Rumraket
July 3, 2022, 9:34pm
708
lee_merrill:
This paper about constructing the MOTB ancestor cites 90% sequence similarity. With about 300 residues, that would be 30 changes, to get to the ancestor, so say about 30 changes to get to a homolog.
No. To get a homolog just means two genes are on separate lineages. They can be completely identical and yet still be homologous because they’re found in different species.
What is it you’re trying to calculate again? If you mean to say extant MotB proteins couldn’t have evolved from an ancestral MotB protein because they’re different from it by about 30 amino acids, I just have to say that you should acquaint yourself with the SARS-Cov2 Omicron spike protein, which was different from the original Wuhan variant by 32 mutations already when it was first detected:
I must repeat what I wrote in this thread :
I’d flip this question around on it’s head and ask, if we can see that two proteins that share something like only 15% sequence similarity are still capable of performing essentially the same function (bind the same molecule or catalyze the same biochemical reaction), then why should we not think this?
If they can be THAT different yet still remain functional in the same way, then why should we think somewhere in the range of similarities between 100% and 15% there is some gap of nonfunctionality?
Presumably two proteins which are totally identical would not merit any doubt at all. So if we make them 99% identical, that’d still plausibly make them able to remain functional. Even if they have some degree of constraint on how much they can change before they stop being able to function, 99% seems to be similar enough that it shouldn’t be a problem. And the same at 98%.
We can imagine we keep going and at some point, maybe we start to think they’re beginning to be so dissimilar it might impact the function? Say we think maybe at 50% similarity we have some intuition that a lot of the protein sequence has changed, so how can it still retain the same structure or function?and yet it still functions. But then doesn’t that immediately imply the entire range spanning 100 to 15% must contain functional sequences? Shouldn’t that cause us to think there really is a pathway all the way from 100% to 15% similarity? We thought maybe 50% was some lower limit of similarity we couldn’t go beyond without breaking the function or structure, and yet now we find one that only has 15% similarity and it remains able to perform the function.
If we can find two proteins that adopt a similar structure which are 90% similar, and others that are 80% similar that still adopt the same structure and function, and then others that are 15%, how is this not exactly what we would expect to have if these proteins really did evolve from a common ancestor over very long periods of time?
And if these proteins are part of some larger structure, and other proteins in that structure exhibit the same pattern, and they show the same sort of gradual decrease in similarity with the distance of relationships between the species that carry them, then what could really justify the idea that they can’t have diverged gradually over that enormous period of time?
2 Likes
