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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

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 Families02:47

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 Networks02:26

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,...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Related Experiment Video

Updated: Jun 27, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

Algorithm to find distant repeats in a single protein sequence.

Nirjhar Banerjee1, Rangarajan Sarani, Chellamuthu Vasuki Ranjani

  • 1Bioinformatics Centre, Centre of Excellence in Structural Biology and Bio-computing, India.

Bioinformation
|December 5, 2008
PubMed
Summary

Researchers developed a new algorithm to identify distant repeats in protein sequences. This method uses Point Accepted Mutation (PAM) scores to analyze amino acid substitutions, aiding evolutionary and structural studies.

Keywords:
distant repeatsgenome sequencesphylogenypoint accepted mutationstructure-function relationship

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Last Updated: Jun 27, 2026

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Published on: January 25, 2019

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Distant repeats in protein sequences are crucial for understanding protein function, structure, and evolution.
  • Analyzing these repeats provides insights into the diversity of gene duplication events throughout evolutionary history.

Purpose of the Study:

  • To develop and present an algorithm for the comprehensive identification of distant repeats within protein sequences.
  • To leverage evolutionary information for a more accurate detection of distant repeats.

Main Methods:

  • The study introduces a novel algorithm designed to detect all distant repeats in a given protein sequence.
  • The Point Accepted Mutation (PAM) matrix is utilized to quantify amino acid substitutions, a key factor in identifying distant repeats.

Main Results:

  • The developed algorithm successfully identifies distant repeats by analyzing amino acid substitution patterns.
  • The application of PAM scores enhances the accuracy of distant repeat detection.

Conclusions:

  • The proposed algorithm offers a valuable tool for researchers studying protein evolution and structure.
  • This method will benefit structural biologists, molecular biologists, biochemists, and those in phylogenetic research.