“Hey Rocky, watch me pull a rabbit out of my hat!”
I realized that I should add just a bit more information to last answer on gene identification, so here it is.
After the last installment, Diego commented:
but still you do not know exactly what part of your DNA sequence is matching to the annotated protein.
Ahh, but we do.
And I was negligent in not showing you.
There are multiple ways to view the GenBank record that we arrived at while following links from our matching sequence.
A very handy way, especially if you’re looking at where sequences align to a larger subject sequence, like a big eucaryotic gene, is to view the GenBank record and the associated annotations as a graph.
To do this, I select Graph from the Display pull-down menu.
And voila! I see a graph and I see where beta lactamase is located on my graph.
I click the graph right above the beta lactamase (bla) arrow and I see where the sequence of the DNA, the sequence of the RNA, and the sequence of the protein all map relative to each other.
Remember, there was a 100% match between my unknown sequence (the match started at 1 and ended at the last nucleotide) and the nucleotides between positions 44, 246 and 44, 665? You can check this here
So, in fact, we do know what part of our query DNA sequence matches (all of it) and where it matches, too.