Biochemistry. 2019 Oct 15;58(41):4169-4182. doi: 10.1021/acs.biochem.9b00735. Epub 2019 Oct 4.
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.
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基因组项目中发现的功能不明蛋白质的分配，需要实验人员能够轻松访问工具和计算资源，以便大规模、用户友好地利用蛋白质、基因组和宏基因组数据库。本文介绍了由酶功能倡议（EFI；可在 https://efi.igb.illinois.edu/ 访问）开发的网络资源，该资源提供了“基因组酶学”工具（“网络工具”），用于：（1）为蛋白质家族生成序列相似性网络（SSN）（EFI-EST）；（2）分析和可视化 SSN 中聚类内的蛋白质基因组上下文（在基因组邻居网络、GNN 和基因组邻居图、GND 中）（EFI-GNT）；（3）基于宏基因组丰度对功能不明 SSN 聚类进行优先级排序，用于功能分配（化学引导功能分析，CGFP）（EFI-CGFP）。EFI-EST 生成的 SSN 用作 EFI-GNT 和 EFI-CGFP 的输入，使工具之间的信息易于传递。网络使用 Cytoscape 进行可视化和分析，Cytoscape 是一种广泛使用的桌面应用程序；GND 和 CGFP 热图汇总了宏基因组的丰度，可在工具内查看。我们提供了一个详细的示例，说明了工具的综合使用，分析了在人类肠道微生物组中发现的糖基自由基酶超家族（IPR004184）。该分析表明：（1）SwissProt 注释并不总是正确的，（2）大规模的基因组上下文分析可以预测新的代谢途径，（3）宏基因组丰度可用于识别/优先考虑功能不明的蛋白质进行功能研究。
