The lengthier that organisms have been detached the greater amount of random mutation would have arisen, and thus the larger the amount of different amino acids in the same proteins.
These changes are probable to be in regions that don't involve the active site, otherwise the protein would not function giving a obsolete organism. Similarly genes that encrypt proteins that are very vital to cellular function will be very similar in many animals despite having a common ancestor hundreds of years ago. This is because a small mutation in a very important gene is likely to stop its function and thus kill the cell. However proteins that are not so indispensable or present in many copies may be very different in different animals
hope it helps
