TIGRFAMs

TIGRFAMs is a collection of protein families, equivalence groups, and hidden Markov models (HMMs) used to annotate proteins by homology. It is primarily focused on functionally equivalent proteins and is maintained by the J. Craig Venter Institute (JCVI). TIGRFAMs differs from other protein family databases by its emphasis on identifying proteins that perform the same function, even if their sequences are divergent.

The TIGRFAMs database contains two primary types of entries:

• TIGRFAMs Families: These entries are manually curated and represent groups of homologous proteins that share a common function. Each family entry includes a description of the function, the biological process in which it participates, and references to relevant publications. Critical residues and functional domains are also often highlighted.

• Equivalence Groups (EQs): These represent functionally equivalent protein families from different organisms. Proteins within an EQ may have diverged significantly in sequence, but they perform the same function within their respective organisms.

TIGRFAMs utilizes hidden Markov models (HMMs) to identify proteins that belong to a particular family or equivalence group. These HMMs are specifically trained to recognize the sequence patterns that are characteristic of each family or EQ. This allows for accurate and reliable annotation of protein sequences, even when those sequences are distantly related to previously characterized proteins.

The TIGRFAMs database is a valuable resource for researchers who are interested in identifying the function of proteins, understanding the evolutionary relationships between proteins, and exploring the diversity of protein functions across different organisms. It is commonly used in genome annotation pipelines to assign functional roles to newly sequenced proteins. The data is publicly accessible and can be downloaded for local analysis.