I don't fully understand your question. Do you have a set of proteins in which you want to identify the motif or you want to gather all proteins with that motif? So in general, one option if to look for the motif in the prosite database (http://prosite.expasy.org/scanprosite/). You can also query databases with http://www.genome.jp/tools/motif/MOTIF2.html transforming your profile into prosite-friendly motifs.
OK maybe I will be try a be more clear. We found that one of the enzyme that we have analysed display extremely high affinity to Met-X-X-Arg sequence. I would like to identified the human protein that contain this sequence. One of the guess of presence of N-terminal Met as start codon translation.
I don't think that blast will do the job. The sequence is too short. I can't do that myself but i can ask my colleague, data scientist. He can do this.
Hi Adam, so MOTIF2 (http://www.genome.jp/tools/motif/MOTIF2.html) seems to be the tool you are looking for. If you pass M-x-x-R to the server and restrict your search to humans you'll find a subset that have that particular motif. As I understand that is what you want. However, this will give you a substantial amount of proteins (the search I did with your query gave me over 1000 hits). This is expected since the motif is very short, and out of 4 sites 2 can be anything (X).