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

Söding, J; Remmert, M; Biegert, A

doi:10.1093/nar/gkl130

Item

ITEM ACTIONSEXPORT

Add to Basket

Local TagsRelease HistoryDetailsSummary

Released

Journal Article

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

MPS-Authors

/persons/resource/persons128572

Söding, J
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

/persons/resource/persons173010

Remmert, M
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

/persons/resource/persons173012

Biegert, A
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

External Resource

No external resources are shared

Fulltext (restricted access)

There are currently no full texts shared for your IP range.

Fulltext (public)

There are no public fulltexts stored in PuRe

Supplementary Material (public)

There is no public supplementary material available

Citation

Söding, J., Remmert, M., & Biegert, A. (2006). HHrep: de novo protein repeat detection and the origin of TIM barrels. Nucleic Acids Research (London), 34(Web Server issue), W137-W142. doi:10.1093/nar/gkl130.

Cite as: https://hdl.handle.net/21.11116/0000-000B-2839-9

Abstract

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 β-propellor fold, ferredoxin-like fold, double psi barrels or (βα)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 βαβα or βα unit. HHrep can be accessed at http://hhrep.tuebingen.mpg.de.