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. 2016 Aug 27;17(1):686. doi: 10.1186/s12864-016-3025-3

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© The Author(s). 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — Common types of incorrectly identified regulatory motifs in phylogenetic footprinting analyses that do not correspond to real TFBSs of the LysR-type family in Gammaproteobacteria. The TFs belonging to the LysR-type family in Gammaproteobacteria are commonly transcribed in a divergent orientation with respect to their TGs. In the intergenic region of the TF-TG, there are two to three IRs, represented by purple (IR1), green (IR2) and red (IR3) boxes. The -35 and -10 boxes of the TG are represented by cream rectangles. The question marks represent motif regions that are not commonly identified, while the exclamation marks represent DNA regions that are not part of the regulatory motif but were identified as such. Due to the molecular bases of the regulatory systems, each TFBS was recognized with different affinities by their corresponding TF. Therefore, their sequence conservation varies, wherein IR1 is the most conserved sequence and IR2 is the least conserved sequence. Additionally, the sequence conservation within an IR sequence also presents important differences. Colored spaces within the boxes represent nucleotides of the motif that are more conserved, while white spaces represent poorly conserved nucleotides. Additionally, nucleotide conservation levels of the motifs are represented with plus signs (+), with +++ (three plus signs) indicating DNA regions with the most conserved nucleotides and + (one plus sign) indicating less conserved DNA regions. In each example, the name of the TF of the regulatory system and its corresponding references are indicated. a Only IR1, the most conserved of the IRs, is identified. b Only the most conserved parts of IR1 and IR3 are identified. c A large DNA region including IR1, the most conserved part of the IR2 and IR3 are identified. Additionally, the DNA regions between IR1 and IR2 that are not recognized by the TF are also incorrectly included. d A contiguous long DNA region, including the contiguous IR1 and IR2 sequences and the sequence between them, are reported as the TF-binding sequence