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Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks.

Janine N Copp1, Eyal Akiva2,3, Patricia C Babbitt2,3

  • 1Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada.

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|July 28, 2018
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Summary
This summary is machine-generated.

Sequence similarity networks (SSNs) help discover novel protein functions by analyzing protein superfamilies. This approach rapidly classifies proteins, revealing unexplored sequences with potential new enzymatic activities.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Vast protein sequence data in public databases offers insights into protein function evolution.
  • Current understanding of protein function is limited compared to nature's diversity.
  • Integrative computational methods are crucial for discovering new protein functions and enzymatic reactions.

Purpose of the Study:

  • To highlight the utility of sequence similarity networks (SSNs) for exploring uncharted protein sequence and function space.
  • To demonstrate the application of SSNs in classifying protein groups and identifying novel functionalities within the nitroreductase (NTR) superfamily.

Main Methods:

  • Utilized sequence similarity networks (SSNs) to analyze protein superfamilies.
  • Investigated complex sequence-structure-function relationships.
  • Applied SSN analysis to the nitroreductase (NTR) superfamily for classification and discovery.

Main Results:

  • SSNs effectively identify previously unexplored protein sequence and function space.
  • SSN investigations provide rapid and efficient classification of protein groups.
  • The approach exposed experimentally uncharacterized sequences within the NTR superfamily with potential novel functions.

Conclusions:

  • SSNs are a powerful tool for discovering new protein functions and enzymatic activities.
  • Integrating SSNs with experimental characterization will broaden the understanding of enzyme functional diversity and physiological roles.
  • This approach accelerates the exploration of the vast, yet largely unknown, functional repertoire of proteins.