TABLE 2.
Analysis of the codon usage of L. lactis and L. monocytogenes bacterium and phage strains
| Amino acid | Codon | % Codon usage |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| L. lactis host strainsa | L. monocytogenes host strainsb | L. monocytogenes phage P35 |
L. lactis phage |
||||||||||
| 1358 | bIL170 | Q54 | P335 | P087 | asccφ28 | c2 | 1706 | KSY1 | |||||
| Ala | GCG | 11.0 | 21.7 | 21.0 | 29.5 | 7.7 | 15.4 | 12.4 | 2.2 | 20.5 | 10.5 | 2.8 | 1.9 |
| GCA | 31.6 | 36.4 | 36.5 | 37.6 | 37.9 | 33.6 | 37.4 | 34.4 | 36.4 | 37.3 | 37.6 | 46.6 | |
| GCT | 41.5 | 31.0 | 32.2 | 13.1 | 47.8 | 36.4 | 39.1 | 56.6 | 33.9 | 41.4 | 52.5 | 47.4 | |
| GCC | 16.0 | 10.9 | 10.3 | 19.8 | 6.6 | 14.7 | 11.0 | 6.8 | 9.3 | 11.0 | 7.2 | 4.2 | |
| Arg | AGG | 4.1 | 3.6 | 3.8 | 4.2 | 10.5 | 5.4 | 5.8 | 3.3 | 5.5 | 10.3 | 4.8 | 5.2 |
| AGA | 22.2 | 21.6 | 24.6 | 7.8 | 45.4 | 25.8 | 32.9 | 26.7 | 30.2 | 35.0 | 36.1 | 46.3 | |
| CGG | 6.1 | 7.8 | 7.3 | 11.8 | 3.8 | 6.7 | 4.7 | 2.6 | 11.0 | 1.7 | 1.2 | 2.8 | |
| CGA | 15.4 | 15.0 | 12.2 | 14.5 | 11.6 | 15.6 | 18.8 | 13.3 | 11.5 | 9.9 | 10.8 | 11.0 | |
| CGT | 40.5 | 33.5 | 33.5 | 16.5 | 19.8 | 27.4 | 29.6 | 48.6 | 32.4 | 33.3 | 42.6 | 31.3 | |
| CGC | 11.8 | 18.5 | 16.8 | 45.3 | 9.0 | 19.1 | 8.3 | 5.5 | 9.3 | 9.9 | 4.6 | 3.5 | |
| Asn | AAT | 79.0 | 68.4 | 67.9 | 32.9 | 62.5 | 52.0 | 70.5 | 67.5 | 75.3 | 46.4 | 77.6 | 64.3 |
| AAC | 21.0 | 31.6 | 32.1 | 67.2 | 37.5 | 48.0 | 29.5 | 32.5 | 24.7 | 53.7 | 22.4 | 35.7 | |
| Asp | GAT | 72.7 | 73.4 | 73.2 | 14.2 | 54.3 | 47.6 | 71.0 | 63.6 | 66.8 | 47.8 | 77.7 | 62.2 |
| GAC | 27.3 | 26.6 | 26.8 | 85.8 | 45.7 | 52.4 | 29.0 | 36.4 | 33.2 | 52.2 | 22.3 | 37.8 | |
| Cys | TGT | 77.3 | 63.9 | 60.5 | 27.4 | 66.1 | 73.3 | 64.2 | 84.4 | 63.4 | 73.3 | 77.6 | 74.1 |
| TGC | 22.7 | 36.1 | 39.5 | 72.6 | 33.9 | 26.7 | 35.9 | 15.6 | 36.6 | 26.7 | 22.4 | 25.9 | |
| Gln | CAG | 16.5 | 15.4 | 15.7 | 36.0 | 20.4 | 17.4 | 19.7 | 11.8 | 9.3 | 17.4 | 11.3 | 12.5 |
| CAA | 83.5 | 84.6 | 84.3 | 64.0 | 79.6 | 82.6 | 80.3 | 88.2 | 90.7 | 82.6 | 88.7 | 87.5 | |
