Clustering of the NUTs and the trees in the forest of life using the classical multidimensional scaling (CMDS) method. (a) The best two-dimensional projection of the clustering of 102 NUTs (brown squares) in a 30-dimensional space. The 14 1:1 NUTs (corresponding to COGs consisting of 1:1 orthologs) are shown as black circles. V1, V2, variables 1 and 2, respectively. (b) The best two-dimensional projection of the clustering of the 3,789 COG trees in a 669-dimensional space. The seven clusters are color-coded and the NUTs are shown by red circles. (c) Partitioning of the trees in each cluster between the two prokaryotic domains: blue, archaea-only (A); green, bacteria-only (B); brown, COGs including both archaea and bacteria (A&B). (d) Classification of the trees in each cluster by COG functional categories [41,42]: A, RNA processing and modification; B, chromatin structure and dynamics; C, energy transformation; D, cell division and chromosome partitioning; E, amino acid metabolism and transport; F, nucleotide metabolism and transport; G, carbohydrate metabolism and transport; H, coenzyme metabolism and transport; I, lipid metabolism; J, translation and ribosome biogenesis; K, transcription; L, replication and repair; M, cell envelope and outer membrane biogenesis; N, cell motility and secretion; O, post-translational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolism; R, general functional prediction only; S, uncharacterized. (e) The mean similarity values between the 102 NUTs and each of the seven tree clusters in the forest of life (colors as in (b)).
Puigbò et al. Journal of Biology 2009 8:59 doi:10.1186/jbiol159