ArticleJournal of molecular biology2023
EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools.
Article in Journal of molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 papers.
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236 citing papers in PubMed.
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- Diversity and Classification of the Actinopeptins: A New Family of Lanthipeptides Within the Genomes from the Phylum Actinomycetota.Antibiotics (Basel, Switzerland) · 2026Article
- A posttranslational modification of fimbriae drives pathogenicity inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Gene amir_2071 of Actinosynnema mirum DSM 43827 encodes a dimethylallyltryptophan synthase superfamily protein responsible for the production of prenylated tyrosine.Folia microbiologica · 2026Article
- DeepHalo: Deep learning-powered exploration of halogenated metabolites uncovering antibacterial depsipeptides.Acta pharmaceutica Sinica. B · 2026Article
- Distribution and Evolutionary Signatures of a Broad-Spectrum Pesticide-Degrading Carboxylesterase TriS From Strain S113.Environmental microbiology · 2026Article
176 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.