| Glu | GAG | 17.9 | 18.1 | 18.5 | 38.0 | 21.2 | 19.0 | 21.5 | 18.2 | 20.0 | 26.2 | 17.4 | 16.8 |
| GAA | 82.1 | 81.9 | 81.5 | 62.0 | 78.8 | 81.0 | 78.5 | 81.8 | 80.0 | 73.8 | 82.6 | 83.2 | |
| Gly | GGG | 12.4 | 13.3 | 13.1 | 20.1 | 8.8 | 21.9 | 10.7 | 3.3 | 19.6 | 15.3 | 5.0 | 5.9 |
| GGA | 37.8 | 29.4 | 30.1 | 15.0 | 33.8 | 34.8 | 40.2 | 29.3 | 37.3 | 27.6 | 29.7 | 31.0 | |
| GGT | 37.0 | 35.8 | 36.0 | 14.2 | 40.4 | 26.4 | 34.2 | 62.9 | 28.6 | 43.1 | 55.8 | 49.4 | |
| GGC | 12.6 | 21.5 | 20.9 | 50.7 | 17.0 | 16.9 | 14.9 | 4.5 | 14.5 | 14.0 | 9.5 | 13.7 | |
| His | CAT | 74.7 | 70.4 | 70.7 | 28.0 | 70.2 | 46.5 | 66.7 | 70.1 | 75.7 | 55.1 | 79.6 | 74.7 |
| CAC | 25.3 | 29.7 | 29.3 | 72.0 | 29.8 | 53.5 | 33.3 | 29.9 | 24.3 | 44.9 | 20.4 | 25.3 | |
| Ile | ATA | 11.3 | 13.2 | 14.5 | 19.5 | 25.1 | 27.7 | 19.3 | 13.6 | 17.0 | 22.1 | 22.6 | 20.4 |
| ATT | 68.2 | 62.2 | 59.8 | 29.5 | 56.9 | 57.6 | 59.9 | 61.1 | 68.0 | 55.5 | 59.3 | 56.5 | |
| ATC | 20.5 | 24.6 | 25.7 | 51.0 | 18.0 | 14.6 | 20.8 | 25.4 | 15.1 | 22.5 | 18.2 | 23.1 | |
| Leu | TTG | 21.3 | 13.2 | 13.1 | 14.8 | 16.7 | 13.3 | 19.8 | 17.0 | 14.6 | 22.0 | 12.6 | 16.1 |
| TTA | 31.6 | 39.4 | 39.8 | 15.5 | 38.7 | 47.1 | 36.1 | 38.0 | 46.2 | 36.7 | 41.3 | 31.9 | |
| CTG | 5.9 | 5.1 | 4.8 | 9.8 | 4.9 | 1.4 | 4.8 | 2.8 | 2.7 | 3.3 | 1.3 | 3.6 | |
| CTA | 7.7 | 14.0 | 14.3 | 10.0 | 14.2 | 14.5 | 9.4 | 11.2 | 9.7 | 17.1 | 12.9 | 14.8 | |
| CTT | 25.6 | 22.3 | 22.2 | 11.8 | 23.8 | 20.7 | 25.1 | 26.4 | 21.2 | 17.2 | 27.4 | 29.8 | |
| CTC | 7.9 | 6.0 | 6.0 | 38.2 | 1.7 | 3.1 | 4.9 | 4.6 | 5.8 | 3.7 | 4.5 | 3.8 | |
| Lys | AAG | 17.2 | 14.3 | 13.9 | 36.0 | 23.6 | 20.2 | 22.3 | 19.8 | 18.0 | 20.4 | 22.4 | 26.5 |
| AAA | 82.8 | 85.7 | 86.1 | 64.0 | 76.4 | 79.8 | 77.7 | 80.2 | 82.0 | 79.6 | 77.6 | 73.5 | |
| Phe | TTT | 75.5 | 67.6 | 66.9 | 30.0 | 69.1 | 65.4 | 73.8 | 64.1 | 83.7 | 64.0 | 71.1 | 61.5 |
| TTC | 24.5 | 32.5 | 33.1 | 70.0 | 30.9 | 34.6 | 26.2 | 35.9 | 16.3 | 36.0 | 28.9 | 38.5 | |
| Pro | CCG | 8.7 | 19.9 | 18.9 | 41.0 | 8.6 | 28.1 | 12.2 | 2.0 | 10.7 | 11.4 | 2.8 | 2.2 |
| CCA | 46.5 | 52.0 | 52.5 | 12.8 | 38.3 | 30.7 | 47.0 | 52.9 | 22.0 | 32.3 | 53.4 | 58.2 | |
