Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Open Badges Research article

LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria

Miaomiao Zhou13*, Daniel Theunissen23, Michiel Wels123 and Roland J Siezen123

Author Affiliations

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

2 TI Food and Nutrition, Wageningen, The Netherlands

3 NIZO food research, Ede, The Netherlands

For all author emails, please log on.

BMC Genomics 2010, 11:651  doi:10.1186/1471-2164-11-651

Published: 23 November 2010

Additional files

Additional file 1:

The overview of LAB-Secretome. Sheet S1: an overview of secretomes included in this research; sheet S2: the presence and absence patterns of the LaCOGs in 26 LAB genomes; sheet S3: the ubiquitous LaCOGs; sheet S4: the niche-specific LaCOGs; sheet S5: the species-specific LaCOGs; sheet S6: the ORFans; S7: the proteins with only distant homologs.

Format: XLS Size: 343KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

False-positive SCL predictions. The false-positive SCL predictions that were corrected using domain composition and homolog information of LaCOGs. Sheet S1: the intracellular proteins that had been wrongly predicted to be extracellular; sheet S2: the N-terminally anchored LaCOGs with C-terminal inside topology.

Format: XLSX Size: 24KB Download file

Open Data

Additional file 3:

The extracellular pseudogenes. The secretome pseudogenes. The pseudogenes with wrongly annotated start/end codons were corrected and concatenated with corresponding gene neighbors. The resulting proteins seem to have homologs in various LaCOGs. The concatenated protein sequences are listed in the last column, with an "x" showing the conjunction site of each sequence.

Format: XLSX Size: 111KB Download file

Open Data

Additional file 4:

Interesting cases of extracellular protein families. The distribution of binding protein families: sheet S1: Nlpc-P60 families; sheet S2: Cell surface hydrolase; sheet S3: Binding proteins.

Format: XLSX Size: 21KB Download file

Open Data