How Is Protein Similarity Calculated for a Pairwise Protein Alignment?

SnapGene uses the BLOMSUM62 scoring matrix (see https://en.wikipedia.org/wiki/BLOSUM) with a threshold of 1, in order to classify aligned residue pairs as Identical, Similar or "Not Similar".

For example, the Proline/Alanine (A/P) pair at position 4 in the above alignment has a BLOMSUM62 score of  -1, which is below the threshold of 1, so the pair is marked "Not Similar".