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. 2014 Jan 2;10(1):e1003294. doi: 10.1371/journal.pcbi.1003294

Figure 1. tRNA isoacceptors and adaptation index.

Figure 1

(A) Illustration of the decoding by tRNA. The alanine (Ala) charged tRNAs that recognize GCU and GCC belong to the same isoacceptor. Decoding is performed according to the wobble rules [73]. Alanine (Ala) is decoded by three groups of isoacceptor tRNAs. The genomic tRNA copy number (CN) from H. sapiens is marked. Specifically, the number of genes for Ala is 43 (the sum of the CN of all isoacceptor groups). Codons are always read by the 5′ to 3′ directionality from DNA or mRNA. (B) The range of codon tAI that can be assigned to each AA in H. sapiens is shown. Codon tAI is determined by the CN of tRNAs for that codon and according to the coupling of tRNA at the wobble position. The tAI for each codon is marked by a colored dot. Tryptophan (Trp) and Methionine (Met) are encoded by a single codon. For the other AAs a range of tAI values are shown according to the number of codons (2, 3, 4 and 6 codons). Note that Arg, Ser and Leu that are decoded by 6 codons each, do not necessarily have a wide range of tAI values. The minimal and maximal tAI values for each of the AAs are colored green and red, respectively. (C) Clustering of multicellular model organisms by the correlation calculated according to a vector of the tAI values (61 codons). The Spearman correlation coefficient between each pair of species is color-coded. The tAI codon values for each organism is listed in Table S1.