A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1

doi:10.1186/1471-2164-9-145

BMC Genomics

Volume 9

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Research article

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1

Christof Francke¹^,2^* , Robert Kerkhoven²^* , Michiel Wels¹^,2^,3 and Roland J Siezen¹^,2^,3

¹TI Food and Nutrition, P.O. Box 557, 6700AN Wageningen, The Netherlands

²Center for Molecular and Biomolecular Informatics (260), NCMLS, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500HB Nijmegen, The Netherlands

³NIZO food research, P.O. Box 20, 6710BA Ede, The Netherlands

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:145doi:10.1186/1471-2164-9-145


Published:	27 March 2008

Additional files

Additional file 1:

The number of LacI-family members in sequenced Firmicutes. The file lists the species whose genome was studied, their abbreviation and the number of LacI-family TFs recovered for each genome.

Format: XLS Size: 59KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

IDs and sequences of LacI-family TFs in sequenced Firmicutes. The file contains the sequences that were considered in this study with their different IDs.

Format: XLS Size: 449KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Multiple sequence alignment of LacI-family TFs of sequenced Firmicutes. The file gives the sequence alignment of the TFs considered in this study.

Format: ALN Size: 684KB Download file

Additional file 4:

Neighbor Joining tree for the LacI-family TFs of sequenced Firmicutes. The file gives the bootstrapped (n = 250) NJ-tree for the LacI-family TF homologs of the Firmicutes, Salmonella and E. coli.

Format: PHB Size: 28KB Download file

Additional file 5:

Multiple sequence alignments and Neighbor joining trees for the two functional domains of the LacI-family TF homologs in L. plantarum. The file contains images of the sequence alignments and the bootstrapped (n = 1000) NJ-trees for the two TF functional domains.

Format: PPT Size: 95KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Additional file 6:

Gene context conservation of the LacI-family TF homologs in L. plantarum WCFS1. The file provides a visualization of context information that was used to define the GOOFEs and contains the motifs used to perform the MAST searches.

Format: PPT Size: 3.2MB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Additional file 7:

LacI-family homologs deviant at position 24 and their putative operators. The file lists the putative binding motifs for several LacITFs with a conserved substitution of the conserved arginine at position 24 (in Figure 2).

Format: XLS Size: 89KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 8:

MAST output. The file contains the parsed output of the MAST searches. A new sheet is provided for each criterion that was applied to constrain the list. The results are color-coded.

Format: XLS Size: 1.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 9:

The functional annotation of the genes and operons regulated by LacI-TFs in L. plantarum. The file contains a functional description of the genes and operons that putatively constitute the minimal regulons depicted in Figure 3 (with relevant references).

Format: RTF Size: 101KB Download file