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Updated: Jul 9, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
The Pfam protein families database
Robert D Finn1, John Tate, Jaina Mistry
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK.
Nucleic Acids Research
|November 28, 2007
Summary
Pfam is a protein family database that now includes 9318 families. This protein domain resource is updated with new sequence data and features an improved website design for better accessibility.
Area of Science:
- Bioinformatics
- Structural Biology
- Genomics
Background:
- Pfam is a widely used database of protein families and domains.
- It represents protein families using multiple sequence alignments and profile hidden Markov models.
- The database is crucial for understanding protein function and evolution.
Purpose of the Study:
- To announce the release of Pfam version 22.0.
- To highlight the expansion of Pfam's data sources.
- To introduce the new, unified website design for improved user experience.
Main Methods:
- Curating protein families using multiple sequence alignments.
- Developing profile hidden Markov models for each family.
- Integrating data from UniProtKB, NCBI GenPept, and metagenomics projects.
- Developing a new, consistent website design across consortium members.
Main Results:
- Pfam release 22.0 contains 9318 protein families.
- The database now incorporates sequences from metagenomics projects.
- A new, consistent, and improved website design is available across multiple international sites.
Conclusions:
- Pfam continues to be a comprehensive and expanding resource for protein domain and family information.
- The integration of diverse sequence data enhances the coverage and utility of Pfam.
- The updated website design improves accessibility and usability for researchers worldwide.
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02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
01:57Protein Complexes with Interchangeable Parts
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...