BLAST does have a few shortcomings. This site uses Akismet to reduce spam. Learn how your comment data is processed. Written by Andrew Porterfield. Identities are residues that are identical in the hit and the query red opsin , when the two are optimally aligned. Positives are residues that are very similar to each other see residue number 1 in the blue opsin—it's threonine in red opsin, and the very similar serine in the blue. Gaps are sometimes introduced into a hit to improve its alignment with the query.
The more identities and positives, and the fewer gaps, the higher the score. Other proteins, which are apparently not visual pigments, have even lower scores.
The higher the score, the better the alignment. Scores are reduced by mismatches and gaps in the best alignment. Calculation of the score is complex, involving a substituion matrix, which is a table that assigns a score to each pair of residues aligned.
The expectation value E of a hit tells whether the hit is likely be result from chance likeness between hit and query, or from common ancestry of hit and query. If E is smaller than 10 , it is sometimes given as 0. The expectation value is the number of hits you would expect to occur purely by chance if you searched for your sequence in a random genome the size of the human genome.
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