Table 1.

Codon usage in E. coli. Codon usage is compared between a set of 40 highly expressed genes (high; see Sharp et al. 2005) and the genome as a whole (all); the data are relative synonymous codon usage values (the ratio of the observed number to that expected if all codons for an amino acid were used equally). Nineteen codons occurring at significantly higher frequencies (see Henry & Sharp 2007) in the high dataset are shown in bold. The data are for E. coli strain K-12 MG1655 (accession number U00096).

		high	all			high	all			high	all			high	all
Phe	UUU	0.45	1.15	Ser	UCU	2.54	0.87	Tyr	UAU	0.48	1.14	Cys	UGU	0.77	0.89
Phe	UUC	1.55	0.85	Ser	UCC	1.52	0.89	Tyr	UAC	1.52	0.86	Cys	UGC	1.23	1.11
Leu	UUA	0.14	0.79	Ser	UCA	0.19	0.74	Ter	UAA	2.85	1.89	Ter	UGA	0.15	0.88
Leu	UUG	0.25	0.77	Ser	UCG	0.06	0.92	Ter	UAG	0	0.23	Trp	UGG	1.00	1.00
Leu	CUU	0.30	0.62	Pro	CCU	0.59	0.64	His	CAU	0.61	1.14	Arg	CGU	4.13	2.27
Leu	CUC	0.23	0.63	Pro	CCC	0.05	0.50	His	CAC	1.39	0.86	Arg	CGC	1.80	2.39
Leu	CUA	0.01	0.22	Pro	CCA	0.52	0.76	Gln	CAA	0.37	0.69	Arg	CGA	0	0.39
Leu	CUG	5.07	2.97	Pro	CCG	2.85	2.10	Gln	CAG	1.63	1.31	Arg	CGG	0.03	0.59
Ile	AUU	0.72	1.52	Thr	ACU	1.89	0.67	Asn	AAU	0.25	0.90	Ser	AGU	0.29	0.91
Ile	AUC	2.27	1.26	Thr	ACC	1.75	1.74	Asn	AAC	1.75	1.10	Ser	AGC	1.40	1.66
Ile	AUA	0.01	0.22	Thr	ACA	0.19	0.53	Lys	AAA	1.45	1.53	Arg	AGA	0.03	0.23
Met	AUG	1.00	1.00	Thr	ACG	0.17	1.07	Lys	AAG	0.55	0.47	Arg	AGG	0	0.14
Val	GUU	2.07	1.03	Ala	GCU	1.83	0.65	Asp	GAU	0.69	1.26	Gly	GGU	2.53	1.35
Val	GUC	0.30	0.86	Ala	GCC	0.32	1.08	Asp	GAC	1.31	0.74	Gly	GGC	1.39	1.61
Val	GUA	1.14	0.62	Ala	GCA	1.09	0.85	Glu	GAA	1.51	1.38	Gly	GGA	0.03	0.44
Val	GUG	0.48	1.49	Ala	GCG	0.76	1.42	Glu	GAG	0.49	0.62	Gly	GGG	0.06	0.60