oriTDB

oriTDB comprises 122 experimentally validated and 22,927 predicted oriTs within bacterial plasmids, Integrative and Conjugative Elements, and Integrative and Mobilizable Elements. Additionally, oriTDB includes details about associated relaxases, auxiliary proteins, type IV coupling proteins, and a gene cluster encoding the type IV secretion system. The database also provides predicted secondary structures of oriT sequences, dissects oriT regions into pairs of inverted repeats, nic sites, and their flanking conserved sequences, and offers an interactive visual representation. Furthermore, oriTDB includes an enhanced oriT prediction pipeline, oriTfinder2, which integrates a functional annotation module for cargo genes in bacterial MGEs.oriTDB数据库收录了细菌质粒、整合接合元件（Integrative and Conjugative Elements）以及整合可移动元件（Integrative and Mobilizable Elements）中的122个经实验验证的转移起始位点（oriT）与22927个预测获得的oriT。此外，该数据库还提供了相关松弛酶（relaxases）、辅助蛋白（auxiliary proteins）、IV型偶联蛋白（type IV coupling proteins）以及编码IV型分泌系统（type IV secretion system）的基因簇的详细信息。该数据库还可提供oriT序列的预测二级结构，将oriT区域划分为反向重复序列对、nic位点及其侧翼保守序列，并支持交互式可视化展示。此外，oriTDB还集成了增强型oriT预测流程oriTfinder2，该流程整合了针对细菌可移动遗传元件（Mobile Genetic Elements，MGEs）负载基因的功能注释模块。

搜集汇总

背景与挑战

背景概述

oriTDB是一个专注于细菌移动遗传元件（MGEs）转移起始（oriT）区域的数据库，包含23,527个oriT区域和972个物种，涉及抗生素抗性基因等货物基因。该数据库提供oriTfinder2预测工具，旨在支持研究基因水平转移和抗菌素耐药性传播。