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TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences

Manjunatha R Karpenahalli, Andrei N Lupas, Johannes Söding
2007 BMC Bioinformatics  
TPRpred detects not only TPR-like repeats, but also the related Pentatrico Peptide Repeats (PPRs) and SEL1-like repeats.  ...  Several resources are available for the prediction of TPRs, however, they often fail to detect divergent repeat units.  ...  Acknowledgements We thank Christian Mayer for re-coding the Perl script in C++ and Andreas Biegert for integrating the program into the MPI Bioinformatics Toolkit.  ... 
doi:10.1186/1471-2105-8-2 pmid:17199898 pmcid:PMC1774580 fatcat:tjtrosjdvrendav7jimqwxy3lm

Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants

Shifeng Cheng, Bernard Gutmann, Xiao Zhong, Yongtao Ye, Mark F. Fisher, Fengqi Bai, Ian Castleden, Yue Song, Bo Song, Jiaying Huang, Xin Liu, Xun Xu (+4 others)
2016 The Plant Journal  
We used the redefined motifs to develop accurate and consistent annotations of PPR sequences from 109 genomes.  ...  The pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants.  ...  ., Lupas, A.N. and Soding, J. (2007) TPRpred: a tool for prediction of TPR-, PPR-and SEL1-like repeats from protein sequences. BMC Bioinformatics 8, 2.  ... 
doi:10.1111/tpj.13121 pmid:26764122 fatcat:k6aplrc5fvcufave3vjb6bufce

Peptide-based quorum sensing systems in Paenibacillus polymyxa [article]

Maya Voichek, Sandra Maaß, Tobias Kroniger, Dörte Becher, Rotem Sorek
2019 bioRxiv   pre-print
Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide.  ...  Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides leads to reprogramming of the transcriptional response.  ...  TPRpred: a tool for prediction of 564 TPR-, PPR-and SEL1-like repeats from protein sequences. BMC Bioinformatics 8, Fekkes, P. & Driessen, A. J.  ... 
doi:10.1101/767517 fatcat:hd4t2jvnf5d6db6v6tsrf2g7ei

Evolution of modular intraflagellar transport from a coatomer-like progenitor

T. J. P. van Dam, M. J. Townsend, M. Turk, A. Schlessinger, A. Sali, M. C. Field, M. A. Huynen
2013 Proceedings of the National Academy of Sciences of the United States of America  
Their N-terminal region contains WD40 repeats, likely forming two β-propeller folds, whereas their C-terminal region contains tetratricopeptide repeats (TPR), likely forming an α-solenoid-like fold.  ...  Such an analysis is necessary because the abundance of the WD40 and TPR domains in noncoatomer subunit proteins requires more than sequence similarity to establish a close phylogenetic relationship.  ...  Karpenahalli MR, Lupas AN, Söding J (2007) TPRpred: A tool for prediction of TPR-, PPR-and SEL1-like repeats from protein sequences. BMC Bioinformatics 8 Fig. S1 .  ... 
doi:10.1073/pnas.1221011110 pmid:23569277 pmcid:PMC3637775 fatcat:gg73egkvlbgdpjum5yv7vowe2u

Characterization of Tetratricopeptide Repeat-Like Proteins in Francisella tularensis and Identification of a Novel Locus Required for Virulence

Vera Dankova, Lucie Balonova, Adela Straskova, Petra Spidlova, Daniela Putzova, Todd Kijek, Joel Bozue, Christopher Cote, Sherry Mou, Patricia Worsham, Barbora Szotakova, Lukas Cerveny (+2 others)
2014 Infection and Immunity  
Proteins containing tetratricopeptide repeat (TPR)-like domains seem to be promising targets to investigate, since these proteins have been reported to be directly involved in virulence-associated functions  ...  Here, we studied the role of theFTS_0201,FTS_0778, andFTS_1680genes, which encode putative TPR-like proteins inFrancisella tularensissubsp.holarcticaFSC200.  ...  ACKNOWLEDGMENTS We thank Karl Klose and Stephen A.  ... 
doi:10.1128/iai.01620-14 pmid:25245806 pmcid:PMC4249281 fatcat:yhpq2czkl5cbvdrdnjfmmg3biq

