What Parameter Is Best To Decide Function Annoatations Of Proteins?

Question

[Naren]

I have two or more hits for COG annotations for same bacterial protein obtained by RPS-BLAST,
The alignment output has Identity, Bit score, E-value, hit legth,
How to decide which hit is best.
I mean to say what parameter should be given priority?
Highest identity, bit score, hit length, OR Lowest E-value?
Is there any way to optimize all the parameters?

Answer 1

[Birdman]

Definitely e-value. You can see it as a corrected p-value. Bit-score is informative about the "quality" of the match, but personally, for this kind of purpose, I select matches using an e-value threshold.