Web-Based Resource for Genomic Enzymology Tools

项目摘要/摘要 这个应用程序请求对基于Web的资源的支持，该资源提供对“基因组”的社区访问 用于1)鉴定功能发现的未鉴定蛋白质的“酶学”工具，包括 存在于人类微生物组和其他元基因组群落中；2)促进功能分配 通过提供对基因组上下文/功能链接的容易访问来获得未表征的蛋白质；以及3)调查 蛋白质家族中的序列-功能空间用于识别功能筛选和 改善所需的生化/生物物理特性(对系统生物学以及 制药和化学应用)。该资源提供了三个集成工具：1)EFI-EST 基于序列相似性网络的蛋白质家族序列功能空间可视化分析 (SSNS)；2)EFI-GNT，用于可视化/分析SSNS中微生物和真菌蛋白的基因组上下文 识别功能连锁蛋白质的基因组邻域网络和基因组邻域图 (例如，新代谢途径中的酶、转运体和转录调节因子)；以及3)EFI-CGFP 将元基因组和/或元转录组丰度映射到簇的化学指导的功能图谱 在SSNS中，用于识别重要的微生物组目标以进行功能表征。该资源启用 无需用户具备计算机编程专业知识和/或本地访问权限即可访问工具 必要的计算基础设施。该资源自2014年以来一直可用；其开发和 传播得到了U54GM093342和P01GM118303的支持。该资源已被访问 被5,000名国内和国际用户引用，并在&gt；300出版物和专利中被引用，证实了其易用性 用途、受欢迎程度和影响力。

PROJECT SUMMARY/ABSTRACT This application requests support for a web-based resource that provides community access to “genomic enzymology” tools to 1) enable identification of uncharacterized proteins for functional discovery, including those that are present in human microbiome and other metagenomic communities; 2) facilitate assignment of function to uncharacterized proteins by providing easy access to genome context/functional linkage; and 3) survey sequence-function space in protein families for identification of candidates for functional screening and improvement of desired biochemical/biophysical properties (useful for systems biology as well as the pharmaceutical and chemical applications). The resource provides three integrated tools: 1) EFI-EST for visualization/analysis of sequence-function space in proteins families using sequence similarity networks (SSNs); 2) EFI-GNT for visualization/analysis of genome context for microbial and fungal proteins in SSNs using genome neighborhood networks and genome neighborhood diagrams to identify functionally linked proteins (e.g., enzymes, transporters, and transcriptional regulators in novel metabolic pathways); and 3) EFI-CGFP for chemically guided functional profiling that maps metagenome and/or meta-transcriptome abundance to clusters in SSNs for identification of important microbiome targets for functional characterization. The resource enables access to the tools without the need for users to have computer programming expertise and/or local access to the necessary computational infrastructure. The resource has been available since 2014; its development and dissemination have been supported by U54GM093342 and P01GM118303. The resource has been accessed by >5,000 domestic and international users and cited in >300 publications and patents, confirming its ease-of- use, popularity, and impact.