So I am familiar with CLUSTAL Omega to compare several proteins for conservations with each other. But I need some expertise on how to seclude a bit more special information from comparing several sequences.

Let's say we have proteins A1, A2, A3, A4.

All of them are from the protein family A and have thus conserved amino acids between each other. While A1 is something like a model for the protein family A, A2 to A4 have a distinct feature that is exclusive to only them that I want to abolish via site-directed mutagenesis.

Doing sequence alignment with A1-A4 and ruling out conservations that are shared by all of them on paper strikes me as a bit of a time-waster. So Is there an easy program solution to find the conserved amino acids that are exclusive to them and them alone, so that I can exclude the protein family conservations that are needed for proper protein function and reduce my amount of mutation targets?