I literally know nothing about these exact proteins, but just because something is better at making a microorganisms reproduce billions of years ago doesn't mean it's the best for us today, just it's still good enough not to have given us a reproductive disadvantage. It also doesn't mean it's the best for us as modern humans. We have shittons of defects that might not matter too much in terms of evolution, but is something we definitely would love to get rid of as humans.

Another good example of how the motto of evolution is "good enough" is oxygen. Our cells are literally constantly poisoning and damaging themselves with oxygen in order to produce energy to function, but it works well enough for us to reproduce before we get too fucked up and die.

Evolution doesn't do anything. Evolution is simply what happens over many, many generations when slight variations within a population gives some individuals a slightly better chance to spread their genes. It's not like evolution is some sort of intelligent force that selectively makes small improvements over time and never goes "backwards".

A good example are those weird ancient deer that thought: "You know, this land thing is way overrated", and became whales. If evolution phased out stuff, we wouldn't have aquatic mammals.