Phylogeny determined by protein domain content

Yang et al. 10.1073/pnas.0408810102.

Supporting Information

Files in this Data Supplement:

Supporting Figure 6
Supporting Figure 7
Supporting Figure 8
Supporting Figure 9
Supporting Figure 10
Supporting Table 1
Supporting Table 2
Supporting Table 3
Supporting Table 4
Supporting Table 5

Supporting Figure 6

Fig. 6. Phylogenetic trees based on the presence or absence of fold superfamilies (FSFs). (A) Archaea neighbor-joining (NJ) unweighted tree. (B) Archaea NJ weighted tree. (C) Archaea unweighted pair group method with arithmetic mean (UPGMA) unweighted tree. (D) Archaea UPGMA weighted tree. (E) Bacteria NJ unweighted tree. (F) Bacteria NJ weighted tree. (G) Bacteria UPGMA unweighted tree. (H) Bacteria UPGMA weighted tree. (I) Eukarya NJ unweighted tree. (J) Eukarya NJ weighted tree. (K) Eukarya UPGMA unweighted tree. (L) Eukarya UPGMA weighted tree. (M) NJ unweighted tree of life. (N) NJ weighted tree of life. (O) UPGMA unweighted tree of life. (P) UPGMA weighted tree of life.

Supporting Figure 7

Fig. 7. Phylogenetic trees based on the abundance of FSFs. (A) Archaea abundance NJ tree. (B) Archaea abundance UPGMA tree. (C) Bacteria abundance NJ tree. (D) Bacteria abundance UPGMA tree. (E) Eukarya abundance NJ tree. (F) Eukarya abundance UPGMA tree. (G) Abundance NJ tree of life. (H) Abundance UPGMA tree of life.

Supporting Figure 8

Fig. 8. The comparison of fold number vs. e value cutoff figure between different release of the Superfamily database: (A) The genomic domain assignment of the early version of Superfamily (Jan 6, 2004). (B) The genomic domain assignment of the current version of Superfamily (July 14, 2004)

Supporting Figure 9

Fig. 9. Structural comparison of the six FSFs in the d.17 fold.

Supporting Figure 10

Fig. 10. Decay curve of unique and ubiquitous FSFs and its simulation.