CW-PRED: A HMM-Based Method for the Classification of Cell Wall-Anchored Proteins of Gram-Positive Bacteria

  • Danai K. Fimereli
  • Konstantinos D. Tsirigos
  • Zoi I. Litou
  • Theodore D. Liakopoulos
  • Pantelis G. Bagos
  • Stavros J. Hamodrakas
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7297)

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 http://bioinformatics.biol.uoa.gr/CW-PRED/.

Keywords

Gram-positive bacteria cell-wall proteins sortase substrates LPXTG-like motifs Hidden Markov Models proteome analysis 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Danai K. Fimereli
    • 1
  • Konstantinos D. Tsirigos
    • 1
  • Zoi I. Litou
    • 1
  • Theodore D. Liakopoulos
    • 2
  • Pantelis G. Bagos
    • 2
  • Stavros J. Hamodrakas
    • 1
  1. 1.Department of Cell Biology and Biophysics, Faculty of BiologyUniversity of AthensAthensGreece
  2. 2.Department of Computer Science and Biomedical InformaticsUniversity of Central GreeceLamiaGreece

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