Pfam(Protein families )

Pfam 27.0

(March 2013, 14831 families)

http://pfam.sanger.ac.uk/

Protein family• A protein family is a group of evolutionarily-

related proteins • Proteins in a family descend from a common ancestor

(homology) and typically have similar three-dimensional structures, functions, and significant sequence similarity. While it is difficult to evaluate the significance of functional or structural similarity, there is a fairly well developed framework for evaluating the significance of similarity between a group of sequences using sequence alignment methods.

• Proteins that do not share a common ancestor are very unlikely to show statistically significant sequence similarity, making sequence alignment a powerful tool for identifying the members of protein families.

Superfamily – family - subfamily

• A common usage is that superfamilies contain families which contain sub-families.

• Many proteins comprise multiple independent structural and functional units or domains. Due to evolutionary shuffling, different domains in a protein have evolved independently. This has led, in recent years, to a focus on families of protein domains. A number of online resources are devoted to identifying and cataloging such domains. 

Superfamily – family - subfamily

• Superfamily: The domains in a fold are grouped into superfamilies, which have at least a distant common ancestor.

• Family: The domains in a superfamily are grouped into families, which have a more recent common ancestor.

• Protein domain: The domains in families are grouped into protein domains, which are essentially the same protein.

• Species: The domains in "protein domains" are grouped according to species.

• Domain: part of a protein.

An example

The human cyclophilin family, as represented by the structures of the isomerase domains of some of its members.

Protein family resources

• There are many biological databases that record examples of protein families and allow users to identify if newly identified proteins belong to a known family. Here are a few examples:

Protein family resources

• Pfam - Protein families database of alignments and HMMs

• PROSITE - Database of protein domains, families and functional sites

• PIRSF - SuperFamily Classification System• PASS2 - Protein Alignment as Structural Superfamilies v

2 • SUPERFAMILY - Library of HMMs representing superfa

milies and database of (superfamily and family) annotations for all completely sequenced organisms

• SCOP and CATH - classifications of protein structures into superfamilies, families and domains

Pfam

• The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

SUPERFAMILY

• SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

• The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level.

• The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences.

SUPERFAMILY

• SUPERFAMILY classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. The superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.

SUPERFAMILY