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. 2006 Jan 1;34(Database issue):D181-6.
doi: 10.1093/nar/gkj001.

TCDB: the Transporter Classification Database for membrane transport protein analyses and information

Milton H Saier Jr  1 , Can V Tran, Ravi D Barabote
Affiliations

TCDB: the Transporter Classification Database for membrane transport protein analyses and information

Milton H Saier Jr et al. Nucleic Acids Res. .

Abstract

The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10,000 references, encompassing approximately 3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at http://www.tcdb.org. The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.

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Figures

Figure 1
Figure 1
The user-friendly front page of TCDB () where its features are easily accessible.
Figure 2
Figure 2
Protein data for the glucose porter (PtsG) of Escherichia coli displayed in the right window of the two-vertical-frame design of the TCDB web application. The six links shown in the upper right hand side of the figure can be accessed directly on screen.
Figure 3
Figure 3
Tools for analyzing transporters.
Figure 4
Figure 4
A plot characterizing a transporter with a 12 TMS topology. The plot integrates hydropathy, amphipathicity and TMS prediction. The curves represent hydropathy and amphipathicity of the proteins, and the bars are putative TMSs. Each of the TMSs is a hyperlink that can be traversed to plot a helical wheel representation of the TMS.
See this image and copyright information in PMC

References

    1. Chimento D.P., Mohanty A.K., Kadner R.J., Wiener M.C. Crystallization and initial X-ray diffraction of BtuB, the integral membrane cobalamin transporter of Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 2003;59:509–511. - PubMed
    1. Kurisu G., Zakharov S.D., Zhalnina M.V., Bano S., Eroukova V.Y., Rokitskaya T.I., Antonenko Y.N., Wiener M.C., Cramer W.A. The structure of BtuB with bound colicin E3 R-domain implies a translocon. Nature Struct. Biol. 2003;10:948–954. - PubMed
    1. Yu E.W., McDermott G., Zgurskaya H.I., Nikaido H., Koshland D.E., Jr Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump. Science. 2003;300:976–980. - PubMed
    1. Abramson J., Smirnova I., Kasho V., Verner G., Iwata S., Kaback H.R. The lactose permease of Escherichia coli: overall structure, the sugar-binding site and the alternating access model for transport. FEBS Lett. 2003;555:96–101. - PubMed
    1. Huang Y., Lemieux M.J., Song J., Auer M., Wang D.N. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science. 2003;301:616–620. - PubMed

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