Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes
Fig 3
Three methods for identifying and ranking the importance of genes distinguishing Calvin cycle-positive genomes from relatives cooperate to yield a consensus ranking.
The rank of genes, i.e. Enzyme Commission numbers (EC) or Pfam families, within each method (x-axes, logarithmic scale) is plotted against the consensus rank from all three methods (y-axis, logarithmic scale). The orange color intensity (square root scale) indicates the median distance between the gene and Rubisco in number of genes in CBB-positive genomes (S6 Dataset), if the gene was found on the same DNA strand as Rubisco more than 200 times. Genes detected 200 times or fewer on the same DNA strand as Rubisco are shown in light purple. Note that ECs and Pfams were ranked separately in the random forest analysis and thereby each rank is shared by one EC and one Pfam. The random forest analysis included only 1,200 genes due to so-called feature selection preceding ranking (see Materials and methods). The gap between ranks 4,714 and 6,824 in the enrichment analysis is due to 2,110 genes sharing the same q value used for ranking (S2 Dataset). Abbreviations: Ald, fructose-bisphosphate aldolase (EC 4.1.2.13, PF01116); ATPsyn, ATP synthase (PF02823); CbbQ, Rubisco activase CbbQ (PF08406); CbbX, Rubisco activase CbbX (PF17866, “AAA_lid_6”); Fbp, fructose-1,6-bisphosphatase (EC 3.1.3.11, PF00316); GP, glycogen phosphorylase (EC 2.4.1.1); Mdh, malate dehydrogenase (EC 1.1.5.4); Rpe, ribulose-phosphate 3-epimerase (EC 5.1.3.1, PF00834); Tkt, transketolase (EC 2.2.1.1).