Question

What does it mean when two protein sequences have global and local pairwise alignment results that are the same (same identity, similarity, and gap percentages)?

Answer 1

when two protein sequences have global and local pairwise alignment results that are the same i.e. same identity, similarity, and gap percentages means that both the proteins are homologous and they share comman ancestor. This means that in terms of evolution both these proteins are very closely related and have recent ancestory. These proteins might have comman function but not always as a single protein have different effect in different tissues. so it says that genetically they are similar but function may depend upon the cellular environment.