Did you consider PFAM database?

'Domain Organizations' are very beautifully prepared. Look at this

You can search what domains are present in a protein sequence with hmmscan tool, searching the sequence against a HMM database of PFAM

My favorites for proteins are

• InterPro (where you can find domains and get lots of information using InterProScan). You can also use InterProScan with nucleic acids
  • The UniProt database

I decided to use Prosite for a project I'm working on because it has the best integration with UniProt. One of the problems with Pfam is that it is not updated nearly as often as UniProt is, and so your domain intervals are sometimes out of synch. Prosite is updated with UniProt, and you can pull the Prosite domains directly from UniProt, i.e.

http://www.uniprot.org/uniprot/?sort=score&desc=&query=id:Q12851&format=tab&columns=id,feature(DOMAIN%20EXTENT)

While I'm not aware of any out of the box packages for searching domains, you can write a custom script to pull the domain information you need fairly easily.