ArticleeLife2014
Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.
Article in eLife, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- Substrate Specificity of a Methyltransferase Involved in the Biosynthesis of the Lantibiotic Cacaoidin.Biochemistry · 2024Article
- Proteome-Wide Bioinformatic Annotation and Functional Validation of the Monotopic Phosphoglycosyl Transferase Superfamily.bioRxiv : the preprint server for biology · 2024Article
- Genome mining of sulfonated lanthipeptides reveals unique cyclic peptide sulfotransferases.Acta pharmaceutica Sinica. B · 2024Article
- Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex.Nature communications · 2023Article
- Oxygenolytic sulfoquinovose degradation by an iron-dependent alkanesulfonate dioxygenase.iScience · 2023Article
- A Variant of the Sulfoglycolytic Transketolase Pathway for the Degradation of Sulfoquinovose into Sulfoacetate.Applied and environmental microbiology · 2023Article
- Mechanistic Studies on Dehydration in Class V Lanthipeptides.ACS chemical biology · 2022Article
- The Birth of Genomic Enzymology: Discovery of the Mechanistically Diverse Enolase Superfamily.Biochemistry · 2021Article
- Comparative genomic analysis of azasugar biosynthesis.AMB Express · 2021Article
- Review
- Mining and unearthing hidden biosynthetic potential.Nature communications · 2021Review
- Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools.Current opinion in biotechnology · 2021Review
- Discovery of novel pathways for carbohydrate metabolism.Current opinion in chemical biology · 2021Review
- PhotoModPlus: A web server for photosynthetic protein prediction from genome neighborhood features.PloS one · 2021Article
- A ferredoxin-dependent dihydropyrimidine dehydrogenase in Clostridium chromiireducens.Bioscience reports · 2020Article
- Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Photosynthetic protein classification using genome neighborhood-based machine learning feature.Scientific reports · 2020Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794). The predictions were verified by measuring in vitro activities for 51 proteins in 12 families in the PRS that represent ∼85% of the sequences; in vitro activities of pathway enzymes, carbon/nitrogen source phenotypes, and/or transcriptomic studies confirmed the predicted pathways. The synergistic use of sequence similarity networks3 and GNNs will facilitate the discovery of the components of novel, uncharacterized metabolic pathways in sequenced genomes.
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Registered trials
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