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When I align two HBB protein sequences wich have 80% identity, I used two kind of score matrices: Blosum62 and PAM30, to figure out the impact on my results.
I noticed that the bit score is higher when I used PAM30 instead of BLOSUM62, which makes sense because PAM30 is based on more closely related species.
However I don't understand why the E-values differs from each other:
PAMP62: Bit score: 251, E value: 8 * 10^91
PAM30: Bit score: 258, E value: 6*10^82
Question: I don't understand why the E-value changes when using an other scoring matrix?
Perhaps this BLAST tutorial by Steve Altschul will be helpful: The Statistics of Sequence Similarity Scores
There is also the BLAST book by Mark Yandell and Ian Korf.