Figure 2

Clustering of selected σ⁷⁰-superfamily of sigma factors. The unrooted tree resulted from a multiple alignment over the whole aa sequence length of σ^H-like factors and known sigma factors from group 3 (sporulation factors of B. subtilis) and group 4 (ECF factors from B. subtilis and Gram-negative bacteria). The multiple alignment was generated using clustalX [19], by introducing first the shortest sequences to ensure a correct alignment of the conserved regions. The tree was drawn with NJplot http://pbil.univ-lyon1.fr/software/njplot.html. Bootstrap values (number of seeds: 1000, number of trials: 100) are indicated for the upper branches. Evolutionary distance is represented by branch length (scale at the bottom). Groups of σ^H-like factors were numbered as previously reported [12] and a fourth group (IV) was added by our analysis. Bsu, Bacillus subtilis 168; EC, E. coli K-12 substr. MG1655; Pae, Pseudomonas aeruginosa PAO1; Ef, Enteroccocus faecalis V583; Lla, Lactococcus lactis Il1403; Lmo, Listeria monocytogenes EGD-e; Genus Clostridium: CBO, C. botulinum A ATCC3502; CP, C. difficile 630. Genus Lactobacillus: Lba, L. acidophilus NCFM; Lsei, L. casei ATCC334; Lgas, L. gasseri ATCC 33323; Lp, L. plantarum WCFS1; Lsa, L. sakei 23 K, Lsl, L. salivarius UCC118; Lac, L. acidophilus NCFM. Genus Staphylococcus: Sau, S. aureus N315; Sca, S. carnosus TM300; SE, S. epidermidis ATCC 12228. Genus Streptococcus: Spn, S. pneumoniae R6; Spy, S. pyogenes ATCC 10782; Sth, S. thermophilus LMD-9. Names of gene products or locus tags are indicated. σ^H-like sigma factors which belong to sporulating bacteria are indicated with an asterisk; those encoded by a gene not located at a similar locus to sigH_Bsu are underlined (dashed line for the particular case of S. pneumoniae, see Figure 1). The best studied σ^H-like sigma factor for each group is in bold type.