Prediction of twin-arginine signal peptides - PubMed (original) (raw)
Prediction of twin-arginine signal peptides
Jannick Dyrløv Bendtsen et al. BMC Bioinformatics. 2005.
Abstract
Background: Proteins carrying twin-arginine (Tat) signal peptides are exported into the periplasmic compartment or extracellular environment independently of the classical Sec-dependent translocation pathway. To complement other methods for classical signal peptide prediction we here present a publicly available method, TatP, for prediction of bacterial Tat signal peptides.
Results: We have retrieved sequence data for Tat substrates in order to train a computational method for discrimination of Sec and Tat signal peptides. The TatP method is able to positively classify 91% of 35 known Tat signal peptides and 84% of the annotated cleavage sites of these Tat signal peptides were correctly predicted. This method generates far less false positive predictions on various datasets than using simple pattern matching. Moreover, on the same datasets TatP generates less false positive predictions than a complementary rule based prediction method.
Conclusion: The method developed here is able to discriminate Tat signal peptides from cytoplasmic proteins carrying a similar motif, as well as from Sec signal peptides, with high accuracy. The method allows filtering of input sequences based on Perl syntax regular expressions, whereas hydrophobicity discrimination of Tat- and Sec-signal peptides is carried out by an artificial neural network. A potential cleavage site of the predicted Tat signal peptide is also reported. The TatP prediction server is available as a public web server at http://www.cbs.dtu.dk/services/TatP/.
Figures
Figure 1
Tat signal peptides. Sequence logo of the positive training set aligned at the two consecutive arginines. None of the variant forms of Tat signal peptides were included. Sequence conservation is shown in bits and constructed as previously described [29].
Figure 2
Server output. Graphical output from the prediction server. Here is shown the prediction results from SUFI_ECOLI, a known Tat substrate. The S-score indicates whether an amino acid belongs to a Tat signal peptide or not. C- and Y-scores indicate the positioning of a potential cleavage site.
References
- Berks BC, Palmer T, Sargent F. The Tat protein translocation pathway and its role in microbial physiology. Adv Microb Physiol. 2003;47:187–254. - PubMed
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