A puzzle for you:
If this is true and similar sequences are indicative of similar functions and not relatedness, why is it that a deficit of a protein in one organism can be corrected by the introduction of that protein from a different species (and thus having a different sequence)? You are assuming that differences in sequence are due to slight differences in function, while most of the time these differences make no difference at all--some of them don't even change the protein amino acid sequence. Why would an intelligent designer make a bunch of proteins with slightly different coding sequences, yet with the same properties? And why would he make it so that organisms that seem to be closely related (lions and house cats) have fewer of these functionally insignificant differences, while those that are distantly related (lions and opossums) have many more? To me it looks like either these differences are another piece of evidence indicating common ancestry and evolutionary relationships or else the intelligent designer is purposefully trying to trick us.
And how does a Creationist, thinking the way Danny Boy does, explain why:
1. some fungi, especially yeasts have a completely different pathway for the biosynthesis of lysine than that found in all other organisms.
2. they still retain some of the "regular" lysine gene sequences, that are apparently both degenerate and inactive.
Surely they would have the same pathway since the function (biosynthesis of lysine) should dictate the activity of the proteins. And they should have no vestiges of any of the "regular genes", since that would dictate gene products that apparently don't exist or are inactive. Maybe the designer realized he made a mistake and attempted to cover it up? And did a bad job while he was at it.
Again, it is only because you *assume* that 'lions and opposums' are 'distantly-related' that you have a 'puzzle'.
That lions and house cats are closely-related is not questioned.
Small differences that do not affect function are the happy consequence of a robust, fault-tolerant design. That you do not recognize that, but choose to see common descent is the result of your 'a priori' commitment to naturalism.
The creator is not trying to trick you. He has given you plenty of evidence of his presence and design of life. You choose to reject it and instead focus on evidence that you can interpret according to your will.
The essence of Hebrews 11:6 is that the potential for unbelief must always exist. Always.