skip to main content
Idioma:

The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways

Zallot, Rémi ; Oberg, Nils ; Gerlt, John A

Biochemistry (Easton), 2019-10, Vol.58 (41), p.4169-4182 [Periódico revisado por pares]

United States: American Chemical Society

Texto completo disponível

Citações Citado por
  • Título:
    The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways
  • Autor: Zallot, Rémi ; Oberg, Nils ; Gerlt, John A
  • É parte de: Biochemistry (Easton), 2019-10, Vol.58 (41), p.4169-4182
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
    R.Z. and J.A.G. identified the web tool features essential for designing experimental strategies for proposing and experimentally testing in vitro activities and in vivo metabolic/physiological functions, N.O. programmed the back-end scripts and designed the graphical interface, and R.Z., N.O., and J.A.G. tested the performance of the web tools.
    Author Contributions
  • Descrição: The assignment of functions to uncharacterized proteins discovered in genome projects requires easily accessible tools and computational resources for large-scale, user-friendly leveraging of the protein, genome, and metagenome databases by experimentalists. This article describes the web resource developed by the Enzyme Function Initiative (EFI; accessed at https://efi.igb.illinois.edu/) that provides “genomic enzymology” tools (“web tools”) for (1) generating sequence similarity networks (SSNs) for protein families (EFI-EST); (2) analyzing and visualizing genome context of the proteins in clusters in SSNs (in genome neighborhood networks, GNNs, and genome neighborhood diagrams, GNDs) (EFI-GNT); and (3) prioritizing uncharacterized SSN clusters for functional assignment based on metagenome abundance (chemically guided functional profiling, CGFP) (EFI-CGFP). The SSNs generated by EFI-EST are used as the input for EFI-GNT and EFI-CGFP, enabling easy transfer of information among the tools. The networks are visualized and analyzed using Cytoscape, a widely used desktop application; GNDs and CGFP heatmaps summarizing metagenome abundance are viewed within the tools. We provide a detailed example of the integrated use of the tools with an analysis of glycyl radical enzyme superfamily (IPR004184) found in the human gut microbiome. This analysis demonstrates that (1) SwissProt annotations are not always correct, (2) large-scale genome context analyses allow the prediction of novel metabolic pathways, and (3) metagenome abundance can be used to identify/prioritize uncharacterized proteins for functional investigation.
  • Editor: United States: American Chemical Society
  • Idioma: Inglês
Links
Voltar para lista de resultados

  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

Buscando em bases de dados remotas. Favor aguardar.