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Table 3 Data describing nucleotide substitution patterns within the conserved regions of the homing endonuclease domains of pairs of VMA inteins. Sd is the number of observed synonymous substitutions; Nd is the number of observed non-synonymous substitutions; S is the number of potential synonymous substitutions; N is the number of potential non-synonymous substitutions; pS is the proportion of observed synonymous substitutions; pN is the proportion of observed non-synonymous substitutions; dS is the Jukes-Cantor correction for multiple hits of pS; dN is the Jukes-Cantor correction for multiple hits of pN. EN describes the experimentally determined activity of the homing endonuclease [9], A= active, I= inactive. The activities of the endonucleases from C. glabrata and D. hansenii have not been determined, but are likely to be inactive. The species in which VMA inteins occur are labelled: Scerev, Saccharomyces cerevisiae; SspDH1A, a wild isolate of S. cerevisiae; Scarioc, S. cariocanus; Tglobosa, Torulaspora globosa; Zbailli, Zygosaccharomyces bailli; Tpret, T. pretoriensis; Zbisporus, Zygosaccharomyces bisporus; Zrouxii, Z. rouxii; Kpolysp, Kluyveromyces polysporus; Sunisp, S. (Kazachstania) unisporus; Sexiguus, S. (Kazachstania) exiguus; Ctropicalis, Candida tropicalis; Sdair, S. (Naumovia) dairenensis; Scastelli, S. (Naumovia) castellii; Cglabrata, C. glabrata; Klactis, K. lactis; Dhansenii, Debaryomyces hansenii. Inteins with active homing endonucleases are marked by asterisks*.

From: The distribution and evolutionary history of the PRP8 intein

  

