TABLE 7.
Comparison of codon usage in tnpA, merA, and the tnp-mer junction of Tn21 family transposons and a distantly related transposon, Tn5041
| Genes compareda
|
D2b | |||
|---|---|---|---|---|
| Gene A | Length (bp) | Gene B | Length (bp) | |
| Tn21 tnpA | 2,967 | Tn501 tnpA | 2,967 | 0.62 |
| Tn5036 tnpA | 2,973 | 0.97 | ||
| Tn5041 tnpA | 2,988 | 2.55 | ||
| Tn21 merA | 1,695 | Tn501 merA | 1,686 | 0.41 |
| Tn5036 merA | 1,686 | 0.50 | ||
| Tn5041 merA | 1,680 | 2.72 | ||
| Tn21 urf2M | 987 | Tn21 merA | 1,695 | 1.00 |
| Tn21 tnpA | 2,967 | 3.21 | ||
| Tn501 orf2 | 990 | 1.31 | ||
| Tn501 merA | 1,686 | 0.98 | ||
| Tn501 tnpA | 2,967 | 3.61 | ||
a
Tn21, Tn501, and Tn5036 belong to the Tn21 family of transposons; Tn5041 is distantly related to them (124).
b
The D2 statistic, calculated with the GCG program Correspond, compares the pattern of codon usage generated by the GCG program CodonFrequency (20). D2 is the sum over all codons of the residual equation D2 = (frequencycodon table 1 − frequencycodon table 2)2. D2 increases as patterns of codon usage become more dissimilar. D2 values of <3.0 are consistent with a common origin for the genes (24). (The significance of D2 decreases with sequence sizes of 1,000 bp).