| CCT | 36.4 | 23.2 | 23.6 | 15.1 | 49.6 | 32.0 | 33.0 | 42.3 | 53.1 | 51.5 | 41.5 | 37.4 | |
| CCC | 8.4 | 5.0 | 5.0 | 31.0 | 3.6 | 9.2 | 7.9 | 2.8 | 14.1 | 4.8 | 2.3 | 2.2 | |
| Ser | AGT | 22.3 | 23.8 | 23.7 | 6.1 | 26.1 | 27.2 | 23.8 | 26.4 | 22.0 | 30.6 | 22.0 | 21.9 |
| AGC | 9.0 | 15.4 | 16.0 | 33.3 | 17.4 | 24.1 | 14.2 | 4.4 | 6.7 | 20.3 | 6.2 | 7.6 | |
| TCG | 5.6 | 11.0 | 11.2 | 26.7 | 4.2 | 7.7 | 5.2 | 3.6 | 5.6 | 4.1 | 2.2 | 2.0 | |
| TCA | 33.0 | 17.4 | 17.7 | 19.2 | 32.6 | 22.6 | 31.0 | 33.8 | 35.7 | 25.3 | 35.2 | 33.6 | |
| TCT | 25.4 | 21.5 | 20.7 | 10.4 | 18.6 | 15.0 | 21.5 | 27.9 | 26.5 | 18.7 | 31.6 | 33.2 | |
| TCC | 4.7 | 11.0 | 10.7 | 4.4 | 1.1 | 3.3 | 4.2 | 3.9 | 3.6 | 1.0 | 2.8 | 1.7 | |
| Thr | ACG | 11.8 | 20.9 | 20.1 | 33.5 | 9.9 | 11.2 | 10.9 | 4.6 | 16.5 | 11.8 | 4.8 | 2.7 |
| ACA | 39.2 | 41.9 | 42.9 | 35.4 | 46.8 | 45.1 | 39.0 | 40.8 | 40.9 | 44.9 | 44.8 | 45.9 | |
| ACT | 36.5 | 26.0 | 26.4 | 12.9 | 37.5 | 32.5 | 39.6 | 45.7 | 29.1 | 37.3 | 46.1 | 47.0 | |
| ACC | 12.5 | 11.2 | 10.6 | 19.3 | 5.7 | 11.2 | 10.5 | 8.9 | 13.5 | 6.0 | 4.2 | 4.4 | |
| Tyr | TAT | 78.2 | 68.0 | 67.4 | 45.3 | 73.0 | 65.8 | 75.4 | 75.7 | 78.9 | 67.0 | 78.8 | 72.3 |
| TAC | 21.8 | 32.0 | 32.6 | 54.7 | 27.0 | 34.2 | 24.6 | 24.3 | 21.1 | 33.0 | 21.2 | 27.7 | |
| Val | GTG | 13.5 | 19.7 | 20.0 | 20.7 | 7.5 | 7.0 | 13.0 | 6.0 | 12.4 | 11.0 | 6.7 | 7.1 |
| GTA | 19.7 | 30.9 | 31.7 | 18.4 | 40.3 | 44.4 | 24.8 | 40.0 | 20.4 | 37.2 | 37.8 | 53.0 | |
| GTT | 48.5 | 37.0 | 36.5 | 14.9 | 39.8 | 39.6 | 47.9 | 47.2 | 50.7 | 40.6 | 48.2 | 30.0 | |
| GTC | 18.3 | 12.4 | 11.8 | 46.0 | 12.4 | 9.1 | 14.4 | 6.8 | 16.5 | 11.3 | 7.3 | 9.6 | |
| Stop | TGA | 19.0 | 18.7 | 19.7 | 27.9 | 25.0 | 27.7 | 26.5 | 21.6 | 14.3 | 30.8 | 18.4 | 21.4 |
| TAG | 12.0 | 9.9 | 8.0 | 16.3 | 9.4 | 10.6 | 20.4 | 14.8 | 21.4 | 12.8 | 18.4 | 18.3 | |
| TAA | 69.0 | 71.4 | 72.2 | 55.8 | 65.6 | 61.7 | 53.1 | 63.6 | 64.3 | 56.4 | 63.2 | 60.3 | |
a
These data represent the means for three L. lactis strains.
b
These data represent the means for two L. monocytogenes strains.