Table 1.
Genes with significant directional changes in their codon usage bias compared to their inferred ancestral sequence
|
Gene |
COUSINanc |
ΔCOUSINall |
ΔCOUSINsyn |
S |
N |
No. of CDSs |
Res. time |
|---|---|---|---|---|---|---|---|
|
Bicarbonate transport system permease CmpB |
0.949 |
+0.014 |
+0.014 |
12 |
3 |
61 |
0.007 |
|
Hypothetical protein |
0.8 |
+0.009 |
+0.009 |
4 |
0 |
35 |
0.007 |
|
Alcohol dehydrogenase |
0.842 |
+0.005 |
+0.005 |
8 |
3 |
46 |
0.007 |
|
Cyclic-di-GMP phosphodiesterase AdeB |
0.811 |
+0.005 |
+0.005 |
6 |
7 |
26 |
0.005 |
|
Hypothetical protein |
1.06 |
+0.003 |
n.s. |
2 |
7 |
43 |
0.005 |
|
4-hydroxy-tetrahydrodipicolate synthase |
0.794 |
+0.002 |
+0.005 |
7 |
5 |
31 |
0.009 |
|
Hypothetical protein |
0.196 |
−0.001 |
−0.001 |
4 |
5 |
25 |
0.006 |
|
Hypothetical protein |
0.861 |
−0.001 |
−0.001 |
3 |
0 |
31 |
0.008 |
|
Putative ribosomal N-acetyltransferase YdaF |
0.801 |
−0.004 |
n.s. |
3 |
5 |
37 |
0.007 |
|
HTH-type transcriptional regulator DmlR |
0.73 |
−0.005 |
−0.008 |
6 |
5 |
23 |
0.008 |
|
Hypothetical protein |
0.499 |
−0.005 |
−0.005 |
7 |
4 |
32 |
0.008 |
|
Hypothetical protein |
0.794 |
−0.006 |
−0.007 |
3 |
1 |
36 |
0.004 |
|
Glycine cleavage system H protein |
0.764 |
−0.008 |
−0.012 |
5 |
4 |
23 |
0.008 |
|
Putative manganese catalase |
0.942 |
−0.008 |
−0.008 |
8 |
10 |
36 |
0.004 |
|
Glutathione S-transferase GST-6.0 |
0.711 |
−0.011 |
−0.009 |
5 |
4 |
23 |
0.008 |
|
Hypothetical protein |
0.711 |
−0.016 |
−0.009 |
8 |
2 |
32 |
0.008 |
COUSINanc.=COUSIN value of the ancestral sequence; ΔCOUSINall=mean change in COUSIN values between ancestral and extant sequences. ΔCOUSINsyn=mean change in COUSIN values between ancestral and extant sequences when only synonymous variation is taken into account. S=number of positions with synonymous variation. N=number of positions with non-synonymous variation. No. of CDSs=number of CDSs in the analysis for each gene. Res. time=mean residence time for each gene.