Nucleic Acids Research Advance Access originally published online on November 28, 2006
Nucleic Acids Research 2007 35(Database issue):D274-D279; doi:10.1093/nar/gkl925
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Nucleic Acids Research, 2007, Vol. 35, Database issue D274-D279
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
The Institute for Genomic Research 9712 Medical Center Drive, Rockville, MD 20850, USA
*To whom correspondence should be addressed. Tel: +1 301 795 7531; Fax: +1 301 838 0208; Email: ipaulsen{at}tigr.org
Received September 8, 2006. Revised October 16, 2006. Accepted October 17, 2006.
TransportDB (http://www.membranetransport.org/) is a comprehensive database resource of information on cytoplasmic membrane transporters and outer membrane channels in organisms whose complete genome sequences are available. The complete set of membrane transport systems and outer membrane channels of each organism are annotated based on a series of experimental and bioinformatic evidence and classified into different types and families according to their mode of transport, bioenergetics, molecular phylogeny and substrate specificities. User-friendly web interfaces are designed for easy access, query and download of the data. Features of the TransportDB website include text-based and BLAST search tools against known transporter and outer membrane channel proteins; comparison of transporter and outer membrane channel contents from different organisms; known 3D structures of transporters, and phylogenetic trees of transporter families. On individual protein pages, users can find detailed functional annotation, supporting bioinformatic evidence, protein/DNA sequences, publications and cross-referenced external online resource links. TransportDB has now been in existence for over 10 years and continues to be regularly updated with new evidence and data from newly sequenced genomes, as well as having new features added periodically.
Present address: Kaixi Chen, Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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