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. 2016 Oct 4;16:231. doi: 10.1186/s12866-016-0850-0

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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. 5 — Example analysis of predicted cdPadR1 binding motif (cdPadR1 motif) as verified by EMSA. a Motif identified by GLAM2 analysis [24] of small dsDNA fragments from within the cdPadR1 promoter (Pr68 and PR122). b cdPadR1 motifs present in three exemplar promoters compared to the cdPadR1 motif. Nucleotides that are in agreement with the reference cdPadR1 motif are highlighted. Pr132 and Pr133 are upstream of CDR20291_2322 (IclR family transcription regulator CDS); Pr135 and Pr136 are upstream of CDR20291_1882 (two-component system response regulator CDS); Pr137 and Pr138 are upstream of CDR20291_1590 (ArsR family transcriptional regulator CDS). b EMSAs of cdPadR1 binding 30 bp (green arrows) and 100 bp (red arrows) promoter regions that contain cdPadR1 motif. DNA only (-) reactions contained 100 nM either 30 or 100 bp dsDNA from promoters listed above. Reactions containing dsDNA and 4 μM cdPadR1 are noted with a plus (+) sign. Final DNA concentration in both reactions was 100 nM. Bound complexes are indicated with black arrows