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

BMC Biotechnology

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

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

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%.

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