Journal ArticleDOI
pLogo: a probabilistic approach to visualizing sequence motifs
TLDR
The pLogo is described, a motif visualization in which residue heights are scaled relative to their statistical significance, in which real-time conditional probability calculations and visualizations are supported.Abstract:
Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at http://plogo.uconn.edu/ and supports real-time conditional probability calculations and visualizations.read more
Citations
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Journal ArticleDOI
Protein kinases PknA and PknB independently and coordinately regulate essential Mycobacterium tuberculosis physiologies and antimicrobial susceptibility
Jumei Zeng,John Platig,Tan-Yun Cheng,Saima Ahmed,Yara Skaf,Lakshmi-Prasad Potluri,Daniel Schwartz,Hanno Steen,D. Branch Moody,Robert N. Husson +9 more
TL;DR: These findings support these kinases as targets for new antituberculosis drugs and provide a valuable resource for targeted investigation of mechanisms by which protein phosphorylation regulates pathways required for growth and virulence in M. tuberculosis.
Journal ArticleDOI
Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors.
Shutao Mei,Rochelle Ayala,Sri H. Ramarathinam,Patricia T. Illing,Pouya Faridi,Jiangning Song,Anthony W. Purcell,Nathan P. Croft +7 more
TL;DR: Analysis of HLA-bound peptides from a variety of allotypes and the distribution of mass spectrometry-detected PTMs is analyzed, finding deamidation of asparagine or glutamine to be highly prevalent and aiding in the design of novel T cell therapeutic targets derived from glycoprotein antigens.
Journal ArticleDOI
Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria.
TL;DR: The first proteomic survey of lysine malonylation in Synechocystis is performed using highly accurate tandem mass spectrometry in combination with affinity purification and 27 proteins involved in photosynthesis were found to be malonylated for the first time, suggesting that lysinesmalonylation may be involved in photoynthesis.
Journal ArticleDOI
Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated proteins and an anti-senescence function of UBC9.
Francis P. McManus,Véronique Bourdeau,Mariana Acevedo,Stéphane Lopes-Paciencia,Lian Mignacca,Frédéric Lamoliatte,John W. Rojas Pino,Gerardo Ferbeyre,Pierre Thibault +8 more
TL;DR: This work proposes both pro- and anti-senescence functions of protein SUMOylation, which were identified in the SUMO proteome of senescent cells in a site-specific manner and were associated with PML nuclear body associated proteins.
Journal ArticleDOI
A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling
Villu Kasari,Villu Kasari,Agnieszka A. Pochopien,Tonu Margus,Tonu Margus,Victoriia Murina,Victoriia Murina,Kathryn Jane Turnbull,Kathryn Jane Turnbull,Yang Zhou,Tracy Nissan,Tracy Nissan,Michael Graf,Jiri Novacek,Gemma C. Atkinson,Marcus J.O. Johansson,Daniel N. Wilson,Vasili Hauryliuk,Vasili Hauryliuk,Vasili Hauryliuk +19 more
TL;DR: Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3 and suggests that New1 is a translation factor that fine-tunes the efficiency of translation termination or ribosome recycling.
References
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Journal ArticleDOI
WebLogo: A Sequence Logo Generator
TL;DR: WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment that provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive.
Journal ArticleDOI
Sequence logos: a new way to display consensus sequences
Thomas D. Schneider,R M Stephens +1 more
TL;DR: From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content at every position in a site or sequence.
Journal ArticleDOI
A C-terminal signal prevents secretion of luminal ER proteins
Sean Munro,Hugh R.B. Pelham +1 more
TL;DR: It is proposed that the KDEL sequence marks proteins that are to be retained in the ER and discuss possible retention mechanisms.
Journal ArticleDOI
The P-loop--a common motif in ATP- and GTP-binding proteins.
TL;DR: Current knowledge of P-loops is discussed with the additional aim of illustrating the fascinating relationship between protein sequence, structure and function.
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