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Comparative analysis of the two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis, by M. de Been, C. Francke, R. Moezelaar, T. Abee and R. J. Siezen

Microbiology vol. 152, part 10, pp. 3035 - 3048

Table S1. Sixteen putative HK and RR genes that have previously been unidentified due to erroneous ORF predictions. [PDF] (13 kb)

Table S2. Domain organization of HKs and RRs. [PDF] (18 kb)

Table S3. From reference codes to NCBI gi-codes. [PDF] (17 kb)

Table S4. Nature of truncated or deleted B. anthracis TCSs in six other B. anthracis strains and B. cereus G9241. [PDF] (19 kb)

Fig. S1. HK tree. [PDF] (6 Mb)
This tree was constructed with all B. cereus group and B. subtilis HK phosphotransferase domains (start of H-box to end of HATPase domain), including similar sequences from other bacterial species. The multiple sequence alignment was made with MUSCLE 3.51 (Edgar, 2004) and the bootstrapped neighbour-joining (NJ) tree was created with CLUSTAL W 1.83 (Thompson et al., 1994). The NJ tree was visualized with Levels of Orthology through Phylogenetic Trees (LOFT) (R. van der Heijden and others, unpublished results). The first three characters of each name represent a species-specific code. This code is followed by a gi-code or a gene name (NCBI) and, finally, by an abbreviation of the species name. In the case of B. cereus group species, the reference codes of Table 2 were used instead of gi-codes/names. A translation of these codes to NCBI codes can be found in Table S3. Based on the tree, HKs were classified into different subfamilies. These subfamilies have been described by Grebe & Stock (1999) and are shown on the right side of the tree. See main paper for details of references cited.

Fig. S2. RR tree. [PDF] (5.6 Mb)
This tree was constructed with all B. cereus group and B. subtilis RR receiver domains, including similar sequences from other bacterial species. Details of tree construction and presentation were as described for the HK tree in the legend of Fig. S1. Based on the tree and the RR output domains detected with Pfam and SMART, RRs were classified into different subfamilies. These subfamilies/output domains are shown on the right side of the tree.

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