Pfam, TIGRfam, Superfamily, Smart....

The Pfam database is one the most important collections of information in the world for classifying proteins. The database categorises 75 per cent of known proteins to form a library of protein families - a 'periodic table' of biology.

TIGRFAMs are protein families based on Hidden Markov Models or HMMs

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments 1. Julian Gough* and 2. Cyrus Chothia

http://supfam.org/SUPERFAMILY/

Even SMART use protein domain HMMs

Editing to Add Python HMM modules

Ghmm http://ghmm.sourceforge.net/ghmm-python-tutorial.html

Hmmus has some C implementations of HMM algorithms with Python bindings http://pypi.python.org/pypi/hmmus/0.2.16

Sarment: Python modules for HMM analysis and partitioning of sequences http://bioinformatics.oxfordjournals.org/content/21/16/3427.full

You may try the Pfam database for the HMM of 11912 protein domain families. You can download the HMM profile for the current release from the Pfam FTP: Pfam-A.hmm.gz. You may use HMMER3 for searches or to analyze the Pfam based HMMs.