The Transporter Classification Database (TCDB): recent advances

doi:10.1093/nar/gkv1103

. 2016 Jan 4;44(D1):D372-9.

doi: 10.1093/nar/gkv1103. Epub 2015 Nov 5.

The Transporter Classification Database (TCDB): recent advances

Milton H Saier Jr¹, Vamsee S Reddy², Brian V Tsu³, Muhammad Saad Ahmed⁴, Chun Li⁴, Gabriel Moreno-Hagelsieb⁵

Affiliations

¹ Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA msaier@ucsd.edu.
² Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA Department of Medical Sciences, Boston University School of Medicine, 72 E Concord St., Boston, MA 02118, USA.
³ Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA.
⁴ Department of Biological Engineering, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, People's Republic of China.
⁵ Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, Canada N2L 3C5.

PMID: 26546518
PMCID: PMC4702804
DOI: 10.1093/nar/gkv1103

The Transporter Classification Database (TCDB): recent advances

Milton H Saier Jr et al. Nucleic Acids Res. 2016.

. 2016 Jan 4;44(D1):D372-9.

doi: 10.1093/nar/gkv1103. Epub 2015 Nov 5.

Authors

Milton H Saier Jr¹, Vamsee S Reddy², Brian V Tsu³, Muhammad Saad Ahmed⁴, Chun Li⁴, Gabriel Moreno-Hagelsieb⁵

Affiliations

¹ Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA msaier@ucsd.edu.
² Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA Department of Medical Sciences, Boston University School of Medicine, 72 E Concord St., Boston, MA 02118, USA.
³ Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA.
⁴ Department of Biological Engineering, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, People's Republic of China.
⁵ Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, Canada N2L 3C5.

PMID: 26546518
PMCID: PMC4702804
DOI: 10.1093/nar/gkv1103

Abstract

The Transporter Classification Database (TCDB; http://www.tcdb.org) is a freely accessible reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB). It consists of more than 10,000 non-redundant transport systems with more than 11 000 reference citations, classified into over 1000 transporter families. Transporters in TCDB can be single or multi-component systems, categorized in a functional/phylogenetic hierarchical system of classes, subclasses, families, subfamilies and transport systems. TCDB also includes updated software designed to analyze the distinctive features of transport proteins, extending its usefulness. Here we present a comprehensive update of the database contents and features and summarize recent discoveries recorded in TCDB.

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References

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[1] Cook G.M., Greening C., Hards K., Berney M. Energetics of pathogenic bacteria and opportunities for drug development. Adv. Microb. Physiol. 2014;65:1–62. - PubMed

[2] Cook G.M., Greening C., Hards K., Berney M. Energetics of pathogenic bacteria and opportunities for drug development. Adv. Microb. Physiol. 2014;65:1–62. - PubMed

[3] Busch W., Saier M.H., Jr The transporter classification (TC) system, 2002. Crit. Rev. Biochem. Mol. Biol. 2002;37:287–337. - PubMed

[4] Busch W., Saier M.H., Jr The transporter classification (TC) system, 2002. Crit. Rev. Biochem. Mol. Biol. 2002;37:287–337. - PubMed

[5] Putman M., van Veen H.W., Konings W.N. Molecular properties of bacterial multidrug transporters. Microbiol. Mol. Biol. Rev. 2000;64:672–693. - PMC - PubMed

[6] Putman M., van Veen H.W., Konings W.N. Molecular properties of bacterial multidrug transporters. Microbiol. Mol. Biol. Rev. 2000;64:672–693. - PMC - PubMed

[7] Delmar J.A., Su C.C., Yu E.W. Bacterial multidrug efflux transporters. Annu. Rev. Biophys. 2014;43:93–117. - PMC - PubMed

[8] Delmar J.A., Su C.C., Yu E.W. Bacterial multidrug efflux transporters. Annu. Rev. Biophys. 2014;43:93–117. - PMC - PubMed

[9] Yen M.R., Choi J., Saier M.H., Jr Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution. J. Mol. Microbiol. Biotechnol. 2009;17:163–176. - PMC - PubMed

[10] Yen M.R., Choi J., Saier M.H., Jr Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution. J. Mol. Microbiol. Biotechnol. 2009;17:163–176. - PMC - PubMed

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The Transporter Classification Database (TCDB): recent advances

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The Transporter Classification Database (TCDB): recent advances

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