How to identify unknown sequence? - No BLAST identity!! (Nov/05/2008 )
except for the gap from 90-180 the scores look a little disconcerting.
how does the actual alignment look?
what is the percent identity?
these factors will help you determine the uniqueness of your sequence.
It's the amino acid sequence that determines what the protein does -- 50% similarity at the DNA level implies it's 50% different. You really need to determine what the amino acid sequence of your ORF is, and use that to identify what you've got...