Table 1.

Translationally optimal codons estimated for synonymous groups in seven bacterial species.

Amino acid1	Synonymous codons	E. coli	S. enterica	B. subtilis	B. thetaiotaomicron	Synechocystis sp.	M. tuberculosis	L. interrogans
Ala	GCA, GCC, GCG, GCU	—3	—	GCAa	GCU	GCC	GCC	GCA
Cys	UGC, UGU	UGC b	UGC	UGC	UGU	—	UGC	—
Asp	GAC, GAU	—	—	—	GAU	—	GAC	—
Glu	GAA,GAG	GAAab	GAA	GAA a	GAA	GAA	GAG	GAA
Phe	UUC,UUU	UUC ab	UUC	—	UUC	—	UUC	—
Gly	GGN	GGC ab	GGC	GGC	GGU	GGU	GGC *	—
His	CAC, CAU	CAC b	—	—	—	—	CAC	—
Ile	AUA, AUC, AUU	AUC ab	AUC	—	AUC	—	AUC	—
Lys	AAA, AAG	AAA ab	AAA	AAA a	AAA	—	AAG	—
Leu 2-fold2	UUA, UUG	UUG b	UUG	UUAa	—	UUG	UUG	—
Leu 4-fold	CUA, CUC, CUG, CUU	CUG a	CUG	CUU	—	CUG*	CUG	—
Asn	AAC, AAU	AAC ab	AAC	—	—	—	AAC	—
Pro	CCA, CCC, CCG, CCU	CCG *ab	CCG	—	—	CCC*	CCG	CCU
Gln	CAA, CAG	CAG ab	CAG	CAA a	—	—	CAG	—
Arg 2-fold	AGA, AGG	AGAa	AGA	AGA	AGA	AGG	AGG	AGA
Arg 4-fold	CGA, CGC, CGG, CGU	CGU a	CGU	CGC	CGU	CGG *	CGC	CGU
Serine 2-fold	AGC, AGU	AGC b	AGC	AGC	—	—	AGC	—
Serine 4-fold	UCA, UCC, UCG, UCU	UCU	UCC	UCA	UCU	UCC	—	UCU
Thr	ACA, ACC, ACG, ACU	ACC ab	ACC	ACAa	ACU	ACC	ACC	ACU
Val	GUA, GUC, GUG, GUU	—		GUU	GUA	—	—
Tyr	UAC, UAU	—		—	—	—	UAC

Bold are translationally optimal codons that also have the highest tRNA availability estimated by tpm from two independent RNA-Seq datasets.

¹Two amino acids (Met and Trp) are omitted because they are each encoded by a single codon.

²The 6-fold degenerate codon families (Leu, Arg, and Ser) are broken into 2 and 4-fold families because of differences in the first codon base.

³An optimal codon cannot be determined by our definition (e.g., RSCU HEG < RSCU LEG violates the second criterion).

^*Predicted preferred codons match optimal codons in only one of the two RNA-Seq data analyzed.

^aTranslationally optimal codons match optimal codons determined by F_op in Ikemura¹⁰ and Kanaya, et al.¹¹.

^bTranslationally optimal codons identified using average tRNA abundance from RNA fingerprinting approach, retrieved from Dong, et al.⁴².