I have done a multiple sequence alignment on my protein using closely related other proteins. I have also found out the percentage identity matrix. I am not sure how to interpret the results though? Thanks for your valuable suggestions.
Before interpretation, you should think what is your purpose of interpretation. Do you want to find conserved region or want to see the evolutionary pattern, or just wanted to know about the phylogeny. May be this discussion can help you. https://www.biostars.org/p/9085/
It appears there is not conserved region among the proteins. Nevertheless, could you attach the raw sequence file, so that we could align and assist you somehow.