will contain residue IDs that don't exist in your PDB file with the original unmutated motif, like for example for the two hits with 1 mutation, residues E38S (wildtype is E38D) and I44N (wildtype is I44T) respectively don't exist in the original PDB file, pyScoMotif mutated those positions, and then found the hit reported in similar_motif_found.

[gry-613]

Hi, could you explain a bit more in detail what you are trying to do ? I'm not sure I understand where the problem is with the output file.

Note that for hits with mutations, the matched_motif will contain residue IDs that don't exist in your PDB file with the original unmutated motif, like for example for the two hits with 1 mutation, residues E38S (wildtype is E38D) and I44N (wildtype is I44T) respectively don't exist in the original PDB file, pyScoMotif mutated those positions, and then found the hit reported in similar_motif_found.

Sorry, I may not have expressed myself very clearly. My confusion lies in the fact that, for example, in the last row of the above image, the n_mutations column indicates that there are three mutations, but the residues in matched motif and similar_motif_found seem to be exactly the same. If I want to know specifically which residues were mutated, how can I get this information?

[gciaberi]

If you look at the matched_motif value of the last row, you can see that positions E69, E38 and E225 are different from your original unmutated motif. Indeed, given that you are using the mutation search approach, the matched_motif column returns mutated versions of your original motif, and similar_motif_found returns matches against that mutated version. So to know which residues were mutated, you just need to compare the full residue IDs of your original unmutated motif with what is reported in matched_motif.

[gry-613]

If you look at the matched_motif value of the last row, you can see that positions E69, E38 and E225 are different from your original unmutated motif. Indeed, given that you are using the mutation search approach, the matched_motif column returns mutated versions of your original motif, and similar_motif_found returns matches against that mutated version. So to know which residues were mutated, you just need to compare the full residue IDs of your original unmutated motif with what is reported in matched_motif.

Thank you, I understand!