CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria

		A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria

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 new Hidden Markov Model (HMM), an extension to the HMM model from Litou et al., was developed for predicting the LPXTG and LPXTG-like cell-wall proteins of Gram-positive bacteria.

An analysis of 177 completely sequenced genomes has been performed as well. We identified in total 1456 cell-wall proteins, from which 1283 have the LPXTG motif, 39 the NPXTG motif, 53 have the LPXTA and 81 the LAXTG motif.

For publication of results, please cite:

Current version:
Fimereli DK, Tsirigos KD, Litou ZI, Liakopoulos TD, Bagos PG and Hamodrakas SJ.
CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria
Springer's Lecture Notes in Computer Science, 2012, Volume 7297/2012, p. 285-290
Original paper:
Litou ZI, Bagos PG, Tsirigos KD, Liakopoulos TD and Hamodrakas SJ.
Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes.
J Bioinform Comput Biol., 2008 Apr;6(2):387-401.

[Supplementary material]
[Introductory Page]
[CW-PRED training set]
contact: pbagos

ucg.gr

University of Athens
Faculty of Biology
Dept. of Cell Biology and Biophysics

Biophysics
& Bioinformatics
Laboratory