I have a multiple alignment of some proteins from the same family. All of them have 2 functional domains. Both of them are presented in Pfam database. There are no overlaps of these two domains in my alignment. I want cut the first domain off from all the proteins in the alignment. But I don't know how conservative is the boundary of first domain is. I don't want to watch each sequence individually and cut off the first domain by hand. Does there exist some way to do it automatically?
Not an automatic way, but faster than doing them all individually:
If you use program Clustal X (and probably also the newer version Clustal Omega, but when I worked with sequence alignments this wasn't out yet so don't know if the GUI is the same), after aligning the sequences you can select the columns that contain the alignment of the first domain, and you can delete these columns (either right-click delete/remove or something similar, or there is an option in the upper menu). If you know that the alignment of the first domain is correct, you can remove the first domain from all sequences with one click.
This is probably also possible in other alignment programs, but I only know about Clustal X for sure.