PeroxiBase: The peroxidase database
PeroxiBase: The peroxidase database
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DOI：
10.1016/j.phytochem.2007.04.005
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发表时间：
2007-06-01
期刊：
影响因子：
3.8
通讯作者：
Dunand, Christophe
中科院分区：
文献类型：
--
作者：
Passardi, Filippo;Theiler, Grgory;Dunand, Christophe
过氧化物酶（EC 1.11）1.X)，由大小多基因家族编码，参与了几个重要的生理和发育过程。分析它们的进化和它们在不同门中的分布无疑有助于阐明它们在几乎所有生物体中极其广泛和多样化的存在的奥秘。PeroxiBase最初是为从植物中详尽收集III类过氧化物酶序列而创建的（Bakalovic， N., Passardi， F.等，2006）。PeroxiBase: III类植物过氧化物酶数据库。植物化学67,534-539)。将III类过氧化物酶数据库扩展到所有能够减少过氧化物分子的蛋白质似乎是必要的。我们的数据库包含血红素和非血红素过氧化物酶序列，这些序列来自于保存在GenBank或UniProt知识库等主要存储库中的注释或未正确注释的序列。这个新的数据库将允许获得进化的蛋白质家族和超家族能够过氧化物酶反应的全球概况。在这个快速发展的领域中，需要对过氧化物酶蛋白序列进行不断的更新和修正。由于缺乏统一的命名法，我们还为每个不同的过氧化物酶族引入了一个独特的缩写。因此，本文旨在报告peroxbase数据库的发展，该数据库可以通过web服务器（http://peroxibase.isb-sib.ch）免费访问。除了新的过氧化物酶分类之外，还创建了新的特定工具来方便过氧化物酶序列的查询、分类和提交。(c) 2007 Elsevier Ltd.版权所有。
Peroxidases (EC 1.11. 1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. Analyzing their evolution and their distribution among various phyla could certainly help to elucidate the mystery of their extremely widespread and diversified presence in almost all living organisms. PeroxiBase was originally created for the exhaustive collection of class III peroxidase sequences from plants (Bakalovic, N., Passardi, F., et al., 2006. PeroxiBase: a class III plant peroxidase database. Phytochemistry 67, 534-539). The extension of the class III peroxidase database to all proteins capable to reduce peroxide molecules appears as a necessity. Our database contains haem and non-haem peroxidase sequences originated from annotated or not correctly annotated sequences deposited in the main repositories such as GenBank or UniProt KnowledgeBase. This new database will allow obtaining a global overview of the evolution the protein families and superfamilies capable of peroxidase reaction. In this rapidly growing field, there is a need for continual updates and corrections of the peroxidase protein sequences. Following the lack of unified nomenclature, we also introduced a unique abbreviation for each different family of peroxidases. This paper thus aims to report the evolution of the PeroxiBase database, which is freely accessible through a web server (http://peroxibase.isb-sib.ch). In addition to new categories of peroxidases, new specific tools have been created to facilitate query, classification and submission of peroxidase sequences. (c) 2007 Elsevier Ltd. All rights reserved.