EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools

J Mol Biol. 2023 Jul 15;435(14):168018. doi: 10.1016/j.jmb.2023.168018. Epub 2023 Feb 17.

Abstract

The Enzyme Function Initiative (EFI) provides a web resource with "genomic enzymology" web tools to leverage the protein (UniProt) and genome (European Nucleotide Archive; ENA; https://www.ebi.ac.uk/ena/) databases to assist the assignment of in vitro enzymatic activities and in vivo metabolic functions to uncharacterized enzymes (https://efi.igb.illinois.edu/). The tools enable (1) exploration of sequence-function space in enzyme families using sequence similarity networks (SSNs; EFI-EST), (2) easy access to genome context for bacterial, archaeal, and fungal proteins in the SSN clusters so that isofunctional families can be identified and their functions inferred from genome context (EFI-GNT); and (3) determination of the abundance of SSN clusters in NIH Human Metagenome Project metagenomes using chemically guided functional profiling (EFI-CGFP). We describe enhancements that enable SSNs to be generated from taxonomy categories, allowing higher resolution analyses of sequence-function space; we provide examples of the generation of taxonomy category-specific SSNs.

Keywords: EFI-EST; EFI-GNT; genome context; sequence similarity networks; taxonomy.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Archaea / enzymology
  • Archaea / genetics
  • Bacteria / enzymology
  • Bacteria / genetics
  • Databases, Genetic*
  • Enzymes* / chemistry
  • Enzymes* / genetics
  • Fungi / enzymology
  • Fungi / genetics
  • Genomics
  • Humans
  • Internet*
  • Metagenome

Substances

  • Enzymes