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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
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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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A. Biegert and J. Soding
De novo identification of highly diverged protein repeats by probabilistic consistency
Bioinformatics, March 15, 2008; 24(6): 807 - 814.
[Abstract] [Full Text] [PDF]


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