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. 2016:2016:9415459.
doi: 10.1155/2016/9415459. Epub 2016 Sep 21.

T4SP Database 2.0: An Improved Database for Type IV Secretion Systems in Bacterial Genomes with New Online Analysis Tools

Na Han  1 , Weiwen Yu  1 , Yujun Qiang  1 , Wen Zhang  1
Affiliations

T4SP Database 2.0: An Improved Database for Type IV Secretion Systems in Bacterial Genomes with New Online Analysis Tools

Na Han et al. Comput Math Methods Med. 2016.

Abstract

Type IV secretion system (T4SS) can mediate the passage of macromolecules across cellular membranes and is essential for virulent and genetic material exchange among bacterial species. The Type IV Secretion Project 2.0 (T4SP 2.0) database is an improved and extended version of the platform released in 2013 aimed at assisting with the detection of Type IV secretion systems (T4SS) in bacterial genomes. This advanced version provides users with web server tools for detecting the existence and variations of T4SS genes online. The new interface for the genome browser provides a user-friendly access to the most complete and accurate resource of T4SS gene information (e.g., gene number, name, type, position, sequence, related articles, and quick links to other webs). Currently, this online database includes T4SS information of 5239 bacterial strains. Conclusions. T4SS is one of the most versatile secretion systems necessary for the virulence and survival of bacteria and the secretion of protein and/or DNA substrates from a donor to a recipient cell. This database on virB/D genes of the T4SS system will help scientists worldwide to improve their knowledge on secretion systems and also identify potential pathogenic mechanisms of various microbial species.

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Conflict of interest statement

None of the authors has conflict of interests.

Figures

Figure 1
Figure 1
The T4SP analysis page where users could upload their DNA sequences on the web page and get the report page about the T4SS genes.
Figure 2
Figure 2
The online blast page.
Figure 3
Figure 3
The blast result page.
Figure 4
Figure 4
The web page covering a genome browser and tables about T4SS genes for the genome in the database or the sequence users submitted.
Figure 5
Figure 5
The data page.
Figure 6
Figure 6
The taxonomy tree in 8 classic levels of bacteria (kingdom, phylum, class, order, family, genus, species, and strain).
See this image and copyright information in PMC

References

    1. Waksman G., Fronzes R. Molecular architecture of bacterial type IV secretion systems. Trends in Biochemical Sciences. 2010;35(12):691–698. doi: 10.1016/j.tibs.2010.06.002. - DOI - PubMed
    1. Wallden K., Rivera-Calzada A., Waksman G. Microreview: type IV secretion systems: versatility and diversity in function. Cellular Microbiology. 2010;12(9):1203–1212. doi: 10.1111/j.1462-5822.2010.01499.x. - DOI - PMC - PubMed
    1. Juhas M., Crook D. W., Hood D. W. Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence. Cellular Microbiology. 2008;10(12):2377–2386. doi: 10.1111/j.1462-5822.2008.01187.x. - DOI - PMC - PubMed
    1. Cascales E., Christie P. J. The versatile bacterial type IV secretion systems. Nature Reviews. Microbiology. 2003;1(2):137–149. doi: 10.1038/nrmicro753. - DOI - PMC - PubMed
    1. Fronzes R., Christie P. J., Waksman G. The structural biology of type IV secretion systems. Nature Reviews Microbiology. 2009;7(10):703–714. doi: 10.1038/nrmicro2218. - DOI - PMC - PubMed

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