Peptide-based quorum sensing systems in Paenibacillus polymyxa

Maya Voichek, Sandra Maaß, Tobias Kroniger, Dörte Becher, Rotem Sorek
2020 Life Science Alliance  
Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide.  ...  Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides leads to reprogramming of the transcriptional response.  ...  We thank the Sorek lab members for fruitful discussions and helpful suggestions.  ... 
doi:10.26508/lsa.202000847 pmid:32764104 fatcat:kpesozyucrcq5aqokknjy62tqa

How do I get the most out of my protein sequence using bioinformatics tools?

Joana Pereira, Vikram Alva
2021 Acta Crystallographica Section D: Structural Biology  
Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest.  ...  However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary  ...  Acknowledgements We would like to thank Andrei Lupas for continued support, Andre Noll, Felix Gabler, Joel Domke, Johannes Wö rner and Seung-Zin Nam for their contributions to the development of the Toolkit  ... 
doi:10.1107/s2059798321007907 pmid:34473083 pmcid:PMC8411974 fatcat:zkl7sre2d5dnlhu2m6nloc4tcq

Multi-genome identification and characterization of chlamydiae-specific type III secretion substrates: the Inc proteins

Pierre Dehoux, Rhonda Flores, Catherine Dauga, Guangming Zhong, Agathe Subtil
2011 BMC Genomics  
Conclusions The Inc proteins represent 7 to 10 % of each proteome and show a great degree of sequence diversity between species.  ...  Samudrala R, Heffron F, McDermott JE: Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems.  ...  Acknowledgements We thank Alice Dautry-Varsat for discussion, Stéphanie Perrinet, Valérie Malardé and Laurence Tastevin for carrying out secretion assays, Scot Ouellette for critically reading the manuscript  ... 
doi:10.1186/1471-2164-12-109 pmid:21324157 pmcid:PMC3048545 fatcat:y6upngbxyfctxkzoycmtwa6mzy

The mechanism of selective kinesin inhibition by kinesin binding protein [article]

Joseph Atherton, Jessica J. A Hummel, Natacha Olieric, Julia Locke, Alejandro Pena, Stephen S Rosenfeld, Michel O Steinmetz, Casper C Hoogenraad, Carolyn A Moores
2020 bioRxiv   pre-print
Kinesin binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment and blocks their cellular function.  ...  KBP is a TPR-containing, crescent-shaped right-handed α-solenoid that sequesters the tubulin-binding surface of the kinesin motor domain, structurally distorting the motor domain and sterically blocking  ...  TPRpred: a tool for prediction of TPR-, PPR-and SEL1-like repeats from protein sequences. BMC Bioinformatics 8, 2 (2007). 59. Zimmermann, L. et al.  ... 
doi:10.1101/2020.07.17.208736 fatcat:yixwdyrwmbhfzhadj7a25jaymi

RNPP-type quorum sensing regulates solvent formation and sporulation inClostridium acetobutylicum [article]

Ann-Kathrin Kotte, Oliver Severn, Zak Bean, Katrin Schwarz, Nigel P Minton, Klaus Winzer
2017 bioRxiv   pre-print
Triplicate mutants were generated for each system inC. acetobutylicumATCC 824 and screened for phenotypic changes.  ...  However, the regulation of its fermentation metabolism, in particular the shift from acid to solvent production, remains poorly understood.  ...  Karpenahalli M, Lupas A, Soding, J. 2007. TPRpred: a tool for prediction of TPR-, 6 PPR-and SEL1-like repeats from protein sequences. BMC Bioinformatics 8:2. 7 25.  ... 
doi:10.1101/106666 fatcat:zi6od5ainnha5i73qho5xatks4