the e-value and the score are entirely positive correlation, and i’m thinking the SCORE is more useful for evaluating a alignment: the e-value 1e-49 and 1e-51 are in the same significant, but the corresponded score 780 and 810 (approximately) are in the difference about 4%……..
as I said above, the score tells you only how good is the alignment. But if you had some short sequence, it may have high score, but be less significant, then worst alignment, yet through longer sequence