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. 2012 Mar 24;29(10):2937–2948. doi: 10.1093/molbev/mss101

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© The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 3. — Comparative analysis of the anti-SD genomes and the non-anti-SD genomes in the phylum Proteobacteria. (A) Maximum likelihood phylogenetic tree. Group 3 non–anti-SD genomes are shown in gray. (B) Predicted 16S rRNA 3′ tail sequences. The regions corresponding to the Escherichia coli anti-SD motif are shaded in gray. (C) SD indexes (dF_SD). Triangle: cutoff value < −3.4535 kcal/mol; Dot: cutoff value < −4.4 kcal/mol. (D) Fractions of the four nucleotides (df_A, df_C, df_G, and df_T) at specific positions between −50 and −1 nt from all protein-coding genes in each genome. The background fraction was subtracted. For details, see Materials and Methods. (i) The class Gammaproteobacteria. (ii) The class Betaproteobacteria. (iii) The class Alphaproteobacteria.