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. 2017 Jan 4;45(D1):D320-D324.
doi: 10.1093/nar/gkw1068. Epub 2016 Nov 28.

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

Liam D H Elbourne  1 , Sasha G Tetu  2 , Karl A Hassan  2 , Ian T Paulsen  3
Affiliations

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

Liam D H Elbourne et al. Nucleic Acids Res. .

Abstract

All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline. The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. For example, TransportDB 2.0 includes tools that allow users to select annotated genomes of interest from the thousands of species held in the database and compare their complete transporter complements.

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Figures

Figure 1.
Figure 1.
TransportDB 2.0 home page and core dynamic elements of the organism pages facilitating interactive data access. (A) Screenshot of the TransportDB 2.0 web portal home page. The home page provides an overview of the database and the current database content in both text format and as an interactive zoomable treemap image at the bottom of the page, which operates in the same manner as the organism treemaps (see B). The organism pages can be accessed by typing into the autocompleting search bar, or by following the ‘Browse Organisms Taxonomically’ button. Selecting an organism will open the organism page, which provides a textual overview of the transporter content of that organism, as well as three alternative avenues to view the transporter annotation data for that organism (panels B–D). (B) A zoomable treemap is present in the top right corner of the organism page. At the top level (top panel) the treemap shows transporter classes, clicking in the box for any class (e.g. Secondary Transporter) shows the transporter families or superfamilies within that class (middle panel), and subsequent clicking on a transporter family (e.g. MFS) shows the constituent members of that family (bottom panel). Clicking on any transporter locus tag will open up the annotation evidence for that transporter. (C) The middle section of the organism pages contain nested tabbed lists of all transport proteins within each family and their accompanying details. (D) The lower section of the page shows a zoomable sunburst diagram depicting the distribution of transporter classes in the inner ring, and transporter families in the middle ring, broken down by substrate specificity at the outer ring. As with the treemap zooming in is achieved by clicking on the desired region. Zooming out is achieved by clicking in the centre of the circle.
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