Table 2 The rates of synonymous (dS) and nonsynonymous (dN) nucleotide substitutions among different functional categories for A. pleuropneumoniae genes
From: Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae
COG categorya | Number of genes analyzed | dS (± se)b | dN (± se)c | r d |
|---|---|---|---|---|
Energy production and conversion | 114 | 44.2 × 10-3 (± 5.2 × 10-3) | 2.7 × 10-3 (± 0.5 × 10-3) | 0.78 |
Cell cycle control and cell division | 26 | 59.7 × 10-3 (± 13.0 × 10-3) | 3.3 × 10-3 (± 0.8 × 10-3) | 0.69 |
Amino acid transport and metabolism | 133 | 80.1 × 10-3 (± 6.6 × 10-3) | 4.1 × 10-3 (± 0.4 × 10-3) | 0.80 |
Nucleotide transport and metabolism | 52 | 53.7 × 10-3 (± 8.3 × 10-3) | 2.5 × 10-3 (± 0.4 × 10-3) | 0.67 |
Carbohydrate transport and metabolism | 109 | 56.8 × 10-3 (± 6.5 × 10-3) | 3.2 × 10-3 (± 0.6 × 10-3) | 0.73 |
Coenzyme transport and metabolism | 92 | 59.5 × 10-3 (± 7.7 × 10-3) | 4.7 × 10-3 (± 0.7 × 10-3) | 0.57 |
Lipid transport and metabolism | 32 | 61.4 × 10-3 (± 11.3 × 10-3) | 3.7 × 10-3 (± 0.9 × 10-3) | 0.75 |
Translation | 151 | 42.9 × 10-3 (± 4.5 × 10-3) | 2.1 × 10-3 (± 0.3 × 10-3) | 0.58 |
Transcription | 78 | 69.4 × 10-3 (± 11.8 × 10-3) | 3.8 × 10-3 (± 0.8 × 10-3) | 0.86 |
Replication, recombination and repair | 94 | 83.3 × 10-3 (± 11.8 × 10-3) | 6.2 × 10-3 (± 1.3 × 10-3) | 0.69 |
Cell membrane and envelope biogenesis | 120 | 63.3 × 10-3 (± 10.8 × 10-3) | 4.8 × 10-3 (± 0.8 × 10-3) | 0.85 |
Posttranslational modification, protein turnover, chaperones | 84 | 55.3 × 10-3 (± 7.2 × 10-3) | 3.6 × 10-3 (± 0.9 × 10-3) | 0.75 |
Inorganic ion transport and metabolism | 124 | 63.5 × 10-3 (± 6.1 × 10-3) | 3.9 × 10-3 (± 0.4 × 10-3) | 0.67 |
Secondary metabolites biosynthesis, transport and catabolism | 12 | 34.3 × 10-3 (± 11.4 × 10-3) | 2.7 × 10-3 (± 0.9 × 10-3) | 0.90 |
General function prediction only | 203 | 65.7 × 10-3 (± 6.1 × 10-3) | 4.6 × 10-3 (± 0.5 × 10-3) | 0.82 |
Function unknown | 177 | 73.6 × 10-3 (± 9.1 × 10-3) | 4.7 × 10-3 (± 0.6 × 10-3) | 0.86 |
Signal transduction mechanisms | 30 | 39.5 × 10-3 (± 8.6 × 10-3) | 2.0 × 10-3 (± 0.4 × 10-3) | 0.60 |
Intracellular trafficking, secretion and vesicular transport | 47 | 66.4 × 10-3 (± 16.5 × 10-3) | 7.0 × 10-3 (± 3.5 × 10-3) | 0.85 |
Defense mechanisms | 22 | 63.6 × 10-3 (± 20.1 × 10-3) | 3.9 × 10-3 (± 1.5 × 10-3) | 0.76 |
Not in COGs | 258 | 56.1 × 10-3 (± 5.9 × 10-3) | 6.6 × 10-3 (± 0.8 × 10-3) | 0.72 |