Thank you for reading this question. I have a question about symbols as a result of pairwise alignment of amino acid sequences obtained using MAFFT or Clustal omega.
The colon (:) indicates that the amino acids are strongly conserved, even if they have changed. The dots (.) indicate that the amino acids have changed and are weakly preserved.
What is the combination of amino acids that show strong preservation and the combination of amino acids that show weak preservation in PAM250 and BLOSUM64?
I want that list, but I couldn't find it on the web.
ClustW's multiple alignment amino acid combinations are listed on the following pages. However, the amino acids S and A are included in both the well-preserved amino acid combination (STA) and the weak combination (CSA), and this table is unlikely to be used for pairwise alignment.
https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Bioinformatics+Tools+FAQ Item of "What do consensus symbols represent in a Multiple Sequence Alignment?"