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Nucleic Acids Research 2006 34(Web Server issue):W137-W142; doi:10.1093/nar/gkl130
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

HHrep: de novo protein repeat detection and the origin of TIM barrels

Johannes Söding*, Michael Remmert and Andreas Biegert

Department of Protein Evolution, Max-Planck-Institute for Developmental Biology Spemannstrasse 35, 72076 Tübingen, Germany

*To whom correspondence should be addressed. Tel: +49 7071 601 451; Fax +49 7071 601 349; Email: johannes.soeding{at}tuebingen.mpg.de

Received February 13, 2006. Revised March 1, 2006. Accepted March 14, 2006.

HHrep is a web server for the de novo identification of repeats in protein sequences, which is based on the pairwise comparison of profile hidden Markov models (HMMs). Its main strength is its sensitivity, allowing it to detect highly divergent repeat units in protein sequences whose repeats could as yet only be detected from their structures. Examples include sequences with ß-propellor fold, ferredoxin-like fold, double psi barrels or (ß{alpha})8 (TIM) barrels. We illustrate this with proteins from four superfamilies of TIM barrels by revealing a clear 4- and 8-fold symmetry, which we detect solely from their sequences. This symmetry might be the trace of an ancient origin through duplication of a ß{alpha}ß{alpha} or ß{alpha} unit. HHrep can be accessed at http://hhrep.tuebingen.mpg.de.


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