Abstract

Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and aids identification of potential cell surface diagnostic markers, drug targets, or vaccine components. PSORTdb comprises ePSORTdb, a manually curated database of experimentally verified protein SCLs, and cPSORTdb, a pre-computed database of PSORTb-predicted SCLs for NCBI’s RefSeq deduced bacterial and archaeal proteomes. We now report PSORTdb 4.0 (http://db.psort.org/). It features a website refresh, in particular a more user-friendly database search. It also addresses the need to uniquely identify proteins from NCBI genomes now that GI numbers have been retired. It further expands both ePSORTdb and cPSORTdb, including additional data about novel secondary localizations, such as proteins found in bacterial outer membrane vesicles. Protein predictions in cPSORTdb have increased along with the number of available microbial genomes, from approximately 13 million when PSORTdb 3.0 was released, to over 66 million currently. Now, analyses of both complete and draft genomes are included. This expanded database will be of wide use to researchers developing SCL predictors or studying diverse microbes, including medically, agriculturally and industrially important species that have both classic or atypical cell envelope structures or vesicles.

中文翻译：

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PSORTdb 4.0：扩展和重新设计的细菌和古细菌蛋白亚细胞定位数据库，包含新的次级定位

摘要

蛋白质亚细胞定位（SCL）对于了解蛋白质功能，基因组注释和帮助鉴定潜在的细胞表面诊断标记物，药物靶标或疫苗成分非常重要。PSORTdb包括ePSORTdb（一个经过人工验证的，经过实验验证的蛋白SCL的数据库）和cPSORTdb（一个由PSORTb预测的SCL的预先计算的数据库，用于NCBI RefSeq推导的细菌和古细菌蛋白质组）。现在，我们报告PSORTdb 4.0（http://db.psort.org/）。它具有网站刷新功能，尤其是对用户更友好的数据库搜索。由于已经取消了GI号，因此它也满足了从NCBI基因组中唯一鉴定蛋白质的需求。它进一步扩展了ePSORTdb和cPSORTdb，包括有关新的二级定位的附加数据，例如细菌外膜囊泡中的蛋白质。cPSORTdb中的蛋白质预测随着可用微生物基因组数量的增加而增加，从发布PSORTdb 3.0时的大约1300万增加到目前的6600万。现在，包括完整和原始基因组的分析。这个扩展的数据库将广泛用于开发SCL预测因子或研究多种微生物的研究人员，包括具有经典或非典型细胞包膜结构或囊泡的医学，农业和工业重要物种。