The Rates of Synonymous (Ks) and Nonsynonymous (Ka) Nucleotide Substitutions among Different Functional Categories for Essential, Nonessential, and Undetermined Escherichia coliGenes
| Ks (±se)[i] | Ka (±se)[ii] | Ka/Ks (±se) | |
| Information storage and processing | |||
| Essential (n = 113) | 19.42 × 10−3 | 0.96 × 10−3 | 3.89 × 10−2 |
| (±2.3 × 10−3) | (±0.2 × 10−3) | (±0.8 × 10−2) | |
| Nonessential (n = 222) | 48.16 × 10−3 | 3.50 × 10−3 | 8.72 × 10−2 |
| (±2.8 × 10−3) | (±0.4 × 10−3) | (±1.1 × 10−2) | |
| Undetermined (n = 113) | 52.31 × 10−3 | 4.62 × 10−3 | 11.69 × 10−2 |
| (±4.4 × 10−3) | (±0.6 × 10−3) | (±1.8 × 10−2) | |
| Significance of the difference[iii] essential vs. nonessential | P = 1.6 × 10−15 | P = 1.6 × 10−7 | P = 6.1 × 10−3 |
| Significance of the difference[iii] essential vs. undetermined | P = 3.2 × 10−12 | P = 1.3 × 10−10 | P = 1.3 × 10−4 |
| Significance of the difference[iii] nonessential vs. undetermined | NS | NS | NS |
| Cellular processes | |||
| Essential (n = 46) | 37.57 × 10−3 | 1.32 × 10−3 | 4.72 × 10−2 |
| (±3.5 × 10−3) | (±0.3 × 10−3) | (±1.5 × 10−2) | |
| Nonessential (n = 408) | 47.17 × 10−3 | 3.01 × 10−3 | 7.86 × 10−2 |
| (±1.9 × 10−3) | (±0.3 × 10−3) | (±0.7 × 10−2) | |
| Undetermined (n = 154) | 40.92 × 10−3 | 4.10 × 10−3 | 8.80 × 10−2 |
| (±2.1 × 10−3) | (±0.5 × 10−3) | (±0.9 × 10−2) | |
| Significance of the difference[iii] essential vs. nonessential | NS | P = 3.6 × 10−2 | NS |
| Significance of the difference[iii] essential vs. undetermined | NS | P = 2.0 × 10−4 | P = 3.7 × 10−4 |
| Significance of the difference[iii] nonessential vs. undetermined | NS | P = 2.8 × 10−3 | P = 3.2 × 10−4 |
| Metabolism | |||
| Essential (n = 34) | 37.18 × 10−3 | 1.09 × 10−3 | 3.19 × 10−2 |
| (±8.1 × 10−3) | (±0.3 × 10−3) | (±1.1 × 10−2) | |
| Nonessential (n = 725) | 54.76 × 10−3 | 2.52 × 10−3 | 5.92 × 10−2 |
| (±1.5 × 10−3) | (±0.1 × 10−3) | (±0.4 × 10−2) | |
| Undetermined (n = 241) | 59.32 × 10−3 | 4.50 × 10−3 | 9.80 × 10−2 |
| (±3.2 × 10−3) | (±0.3 × 10−3) | (±0.8 × 10−2) | |
| Significance of the difference[iii] essential vs. nonessential | P = 1.2 × 10−4 | P = 1.2 × 10−3 | P = 2.7 × 10−3 |
| Significance of the difference[iii] essential vs. undetermined | P = 8.2 × 10−5 | P = 4.9 × 10−8 | P = 1.7 × 10−6 |
| Significance of the difference[iii] nonessential vs. undetermined | NS | P = 3.6 × 10−13 | P = 8.2 × 10−11 |
| Poorly Characterized | |||
| Essential (n = 12) | 28.75 × 10−3 | 1.75 × 10−3 | 11.20 × 10−2 |
| (±6.0 × 10−3) | (±0.3 × 10−3) | (±4.2 × 10−2) | |
| Nonessential (n = 439) | 49.59 × 10−3 | 5.93 × 10−3 | 13.08 × 10−2 |
| (±2.1 × 10−3) | (±0.6 × 10−3) | (±0.9 × 10−2) | |
| Undetermined (n = 599) | 45.51 × 10−3 | 5.51 × 10−3 | 12.60 × 10−2 |
| (±1.7 × 10−3) | (±0.5 × 10−3) | (±0.8 × 10−2) | |
| Significance of the difference[iii] essential vs. nonessential | NS | NS | NS |
| Significance of the difference[iii] essential vs. undetermined | NS | NS | NS |
| Significance of the difference[iii] nonessential vs. undetermined | NS | NS | NS |
[i] The average synonymous substitution (nucleotide substitutions that do not change the encoded amino acid sequence) rate (Ks) for all orthologous genes within a given fitness class and species is shown with the standard error (in parentheses).
[ii] The average nonsynonymous substitution (nucleotide substitutions that change the encoded amino acid sequence) rate (Ka) for all orthologous genes within a given fitness class and species is shown with the standard error (in parentheses).
[iii] Statistical significance of the difference between the essential and nonessential classes for a given measurement as determined using the Mann-Whitney U test.