Chlamydiae Database

ChlamDB is a comparative genomics database covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using accessions numbers of the most widely used databases including COG, KEGG ortholog, KEGG pathway, KEGG module, Pfam and InterPro. Candidate effectors of the Type III secretion system (T3SS) were identified using four in silico methods. The identification of orthologs among all PVC genomes allows users to perform large-scale comparative analyses and to identify orthologs of any protein in all genomes integrated in the database. Phylogenetic relationships of PVC proteins and their closest homologs in RefSeq, comparison of transmembrane domains and Pfam domains, conservation of gene neighborhood and taxonomic profiles can be visualized using dynamically generated graphs, available for download. As a central resource for researchers working on chlamydia, chlamydia-related bacteria, verrucomicrobia and planctomyces, ChlamDB facilitates the access to comprehensive annotations and integrates multiple tools for comparative genomic analyses.ChlamDB是一款覆盖衣原体门（Chlamydiae phylum）全部类群，以及隶属于浮霉菌门-疣微菌门-衣原体门（Planctomycetes-Verrucomicrobiae-Chlamydiae, PVC）超门的近缘物种的比较基因组学数据库。用户可借助当前主流数据库的登录号对基因组进行比对、分析与检索，涵盖的数据库包括COG、KEGG直系同源基因（KEGG ortholog）、KEGG通路（KEGG pathway）、KEGG模块（KEGG module）、Pfam及InterPro。研究团队采用四种计算机模拟（in silico）方法，鉴定出Ⅲ型分泌系统（Type III secretion system, T3SS）的候选效应蛋白。通过对所有PVC类群基因组中的直系同源基因进行鉴定，该数据库可支持用户开展大规模比较基因组分析，并检索数据库整合的全部基因组内任意蛋白质的直系同源物。PVC蛋白及其在RefSeq参考序列数据库中的近缘同源蛋白的系统发育关系、跨膜结构域与Pfam结构域的比对结果、基因邻接保守性及分类学特征，均可通过动态生成的可视化图表进行展示，且所有图表均支持下载。作为面向衣原体、衣原体相关细菌、疣微菌及浮霉菌研究人员的核心科研资源，ChlamDB可为用户提供全面的基因组注释信息，并集成多款比较基因组学分析工具。

搜集汇总

背景与挑战

背景概述

ChlamDB是一个比较基因组学数据库，涵盖Chlamydiae门及其相关的Planctomycetes-Verrucomicrobiae-Chlamydiae（PVC）超门，包含277个基因组。它提供详细的蛋白质注释、预计算同源搜索和系统发育分析，并集成多种工具以支持大规模比较基因组学研究。