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Introduction

Bacterial mobile genetic elements (MGEs), play a critical role in disseminating pathogenesis and antimicrobial-resistance determinants. These elements, such as conjugative plasmids, Integrative and Conjugative Elements (ICEs), and Integrative and Mobilizable Elements (IMEs), typically consist of four modules in their conjugative regions: the origin-of-transfer (oriT) region, relaxase gene, type IV coupling protein (T4CP) gene, a gene cluster coding for bacterial type IV secretion system (T4SS), as well as the cargo genes in the MGEs. Focusing on the conjugative modules, oriTDB currently contains comprehensive information on the oriT regions, relaxases, auxiliary proteins, T4CP, T4SS and their associations in MGEs.


Key features

  • Data Repository: oriTDB contains a comprehensive collection of curated datasets of conjugative modules found in plasmids, ICEs and IMEs, which include oriT regions, relaxases, auxiliary proteins, T4CP, and T4SS. In addition, oriTDB also collects a relaxosome dataset and catalogs them as relaxosome entries. These data are categorized based on experimental validation or in silico prediction, allowing users to select the relevant category for browsing and downloading the required data in oriTDB.

  • Statistics contents: Using the dataset obtained from oriTDB, a statistics analysis was conducted regarding the following: 1. the taxonomic distribution of conjugative modules collected in oriTDB. 2. the distribution of the oriT-carrying plasmids, ICEs and IMEs.


    • Key functions

  • Fuzzy search and filters: oriTDB supports fuzzy searching within its database to accommodate user search queries. Users can apply filters on the browsing interface and search results to refine and access the required data.

  • Interactive visualization: for the complex content displayed on interfaces such as browse, statistics, and results, oriTDB offers interactive charts, graphs, and visualizations to help users understand the corresponding information more intuitively.

  • Online oriT region prediction: users can use the prediction tool oriTfinder2 provided by oriTDB to detect oriT regions in submitted GenBank or FASTA files without the need for registration, and there is no limit on the using times.

  • Data and tool sharing: The data and datasets collected in oriTDB can be freely downloaded by users, and the oriTfinder2 prediction tool also offers a local version.


    • Data collection

    Compared to the oriTDB 1.0 released in 2018, we updated our datasets by text mining and in silico prediction:

    Number of elements derived from experimental data Number of elements derived from predicted data Total
    oriTDB (released in 2018)
    oriT Plasmid 42 954 996
    ICE 6 67 73
    IME 4 2 6
    Relaxase 27 956 983
    Auxiliary protein 29 73 102
    T4CP 12 452 464
    oriTDB (updated in 2024)
    oriT Plasmid 91 22,390 22,481
    ICE 18 482 500
    IME 13 55 68
    Relaxase 50 13,066 13,116
    Auxiliary protein 44 7,614 7,658
    T4CP 16 16,969 16,985
    Relaxosome 6 15 21

    Usage

    How to use oriTDB?



    The web-based oriTDB database contains seven major parts: Home, Browse, Statistics, Tools, Download, References and Help. Users can browse and download resources according to their needs on the corresponding pages.


    By entering a specific name of an MGE or a species in the search bar, users can quickly obtain detailed information about the oriT carried by a particular MGE or a category of species.

    On the "Browse" page



    The oriTDB database has classified the collected data on the oriT region, relaxase, auxiliary protein, T4CP, T4SS and relaxosome datasets into two major groups based on their sources (plasmids, ICEs, IMEs, vectors, and artificial transposons) and evidence (experimental validation and in silico prediction). Furthermore, users can conduct a fuzzy search using the search bar. Entries displayed in the browsing interface or search results can be selected to access the corresponding interface and obtain more detailed information.

    On the "Statistics" page




    In this interface, the taxonomic distribution of the conjugative modules and the category distribution of cargo genes archived by oriTDB are displayed and illustrated through interactive pie charts. For the taxonomic distribution section, by clicking on the corresponding species in the pie chart, users can efficiently explore the MGEs of that species archived in oriTDB. For the cargo genes section, such as ARGs, by clicking on an ARG family in the pie chart, users can view in detail the distribution of ARG genes belong to this family. The same applies to other types of cargo genes, such as virulence factors, metal resistance genes and anti-CRISPRs.

    On the "Tools" page


    In this interface, oriTDB offers three online tools: oriTfinder2, BLAST search, and HMMER search:

  • oriTfinder2 prediction tool:

    • Users can identify the origin-of-transfer regions in DNA sequences of bacterial mobile genetic elements, such as plasmids, ICEs, and IMEs, through this online tool. The prediction strategy used by oriTfinder2 are displayed as follows:

  • BLAST search:

    • Users can perform BLAST search for query DNA/protein sequences against experimentally validated sequences archived in oriTDB through this online tool.

  • HMMER search:

    • Users can perform hmmscan search against the profile HMMs of relaxases and T4CPs in oriTDB through this online tool.

    On the "Download" page



    This interface provides the download for the local version of oriTfinder2. Users can also find all the datasets archived in oriTDB on this page and download them for free.

    On the "References" page




    This interface includes all the oriT-related references collected by oriTDB and has classified them according to the conjugative modules (oriT region, relaxosome, relaxase, auxiliary protein, and T4CP). oriTDB also supports the search of included references using keywords such as author, article title, journal, year, and PubMed ID.

    FAQs

    Q1. How to use oriTDB?


    A1: You can quickly understand the core functions of oriTDB through the browse interface, and get more detailed through this Help manual.

    Q2. In the entries collected by oriTDB, some content is displayed as "-", what does this mean?


    A2: If "-" appears in an experimentally validated entry, it indicates that we were unable to find corresponding data in the reference literature; if "-" appears in an in silico predicted entry, it means that the corresponding content was not predicted by oriTfinder.

    Q3: How could I contact you if I find an error or have suggestions for oriTDB?


    A3: Please do not hesitate to contact us through the mailing of hyou@sjtu.edu.cn.

    Q4. Can I submit data to oriTDB?


    A4: You can contact Prof. Ou for cooperation through the mailing of hyou@sjtu.edu.cn.