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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 form...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

Protein and Protein Structures

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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...

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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Related Experiment Video

Updated: Jun 13, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

High quality protein sequence alignment by combining structural profile prediction and profile alignment using

Florian Teichert¹, Jonas Minning, Ugo Bastolla

¹Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr, Darmstadt, Germany.

BMC Bioinformatics

|May 18, 2010

Summary

This study introduces SABERTOOTH, a novel sequence alignment method that improves accuracy for distantly related proteins. The tool outperforms existing methods in the "twilight zone" of protein similarity, offering high-quality alignments where traditional methods fail.

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Last Updated: Jun 13, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

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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
Computational Biology
Structural Bioinformatics

Background:

Protein sequence alignment is crucial but unreliable for distantly related proteins (twilight zone).
Structure alignment offers better quality for distant pairs but requires structural data, which is often unavailable.
Accurate sequence alignment methods are needed for remotely homologous proteins.

Purpose of the Study:

To develop a sequence alignment method that extends accurate alignment to distantly related proteins.
To improve sequence alignment quality in the absence of structural data.

Main Methods:

Combined prediction of structural profiles from protein sequences with profile alignment using the SABERTOOTH tool.
Utilized an artificial neural network to predict protein contact vectors based on PSI-BLAST position-specific scoring matrices.
Assessed alignment quality using structural similarity and the significance score's ability to recognize evolutionary relationships, benchmarked against the SCOP database.

Main Results:

SABERTOOTH produced higher quality sequence alignments compared to Clustal W, T-Coffee, MUSCLE, and PSI-BLAST.
HHpred outperformed SABERTOOTH at family and superfamily levels.
SABERTOOTH demonstrated advantages for alignments at the SCOP fold level, particularly for distantly related proteins.

Conclusions:

SABERTOOTH is an automatic tool for high-quality pairwise sequence alignments, especially beneficial for remotely related proteins.
The method leverages predicted structural profiles for improved alignment accuracy.
Source code is available for academic users.