protein local sequence alignment result interpretation

Question

[kng]

why does the count of similarity + identity +any gap not equal to the total number of sequences in results from local sequence alignment of protein?

My query sequence was 249 long. The target is 3000 long. Local alignment only counted 241 . and calculated, Identity= 177/241 (73.4%), Similarity= 211/241 (87.6%) and Gaps 1/241 ( 0.4%).

1) Should it not count all 249 from my query for calculations? 2) Should not total - identical equal similar + gaps?

Can someone help me understand these numbers?

Answer 1

[Mensur Dlakic]

All fractions are expressed with the length of aligned region as a reference. It doesn't matter how long the query or the match are.

Percent identity should be self-explanatory, and identical residues are highlighted on the middle row between Query and Sbjct. Similarity is the sum of identical and similar residues. By default, all identical residues are also similar, which means that similarity is a more general property that includes identity. Conservative substitutions are shown as + sign in the middle row. In your case, there are 177 identical residues and (211-177) conservative substitutions, for a total of 211 similar residues.