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A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis

Marnix H Medema18, Miaomiao Zhou2*, Sacha AFT van Hijum235, Jolein Gloerich4, Hans JCT Wessels4, Roland J Siezen235 and Marc Strous167

Author Affiliations

1 Department of Microbiology, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, the Netherlands

2 Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands

3 NIZO food research, PO Box 20, 6710 BA Ede, the Netherlands

4 Nijmegen Proteomics Facility, Laboratory of Pediatrics & Neurology, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands

5 TI Food and Nutrition, Kluyver Centre for Genomics of Industrial Fermentation, Wageningen, the Netherlands

6 MPI for Marine Microbiology, Celsiusstr. 1 D-28359, Bremen, Germany

7 CeBiTec, University of Bielefeld, Universitätsstraße 27, D-33615, Bielefeld, Germany

8 Current Address: Department of Microbial Physiology and Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, the Netherlands

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BMC Genomics 2010, 11:299  doi:10.1186/1471-2164-11-299

Published: 12 May 2010

Additional files

Additional file 1:

Experimental training sets. The experimental training sets and the K. stuttgartiensis proteome subsets based on signal peptide predictions.

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Additional file 2:

Predicted anammoxosomal proteome. Details on the anammoxosomal proteome prediction.

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Additional file 3:

Experimental and computational analysis of the signal peptides. Methodological details of signal peptide mass spectrometry and analysis on signal peptides using motif searches, statistical analysis and HMMs. Supplemental figure S2 and S3 depict the signal peptide predictions by the 15 predictors on the training sets and weblogos of K. stuttgartiensis TMHs showing phenylalanine overrepresentation compared to E. coli.

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