Through series of analysis, I got some sequences for species A, I want to confirm if these genes (sequences) also existed in species B, so I want to use NCBI tblastn to do that. Here is the result for one of the sequence, I want to know if we will say this sequence also exist in species B, we need to focus on the e-value or percent identity? if yes, what will be the exact number for e-value and percent identify?
none of these individual values will give you a definitive answer to your question. All the stats blast reports have their own meaning and purpose.
To answer your question you will have to take most of them into account, it has to have a low evalue, and enough % identity/positives but also enough query coverage ....
Image the case where you will have a perfect match of 40AA (out of in 300 in total for you query): I assume you will then not conclude that the query also exists in the target species (thought it will likely have a low evalue, high %id, but the %coverage of query will be very low). On the other end of the spectrum: a fully covered query sequence but with low %id and OK evalue will also not do it.
bottom line: you take all measures into account. I would advise that it needs to have enough %coverage, with good %id and low evalue ... I can understand it might be frustrating to not get actual numbers advise but those are hard to set/give as it depends of several factors as well (eg. phylogenetic distance between query and target, ...)
I got it! I will focus p-value, identity and coverage, before I say that sequence also exist in another species. Thank you!!