ez-CAZy是连接糖苷水解酶序列与酶活性的参考注释数据库。

IF 3.8 2区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES
Daniel S Erdody, Nicholas G Griffin, Renaud Berlemont
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引用次数: 0

摘要

糖苷水解酶(Glycoside Hydrolases, GH)是一种碳水化合物活性酶,在碳水化合物的降解中起着至关重要的作用,影响着生态系统功能、人类健康和生物技术应用。CAZy数据库中GHs的功能注释由于缺乏特定于序列的定义、注释工具以及依赖于广义的“多数规则”活动假设而受到阻碍。在这里,我们介绍ez-CAZy,一个定制的参考数据库,旨在将GH序列以及其他CAZy与其酶活性联系起来。通过使用隐马尔可夫模型配置文件和其他可公开访问的工具重新注释超过7,000个生物化学特征的GHs,我们提供了详细的序列元数据,领域架构和功能预测。我们的分析揭示了GH家族中酶活性和多结构域结构的聚类分布,有助于对新发现的序列进行更精确的功能预测。ez-CAZy的预测准确性使用超过500个最近表征的GHs进行验证,证明了功能注释。ez-CAZy解决了GH注释管道中的关键空白,并提供了一个公开访问的工具来支持序列分析和酶研究。这项工作强调了标准化酶表征和扩展底物测试的必要性,以提高未来研究的注释准确性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
ez-CAZy a reference annotation database for linking glycoside hydrolase sequence to enzymatic activity.

Glycoside Hydrolases (GH) are carbohydrate-active enzymes that play a critical role in the degradation of carbohydrates, impacting ecosystem function, human health, and biotechnological applications. The functional annotation of GHs within the CAZy database is hindered by the lack of sequence-specific definitions, annotation tools, and reliance on generalized "majority rule" activity assumptions. Here, we introduce ez-CAZy, a custom reference database designed to link GH sequences, as well as other CAZy, to their enzymatic activities. By reannotating over 7,000 biochemically characterized GHs using Hidden Markov Model profiles and other publicly accessible tools, we provide detailed sequence metadata, domain architectures, and functional predictions. Our analysis reveals the clustered distribution of enzymatic activities and multi-domain architectures within GH families, facilitating more precise functional predictions for newly identified sequences. The predictive accuracy of ez-CAZy was validated using over 500 recently characterized GHs, demonstrating functional annotation. ez-CAZy addresses critical gaps in GH annotation pipelines and offers a publicly accessible tool to support sequence analysis and enzymatic research. This work underscores the need for standardized enzyme characterization and expanded substrate testing to enhance annotation accuracy in future studies.

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来源期刊
Scientific Reports
Scientific Reports Natural Science Disciplines-
CiteScore
7.50
自引率
4.30%
发文量
19567
审稿时长
3.9 months
期刊介绍: We publish original research from all areas of the natural sciences, psychology, medicine and engineering. You can learn more about what we publish by browsing our specific scientific subject areas below or explore Scientific Reports by browsing all articles and collections. Scientific Reports has a 2-year impact factor: 4.380 (2021), and is the 6th most-cited journal in the world, with more than 540,000 citations in 2020 (Clarivate Analytics, 2021). •Engineering Engineering covers all aspects of engineering, technology, and applied science. It plays a crucial role in the development of technologies to address some of the world''s biggest challenges, helping to save lives and improve the way we live. •Physical sciences Physical sciences are those academic disciplines that aim to uncover the underlying laws of nature — often written in the language of mathematics. It is a collective term for areas of study including astronomy, chemistry, materials science and physics. •Earth and environmental sciences Earth and environmental sciences cover all aspects of Earth and planetary science and broadly encompass solid Earth processes, surface and atmospheric dynamics, Earth system history, climate and climate change, marine and freshwater systems, and ecology. It also considers the interactions between humans and these systems. •Biological sciences Biological sciences encompass all the divisions of natural sciences examining various aspects of vital processes. The concept includes anatomy, physiology, cell biology, biochemistry and biophysics, and covers all organisms from microorganisms, animals to plants. •Health sciences The health sciences study health, disease and healthcare. This field of study aims to develop knowledge, interventions and technology for use in healthcare to improve the treatment of patients.
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