1. Pfam(Protein families )
(March 2013, families)

3. 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.

4. 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. 

5. 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.

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

7. 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:

8. 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 v2
SUPERFAMILY - Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms
SCOP and CATH - classifications of protein structures into superfamilies, families and domains

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

12. 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.

13. 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.

14. SUPERFAMILY