When comparing differences in an amino acid residue at one position between the different proteins in the multiple alignment, what factors do you think would be used to determine if a difference in an amino acid is a conserved change?

To understand the utility in sequence comparison and in the search for proteins that have a common evolutionary origin, you need to be clear about some concepts about how to evolve proteins. The idea that is accepted is that throughout the evolution some species are giving rise to new ones. Behind this is the genetic variation of organisms, that is, the evolution of genomes and their genes, as well as the proteins encoded by them.

Explanation:

Three ways can be distinguished by which genes evolve, and by proteins: mutation, duplication and shuffling of domains. When differences between homologous protein sequences are observed, these differences change to do with the way of life of the organism, an example of this, bacteria that live in hot springs at very high temperatures have proteins with a very high denaturation temperature, and these proteins are usually richer in cysteines. On the other hand, the fact that in positions of the sequences they remain unchanged (preserved positions), means that these have a special importance for the maintenance of the structure or function of the protein and its modification has not been tolerated throughout of evolution