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Open Access Highly Accessed Research article

The proteolytic system of lactic acid bacteria revisited: a genomic comparison

Mengjin Liu12*, Jumamurat R Bayjanov1, Bernadet Renckens1, Arjen Nauta2 and Roland J Siezen134

Author Affiliations

1 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, the Netherlands

2 FrieslandCampina Research, Deventer, the Netherlands

3 NIZO food research, Ede, the Netherlands

4 TI Food and Nutrition, Wageningen, the Netherlands

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BMC Genomics 2010, 11:36  doi:10.1186/1471-2164-11-36

Published: 15 January 2010

Additional files

Additional file 1:

Multiple sequence alignment of core regions of proteins from both the PepI/R/L and EstA families. A manually curated multiple sequence alignment of the concatenated sequences of the four core regions of the PepI/PepR/PepL and EstA superfamily members identified by the protein structure superposition. On basis of this MSA, a family tree was constructed, and is shown in Figure 5.

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Additional file 2:

Proteolytic components in LAB. The file contains a table with GI codes of all the genes listed in Figure 1.

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Open Data

Additional file 3:

Superfamily tree of PepF members. The bootstrapped (n = 1000) neighbor-joining tree for PepF members in LAB

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Open Data

Additional file 4:

Comparison of important residues of the conserved core regions and the cap region. The file contains a table describing the four structurally conserved regions and the cap regions. The identified residues within those regions, which are functionally important and/or conserved in PepI/R/L or EstA families, are highlighted

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Additional file 5:

PepX superfamily tree. The file contains a bootstrapped (n = 1000) NJ tree for PepX family homologs of LAB

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Open Data