Cronometer uses various sources to get its nutrients. But when it comes to the wide variety of processed foods, it has to rely on the package. It's more than likely that the package does not go into the details of things like amino acids.
I just checked. My cronometer did not have Barilla Red Lentil pasta in its database. But I just randomly choose a different brand and it gave the number of grams of protein and not any of the amino acids. Then I checked the label on the package and it was the same thing.
So it probably isn't that it doesn't contain lysine. It just doesn't know how much.
OHMYGOSH! I just had a profound revelation!
I have noticed a number of times with Cronometer that although I get adequate amounts of protein - sometimes I'm lacking in a few (or a bunch) of amino acids. I had puzzled about that many times. I had actually come up with a number of complex reasons for it. No reason to go into that here.
Now, I don't eat processed food every day. But I do have a few favorites that come up at least once a week. Like my Trader Joe's bagels and the occasional Cliff Bar. They have lots of protein but no amino acids are listed and therefore no amino acids show up in Cronometer.
Oh! and the Trader Joe's super firm tofu - same thing.
I will start paying attention to that.
Thank you for your question.
Dr. Watson, we have solved the mystery of the missing amino acids.