Designing degenerate primers using alignment of protein sequences from other species
Try going through this tutorial: http://www.scs.illinois.edu/schulten/tutorials/ef-tu/eftu_tutorial.pdf
It is a nice introduction on how to use multiseq and identify conserved domains from AA or nt sequences across many taxa.

Also check out http://fungene.cme.msu.edu/ 
The RDP staff at Michigan State University are the masters of doing exactly what you're trying to do.