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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...

Conservation of Protein Domains

Conservation of Protein Domains

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Phylogeny

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

Phylogenetic Trees

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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Related Experiment Video

Updated: Aug 12, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

How Often Does Filtering of Alignment Columns Improve the Phylogenetic Inference of Two-Domain Proteins?

Andrey I Sigorskikh¹, Daria D Latortseva¹, Anna S Karyagina^2,3,4

¹Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.

Biochemistry. Biokhimiia

|January 30, 2023

Summary

Filtering protein sequence alignments improves phylogenetic reconstruction quality for full-length eukaryotic proteins. Excluding less conserved regions like linkers and termini can negatively impact accuracy.

Keywords:

evolutionary domains filtration of multiple sequence alignment phylogenetic inference

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Last Updated: Aug 12, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Bioinformatics
Evolutionary Biology
Computational Biology

Background:

Protein phylogeny reconstruction relies on multiple sequence alignments.
Heterogeneous conservation across protein regions (domains, linkers, termini) poses challenges for alignment quality.
Alignment column filtering is a common strategy to address these challenges.

Purpose of the Study:

To investigate the impact of alignment filtering on protein phylogeny reconstruction.
To evaluate different approaches using proteins with two evolutionary domains.
To assess the influence of sequence length and conservation levels on phylogenetic accuracy.

Main Methods:

Comparative analysis of phylogenetic reconstruction methods.
Application of alignment column filtering techniques.
Utilizing multi-domain proteins with varying conservation patterns.

Main Results:

Alignment filtering improved phylogenetic reconstruction quality for full-length eukaryotic protein sequences on average.
Excluding less conserved regions (linkers, termini) generally worsened phylogenetic reconstruction quality.
The effectiveness of filtering is dependent on sequence length and protein type (eukaryotic).

Conclusions:

Full-length sequence analysis with appropriate filtering can enhance eukaryotic protein phylogeny.
Selective exclusion of variable regions may not always be beneficial for phylogenetic accuracy.
Careful consideration of sequence regions and filtering strategies is crucial for robust protein phylogeny reconstruction.