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PathFams: statistical detection of pathogen-associated protein domains
BMC Genomics ( IF 4.4 ) Pub Date : 2021-09-14 , DOI: 10.1186/s12864-021-07982-8
Briallen Lobb 1 , Benjamin Jean-Marie Tremblay 1 , Gabriel Moreno-Hagelsieb 2 , Andrew C Doxey 1
Affiliation  

A substantial fraction of genes identified within bacterial genomes encode proteins of unknown function. Identifying which of these proteins represent potential virulence factors, and mapping their key virulence determinants, is a challenging but important goal. To facilitate virulence factor discovery, we performed a comprehensive analysis of 17,929 protein domain families within the Pfam database, and scored them based on their overrepresentation in pathogenic versus non-pathogenic species, taxonomic distribution, relative abundance in metagenomic datasets, and other factors. We identify pathogen-associated domain families, candidate virulence factors in the human gut, and eukaryotic-like mimicry domains with likely roles in virulence. Furthermore, we provide an interactive database called PathFams to allow users to explore pathogen-associated domains as well as identify pathogen-associated domains and domain architectures in user-uploaded sequences of interest. PathFams is freely available at https://pathfams.uwaterloo.ca .

中文翻译:

PathFams:病原体相关蛋白域的统计检测

在细菌基因组中鉴定的大部分基因编码功能未知的蛋白质。确定这些蛋白质中的哪些代表潜在的毒力因子,并绘制它们的关键毒力决定因素,是一个具有挑战性但重要的目标。为了促进毒力因子的发现,我们对 Pfam 数据库中的 17,929 个蛋白质域家族进行了综合分析,并根据它们在致病性与非致病性物种中的过度表达、分类学分布、宏基因组数据集中的相对丰度和其他因素对它们进行了评分。我们确定了病原体相关域家族、人类肠道中的候选毒力因子以及在毒力中可能起作用的真核样拟态域。此外,我们提供了一个名为 PathFams 的交互式数据库,允许用户探索病原体相关域,并在用户上传的感兴趣序列中识别病原体相关域和域架构。PathFams 可在 https://pathfams.uwaterloo.ca 上免费获得。
更新日期:2021-09-14
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