Table 2.
Summary of the six rarest codons in the Pf-5 genome.
| Codon | Amino acid | Codon usage frequency (per 1000 codons) | Total genome (6144 genes) | Toxoflavin (PFL_1028–1037) | Orfamide A (PFL_2142–2150) | HCN (PFL_2577–2579) | Pyoluteorin (PFL_2784–2800) | Rhizoxin (PFL_2989–2997) | Pyrrolnitrin (PFL_3604–3607) | DAPG (PFL_5951–5958) | All seven clusters (60 genes) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Of total codons | Of total synonymous codons | # CDS | % | # CDS | % | # CDS | % | # CDS | % | # CDS | % | # CDS | % | # CDS | % | # CDS | % | # CDS | % | ||
| AGA | Arg | 0.6 | 9.9 | 917 | 15 | 4 | 40 | 2 | 22 | 0 | 0 | 7 | 41 | 5 | 56 | 2 | 50 | 4 | 50 | 24 | 40 |
| UUA | Leu | 0.8 | 6.2 | 1049 | 17 | 2 | 20 | 0 | 0 | 1 | 33 | 2 | 12 | 6 | 67 | 1 | 25 | 2 | 25 | 14 | 23 |
| AUA | Ile | 1.2 | 25.2 | 1547 | 25 | 3 | 30 | 3 | 33 | 2 | 67 | 14 | 82 | 9 | 100 | 2 | 50 | 3 | 38 | 36 | 60 |
| CUA | Leu | 1.5 | 12.3 | 1967 | 32 | 2 | 20 | 2 | 22 | 0 | 0 | 7 | 41 | 7 | 78 | 2 | 50 | 4 | 50 | 24 | 40 |
| UCU | Ser | 1.6 | 77.8 | 2052 | 33 | 1 | 10 | 2 | 22 | 1 | 33 | 10 | 59 | 7 | 78 | 2 | 50 | 3 | 38 | 26 | 43 |
| UGU | Cys | 1.6 | 154.0 | 2226 | 36 | 1 | 10 | 7 | 78 | 1 | 33 | 11 | 65 | 9 | 100 | 3 | 75 | 4 | 50 | 36 | 60 |
#CDS means coding sequences. % indicates the percentage of rare codon-containing genes in the total genome of Pf-5 or in each antibiotic gene cluster.