I am trying to group peptide sequences according to the protein functions for further filtering and analysis, and I wonder what is the best and the most comprehensive source of protein function annotations. I downloaded the NCBI RefSeq and UniProt (both Swiss and Trembl) separately with annotations that were provided, but there are a few other (some of which are a lot smaller) sets of peptide sequences and annotations available around various sources online. Is there some centralized location with almost all protein function annotations available from where I could get the entries in a text, MySQL, or some other format? Also, it would be great to be able to cross-reference to map the matching entries to my existing NCBI RefSeq and UniProt entries.
Any advice would be appreciated
PS. I am aware of existing posts covering a similar topic, but I did not see any recent comments there. So I'm hoping, with the new post, to get up to date.