TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available. For each organism, its complete membrane transport complement was identified, classified into protein families according to the TC classification system, and functional predictions are provided. Complete lists of the transporters from each organism are accessible from the pull down menus on this page.
For each organism, a summary page is available, overviewing the whole transporter system, including transporter types and individual transporter families. For individual transporter types, a detailed list of transporters with their possible substrates is shown with links to individual protein page which contains protein sequence and annotation information. You can also compare the transporter system from two or more different organisms.
A search engine is set up for easy search in our transporter database for transporter type, family, individual proteins and their substrates. You can also blast search your protein sequence against our transporter database.
With the rapid development of genomic sequencing both in TIGR and in other institutes, more and more genomes are available for the analysis of their transporter system. We will keep updating this site with the newly published genomes. If you have any suggestions, corrections, or comments on our site, please contact us. We are currently working on providing additional functionality for this database.

Click to see the complete list of organisms in TransportDB arrow

The Very Very Latest News

8/08/16 - TransportDB2.0 is live, select the link on the left hand side. It is now being regularly updated with genomes from NCBI RefSeq, and has a new look that reflects a change in the underlying code that should allow the addition of new visualisation and analysis tools.

The Very Latest News

15/03/13 - The RefSeq database has been analysed with the new TransAAP, try the link on the left. This is a beta release, the analysis options are limited, and we are still reviewing the results from the now completely automated transporter annotation. Updates will occur intermittently and hopefully regularly! We're also now using the Australian date format (dd/mm/yy)....

3/30/11:TransportDB is back online! It will now appear at The back story is we've moved from Godaddy to HostGator, there may be some bugs, please feel free to report any found. Hopefully we will now be able to get on with the long awaited update to the TransportDB website and improvements to TransAAP (getting it running again to start with, the also long awaited Linux cluster has arrived and is in the process of being set up).

3/04/11:TransportDB is offline as Godaddy decided that our database is too big!.
After a long transition from JCVI to Macquarie University, we are currently moving to another web server (this should be done with the next two weeks), and are still setting up adequate hardware to run the transporter analyses, and are also still in the process of putting TransportDB v2.0 together. This is going to be an incremental process, but in the medium to long term we should be putting most of the 1000 new genomes from NCBI up.

Our apologies to TransAAP users, the pipeline has been moribund (due to hardware and web hosting issues as above) and will be back in business when the server issues have been resolved. Clearing the backlog is going to take a while, please bear with us.

5/30/07:TransportDB was updated with addition of recently published genomes.
TransportDB data can be download as tab-delimited format
Add a YouTube video on F-ATPase
The pubmed data on transporters have been updated

4/30/07: A new section was added to TransportDB:
"TransAAP": Transporter Automatic Annotation Pipeline

9/8/06:TransportDB was updated with addition of recently published genomes.
Two new sections was added:
"Structure" section lists 3-dimensional structures of membrane transporters.
"Outer Membrane Channels" lists all outer membrane porins/channels in various organisms.

3/15/06:TransportDB was updated with 70+ addition of recently published prokaryotic and eukaryotic genomes.
Click here for a complete list of genomes analyzed.

9/15/05:Please check our recent publication on PLoS Comput Biol.:
"Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes."

Comparative genomic analyses of the transporters described in this database have been published in part in:
Ren Q. and Paulsen I.T. (2007) Large-Scale Comparative Genomic Analyses of Cytoplasmic Membrane Transport Systems in Prokaryotes. Journal of Molecular Microbiolgy and Biotechnology 12:165-79.

Ren Q. and Paulsen I.T. (2005) Comparative Analyses of Fundamental Differences in Membrane Transport Capabilities in Prokaryotes and Eukaryotes. PLoS Computational Biology1(3): e27. [PubMed] [PDF]

Paulsen, I.T. et al. (1998a) Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. Journal of Molecular Biology 277: 573-592. [PubMed]

Paulsen I.T. et al. (1998b) Unified inventory of established and putative transporters encoded within the complete genome of Saccharomyces cerevisiae. FEBS Letters 430: 116-125. [PubMed]

Paulsen I.T. et al. (2000) Microbial genome analyses: comparative transport capabilities in eighteen prokaryotes. Journal of Molecular Biology 301: 75-100. [PubMed]

TransportDB was described in great details in:
Ren, Q. et al. (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Research. 35: D274-279. [Abstract] [Full Text(PDF)]

Ren, Q. et al. (2004) TransportDB: A Relational Database of Cellular Membrane Transport Systems. Nucleic Acids Research. 32: D284-D288. [Abstract] [Full Text(PDF)]

Copyright © 2002-20013 Last updated Thursday September 8, 2016; 01:58:19 AM
Questions may be sent to: Ian T. Paulsen Liam D. H. Elbourne
Principle Investigator: Ian T. Paulsen
Database Administrator and Developer: Liam D. H. Elbourne
Development Team: Sasha Tetu Karl Hassan
Previous Contributors: Qinghu Ren (previous Lead Developer) Katherine H. Kang Kaixi Chen Seth Goldman
Joy Garg Jason Tchieu Joan Chen Marek K. Sliwinski
Crystal structure adapted from: Dr. Mark Sansom Dr. Da-Neng Wang