Comparisons of the amino acid sequences of proteins or the nucleotide sequences of genes can shed light on the evolutionary divergence of related organisms. Would you expect all the proteins or genes of a given set of organisms living on Earth today to show the same degree of divergence? Why or why not?
Here is a paraphrased version that you might understand better.
Scientists can use differences in the primary structure of a protein found in many different organisms to learn about the evolutionary relationship between them. (We can compare how closely related bats are to sheep by comparing differences in their protein structure) Would you expect all of the proteins in a group of animals (all bats in the world for example) to be equally different from those found in sheep? Why or Why not?