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Table 3 Codon usage frequency table for optimal expression in E. coli.

From: Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

AA Codon Freq AA Codon Freq
Ala GCA 0.28 Leu CTT 0.05
Ala GCC 0.07 Leu TTA 0.03
Ala GCG 0.21 Leu TTG 0.02
Ala GCT 0.45 Lys AAA 0.81
Arg AGA 0.02 Lys AAG 0.19
(Arg) AGG 0 Met ATG 1
(Arg) CGA 0 Phe TTC 0.79
Arg CGC 0.24 Phe TTT 0.21
(Arg) CGG 0.01 Pro CCA 0.08
Arg CGT 0.73 (Pro) CCC 0.01
Asn AAC 0.91 Pro CCG 0.82
Asn AAT 0.09 Pro CCT 0.08
Asp GAC 0.72 Ser AGC 0.15
Asp GAT 0.28 (Ser) AGT 0.01
Cys TGC 0.8 Ser TCA 0.02
Cys TGT 0.2 Ser TCC 0.39
Gln CAA 0.14 Ser TCG 0.04
Gln CAG 0.86 Ser TCT 0.39
Glu GAA 0.83 Stop TAA 0.83
Glu GAG 0.17 Stop TAG 0.17
(Gly) GGA 0 Stop TGA 0
Gly GGC 0.5 Thr ACA 0.02
(Gly) GGG 0.01 Thr ACC 0.56
Gly GGT 0.48 Thr ACG 0.05
His CAC 0.83 Thr ACT 0.36
His CAT 0.17 Trp TGG 1
Ile ATA 0.02 Tyr TAC 0.8
Ile ATC 0.86 Tyr TAT 0.2
Ile ATT 0.12 Val GTA 0.21
(Leu) CTA 0.01 Val GTC 0.07
Leu CTC 0.06 Val GTG 0.15
Leu CTG 0.83 Val GTT 0.57
  1. Frequency refers to the percentage occurrence of synonymous codons encoding amino acids in E. coli highly expressed proteins. The nucleic acid sequences of the following genes were combined into a single pseudo-gene and then used in the Kazusa Countcodon program http://www.kazusa.or.jp/codon with eubacterial translation exceptions to generate a codon usage table for that pseudo-gene: ompA (V00307), atpE (V00266), cybB (AP009048), cybC (U14003), sdhC (AP009048), groEL (AP009048), tufA (AP009048), rpsA (AP009048), rpsB (NC_000913), rpoA (AP009048), rpoB (AP009048), rpoC (AP009048), pheS (AP009048), pheT (AP009048), lysS (AP009048). Codons in parentheses fall below the 2% frequency cutoff, and are not used during back-translation when the threshold for codon usage is set at 2%.