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
IIIIII IIIIII
Phettt 55.0929.0867.14 Leuctt 9.705.5619.00
ttc 44.9170.9232.86 ctc 10.408.039.04
Leutta 10.993.4420.09 cta 3.090.836.81
ttg 13.025.4715.05 ctg 52.7976.6729.99
Sertct 13.2632.4119.63 Procct 13.7111.2328.30
tcc 15.0226.5611.34 ccc 11.191.6316.26
tca 10.834.7922.09 cca 18.6315.2531.50
tcg 16.887.3910.60 ccg 56.4771.8923.94
Tyrtat 54.4235.2369.60 Hiscat 56.8029.7761.69
tac 45.5864.7730.40 cac 43.2070.2338.31
TERtaa     Glncaa 33.4018.6537.06
tag     cag 66.6081.3562.94
Cystgt 40.9038.8555.71 Argcgt 38.9964.2526.05
tgc 59.1061.1544.29 cgc 42.2332.9721.94
TERtga     cga 5.521.0712.80
Trptgg 100.00100.00100.00 cgg 8.970.8013.62
Ileatt 51.2033.4947.57 Valgtt 23.7439.7734.33
atc 44.3765.9426.65 gtc 22.4813.4518.95
ata 4.430.5725.78 gta 14.8619.9721.78
Metatg 100.00100.00100.00 gtg 38.9226.8124.94
Thract 14.8529.0826.83 Alagct 14.5227.5422.86
acc 46.8353.6024.45 gcc 27.6216.1423.67
aca 10.524.6727.93 gca 19.6324.0131.27
acg 27.8112.6520.80 gcg 38.2332.3022.19
Asnaat 40.8717.2564.06 Aspgat 62.8346.0570.47
aac 59.1382.7535.94 gac 37.1753.9529.53
Lysaaa 75.4478.5572.21 Glugaa 68.3375.3566.25
aag 24.5621.4527.79 gag 31.6724.6533.75
Seragt 13.964.5218.73 Glyggt 32.9150.8431.79
agc 30.0424.3317.61 ggc 43.1742.8324.51
Argaga 1.750.6215.63 gga 9.191.9724.75
agg 1.540.299.96 ggg 14.744.3618.95


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