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Fig. 9 | BMC Genomics

Fig. 9

From: Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model

Fig. 9

Consensus sequence for the TFBSs of the LysR-type TF family. The T-n11-A motif was originally proposed by Goethals et al. [51] as the consensus sequence recognized by members of the LysR-type family. Considering the results of our PProCoM analysis of the TFBSs of six representative members of this family in Gammaproteobacteria, we defined a new and extended version of this motif: 5′-CTATA-n9-TATAG-3′. Additionally, examples of the sequence consensus of the TFBSs of other members of the LysR-type family that have been experimentally verified are also shown and include the distal TFBSs of CatR of the Gammaproteobacteria Pseudomonas putida [53], OccR of the Alphaproteobacteria Agrobacterium tumefaciens [53, 54] and PcaQ of the Alphaproteobacteria Sinorhizobium meliloti [56]. Dots within the inter-motif sequences were used to align the conserved nucleotides of the consensus sequences

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BMC Genomics

ISSN: 1471-2164

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