Table 2

The rates of synonymous (dS) and nonsynonymous (dN) nucleotide substitutions among different functional categories for A. pleuropneumoniae genes

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


a Two COG functional categories including one gene (i.e. "RNA processing and modification" and "Extracellular structures") are not showed.

b The average rate (dS) of synonymous substitutions (nucleotide mutations that do not alter the amino acid sequence) for all orthologous genes within a give COG role category is displayed, followed by the standard error that is represented in parentheses.

c The average rate (dN) of nonsynonymous substitutions (nucleotide mutations that alter the amino acid sequence) for all orthologous genes within a give COG role category is displayed, followed by the standard error that is represented in parentheses.

d Correlation coefficient between the values of dS and dN.

Xu et al. BMC Evolutionary Biology 2011 11:203   doi:10.1186/1471-2148-11-203

Open Data