Protein sequencing gaps - (Mar/19/2012 )

I have sequenced may interest gene and I aligned my protein with proteins in the databass .
I found that there are gaps in the sequence alignment .
Why there are gaps when i aligned my protein and how I could potentially ‘remove’ them from a subsequent blastx search/alignment ??

The gaps may or may not be due to alterations in the gene if you are looking at a different species, could also be sequencing error, cloning error, ...