This is kind of a stupid question. Suppose I have a contig sequence and I want to know what kind of protein it might encode (if it does). I run it against NCBI ORF Finder and then choose to do a blast and cognitor for the longest reading frame. Get a few hits, and conserved domains for a protein. Next I run the same contig thru NCBI blastx, and get hits for a couple of proteins. But the protein I found through the longest reading frame has a lower score in blastx.
How do I choose which protein it might be?