EzSEA: an interactive web interface for enzyme sequence evolution analysis.

IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2025-05-20 eCollection Date: 2025-01-01 DOI:10.1093/bioadv/vbaf118

Angela K Jiang, Jerry Zhao, Xiaofang Jiang

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引用次数: 0

Abstract

Motivation: Enzymes catalyze essential chemical reactions, driving metabolism, immunity, and growth. Understanding their evolution requires identifying mutations that shaped their functions and substrate interactions. Current methods lack integration of evolutionary history and intuitive visualization tools.

Results: We develop Enzyme Sequence Evolution Analysis (EzSEA), a web interface that identifies putative functionally important mutations by performing the following steps: structural prediction, homology search, multiple sequence alignment and trimming, phylogenetic tree inference, ancestral sequence reconstruction, and enzyme delineation. The EzSEA web application enables intuitive visualization of results, highlighting key mutations and phylogenetic tree branches that putatively delineate the enzyme of interest. Finally, we validate EzSEA by identifying previously experimentally verified key mutations in the gut bacteria enzyme bilirubin reductase.

Availability and implementation: EzSEA is freely available on the web at https://jianglabnlm.com/ezsea/.

查看原文本刊更多论文

EzSEA：一个用于酶序列进化分析的交互式网络界面。

动机：酶催化必要的化学反应，驱动新陈代谢、免疫和生长。了解它们的进化需要确定影响它们功能和底物相互作用的突变。目前的方法缺乏进化历史和直观可视化工具的集成。结果：我们开发了酶序列进化分析（EzSEA），这是一个网络界面，通过以下步骤识别假定的功能重要突变：结构预测、同源性搜索、多序列比对和修剪、系统发育树推断、祖先序列重建和酶描述。EzSEA web应用程序可以直观地可视化结果，突出显示关键突变和系统发育树分支，这些分支可以推定地描述感兴趣的酶。最后，我们通过鉴定先前实验验证的肠道细菌酶胆红素还原酶的关键突变来验证EzSEA。可用性和实施：EzSEA可以在https://jianglabnlm.com/ezsea/网站上免费获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量