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Table 2 Results of lineage-specific positive selection analysis of the slpA gene

From: Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response

Branch

Model

P

lnL

Estimation of parameters

PS Sites

1

A

3

−16283.290

p0 = 0.612 p1 = 0.379

p2 = 0.004 p3 = 0.002

Background:

ω0 = 0.081 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.081 ω1 = 1.000 ω2 = 999.0

BEB

3 > 0.99

2

A

3

−16287.406

p0 = 0.613 p1 = 0.379

p2 = 0.004 p3 = 0.002

Background:

ω0 = 0.081 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.081 ω1 = 1.000 ω2 = 999.0

BEB

3 > 0.99

3

A

3

−16273.156

p0 = 0.546 p1 = 0.325

p2 = 0.080 p3 = 0.047

Background:

ω0 = 0.077 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.078 ω1 = 1.000 ω2 = 305.086

BEB

52 > 0.50

11 > 0.95

1 > 0.99

4

A

3

−16254.536

p0 = 0.534 p1 = 0.326

p2 = 0.086 p3 = 0.052

Background:

ω0 = 0.076 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.078 ω1 = 1.000 ω2 = 49.513

BEB

51 > 0.50

21 > 0.95

8 > 0.99

7

A

3

−16267.493

p0 = 0.577 p1 = 0.364

p2 = 0.035 p3 = 0.022

Background:

ω0 = 0.082 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.082 ω1 = 1.000 ω2 = 999.000

BEB

15 > 0.50

8

A

3

−16286.517

p0 = 0.599 p1 = 0.369

p2 = 0.019 p3 = 0.012

Background:

ω0 = 0.080 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.080 ω1 = 1.000 ω2 = 65.618

BEB

9 > 0.50

1 > 0.95

9

A

3

−16280.189

p0 = 0.585 p1 = 0.366

p2 = 0.029 p3 = 0.018

Background:

ω0 = 0.080 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.081 ω1 = 1.000 ω2 = 998.998

BEB

11 > 0.50

1 > 0.95

11

A

3

−16289.170

p0 = 0.593 p1 = 0.372

p2 = 0.020 p3 = 0.013

Background:

ω0 = 0.082 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.081 ω1 = 1.000 ω2 = 998.975

BEB

3 > 0.50

12

A

3

−16288.187

p0 = 0.604 p1 = 0.367

p2 = 0.017 p3 = 0.010

Background:

ω0 = 0.080 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.080 ω1 = 1.000 ω2 = 998.952

BEB

6 > 0.50

1 > 0.95

13

A

3

−16280.744

p0 = 0.601 p1 = 0.341

p2 = 0.036 p3 = 0.020

Background:

ω0 = 0.079 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.079 ω1 = 1.000 ω2 = 32.021

BEB

18 > 0.50

1 > 0.99

14

A

3

−16287.185

p0 = 0.606 p1 = 0.376

p2 = 0.010 p3 = 0.006

Background:

ω0 = 0.079 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.081 ω1 = 1.000 ω2 = 67.858

BEB

3 > 0.50

2 > 0.95

15

A

3

−16278.296

p0 = 0.598 p1 = 0.354

p2 = 0.029 p3 = 0.017

Background:

ω0 = 0.077 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.078 ω1 = 1.000 ω2 = 8.993

BEB

12 > 0.50

4 > 0.95

1 > 0.99

18

A

3

−16277.205

p0 = 0.560 p1 = 0.337

p2 = 0.063 p3 = 0.038

Background:

ω0 = 0.078 ω1 = 1.000 ω2 = 1.000

Foreground:

ω0 = 0.077 ω1 = 1.000 ω2 = 94.127

BEB

45 > 0.50

7 > 0.95

2 > 0.99

  1. The table shown the number of residues predicted to be under positive selection for each site-specific model in the analyses. All models tested are displayed, along with number of parameters (P), log likelihood scores (L), estimates of parameters (where p = proportion of sites under a particular omega value, and ω = the ratio of non-synonymous substitution per non-synonymous site to synonymous substitution per synonymous site (DN/DS). The number of positively selected sites with a given posterior probability is also given