Web-Based Resource for Genomic Enzymology Tools

基于网络的基因组酶学工具资源

• 批准号: 10548888
• 负责人: JOHN A GERLT
• 金额: $ 56.12万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-10 至 2026-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10548888
• 关键词: Amino Acid Sequence; Amino Acid Sequence Databases; Archaea; Archaeal Proteins; Archives; Bacteria; Bacterial Proteins; Biochemical; Bioinformatics; Chemicals; Color; Communities; Data Set; Databases; Democracy; Development; Disease; Environment; Enzymatic Biochemistry; Enzymes; European; Expressed Sequence Tags; Family; Fungal Proteins; Genes; Genetic Transcription; Genome; Genomics; Guilt; Human Microbiome; Individual; International; Intestines; Knowledge; Legal patent; Maps; Metabolic; Metabolic Pathway; Metagenomics; National Institute of General Medical Sciences; Natural Products; Neighborhoods; Non-Insulin-Dependent Diabetes Mellitus; Nucleotides; Occupations; Ontology; Pharmacologic Substance; Physiological; Pregnancy; Protein Family; Proteins; Publications; Request for Applications; Resources; Running; Sequence Analysis; Surveys; Systems Biology; Visualization; bioinformatics tool; biophysical properties; candidate identification; computer infrastructure; computer program; fungus; genome analysis; genome database; genome resource; improved; in vitro activity; in vivo; interest; link protein; metagenome; metatranscriptome; microbial; microbiome; novel; online resource; prototype; response; screening; small molecule libraries; tool

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.

项目概要/摘要 该应用程序请求支持基于网络的资源，该资源为社区提供对“基因组”的访问 酶学”工具，1) 能够识别未表征的蛋白质以进行功能发现，包括那些 存在于人类微生物组和其他宏基因组群落中； 2) 便于职能分配 通过提供对基因组背景/功能联系的轻松访问来识别未表征的蛋白质； 3）调查 蛋白质家族中的序列功能空间，用于识别功能筛选的候选者 改善所需的生化/生物物理特性（对于系统生物学以及 制药和化学应用）。该资源提供了三个集成工具：1) EFI-EST 使用序列相似性网络对蛋白质家族中的序列功能空间进行可视化/分析 （SSN）； 2) EFI-GNT 用于可视化/分析 SSN 中微生物和真菌蛋白的基因组背景 基因组邻域网络和基因组邻域图来识别功能相关的蛋白质 （例如，新代谢途径中的酶、转运蛋白和转录调节因子）； 3) EFI-CGFP 用于 化学引导的功能分析，将宏基因组和/或宏转录组丰度映射到簇 在 SSN 中识别重要的微生物组目标以进行功能表征。该资源使 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这些工具 必要的计算基础设施。该资源自 2014 年起提供；它的发展和 传播得到了 U54GM093342 和 P01GM118303 的支持。资源已被访问 被超过 5,000 名国内外用户认可，并被超过 300 份出版物和专利引用，证实了其易于使用 使用、流行度和影响。