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Related Concept Videos

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 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...
Multi-species Conserved Sequences02:51

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...
Evolutionary Relationships through Genome Comparisons02:54

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...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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Evolutionarily consistent families in SCOP: sequence, structure and function.

Ralph B Pethica1, Michael Levitt, Julian Gough

  • 1Department of Computer Science, University of Bristol, The Merchant Venturers Building, Room 3,16, Woodland Road, Bristol, UK. pethica@cs.bris.ac.uk

BMC Structural Biology
|October 20, 2012
PubMed
Summary
This summary is machine-generated.

The SCOP protein domain classification system

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

Published on: August 16, 2017

Area of Science:

  • Protein bioinformatics
  • Structural biology
  • Evolutionary biology

Background:

  • The Structural Classification of Proteins (SCOP) database organizes protein domains hierarchically.
  • Superfamilies in SCOP are well-defined by evolutionary, structural, and functional evidence.
  • The basis for SCOP family groupings within superfamilies is less clear, prompting investigation into their evolutionary consistency.

Purpose of the Study:

  • To determine if SCOP families group protein domains based on sequence similarity, structural similarity, or common function.
  • To assess the phylogenetic validity of SCOP family classifications within superfamilies.

Main Methods:

  • Generated phylogenetic trees using multiple sequence alignments.
  • Constructed phylogenetic trees based on structural distances.
  • Created phylogenetic trees from Gene Ontology (GO) terms and Enzyme Commission (EC) numbers.
  • Compared the topologies and confidence values of these trees against SCOP family classifications.

Main Results:

  • SCOP family groupings demonstrate high evolutionary consistency with sequence-based phylogenetics.
  • Trees derived from structural distances show good correlation with SCOP families, but with some inconsistencies.
  • Phylogenetic trees based on functional data (GO terms, EC numbers) are less consistent with SCOP families than sequence or structure-based trees.

Conclusions:

  • SCOP family classifications are largely evolutionarily sound, particularly when supported by sequence data.
  • While structural data generally aligns with SCOP families, functional annotations are more variable.
  • Most GO and EC terms are specific to individual SCOP families or subsets thereof, rather than superfamilies.