EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.
EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.
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DOI：
10.1093/nar/gkv1269
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Rattei T
中科院分区：
文献类型：
--
作者：
Eichinger V;Nussbaumer T;Platzer A;Jehl MA;Arnold R;Rattei T
蛋白质分泌系统在细菌与宿主的相互作用中起着关键作用。effecvedb （http://effectivedb.org）包含预先计算的细菌分泌蛋白和完整分泌系统的预测。在这里，我们描述了一个主要的数据库更新，这是以前的特色NAR数据库问题。EffectiveDB结合多种工具识别III型分泌信号、III型伴侣蛋白的保守结合位点、IV型分泌肽、真核样结构域和宿主亚细胞靶向信号。除了分析任意蛋白质序列集合，新版本的effecvedb还提供了一个“基因组模式”，其中可以筛选来自几乎完整基因组或宏基因组箱的蛋白质序列，以确定三种重要分泌系统（III型，IV型，VI型）的存在。effecvedb包含对目前来自EggNOG 4.0数据库的1677个细菌基因组和来自NCBI RefSeq的其他细菌基因组的预计算预测。这个新的、用户友好的、信息丰富的门户网站提供了一个提交工具，用于在用户提供的数据上运行effecvedb预测工具。
Protein secretion systems play a key role in the interaction of bacteria and hosts. EffectiveDB (http://effectivedb.org) contains pre-calculated predictions of bacterial secreted proteins and of intact secretion systems. Here we describe a major update of the database, which was previously featured in the NAR Database Issue. EffectiveDB bundles various tools to recognize Type III secretion signals, conserved binding sites of Type III chaperones, Type IV secretion peptides, eukaryotic-like domains and subcellular targeting signals in the host. Beyond the analysis of arbitrary protein sequence collections, the new release of EffectiveDB also provides a ‘genome-mode’, in which protein sequences from nearly complete genomes or metagenomic bins can be screened for the presence of three important secretion systems (Type III, IV, VI). EffectiveDB contains pre-calculated predictions for currently 1677 bacterial genomes from the EggNOG 4.0 database and for additional bacterial genomes from NCBI RefSeq. The new, user-friendly and informative web portal offers a submission tool for running the EffectiveDB prediction tools on user-provided data.