Selenzyme: Enzyme selection tool for pathway design
Selenzyme: Enzyme selection tool for pathway design
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Selenzyme：用于途径设计的酶选择工具
DOI：
10.1101/188979
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Carbonell P
中科院分区：
文献类型：
--
作者：
Carbonell P
合成生物学将工程原理应用于生物学，以创造自然界中从未见过的生物功能。合成生物学最令人兴奋的应用之一是设计新的生物体，这些生物体能够以更绿色、可持续的方式生产有价值的化学品，包括药物和生物材料。然而，选择合适的酶来催化每个反应步骤以产生所需的目标化合物并不是微不足道的。在这里，我们介绍Selenzyme，一个免费的在线酶选择工具，用于代谢途径设计。用户被引导通过几个决策步骤，以入围最佳候选人为给定的途径步骤。该工具基于现有数据库和工具以图形方式呈现有关酶的关键信息，例如：序列和催化反应的相似性;源生物与预期宿主物种之间的系统发育距离;突出显示保守区域、预测催化位点和活性区域以及相关特性（例如预测溶解度和跨膜区域）的多重比对。Selenzyme为生物加工中的自动化工作流程提供定制的序列选择。可用性和实施该工具作为途径设计阶段的一部分集成到设计-构建-测试-学习SYNBIOCHEM管道中。Selenzyme网络服务器可在http://selenzyme.synbiochem.co.uk.Supplementary上获得信息补充数据可在Bioinformatics online上获得。
SummarySynthetic biology applies the principles of engineering to biology in order to create biological functionalities not seen before in nature. One of the most exciting applications of synthetic biology is the design of new organisms with the ability to produce valuable chemicals including pharmaceuticals and biomaterials in a greener; sustainable fashion. Selecting the right enzymes to catalyze each reaction step in order to produce a desired target compound is, however, not trivial. Here, we present Selenzyme, a free online enzyme selection tool for metabolic pathway design. The user is guided through several decision steps in order to shortlist the best candidates for a given pathway step. The tool graphically presents key information about enzymes based on existing databases and tools such as: similarity of sequences and of catalyzed reactions; phylogenetic distance between source organism and intended host species; multiple alignment highlighting conserved regions, predicted catalytic site, and active regions and relevant properties such as predicted solubility and transmembrane regions. Selenzyme provides bespoke sequence selection for automated workflows in biofoundries.Availability and implementationThe tool is integrated as part of the pathway design stage into the design-build-test-learn SYNBIOCHEM pipeline. The Selenzyme web server is available at http://selenzyme.synbiochem.co.uk.Supplementary informationSupplementary data are available atBioinformaticsonline.