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Protein Families

Protein 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...

Protein Families

Protein 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...

Conservation of Protein Domains

Conservation 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...

Conservation of Protein Domains Over Different Proteins

Conservation 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...

Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Updated: May 19, 2026

Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis

Embryo Microinjection and Electroporation in the Chordate Ciona intestinalis

Published on: October 16, 2016

The chordate proteome history database.

Anthony Levasseur¹, Julien Paganini, Jacques Dainat

¹INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix Marseille Université, ESIL Polytech, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.

Evolutionary Bioinformatics Online

|August 21, 2012

Summary

This summary is machine-generated.

The Chordate Proteome History Database analyzes protein evolution in chordates, identifying genomic events and functional information. This resource aids in understanding genome evolution and protein domain changes.

Keywords:

family size functional inference genome evolution ortholog groups phylogenetic reconstruction protein architecture

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Published on: October 16, 2016

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Published on: April 11, 2019

Area of Science:

Genomics
Evolutionary Biology
Bioinformatics

Background:

Understanding the evolutionary history of proteomes is crucial for deciphering genomic changes.
Previous analyses lacked integrated approaches to link phylogenetic relationships with genomic events.

Purpose of the Study:

To characterize and study the evolutionary histories of the chordate proteome.
To detect genomic events and perform automatic functional searches within chordate protein families.
To develop a database integrating phylogenetic analysis, gene family evolution, and functional annotation.

Main Methods:

Performed phylogenetic analyses using high-quality multiple sequence alignments and a robust pipeline.
Developed novel approaches to identify orthologs/paralogs and predict gene duplication/gain/loss events.
Created phylogroups by correcting OrthoMCL clusters with phylogenetic trees to deduce gene family dynamics.

Main Results:

Identified and localized key genomic events, including domain gains, losses, and shuffling, on phylogenetic trees.
Established phylogroups enabling the deduction of gene family size and lineage-specific gene gain/loss.
Enabled database searches based on protein identifiers, keywords, domains, and evolutionary events like domain exchange.

Conclusions:

The Chordate Proteome History Database is the first to integrate group clustering, phylogeny, and automatic functional searches.
It provides a unique resource for studying genome evolution, detecting novel protein architectures, and understanding evolutionary events in chordates.