Using evolutionary profiles derived from both sequence and structure information, we construct coarse-grained models of the evolution of structure, function, and folding of the
amino-acyl t-RNA synthetases (AARS). These proteins together with the cognate tRNAs establish the genetic code in all organisms. The evolutionary profiles for each of the twenty some proteins at both the subgroup and class level are derived from the multidimensional QR factorization of sequence and structure alignments which have been orthogonally encoded. The resulting optimal set of proteins best represent the variation observed in the phylogenetic analysis of sequence, structure, and function of the entire set. Applications of the representative sets and their profiles for gene annotation and prediction of folding nuclei are given.
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