Table 3.
Codon usage of pltR gene in Pf-5 and the codon-modified pltR derivatives.
| Amino Acid | Codon | Frequency(/1000)# | Numbers of codon in pltR | ||||||
|---|---|---|---|---|---|---|---|---|---|
| WT | LK298 | LK361 | LK362 | LK363 | LK364 | LK365 | |||
| Ala | GCA | 7.8 | 7 | 0 | 7 | 7 | 0 | 7 | 7 |
| Ala | GCU | 7.8 | 2 | 0 | 2 | 0 | 2 | 2 | 2 |
| Ala | GCG | 28.4 | 7 | 8 | 7 | 7 | 11 | 7 | 7 |
| Ala | GCC | 67.4 | 7 | 15 | 7 | 9 | 10 | 7 | 7 |
| Arg | AGA | 0.6 | 6 | 0 | 6 | 6 | 6 | 0 | 0 |
| Arg | AGG | 1.6 | 1 | 0 | 1 | 1 | 1 | 0 | 1 |
| Arg | CGA | 2.3 | 1 | 0 | 1 | 1 | 0 | 1 | 1 |
| Arg | CGU | 9.2 | 0 | 2 | 0 | 0 | 0 | 0 | 0 |
| Arg | CGG | 14.2 | 4 | 3 | 4 | 4 | 4 | 6 | 6 |
| Arg | CGC | 36.6 | 6 | 13 | 6 | 6 | 7 | 11 | 10 |
| Asn | AAU | 5.9 | 5 | 1 | 5 | 5 | 5 | 5 | 5 |
| Asn | AAC | 23.6 | 6 | 10 | 6 | 6 | 6 | 6 | 6 |
| Asp | GAU | 14.9 | 6 | 3 | 6 | 6 | 6 | 6 | 6 |
| Asp | GAC | 20.6 | 10 | 13 | 10 | 10 | 10 | 10 | 10 |
| Cys | UGU | 1.6 | 3 | 0 | 3 | 3 | 0 | 3 | 3 |
| Cys | UGC | 8.8 | 6 | 9 | 6 | 6 | 9 | 6 | 6 |
| End | UAG | 0.4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| End | UAA | 0.7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| End | UGA | 1.9 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Gln | CAA | 10.3 | 7 | 1 | 7 | 7 | 7 | 7 | 7 |
| Gln | CAG | 40.4 | 5 | 11 | 5 | 5 | 5 | 5 | 5 |
| Glu | GAA | 26.5 | 15 | 8 | 15 | 15 | 15 | 15 | 15 |
| Glu | GAG | 28 | 3 | 10 | 3 | 3 | 3 | 3 | 3 |
| Gly | GGA | 2.7 | 4 | 0 | 4 | 0 | 4 | 4 | 4 |
| Gly | GGU | 11.4 | 2 | 0 | 2 | 0 | 2 | 2 | 2 |
| Gly | GGG | 13.7 | 1 | 1 | 1 | 2 | 1 | 1 | 1 |
| Gly | GGC | 52.7 | 11 | 17 | 11 | 16 | 11 | 11 | 11 |
| His | CAU | 7 | 9 | 4 | 9 | 9 | 9 | 9 | 9 |
| His | CAC | 15.9 | 4 | 9 | 4 | 4 | 4 | 4 | 4 |
| Ile | AUA | 1.2 | 7 | 0 | 0 | 7 | 7 | 7 | 7 |
| Ile | AUU | 7.6 | 3 | 0 | 3 | 3 | 3 | 0 | 3 |
| Ile | AUC | 37.2 | 14 | 24 | 21 | 14 | 14 | 17 | 14 |
| Leu | UUA | 0.8 | 1 | 0 | 1 | 1 | 1 | 0 | 1 |
| Leu | CUA | 1.5 | 4 | 0 | 0 | 4 | 4 | 4 | 4 |
| Leu | CUU | 3.8 | 10 | 0 | 0 | 10 | 10 | 10 | 10 |
| Leu | UUG | 13.2 | 8 | 0 | 8 | 8 | 0 | 8 | 8 |
| Leu | CUC | 16.5 | 9 | 18 | 15 | 9 | 10 | 10 | 9 |
| Leu | CUG | 86.2 | 16 | 30 | 24 | 16 | 23 | 16 | 16 |
| Lys | AAA | 7 | 8 | 3 | 8 | 8 | 8 | 8 | 8 |
| Lys | AAG | 24.8 | 10 | 15 | 10 | 10 | 10 | 10 | 10 |
| Met | AUG | 21.4 | 5 | 5 | 5 | 5 | 5 | 5 | 5 |
| Phe | UUU | 7.1 | 3 | 0 | 3 | 3 | 0 | 3 | 3 |
| Phe | UUC | 28.7 | 7 | 10 | 7 | 7 | 10 | 7 | 7 |
| Pro | CCA | 4.1 | 2 | 0 | 2 | 0 | 2 | 2 | 2 |
| Pro | CCU | 4.1 | 3 | 0 | 3 | 0 | 3 | 3 | 3 |
| Pro | CCC | 16.3 | 5 | 2 | 5 | 7 | 5 | 5 | 5 |
| Pro | CCG | 25.7 | 7 | 15 | 7 | 10 | 7 | 7 | 7 |
| Ser | UCU | 1.6 | 1 | 0 | 1 | 1 | 0 | 1 | 1 |
| Ser | UCA | 1.7 | 5 | 1 | 5 | 5 | 5 | 5 | 5 |
| Ser | AGU | 4.4 | 3 | 0 | 3 | 3 | 3 | 0 | 3 |
| Ser | UCG | 8.8 | 8 | 7 | 8 | 8 | 8 | 8 | 8 |
| Ser | UCC | 12.7 | 4 | 8 | 4 | 4 | 4 | 6 | 4 |
| Ser | AGC | 27.5 | 13 | 18 | 13 | 13 | 14 | 14 | 13 |
| Thr | ACA | 1.7 | 4 | 1 | 4 | 4 | 4 | 4 | 4 |
| Thr | ACU | 3.6 | 3 | 0 | 3 | 0 | 3 | 3 | 3 |
| Thr | ACG | 5.6 | 3 | 2 | 3 | 3 | 3 | 3 | 3 |
| Thr | ACC | 34.7 | 12 | 19 | 12 | 15 | 12 | 12 | 12 |
| Trp | UGG | 14.7 | 3 | 3 | 3 | 3 | 3 | 3 | 3 |
| Tyr | UAU | 6.6 | 2 | 0 | 0 | 2 | 2 | 2 | 2 |
| Tyr | UAC | 18.8 | 4 | 6 | 6 | 4 | 4 | 4 | 4 |
| Val | GUU | 4.3 | 4 | 0 | 0 | 4 | 4 | 4 | 4 |
| Val | GUA | 4.6 | 3 | 0 | 0 | 3 | 3 | 3 | 3 |
| Val | GUC | 20.6 | 5 | 10 | 8 | 5 | 5 | 5 | 5 |
| Val | GUG | 38.8 | 6 | 8 | 10 | 6 | 6 | 6 | 6 |
#
Frequency indicates the codon usage frequency of a specific codon per 1000 total codons used in the annotated coding sequences of Pf-5.