Table 1.
Average environmental relative amino acid abundance (eRAAA) across habitats calculated from the literature.
Figure 1.
Characterization of different environments by their relative amino acid composition.
A) scatter plot by Principal Component Analysis according to the type of environment; B) Hierarchical clustering analysis. The length of branches represents the degree of dissimilarity between clusters. The x-axis of the heat map represents the 20 amino acids by alphabetical order of the three-letter code name. Determinations of Asp/Asn and Glu/Gln were considered together for the analysis, because environmental measurements did not distinguish between the two amino acids in the pairs. The y- axis of the heatmap represents the individual environments where amino acid abundance was determined. Over- and under-representation of amino acid residues in each environment are represented in green and red colored squares, respectively.
Table 2.
Spearman rank correlation coefficients between estimated amino acid compositions (based on CAI and δ predictors) and experimentally-determined amino acid abundances.
Figure 2.
Characterization of the relative amino acid composition of the proteomes from different organisms.
A) scatter plot by Principal Component Analysis according to the type of environment; B) Hierarchical clustering analysis. The length of branches represents the degree of dissimilarity between clusters. The x-axis of the heat map represents the 20 amino acids by alphabetical order of the three-letter code name. The y- axis of the heatmap represents the individual organisms where amino acid abundance was estimated. Over- and under-representation of amino acid residues in each organism are represented in green and red colored squares, respectively.
Table 3.
Linear regression models for the effect of GC content, Phylogeny and Habitat on the relative cellular amino acid abundance.
Figure 3.
Relative amino acid composition, weighted by δ index, of each organism plotted against average GC content.
Figure 4.
Spearman Rank Correlations between the RAAA of organisms and environments.
Asterisks represent significance at p<0.01 (**) and p<0.001 (***).