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Related Experiment Videos

Using the CATH domain database to assign structures and functions to the genome sequences.

F Pearl1, A E Todd, J E Bray

  • 1Department of Biochemistry and Molecular Biology, University College, London, UK.

Biochemical Society Transactions
|May 18, 2000
PubMed
Summary

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The CATH database aids protein structure analysis. Sensitive sequence search methods like PSI-BLAST can annotate microbial genomes, but functional conservation varies, requiring careful assessment in some protein families.

Area of Science:

  • Structural bioinformatics
  • Genomic annotation
  • Computational biology

Background:

  • The CATH database classifies protein structures, aiding evolutionary and functional analysis.
  • Sequence search methods are crucial for identifying homologous proteins across databases.
  • Understanding protein function is vital for deciphering biological mechanisms.

Purpose of the Study:

  • To evaluate the effectiveness of sequence search methods for annotating microbial genomes using the CATH database.
  • To assess the reliability of inferring protein function based on structural and evolutionary relationships.

Main Methods:

  • Utilized the CATH database of protein structures.
  • Tested various sequence search methods, including gapped BLAST and Position Specific Iterated Basic Local Alignment Tool (PSI-BLAST).

Related Experiment Videos

  • Analyzed functional conservation within CATH's fold groups and homologous superfamilies.

    • Main Results:

    • PSI-BLAST and gapped BLAST can assign structural data to 22-36% of microbial genomes.
    • Functional conservation is high in enzyme families (nearly 55%), but divergence occurs in some large families.
    • Caution is advised when inferring function in highly populated families due to potential divergence.

    Conclusions:

    • Sensitive sequence search algorithms can enhance microbial genome annotation.
    • Functional inference based on homology requires careful consideration of potential divergence, especially in large protein families.
    • Further assessment of key residue substitutions is recommended for accurate functional prediction.