I am interested in studying the evolution of a certain motif in homologous proteins. Actually, I generated a set of non-homologous proteins to study the conservation of the same motif and found out that in the case of non-homologous proteins, it was highly conserved. Now, I want to further investigate whether it is conserved in the homologues of each protein in the non-homologous data-set that I generated. How can I move on with such an analysis? Does analyzing the data in such a manner make sense or not ?