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. 2014 Mar 6;9(3):e90447. doi: 10.1371/journal.pone.0090447

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© 2014 Shimada 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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[A] The known consensus sequences of RpoD-dependent promoter, TTGAAC (-35) and TATAAT (-10) separated by 17 plus/minus 2 bp, were searched for all type-A (177) and type-B (315) spacers (see Experimental Procedure for the analysis method). Most of the constitutive promoters carry high-levels of the consensus sequence as listed in Table 1. The composition of promoter -35 and -10 sequence was classified into 8 groups based on the conservation level of consensus sequences. About 89% of type-A promoters and 82% of type-B promoters (or 86% of A- plus B-type promoters) contain the sequence higher than 4/6 agreement with the consensus sequence at both -35 or -10 positions (A1), while only 39% of a total of 582 known promoters carries this level of consensus sequences (B1). [B] The whole set of constitutive promoter sequences were subjected to Logo analysis [73]. The Logo patterns of -35 and -10 sequences are essentially the same among the constitutive promoters within type-A and type-B spacers. The Logo pattern of the whole set of constitutive promoters was compared with the Logo pattern generated using the total of 582 experimentally identified promoters [19], [20]. The contribution of each base of the consensus -35 and -10 sequences is significantly different between the constitutive promoters and the set of known promoters.