I thought I would leave the following as I typed it, but I have changed my mind. Ideally, one would say that, “the [protein] is an order of magnitude greater …”. Unfortunately, this would require re-ordering the paragraph, and the current order is better. So… skip to after the (second) line.
For my money, “pales etc.” is just not a strong enough expression here. “Pales in comparison with”, I venture is used when the first case is impressive, but the second case is so much greater that it makes the first case look entirely unimpressive. An example might be that company X has 140,000 PDB structures, but company Y has 600,000; it is not just somewhat better, but indeed makes the other look… er, pale. Again: “I can run the mile in 7:05, but this pales in comparison with Matthew, who can do it in 5:17.”
I would suggest here, perhaps, “is an order of magnitude smaller than”. This is about, for example, 10^5 vs 10^6, or 10^5 vs 10^7. (One can resort to saying, “several orders of magnitude” if comparing (e.g.) computer storage in 1980 with computer storage today.)
I would say that the expression, “pales in comparison with”, connotes [implies] the same order of magnitude — connotes that the things being compared might have been expected to be about the same — my mile in 7:05 is pretty good for a typical person, but Matthew is an elite athlete who has been training for a year. (This is not to say that you can not say, “pales in comparison with”, about something that is 1/10th as good; one might say, “The {imaginary machine gun} fires 400 rounds per minute, but that pales in comparison with the {imaginary machine gun}, which fires 5000 rounds per minute”… although (again) these are both machine guns.)
That is to say that — although 140 thousand is indeed impressive — (I venture) it is implicit that they are of the same order of magnitude.
I am thinking, then, that you might say, “pales into insignificance beside” [noting that Michael Harvey mentioned this], which is a way of making the expression stronger, or… “is trivial in comparison with”.