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Related Experiment Videos

Searching for common sequence patterns among distantly related proteins

M Suyama1, T Nishioka, J Oda

  • 1Institute for Chemical Research, Kyoto University, Uji-city, Japan.

Protein Engineering
|November 1, 1995
PubMed
Summary

A new program, Gap Allowing Pattern Explorer (GAPE), identifies conserved amino acid sequence motifs in proteins, even with gaps. This tool aids in discovering functionally important residues involved in ligand recognition.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Protein Sequence Analysis

Background:

  • Identifying conserved amino acid motifs is crucial for understanding protein function and evolution.
  • Existing methods often struggle with sequence variations and gaps, limiting motif discovery.
  • Distantly related proteins may share functional motifs despite significant sequence divergence.

Purpose of the Study:

  • To develop a novel computational tool, Gap Allowing Pattern Explorer (GAPE), for extracting conserved amino acid sequence motifs.
  • To enable motif discovery in protein sequences that contain gaps or insertions.
  • To identify functionally significant residues involved in ligand recognition.

Main Methods:

  • The GAPE program generates all possible amino acid patterns up to five residues.

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  • It selects subsequences matching patterns, ignoring distances between residues.
  • Motifs are extracted by fixing distances between residues, with options to relax constraints for gap identification.

    • Main Results:

    • GAPE successfully identified conserved motifs in pyridoxal-phosphate and ATP-related protein sequences.
    • Extracted motifs with low occurrence expectation contained amino acid residues critical for ligand binding.
    • The program effectively handles sequence gaps, expanding motif discovery capabilities.

    Conclusions:

    • The Gap Allowing Pattern Explorer (GAPE) is an effective tool for identifying conserved protein motifs, including those with gaps.
    • The identified motifs highlight key residues involved in protein-ligand interactions.
    • GAPE enhances the ability to study evolutionary relationships and functional sites in diverse protein families.