To answer your question directly, there is no inherent difference between plant and animal amino acids. If the amino acid profile of one source is identical to another, its potential value or utility is also identical. Most amino acid are, after all, created by plants, and subsequently consumed and utilised by the grazing and foraging animals that we farm for meat. And those amino acids are passed down the food chain from plant to animal, and animal to human. The rate of absorption of each amino acid is proportional to its relative concentration, and the rate at which it is characteristically absorbed.
Some amino acids are sythesised by animals, however. Of the 21 amino acids common to all life, human beings are incapable of synthesising nine. These are the ‘essential’ amino acids. An additional six are deemed ‘conditionally essential’, since the rate of their synthesis is inadequate under certain conditions. Nevertheless, regardless of the source, the amino acids are chemically identical, and therefore indistinguishable by the body.
What does vary from source to source are so-called ‘anti-nutritional factors’, which broadly describe components that inhibit the digestibility, absorption, and/or utility of the available protein. These factors include certain food chemicals accompanying the protein sources, as well as the products of heat (i.e. Maillard reactions) and chemical processing—and they apply to both animal and plant sources.
The widely-used Protein Digestibility Corrected Amino Acid Score (PDCAAS) rating was developed jointly by the Food and Agriculture Organization (FAO) and World Health Organisation (WHO) in 1989. Although it is now over 30 years old, it remains a good general indicator of protein bio-availability, defined as “the proportion of the total amino acid that is digested and absorbed in a form suitable for protein synthesis.” However, the rating has a number of limitations, including its inability to account for endogenous (inside the body) losses of amino acids due to the aforementioned anti-nutritional factors, and the fact that protein from one source is not consumed in isolation from other food sources. The ‘quality’ and bio-availability of any protein source is likely dependent on all other components of the diet.
All of that said, we can assume that limiting intake of known anti-nutritional factors—glucosinolates, trypsin inhibitors, haemagglutinins, tannins, gossypol, uricogenic nucleobases, and Maillard reaction chemcials such as oxidized forms of sulphur amino acids, D-amino acids, and lysinoalanine (LAL)—will maximise the bio-availability of our dietary protein.
I hope that is helpful.