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Updated: Jul 5, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Identifying protein domains with the Pfam database.
Robert Finn1, Sam Griffiths-Jones, Alex Bateman
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, United Kingdom.
Current Protocols in Bioinformatics
|April 23, 2008
Summary
The Pfam database provides protein domain families, including alignments and models. This guide details accessing and utilizing Pfam data, such as families, alignments, and annotations, locally or remotely.
Area of Science:
- Bioinformatics
- Structural Biology
- Genomics
Background:
- Protein domains are fundamental units of proteins, crucial for function and evolution.
- Databases like Pfam organize protein domain information for researchers.
- Understanding protein domain families aids in functional prediction and comparative genomics.
Purpose of the Study:
- To provide comprehensive guidance on accessing and utilizing the Pfam database.
- To explain the structure and content of Pfam entries, including families, alignments, and annotations.
- To detail methods for using Pfam data both remotely via the web and locally.
Main Methods:
- Description of Pfam database structure and content.
- Explanation of how to access Pfam entries (families, alignments, annotation).
- Instructions for local and remote usage of the Pfam database.
Main Results:
- Pfam entries are structured around protein domain families.
- Each family includes multiple sequence alignments and profile hidden Markov models (HMMs).
- Associated data includes annotation, literature references, and cross-database links.
Conclusions:
- The Pfam database is a valuable resource for protein domain family information.
- Effective utilization of Pfam data requires understanding its structure and access methods.
- The guide facilitates efficient use of Pfam for research in bioinformatics and related fields.
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02:47Protein Families
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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...
02:26Conservation 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...
02:26Conservation of Protein Domains
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...
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02:04Protein-protein Interfaces
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02:26Protein Networks
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