If I have a set of orthologous proteins, it is assumed that these will have a shared function due to the maintenance of evolutionary pressure following speciation (as I understand).
If I have a set of proteins that fall within a single PFAM, is the assumption of shared functionality as strong as it would be for the ortholog group? I am guessing not, as the second paragraph of the reference's introduction explicitly says they do not always share function. But then, no assumption is complete, so I imagine there will also be orthologs that do not share function.
I assume there is a degree of uncertainty regarding how high quality the group of orthologs is (e.g. if it is found by RSD or RBH or tree based methods). But with that in mind, would you say the assumption of shared functionality is stronger for the PFAM group or for the orthologous group?
Reference: Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D427–D432, https://doi.org/10.1093/nar/gky995
Edit - for anyone interested there's some interesting discussion here - Pfam Based Functional Annotaion