Protein families in HMMs
- Pfam
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
Pfam 26.0 (November 2011, 13672 families)
Pfam 30.0 (June 2016, 16306 entries)
Go to the web - TIGRFAMs
TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins
13.0, 4284 families, August 15 2012
15.0, 4488 families, September 16 2014
Go to the web - PANTHER
PANTHER version 8.0 contains 7729 protein families, each with a phylogenetic tree relating modern-day genes in 48 organisms.
PANTHER version 11.1 contains 13096 protein families, each with a phylogenetic tree relating modern-day genes in 104 organisms.
Go to the web
Protein families in sequences
- ko families (used in KEGG)
- FIG families (used in SEED)