The d b * ± sd values in logarithmic scale, corresponding
to 0.00550 and 0.0231 (d b * = 0.01128) in the original scale, were used as threshold values for the three zones (N = 687; five OGs with d b = 0 were excluded from 692 OGs satisfying the above criteria (i)-(iii)). Amino acid sequences of the genes were aligned by the einsi command of the MAFFT program [128], from which a neighbor-joining tree was constructed by the ClustalW program [135]. A branch-site likelihood ratio test of positive selection was carried Metabolism inhibitor out using PAML [60] based on the multiple alignment by the einsi command of MAFFT [128]. Only residues aligned at the same site by the einsi command and by PRANK (with codon option) LY333531 cost [136] were considered. Positively-selected residues were mapped on the p55 structure
of VacA using PyMol). Statistics The equality of means for phylogenetic profiling between East Asian and European QNZ order strains was tested by Kruskal-Wallis one-way analysis of variance by ranks, a non-parametric method for testing equality of population medians among groups. The tests were conducted using the R statistics package [137]. Accession Numbers The accession numbers of the H. pylori genome sequences reported in this paper are: F16 [DDBJ:AP011940.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011940.1 ], F30 [DDBJ:AP011941.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011941.1,
DDBJ:AP011942.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011942.1], F32 [DDBJ:AP011943.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011943.1, 2-hydroxyphytanoyl-CoA lyase DDBJ:AP011944.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query= AP011944.1] and F57 [DDBJ:AP011945.1 http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry2.pl?database=ver_ddbj&query=AP011945.1]. Author information Current position of MK: Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, 237-0061, Japan Acknowledgements YF, TT, NH, NT and IK are grateful to Hitomi Mimuro and Chihiro Sasakawa for introduction to H. pylori experiments. This work was supported by the Institute for Bioinformatics Research and Development, the Japan Science and Technology Agency. I.U. was supported by a Grant-in-Aid for Scientific Research (20310125) from the Japan Society for the Promotion of Science. N. H. was supported by grants from Ministry of Education, Culture, Sports, Science and Technology-Japan (MEXT), by Takeda Foundation, by Sumitomo Foundation, by Kato Memorial Bioscience Foundation and by Naito Foundation. I.K.