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HHrep specifications

Information


Unique identifier OMICS_10028
Name HHrep
Interface Web user interface
Restrictions to use None
Input data Protein sequence(s)
Computer skills Basic
Stability No
Maintained No

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Publication for HHrep

HHrep citations

 (12)
library_books

The Conserved Actinobacterial Two Component System MtrAB Coordinates Chloramphenicol Production with Sporulation in Streptomyces venezuelae NRRL B 65442

2017
Front Microbiol
PMCID: 5487470
PMID: 28702006
DOI: 10.3389/fmicb.2017.01145

[…] s to see if expression of TB-MtrA or the gain-of-function Y102C TB-MtrA in S. venezuelae would switch on chloramphenicol production. We also modeled Sv-MtrA onto the published TB-MtrA structure using HHrep (; ) and made the equivalent Y99C (predicted gain-of-function) change in Sv-MtrA (Figure ). We made expression constructs for all three, driven by the S. venezuelae mtrA promoter, and introduced […]

library_books

Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore Forming Proteins

2016
PLoS One
PMCID: 4827864
PMID: 27064789
DOI: 10.1371/journal.pone.0152733

[…] central regions of an alignment. Thus, all segments analyzed are derived from contiguous portions of proteins.The Ancient Rep (AR) and GSAT programs [] were used to identify internal repeats, and the HHRep [] and HHRepID [] programs provided independent search approaches. The AR program compares potential transmembrane repeat sequences (e.g., transmembrane regions predicted by HMMTOP) within a sin […]

library_books

Atomic Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N Terminal Domain

2015
J Mol Biol
PMCID: 4590430
PMID: 26343760
DOI: 10.1016/j.jmb.2015.08.023

[…] erved surfaces were determined using ConSurf . Figures were generated using PyMOL. Regions of disorder in Apc4 and Apc5 were predicted using OnD-CRF . TPR predictions were performed using TPRpred and HHrep . Protein structure predictions were performed using Phyre2 protein recognition server . […]

library_books

Tandem Repeats in Proteins: Prediction Algorithms and Biological Role

2015
Front Bioeng Biotechnol
PMCID: 4585158
PMID: 26442257
DOI: 10.3389/fbioe.2015.00143

[…] ability to detect very long PTRs (≥ 4000 AA), with XSTREAM and PTRStalker emerging as the best choice for this task. A second test is aimed at detecting dimeric proteins by five tools (RADAR, TRUST, HHRep, HHRepID, and PTRStalker), with PTRStalker, TRUST, and HHRepID being able to successfully uncover such dimeric structures in some of the tested proteins. In Jorda and Kajava (), four methods (T- […]

library_books

Three dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by cross linking and molecular modelling

2015
Open Biol
PMCID: 4345284
PMID: 25716199
DOI: 10.1098/rsob.150005

[…] t in more than one third of the homologues; (v) strong indications of disruption of the sequence repeat pattern (not spanning multiples of seven positions) as revealed through alignment analyses with HHrep, HHrepID, and/or the COILS/PCOILS outputs at the Bioinformatics Toolkit site [] corroborated by other heuristics. Ideally, we would like the fragment boundaries to coincide with locations where […]

library_books

Brefeldin A inhibited guanine nucleotide exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM type α helical structure

2014
BMC Res Notes
PMCID: 4096751
PMID: 24997568
DOI: 10.1186/1756-0500-7-435

[…] ail.mit.edu/cb/paircoil2/) [] and COILS (http://www.ch.embnet.org/software/COILS_form.html) []. Sequence repeats were predicted using REP (http://www.bork.embl.de/~andrade/papers/rep/search.html) [], HHrep (http://toolkit.tuebingen.mpg.de/hhrep) [] and REPRO (http://www.ibi.vu.nl/programs/reprowww/) []. Fold recognition was performed using FUGUE (http://tardis.nibio.go.jp/fugue/) and HHpred (http: […]

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HHrep institution(s)
Department for Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany; Gene Center Munich, University of Munich (LMU), Munich, Germany

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