If I have the peptide sequence and uses the BASTp in the NCBI, five columns appear Max score, total score, Query cover, E value, Identity. How can I know if this peptide is unique to a the whole group of proteins or unique to a specific protein?
Many thanks
Hi Eman,
Based on BLASTp alignment, you can check if there are any sequences that have alignment that have 100% identity and Query cover, and then analyze whether the outputs are all from the same protein or class of protein, or if other proteins of different functions also have this sequence. I also suggest selecting the most relevant sequences and making a filogram / cladogram to better understand the origin of this peptide and to verify if this peptide has any important biological function.
I hope I was helpfull.
Thanks Leondro.
What is the role of E value then? and what if the identity was 100% and the Query cover wasn't?
The Expect value (E) is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. In other words, the lower the E-value (closer it is to zero), the more significant is the match. However, keep in mind that virtually identical short alignments have relatively high E values
About identity and cover, in this case there was a complete alignment, however there are gaps in the aligned sequence, which reflects that the proteins are not totally equal.
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