-->E. coli Codon Usage

Codon Usage in E. coli
from H?NAUT 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



- tRNAs for codons in yellow highlights are supplied by Bl21-CodonPlus cells (Stratagene).
- Additional tRNA for GGA (orange) is supplied by Rosetta cells (Novagen).
- Further, tRNA for CGG (orange) is contained in Rosetta 2 strains (Novagen).

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]