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. 2025 Jan 6;53(D1):D163-D168.
doi: 10.1093/nar/gkae869.

oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements

Guitian Liu  1   2 , Xiaobin Li  3 , Jiahao Guan  2 , Cui Tai  2 , Yuqing Weng  4 , Xiaohua Chen  1 , Hong-Yu Ou  1   2
Affiliations

oriTDB: a database of the origin-of-transfer regions of bacterial mobile genetic elements

Guitian Liu et al. Nucleic Acids Res. .

Abstract

Conjugation and mobilization are two important pathways of horizontal transfer of bacterial mobile genetic elements (MGEs). The origin-of-transfer (oriT) region is crucial for this process, serving as a recognition site for relaxase and containing the DNA nicking site (nic site), which initiates the conjugation or mobilization. Here, we present a database of the origin-of-transfer regions of bacterial MGEs, oriTDB (https://bioinfo-mml.sjtu.edu.cn/oriTDB2/). Incorporating data from text mining and genome analysis, 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. This resource is intended to support research on bacterial conjugative or mobilizable elements and promote an understanding of their cargo gene functions.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Overview of the dissection and visualization of the oriT region in oriTDB. (A) The detailed information of the oriT_R388 region in the plasmid R388 of Escherichia coli. The oriT region was dissected into pairs of IRs, nic sites, and their flanking conserved sequences (blue dashed box). (B) Visual representation of the oriT_R388 region. The sequence of oriT is presented in the interactive visualization form (red dashed box), with the IR pairs in the oriT region as aqua arrows, and the nic sites as orange rectangles. (C) The RNAfold-predicted secondary structure of the single strand oriT_R388 region. (D) The AlphaFold2-predicted structure of the relaxase protein TrwC_R388 related to oriT_R388.
Figure 2.
Figure 2.
Species distribution and cargo genes categorization of the oriT-carrying plasmids predicted by oriTfinder2. (A) Species distribution of the oriT-carrying plasmids. (B) The number of the conjugative, mobilizable (oriT) and mobilizable (oriT+ relaxase) plasmids. (C) The number of the six categorized cargo genes in the oriT-carrying plasmids. (D) The proportion of the three categorized oriT-carrying plasmids in the six categorized cargo genes.
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