We find that many people are interested in learning more about the domains in their proteins of interest. A great tool to use to examine the domains, their architecture/organization, and their relationships is SMART, the Simple Modular Architecture Research Tool. It is developed and maintained by the Bork lab at EMBL (a source of many great tools). This appetizer movie may get you interested in examining your proteins of interest with the SMART analysis. We show you how to find hundreds of proteins with “transmembrane receptor” domains in about 3 minutes.
We have a complete tutorial on SMART that presents the information in much more detail.