I have several lists of proteins from mass spec (interactome data). The question I have to answer now, is: share these proteins common motifs? We are mainly interessted in ubiquitin binding motifs. So far I used NCBI's Batch CD-search and restricted the results to superfamilies. But I think we are lacking some information here. For example some kind of normalization of the data (if a motif occurs 10 times in all human proteins and we pull 9 of them, this would be an interesting result, if it occurs 30,000 times and we found 300 of them: not so interesting). Any ideas, tipps or hints?