Table 3

Genes that show evidence for positive Darwinian selection

Name (Systematic)

Cluster ID a

COG b

Putative function of coding products

2Δℓc

Q-value

p d

ωe

Positively selected sites f


napA

APO_0068

C

Periplasmic nitrate reductase

10.03

0.189

0.000

1.02

glpA

APO_0197

C

Anaerobic glycerol-3-phosphate dehydrogenase subunit A

12.26

0.096

0.009

11.45

fumC

APO_0306

C

Fumarate hydratase

15.63

0.032

0.004

99.56

prlC

APO_0109

E

Oligopeptidase A

14.72

0.042

0.000

607.84

argH

APO_0322

E

Argininosuccinate lyase

13.10

0.071

0.014

10.79

423

gntT

APO_0415

E

Transporter, gluconate/H+ symporter (GntP) family

11.74

0.106

0.008

13.97

190, 193

proA

APO_0424

E

Gamma-glutamyl phosphate reductase

10.02

0.189

0.051

3.29

artP

APO_0998

E

Arginine transport ATP-binding protein

14.75

0.042

0.004

521.75

225

leuD

APO_1132

E

3-isopropylmalate dehydratase small subunit

11.14

0.135

0.032

57.70

cpdB

APO_0120

F

2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase

19.13

0.010

0.032

3.82

9, 99, 554

purD

APO_0394

F

Phosphoribosylamine--glycine ligase

13.44

0.062

0.061

34.74

glgP

APO_00f74

G

Maltodextrin phosphorylase

14.13

0.054

0.019

9.66

13, 27, 392

kdgK

APO_0752

G

2-dehydro-3-deoxygluconokinase

9.98

0.190

0.042

8.28

hemN

APO_0325

H

Oxygen-independent coproporphyrinogen-III oxidase

21.87

0.005

0.015

27.37

38, 136, 428

lipB

APO_1067

H

Octanoyltransferase

10.14

0.189

0.000

1.00

valS

APO_0044

J

Valyl-tRNA synthetase

22.18

0.005

0.016

3.82

47, 792

rumA

APO_0356

J

23S rRNA (uracil-5-)-methyltransferase

26.17

0.002

0.003

47.26

20

trmA2

APO_0540

J

tRNA (uracil-5-)-methyltransferase

10.70

0.160

0.028

4.08

24, 210

yhgF

APO_0081

K

Transcriptional accessory protein

18.60

0.010

0.024

3.78

10, 142

lysR

APO_0797

K

Transcriptional regulatory protein

18.79

0.010

0.012

10.60

284, 287, 292

parC

APO_0090

L

DNA topoisomerase 4 subunit A

13.47

0.062

0.003

10.50

357

mutM

APO_0873

L

Heptosyltransferase family

12.15

0.096

0.077

14.90

270

tatD

APO_0977

L

Deoxyribonuclease

13.73

0.059

0.198

2.42

188, 204, 234

hcsA

APO_0102

M

Capsule polysaccharide modification protein

10.07

0.189

0.027

3.16

483

hcsB

APO_0367

M

Capsule polysaccharide modification protein

18.72

0.010

0.034

18.52

13, 136, 366

ompP2B

APO_0561

M

Outer membrane protein P2-like protein

16.15

0.026

0.095

8.07

306, 317, 320

mscL

APO_1465

M

Large-conductance mechanosensitive channel

12.17

0.096

0.044

103.40

97

ptrA

APO_0039

O

Protease III

17.69

0.013

0.049

6.26

43, 44, 50, 91, 617, 909

glnD

APO_0064

O

uridylyltransferase

17.93

0.013

0.024

12.23

17, 190, 514, 551

sppA

APO_0149

O

Protease 4

10.42

0.173

0.030

9.37

lonH

APO_0207

O

Lon protease

15.24

0.035

0.013

106.47

19

nrfG

APO_0983

O

Formate-dependent nitrite reductase complex subunit

12.29

0.096

0.084

27.77

tehA

APO_0711

P

Tellurite resistance protein

11.70

0.106

0.007

70.81

252

cysW

APO_0883

P

Sulfate transport system permease protein

13.80

0.059

0.074

3.68

145

-

APO_0030

R

Helicase

12.14

0.096

0.051

2.56

pqiB

APO_0055

R

Paraquat-inducible protein B

20.31

0.008

0.046

3.62

259, 318, 384

tldD

APO_0268

R

Protease

10.16

0.189

0.009

15.91

377, 379

-

APO_0269

R

Hypothetical protein

10.02

0.189

0.000

1.00

463

pcaK

APO_0359

R

Major facilitator transporter

12.09

0.096

0.022

5.96

195, 238, 416, 417

thiH

APO_0509

R

Thiazole biosynthesis protein

18.32

0.011

0.012

12.98

15, 55

murQ

APO_0754

R

N-acetylmuramic acid 6-phosphate etherase

17.69

0.013

0.059

4.05

54, 99, 293

-

APO_0792

R

Nucleoside-diphosphate sugar epimerase

11.92

0.102

0.060

9.71

rssA

APO_0839

R

Patatin

11.22

0.132

0.019

41.55

225

cof

APO_0888

R

Hydrolases of the HAD superfamily

10.62

0.160

0.000

25.15

smtA

APO_0969

R

Methyltransferase

10.66

0.160

0.045

101.87

134, 204

aphA

APO_1107

R

Membrane protein affecting hemolysin expression

10.83

0.153

0.012

24.96

46

recX

APO_1397

R

Regulatory protein

19.96

0.008

0.008

37.09

47

ytfN

APO_0025

S

Hypothetical protein

14.07

0.054

0.002

239.60

553

-

APO_0098

S

Oligopeptide transporter

20.79

0.007

0.012

15.91

82, 127, 546

glnE

APO_0041

T

Glutamate-ammonia-ligase adenylyltransferase

11.88

0.102

0.023

3.60

53

typA

APO_0150

T

GTP-binding protein

33.59

0.000

0.006

15.43

395, 567, 569

apaA

APO_0772

T

ABC transporter, periplasmic binding protein

13.49

0.062

0.031

7.10

103, 147

-

APO_0051

-

Hypothetical protein

19.00

0.010

0.088

5.16

105

guaB

APO_0259

-

Inosine-5'-monophosphate dehydrogenase

15.25

0.035

0.013

4.98

448

-

APO_0393

-

Hypothetical protein

24.92

0.002

0.027

57.62

97, 104, 134, 355

-

APO_0571

-

Hypothetical protein

12.27

0.096

0.020

28.21

199, 275, 283

wecF

APO_0577

-

TDP-Fuc4NAc:lipid II Fuc4NAc transferase

22.68

0.005

0.035

14.23

70, 92, 182, 183, 289


a Protein designations were taken from the A. pleuropneumoniae ortholog annotation that was summarized in our recent publication [19].

b The abbreviations of COG function categories were assigned based on Figure 1.

c 2Δℓ denote the statistic of likelihood ratio test.

d The proportion of the amino acid sites under positive selection.

e ω is equal to the ratio of dN to dS (Number of nonsynonymous changes per nonsynonymous sites/Number of synonymous changes per synonymous site) for amino acid sites under positive selection (model M2a).

f Positively selected sites identified with posterior probability P > 95%.

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

Open Data