Web-Based Resource for Genomic Enzymology Tools

项目概要/摘要 此应用程序请求支持一个基于Web的资源，该资源为社区提供对“基因组 酶学”工具，以1）能够识别未表征的蛋白质的功能发现，包括那些 存在于人类微生物组和其他宏基因组群落中; 2）促进功能分配 通过提供对基因组背景/功能连锁的简单访问，对未表征的蛋白质进行分析;以及3）调查 蛋白质家族中的序列-功能空间，用于鉴定功能筛选的候选物， 改善所需的生物化学/生物物理性质（可用于系统生物学以及 制药和化学应用）。该资源提供了三个综合工具： 使用序列相似性网络可视化/分析蛋白质家族中的序列-功能空间 2）EFI-GNT，用于SSN中微生物和真菌蛋白质的基因组背景的可视化/分析，使用 基因组邻域网络和基因组邻域图，以识别功能相关的蛋白质 (e.g.,酶、转运蛋白和转录调节因子）;和3）EFI-CGFP， 化学引导的功能分析，将宏基因组和/或元转录组丰度映射到簇 在SSN中用于鉴定功能表征的重要微生物组靶标。资源使 访问工具，而无需用户具有计算机编程专业知识和/或本地访问 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 U 54 GM 093342和P01 GM 118303支持了传播。资源已被访问 被超过5,000名国内外用户使用，并被超过300项出版物和专利引用，证实了其易用性。 使用、受欢迎程度和影响。

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.