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CW-PRED: A HMM-Based Method for the Classification of Cell Wall-Anchored Proteins of Gram-Positive Bacteria
Danai K. Fimereli1, Konstantinos D. Tsirigos1, Zoi I. Litou1, Theodore D. Liakopoulos2, Pantelis G. Bagos2, and Stavros J. Hamodrakas1
1Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece
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2Department of Computer Science and Biomedical Informatics, University of Central Greece, Papasiopoulou 2-4, Lamia 35100, Greece
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Abstract. Gram-positive bacteria have surface proteins that are often implicated in virulence. A group of extracellular proteins attached to the cell wall contains an LPXTG-like motif that is target for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A Hidden Markov Model (HMM) was developed for predicting the LPXTG and LPXTG-like cell-wall proteins of Gram-positive bacteria. The model is the first capable of predicting alternative (i.e. other than LPXTG-containing) substrates. Our analysis of 177 completely sequenced genomes identified 1456 cell-wall proteins, a number larger compared to the previously available methods. Among these, apart from the previously identified 1283 proteins carrying the LPXTG motif, we identified 39 newly identified proteins carrying NPXTG, 53 carrying LPXTA and 81 carrying the LAXTG motif. The tool is freely available for academic use at
Keywords: Gram-positive bacteria, cell-wall proteins, sortase substrates, LPXTG-like motifs, Hidden Markov Models, proteome analysis
LNAI 7297, p. 285 ff.
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© Springer-Verlag Berlin Heidelberg 2012