Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria

Bacterial lipoproteins are a diverse and functionally important group of proteins that are amenable to bioinformatic analyses because of their unique signal peptide features. Here we have used a dataset of sequences of experimentally verified lipoproteins of Gram-positive bacteria to refine our prev...

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Bibliographic Details
Published in:World journal of microbiology & biotechnology 2008-11, Vol.24 (11), p.2377-2382
Main Authors: Rahman, Obaidur, Cummings, Stephen P, Harrington, Dean J, Sutcliffe, Iain C
Format: Article
Language:English
Subjects:
Amino acids
Applied Microbiology
Bacteria
Biochemistry
Bioinformatics
Biological and medical sciences
Biomedical and Life Sciences
Biotechnology
Datasets
Environmental Engineering/Biotechnology
Fundamental and applied biological sciences. Psychology
Genomes
Gram-negative bacteria
Gram-positive bacteria
Life Sciences
Lipoproteins
Localization
Microbiology
Peptides
Proteins
Review
Studies
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Description
Summary:Bacterial lipoproteins are a diverse and functionally important group of proteins that are amenable to bioinformatic analyses because of their unique signal peptide features. Here we have used a dataset of sequences of experimentally verified lipoproteins of Gram-positive bacteria to refine our previously described lipoprotein recognition pattern (G+LPP). Sequenced bacterial genomes can be screened for putative lipoproteins using the G+LPP pattern. The sequences identified can then be validated using online tools for lipoprotein sequence identification. We have used our protein sequence datasets to evaluate six online tools for efficacy of lipoprotein sequence identification. Our analyses demonstrate that LipoP (http://www.cbs.dtu.dk/services/LipoP/) performs best individually but that a consensus approach, incorporating outputs from predictors of general signal peptide properties, is most informative.
ISSN:0959-3993
1573-0972
DOI:10.1007/s11274-008-9795-2