We have obtained an alignment with 59 matches, which is still very good, again showing the high degree of conservation of this particular protein sequence, even between organisms so different as humans and worms. Let us start with Drosophila melanogaster, the fruit fly. Fortunately, this is not the case, as can be shown by comparing the human cytochrome c sequence to cytochrome c sequences from other organisms. If sequence similarities were restricted to closely related species, such as humans and mice, sequence comparison would be of limited use. This is a primary motivation for comparing sequences. For many other newly discovered proteins, however, we can formulate hypotheses for their function based on similarity with known proteins. In the case of cytochrome c, independent bench experiments determined the function of each of the two proteins. Many of the protein sequences in mice and humans are similar for this reason, and this gives us a powerful tool to find clues about protein function. It is likely that this ancestor had a cytochrome c protein, and the sequences above are descendants of that primitive sequence, just as each species is as a whole (but please note the caveats in the next section). Humans and mice are mammals, and they share an ancestor that probably existed about 80 million years ago. It is no coincidence that two proteins, although from two different species, have the same function with highly similar sequences. Intuition suggests that this is a high level of similarity, and indeed it is. This gives us our first measure of similarity between these two sequences: they are 91% (95/104) identical. Thus, we can immediately see that there are exactly nine positions where these two sequences differ, of a total of 104 positions. Notice also that there are asterisks below the second sequence to show positions where there is a match between a residue (or character) in the first sequence and a character in the second sequence. Notice that the alignment had to be broken into two sections, because the sequences are too long to fit in a single line.

Bioedit sequence similarity