E. coli Codon Usage

Codon Usage in E. coli
from HÉNAUT and DANCHIN:Analysis and Predictions from Escherichia coli sequences.
Escherichia coli and Salmonella, Vol. 2, Ch. 114:2047-2066, 1996, Neidhardt FC ed., ASM press, Washington, D.C.

Amino
Acid Codon Class Amino
Acid Codon Class

I II III I II III

Phe ttt 55.09 29.08 67.14 Leu ctt 9.70 5.56 19.00

ttc 44.91 70.92 32.86 ctc 10.40 8.03 9.04

Leu tta 10.99 3.44 20.09 cta 3.09 0.83 6.81

ttg 13.02 5.47 15.05 ctg 52.79 76.67 29.99

Ser tct 13.26 32.41 19.63 Pro cct 13.71 11.23 28.30

tcc 15.02 26.56 11.34 ccc 11.19 1.63 16.26

tca 10.83 4.79 22.09 cca 18.63 15.25 31.50

tcg 16.88 7.39 10.60 ccg 56.47 71.89 23.94

Tyr tat 54.42 35.23 69.60 His cat 56.80 29.77 61.69

tac 45.58 64.77 30.40 cac 43.20 70.23 38.31

TER taa Gln caa 33.40 18.65 37.06

tag cag 66.60 81.35 62.94

Cys tgt 40.90 38.85 55.71 Arg cgt 38.99 64.25 26.05

tgc 59.10 61.15 44.29 cgc 42.23 32.97 21.94

TER tga cga 5.52 1.07 12.80

Trp tgg 100.00 100.00 100.00 cgg 8.97 0.80 13.62

Ile att 51.20 33.49 47.57 Val gtt 23.74 39.77 34.33

atc 44.37 65.94 26.65 gtc 22.48 13.45 18.95

ata 4.43 0.57 25.78 gta 14.86 19.97 21.78

Met atg 100.00 100.00 100.00 gtg 38.92 26.81 24.94

Thr act 14.85 29.08 26.83 Ala gct 14.52 27.54 22.86

acc 46.83 53.60 24.45 gcc 27.62 16.14 23.67

aca 10.52 4.67 27.93 gca 19.63 24.01 31.27

acg 27.81 12.65 20.80 gcg 38.23 32.30 22.19

Asn aat 40.87 17.25 64.06 Asp gat 62.83 46.05 70.47

aac 59.13 82.75 35.94 gac 37.17 53.95 29.53

Lys aaa 75.44 78.55 72.21 Glu gaa 68.33 75.35 66.25

aag 24.56 21.45 27.79 gag 31.67 24.65 33.75

Ser agt 13.96 4.52 18.73 Gly ggt 32.91 50.84 31.79

agc 30.04 24.33 17.61 ggc 43.17 42.83 24.51

Arg aga 1.75 0.62 15.63 gga 9.19 1.97 24.75

agg 1.54 0.29 9.96 ggg 14.74 4.36 18.95

Genes are clustered by using factorial correspondence analysis into three classes. Class I contains genes involved in most metabolic processes. Class II genes correspond to genes highly and continuously expressed during exponential growth. Class III genes are implicated in horizontal transfer of DNA. One can see that the distribution of codons in class III genes is more or less even, whereas it is extremely biased in class II genes (in particular, codons terminated in A are selected against).

[Codon Usage]

M. Maduro

Amino Acid	Codon	Class			Amino Acid	Codon	Class
Amino Acid	Codon	I	II	III	Amino Acid	Codon	I	II	III
Phe	ttt	55.09	29.08	67.14	Leu	ctt	9.70	5.56	19.00
Phe	ttc	44.91	70.92	32.86		ctc	10.40	8.03	9.04
Leu	tta	10.99	3.44	20.09		cta	3.09	0.83	6.81
Leu	ttg	13.02	5.47	15.05		ctg	52.79	76.67	29.99
Ser	tct	13.26	32.41	19.63	Pro	cct	13.71	11.23	28.30
	tcc	15.02	26.56	11.34		ccc	11.19	1.63	16.26
	tca	10.83	4.79	22.09		cca	18.63	15.25	31.50
	tcg	16.88	7.39	10.60		ccg	56.47	71.89	23.94
Tyr	tat	54.42	35.23	69.60	His	cat	56.80	29.77	61.69
Tyr	tac	45.58	64.77	30.40	His	cac	43.20	70.23	38.31
TER	taa				Gln	caa	33.40	18.65	37.06
TER	tag				Gln	cag	66.60	81.35	62.94
Cys	tgt	40.90	38.85	55.71	Arg	cgt	38.99	64.25	26.05
Cys	tgc	59.10	61.15	44.29		cgc	42.23	32.97	21.94
TER	tga					cga	5.52	1.07	12.80
Trp	tgg	100.00	100.00	100.00		cgg	8.97	0.80	13.62
Ile	att	51.20	33.49	47.57	Val	gtt	23.74	39.77	34.33
	atc	44.37	65.94	26.65		gtc	22.48	13.45	18.95
	ata	4.43	0.57	25.78		gta	14.86	19.97	21.78
Met	atg	100.00	100.00	100.00		gtg	38.92	26.81	24.94
Thr	act	14.85	29.08	26.83	Ala	gct	14.52	27.54	22.86
	acc	46.83	53.60	24.45		gcc	27.62	16.14	23.67
	aca	10.52	4.67	27.93		gca	19.63	24.01	31.27
	acg	27.81	12.65	20.80		gcg	38.23	32.30	22.19
Asn	aat	40.87	17.25	64.06	Asp	gat	62.83	46.05	70.47
Asn	aac	59.13	82.75	35.94	Asp	gac	37.17	53.95	29.53
Lys	aaa	75.44	78.55	72.21	Glu	gaa	68.33	75.35	66.25
Lys	aag	24.56	21.45	27.79	Glu	gag	31.67	24.65	33.75
Ser	agt	13.96	4.52	18.73	Gly	ggt	32.91	50.84	31.79
Ser	agc	30.04	24.33	17.61		ggc	43.17	42.83	24.51
Arg	aga	1.75	0.62	15.63		gga	9.19	1.97	24.75
Arg	agg	1.54	0.29	9.96		ggg	14.74	4.36	18.95