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. 2012 Mar 29;7(3):e34067. doi: 10.1371/journal.pone.0034067

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Balasubramanian et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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The putative AmpR binding site was refined using IEM algorithm and used to search the upstream promoter elements of AmpR-regulated and AmpR-β-lactam regulated genes (listed in Tables S3, S4) in PAO1 and other P. aeruginosa strains. DOOR database [142], [143] was used to identify the operons. The RSAT tool [137] was used to identify PAO1 promoter sequences containing the identified AmpR- and AmpR-β-lactam-regulated genes. The output is represented using WebLogo [136] for the AmpR-dependent genes from IEM (A) and RSA (B), and AmpR-β-lactam dependent genes from IEM (C) and RSA (D).