Finding homologous protein sequence using blastp led to the same sequence as output

Question

[hamid sta]

Hi ! I am going through a project where i need to rely on blast to find homologous sequence of a sepcific protein sequence,let's called it A . To do so , i rely on blastp (prot against prot) . However, the problem is that the output of my research look like the exact same sequence as input . here is a look :

My goal is to find related sequence and then to perform a multiple alignement comparison between all related sequence to find conserved part . But here it look like that all output sequences of my blastp are the very same . Should i include them in my multiple comparison ? it's the same species and even the same strain ! Even though i put "non redundant protein" as parameters of my blast , the protein are the same to me, from the same species to the same strain , how is that possible ?

Thank you for all answer !

Answer 1

[Mensur Dlakic]

It is normal to have some sequences in the database that are identical to your sequence of interest. People sequence the same genome multiple times, or related strains that will have that particular sequence be identical.

If you scroll further down there will be some sequences that are different. Even in the list you showed most sequences do not have 100% coverage to your sequence of interest, so they are not technically identical. Only one sequence is 100% identical with 100% coverage, which is why it has the highest score (909).