Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States.
Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
J Mol Biol. 2023 Jul 15;435(14):168018. doi: 10.1016/j.jmb.2023.168018. Epub 2023 Feb 17.
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.
酶功能倡议(EFI)提供了一个带有“基因组酶学”网络工具的网络资源,利用蛋白质(UniProt)和基因组(欧洲核苷酸档案库;ENA;https://www.ebi.ac.uk/ena/)数据库,协助将体外酶活性和体内代谢功能分配给未鉴定的酶(https://efi.igb.illinois.edu/)。这些工具支持(1)使用序列相似性网络(SSN;EFI-EST)探索酶家族中的序列-功能空间,(2)轻松访问 SSN 簇中细菌、古菌和真菌蛋白质的基因组背景,以便鉴定同功家族并从基因组背景推断其功能(EFI-GNT);(3)使用化学指导的功能分析(EFI-CGFP)确定 NIH 人类宏基因组计划宏基因组中 SSN 簇的丰度。我们描述了可以从分类学类别生成 SSN 的增强功能,从而能够更精细地分析序列-功能空间;我们提供了生成特定于分类学类别的 SSN 的示例。