Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools

Remi Zallot, Nils Oberg, John A. Gerlt

Research output: Contribution to journalReview articlepeer-review

Abstract

The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be ‘user-friendly’ so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterized enzymes. We developed a suite of genomic enzymology tools (https://efi.igb.illinois.edu/) to (1) generate sequence similarity networks (SSNs) for exploration of sequence-function space in protein families (EFI-EST) and (2) provide genome context for members of protein families (EFI-GNT). Integrated analysis of this complementary information allows to generate testable hypotheses about new functions. After a brief overview of EFI-EST and EFI-GNT, we describe applications that illustrate their use.

Original languageEnglish (US)
Pages (from-to)77-90
Number of pages14
JournalCurrent Opinion in Biotechnology
Volume69
DOIs
StatePublished - Jun 2021

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Biomedical Engineering

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