The calculation of functionally equivalent proteins is very similar to the comparison of the GO sets. The selection buttons can be used to build the first query and, after adding the "FUNSIM" operator, they can be used to build the second query. The query to calculate functional related and functionally equivalent proteins between two sets of proteins with the PHP domain reads:
GENE WHERE PFAM:PF02811 FUNSIM GENE WHERE PFAM:PF02811
This query uses the maximum score and the average score for the comparison. Comparing two proteomes with each other is a lengthy operation since all proteins from the first one have to be compared to all proteins from the second proteome. If one is interested in a specific biological process, molecular function or protein family, the query can be redefined to return only the interesting proteins. This reduces the computation time tremendously. The funSim results contain the proteins with the highest funSim, the highest MFscore, and the highest BPscore for each query protein. The results from such a query can be split in three parts.
The first part contains the accession number of the query gene product. The second part consists of the rank, the accession number and the average scores for the target gene product. The table contains the funSimLin, avg, the MFScoreLin, avg, BPScoreLin, avg, and the funSimRel, avg. The last part contains the same information as the second but all scores calculated with GOScoremax.