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REPORTS
12. Y. Ohshima, K. Sato, Y. Sumiyoshi, Y. Endo, J. Am. Chem. treatment of triple excitations) were performed using 29. M. J. Frisch et al., Gaussian 03, Revision C.02, Gaussian,
Soc. 127, 1108 (2005). Molpro 2002.6. Inc., (Wallingford, CT, 2004).
13. C. S. Brauer et al., Chem. Phys. Lett. 401, 420 (2005). 18. R. A. Kendall, T. H. Dunning Jr., R. J. Harrison, J. Chem. 30. Molpro is a package of ab initio programs written by H.-J.
14. M. I. Lester, B. V. Pond, D. T. Anderson, L. B. Harding, Phys. 96, 6796 (1992). Werner et al.
A. F. Wagner, J. Chem. Phys. 113, 9889 (2000). 19. H. C. Longuet-Higgins, Mol. Phys. 6, 445 (1963). 31. This work was supported by a Grant-in-Aid for priority
15. Y. Sumiyoshi, H. Katsnuma, K. Suma, Y. Endo, J. Chem. 20. The character table of the group G4 is given in (23). research entitled ‘‘Radical Chain Reactions’’ (grant
Phys. 123, 054324 (2005). 21. Y. Endo, H. Kohguchi, Y. Ohshima, Faraday Discuss. 97, no.13127101). K.S. acknowledges the support of the
16. K. Suma, Y. Sumiyoshi, Y. Endo, J. Chem. Phys. 121, 341 (1994). Research Fellowships of the Japan Society for the Promotion
8351 (2004). 22. M. Iida, Y. Ohshima, Y. Endo, J. Chem. Phys. 94, 6989 (1991). of Science for Young Scientists (JSPS No. 16-10895).
17. The Gaussian 03 suite of programs (29) and Molpro 23. Materials and methods are available as supporting
2002.6 suite of programs (30) were used for ab initio material on Science Online. Supporting Online Material
calculations. The centrifugal distortion constants were 24. J. A. Odutola, T. R. Dyke, J. Chem. Phys. 72, 5062 (1980). www.sciencemag.org/cgi/content/full/311/5765/1278/DC1
obtained by B3LYP/aug-cc-pVTZ [the Becke 3-parameter- 25. W. Klopper, J. G. C. M. van Duijneveldt-van de Rijdt, F. B. Materials and Methods
Lee-Yang-Parr density functional method using Dunning’s van Duijneveldt, Phys. Chem. Chem. Phys. 2, 2227 (2000). Tables S1 to S4
correlation-consistent polarized triple split valence 26. A. A. Nanayakkara, G. G. Balintkurti, I. H. Williams, Fig. S1
basis set with diffuse functions (18)] of Gaussian 03. J. Phys. Chem. 96, 3662 (1992). References
Other ab initio calculations with SCF, B3LYP, and 27. K. V. Chance et al., J. Mol. Spectrosc. 183, 418 (1997).
RCCSD(T) (the restricted single and double excitation 28. K. Suma, W. Funato, Y. Sumiyoshi, Y. Endo, J. Chem. Phys. 19 December 2005; accepted 31 January 2006
coupled-cluster approach with noniterative perturbational 122, 184302 (2005). 10.1126/science.1124022
Fig. 1. Overview of the procedure. The white boxes represent the major steps chloroplast paralogs from corresponding multiple alignments. We built domain-
for building the pan-domain phylogeny presented here. Steps in gray represent specific alignments by using corresponding proteins encoded by the 31
automatable parts of the procedure that need to be carried out for including orthologs and aligned the resulting profiles. With this procedure, we maximized
further species. For the 31 clusters of orthologous groups (COGs) used in the the number of positions of the global alignment and reduced the number of
analysis, we manually derived 1:1 orthologs by removing mitochondrial and misaligned residues. For a detailed description of the methods, see (8).