Are you sure that you wouldn't be better off making a profile of your sequences from a multiple alignment and using that to search your database, instead? E.g. using the EMBOSS program prophecy to create a profile from your multiply-aligned sequences and then using the EMBOSS program prophet to search your database.
If you have a multiple alignment of the sequences, you can load said alignment in JalView. JalView has a consensus line by default running along the bottom of alignment, you can right-click this and 'Copy consensus sequence'. Then you can paste the contents of your clipboard into a new text file - and you have your consensus sequence.
It's a bit of a hack, and you're relying on JalView making a sensible consensus, but it will give you what you are after.