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

Oberg, Nils, Zallot, Rémi ORCID: https://orcid.org/0000-0002-7317-1578 and Gerlt, John A (2023) EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. Journal of Molecular Biology, 435 (14). 168018. ISSN 0022-2836

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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.

Item Type:	Article (Article)
Peer-reviewed:	Yes
Date Deposited:	25 Jul 2024 14:56
Publisher:	Elsevier
Additional Information:	For copyright reasons, the full-text version of this article is not available via e-space repository. Access to full-text is available through the publisher's website: https://doi.org/10.1016/j.jmb.2023.168018
Divisions:	Faculties > Science and Engineering
Subject terms:	Humans, Bacteria, Fungi, Archaea, Enzymes, Genomics, Internet, Databases, Genetic, Metagenome, EFI-EST, EFI-GNT, genome context, sequence similarity networks, taxonomy, Humans, Bacteria, Genomics, Internet, Metagenome, Enzymes, Archaea, Fungi, Databases, Genetic, Humans, Bacteria, Fungi, Archaea, Enzymes, Genomics, Internet, Databases, Genetic, Metagenome, EFI-EST, EFI-GNT, genome context, sequence similarity networks, taxonomy, Humans, Bacteria, Genomics, Internet, Metagenome, Enzymes, Archaea, Fungi, Databases, Genetic, 0304 Medicinal and Biomolecular Chemistry, 0601 Biochemistry and Cell Biology, 0605 Microbiology, Biochemistry & Molecular Biology, 0304 Medicinal and Biomolecular Chemistry, 0601 Biochemistry and Cell Biology, 0605 Microbiology, Biochemistry & Molecular Biology
URI:	https://e-space.mmu.ac.uk/id/eprint/633428
DOI:	https://doi.org/10.1016/j.jmb.2023.168018
ISSN	0022-2836
e-ISSN	1089-8638

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