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Related Concept Videos

Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...

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DeepES: deep learning-based enzyme screening to identify orphan enzyme genes.

Keisuke Hirota1, Felix Salim1, Takuji Yamada1,2,3,4

  • 1School of Life Science and Technology, Institute of Science Tokyo, Tokyo, 152-8550, Japan.

Bioinformatics (Oxford, England)
|February 5, 2025
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Summary

DeepES, a deep learning tool, identifies orphan enzyme genes by analyzing protein sequences and reaction classes. This approach aids in understanding enzyme functions and discovering novel genes, like those in human gut bacteria.

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Area of Science:

  • Bioinformatics
  • Enzymology
  • Computational Biology

Background:

  • Advances in sequencing technology provide vast protein sequence data.
  • Many enzymes remain unannotated ('orphan enzymes'), limiting functional understanding.
  • Existing tools struggle with annotating these orphan enzymes.

Purpose of the Study:

  • To develop a deep learning-based tool, DeepES, for identifying orphan enzyme genes.
  • To focus on discovering enzymes within specific biosynthetic gene clusters and reaction classes.
  • To bridge the gap in understanding the link between protein sequences and enzymatic reactions.

Main Methods:

  • DeepES utilizes protein sequences as input.
  • It integrates outputs from binary classifiers for different reaction classes.
  • The tool evaluates the presence of specific biosynthetic gene clusters.

Main Results:

  • DeepES effectively captures functional similarity between protein sequences.
  • The tool successfully identified candidate genes for 236 orphan enzymes.
  • Applied to metagenome-assembled genomes, it found enzymes involved in short-chain fatty acid production in gut bacteria.

Conclusions:

  • DeepES is a valuable tool for exploring orphan enzyme genes.
  • It enhances functional annotation by identifying enzymes with unknown roles.
  • The findings contribute to understanding microbial metabolism, particularly in the human gut.