ArticleBiochemistry2019
The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways.
Article in Biochemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 455 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
455 citing papers in PubMed.
- A Divergent Mitochondrial Cytochrome c in Malaria Parasites With an Anomalously Low Redox Potential.Journal of molecular biology · 2026Article
- Late-Stage Posttranslational Assembly of Fosfazinomycins.bioRxiv : the preprint server for biology · 2026Article
- Regulatory divergence and functional diversification of a c-di-GMP-controlled sigma factor in Actinomycetota.mSystems · 2026Article
- Structural and Functional Siderophore Remodeling by Enzymatic Delipidation.Angewandte Chemie (International ed. in English) · 2026Article
- Identification of a putative RocS homolog through phenotypic profiling of uncharacterized essential genes inbioRxiv : the preprint server for biology · 2026Article
- A sequence motif enables widespread use of noncanonical redox cofactors in natural enzymes.Nature chemical biology · 2026Article
- Pyridoxal-phosphate-dependent biosynthesis of aminovaleramide by AvaS in tRNA.Nature chemical biology · 2026Article
- Discovery and structural analysis of glycoside hydrolase family 176 α-1,2 glucosidase from Arthrobacter humicola A8F5.The Journal of biological chemistry · 2026Article
- Leveraging latent space models for enzyme discovery and sampling.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Targeted identification of new phaterpenes and elucidation of the relevant biosynthetic pathway inSynthetic and systems biotechnology · 2026Article
- A cloaked glutamate decarboxylase sustains the GABA shunt inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- CenIR, an essential BlaIR-family regulatory system inJournal of bacteriology · 2026Article
- Diversity and Classification of the Actinopeptins: A New Family of Lanthipeptides Within the Genomes from the Phylum Actinomycetota.Antibiotics (Basel, Switzerland) · 2026Article
- Functional divergence and conservation in the QueC protein family (PF06508): from tRNA modification to anti-phage defense.The Biochemical journal · 2026Article
- A posttranslational modification of fimbriae drives pathogenicity inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Kinetically Divergent Dimanganese-Tyrosyl Radical Cofactor Assembly in Listeria monocytogenes Class I Ribonucleotide Reductase.Biochemistry · 2026Article
- Article
- Evolutionarily divergent DUF4465 domains have a common vitamin BFEBS open bio · 2026Article
- Coordinated regulation of trimethylamine catabolism in abundant marine bacteria.Applied and environmental microbiology · 2026Article
- Nature's Anaerobic Toolkit: Glycyl Radical Enzymes and Their Expanding Functional and Mechanistic Diversity.Biochemistry · 2026Review
395 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.