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
I think when they started Pfam, the idea was to have entries for individual protein families - thus the name. This in turn means that the intent was to have only orthologs as members of each Pfam entry. However, this is really difficult to do without experiments, and HMMs are so sensitive that they inevitably pull in matches to non-orthologs. I think that's why Pfam eventually ended up being a mix of mostly protein families (orthologs) and superfamilies (a mix of ortho-, para- and homologs).
Ah very interesting, thanks for your comment! Would you consider all members of a Pfam (= a protein family, not a superfamily, unless I misunderstand) to be orthologous then? I thought that they were grouped into Pfams according to domain sharing, which doesn't necessarily imply orthology
Pfam is domain-centric, so I was taking about orthology at the domain level. In many cases, especially in prokaryotes, proteins have a single domain, so the domain orthology is the same as orthology in the general sense.
There is a large number of single-domain and single-copy proteins in prokaryotes, which by definition means that all their members are orthologs. Just about all ribosomal proteins, translation factors, single-chain polymerases, etc belong to orthologous Pfam entries.