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Quantitative sequence-function relationships in proteins based on gene ontology.

Vineet Sangar1, Daniel J Blankenberg, Naomi Altman

  • 1Department of Biochemistry and Molecular Biology, Center of Computational Biology and Genomics, The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA. vus102@psu.edu

BMC Bioinformatics
|August 10, 2007
PubMed
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This summary is machine-generated.

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Annotation transfer for homologous proteins is reliable for sequences with over 50% residue identity. Beyond this threshold, the risk of assigning a dissimilar function to a protein is low, though not zero.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Evolution

Background:

  • The assumption that homologous proteins share function is crucial for transferring annotations in biological databases.
  • However, the complex relationship between amino acid sequence divergence and functional divergence necessitates caution.
  • This study quantitatively investigates this relationship using the Gene Ontology (GO) classification.

Purpose of the Study:

  • To quantitatively assess the relationship between sequence and function divergence in homologous proteins.
  • To determine a reliable threshold for transferring functional annotations between proteins based on sequence similarity.
  • To evaluate the accuracy of annotation transfer in protein families.

Main Methods:

  • Analyzed 6828 protein families from the PFAM database.

Related Experiment Videos

  • Correlated sequence divergence from pairwise alignments with functional divergence measured by path lengths in the Gene Ontology graph.
  • Accounted for proteins possessing multiple functions.

    • Main Results:

    • A dramatic decrease in divergent functions was observed for homologous proteins with over 50% residue identity.
    • Annotation transfer errors (assigning a dissimilar function) occur in fewer than 6% of cases for proteins exceeding this 50% identity threshold.
    • While the chance of completely incorrect annotation is low for highly similar proteins, it remains non-zero due to phenomena like recruitment.

    Conclusions:

    • The study provides insights into the general features of protein function evolution.
    • Establishes a guideline for the reliability of annotation transfer based on sequence similarity.
    • Highlights the importance of sequence identity as a predictor for accurate functional annotation transfer.