Sd

Nd

S

N

pS

pN

dS

dN

dS/dN

EN

*Scerev

*SspDH1A

9.00

0.00

52.00

158.00

0.17

0.00

0.20

0.00

NA

AA

*Scerev

*Scarioc

13.00

4.00

52.33

157.67

0.25

0.03

0.30

0.03

11.69

AA

*Scerev

Tglobosa

31.88

36.12

52.50

157.50

0.61

0.23

1.24

0.27

4.54

AI

*Scerev

*Zbailli

31.50

34.50

51.50

158.50

0.61

0.22

1.27

0.26

4.93

AA

*Scerev

Tpret

34.62

41.38

52.83

157.17

0.66

0.26

1.55

0.32

4.79

AI

*Scerev

Zbisporus

27.00

38.00

49.33

151.67

0.55

0.25

0.98

0.30

3.22

AI

*Scerev

Zrouxii

22.38

41.62

48.50

152.50

0.46

0.27

0.72

0.34

2.11

AI

*Scerev

Kpolysp

30.88

57.12

48.00

162.00

0.64

0.35

1.46

0.48

3.07

AI

*Scerev

Sdair

34.75

61.25

51.50

158.50

0.67

0.39

1.72

0.54

3.18

AI

*Scerev

Sunisp

27.62

70.38

52.17

157.83

0.53

0.45

0.92

0.68

1.36

AI

*Scerev

Sexiguus

24.00

71.00

50.67

159.33

0.47

0.45

0.75

0.68

1.11

AI

*Scerev

Ctropicalis

28.75

70.25

52.17

157.83

0.55

0.45

1.00

0.68

1.47

AI

*Scerev

Scastelli

35.88

56.12

51.00

159.00

0.70

0.35

2.08

0.48

4.37

AI

*Scerev

Cglabrata

25.38

67.62

45.83

143.17

0.55

0.47

1.01

0.75

1.35

AI

*Scerev

Klactis

33.12

70.88

49.50

151.50

0.67

0.47

1.67

0.73

2.28

AI

*Scerev

Dhansenii

32.62

50.38

52.83

154.17

0.62

0.33

1.30

0.43

3.03

AI

*SspDH1A

*Scarioc

15.00

4.00

52.33

157.67

0.29

0.03

0.36

0.03

13.99

AA

*SspDH1A

Tglobosa

28.12

35.88

52.50

157.50

0.54

0.23

0.94

0.27

3.46

AI

*SspDH1A

*Zbailli

29.25

34.75

51.50

158.50

0.57

0.22

1.06

0.26

4.09

AA

*SspDH1A

Tpret

35.38

41.62

52.83

157.17

0.67

0.26

1.67

0.33

5.13

AI

*SspDH1A

Zbisporus

23.75

38.25

49.33

151.67

0.48

0.25

0.77

0.31

2.51

AI

*SspDH1A

Zrouxii

23.62

41.38

48.50

152.50

0.49

0.27

0.79

0.34

2.33

AI

*SspDH1A

Kpolysp

30.38

56.62

48.00

162.00

0.63

0.35

1.39

0.47

2.96

AI

*SspDH1A

Sdair

33.50

61.50

51.50

158.50

0.65

0.39

1.51

0.55

2.77

AI

*SspDH1A

Sunisp

26.88

71.12

52.17

157.83

0.52

0.45

0.87

0.69

1.26

AI

*SspDH1A

Sexiguus

23.75

71.25

50.67

159.33

0.47

0.45

0.74

0.68

1.08

AI

*SspDH1A

Ctropicalis

27.00

70.00

52.17

157.83

0.52

0.44

0.88

0.67

1.31

AI

*SspDH1A

Scastelli

34.62

56.38

51.00

159.00

0.68

0.35

1.77

0.48

3.68

AI

*SspDH1A

Cglabrata

27.12

67.88

45.83

143.17

0.59

0.47

1.17

0.75

1.56

AI

*SspDH1A

Klactis

33.88

71.12

49.50

151.50

0.68

0.47

1.83

0.74

2.48

AI

*SspDH1A

Dhansenii

32.62

50.38

52.83

154.17

0.62

0.33

1.30

0.43

3.03

AI

*Scarioc

Tglobosa

31.50

35.50

52.83

157.17

0.60

0.23

1.19

0.27

4.42

AI

*Scarioc

*Zbailli

32.88

33.12

51.83

158.17

0.63

0.21

1.40

0.25

5.71

AA

*Scarioc

Tpret

38.12

41.88

53.17

156.83

0.72

0.27

2.34

0.33

7.10

AI

*Scarioc

Zbisporus

27.50

37.50

49.33

151.67

0.56

0.25

1.02

0.30

3.40

AI

*Scarioc

Zrouxii

28.12

38.88

48.50

152.50

0.58

0.25

1.11

0.31

3.57

AI

*Scarioc

Kpolysp

27.88

59.12

48.33

161.67

0.58

0.37

1.10

0.50

2.19

AI

*Scarioc

Sdair

34.62

63.38

51.83

158.17

0.67

0.40

1.66

0.57

2.90

AI

*Scarioc

Sunisp

31.12

69.88

52.50

157.50

0.59

0.44

1.17

0.67

1.75

AI

*Scarioc

Sexiguus

25.75

72.25

51.00

159.00

0.50

0.45

0.84

0.70

1.20

AI

*Scarioc

Ctropicalis

27.38

68.62

52.50

157.50

0.52

0.44

0.89

0.65

1.37

AI

*Scarioc

Scastelli

38.88

57.12

51.33

158.67

0.76

0.36

NA

0.49

NA

AI

*Scarioc

Cglabrata

23.50

69.50

45.83

143.17

0.51

0.49

0.86

0.78

1.10

AI

*Scarioc

Klactis

35.12

72.88

49.50

151.50

0.71

0.48

2.19

0.77

2.85

AI

*Scarioc

Dhansenii

29.75

49.25

52.83

154.17

0.56

0.32

1.04

0.42

2.50

AI

Tglobosa

*Zbailli

24.50

13.50

52.00

158.00

0.47

0.09

0.74

0.09

8.18

IA

Tglobosa

Tpret

28.50

19.50

53.33

156.67

0.53

0.12

0.93

0.14

6.87

II

Tglobosa

Zbisporus

26.12

35.88

49.33

151.67

0.53

0.24

0.92

0.28

3.23

II

Tglobosa

Zrouxii

22.50

31.50

48.50

152.50

0.46

0.21

0.72

0.24

2.99

II

Tglobosa

Kpolysp

24.50

65.50

48.50

161.50

0.51

0.41

0.84

0.58

1.44

II

Tglobosa

Sdair

32.00

64.00

52.00

158.00

0.62

0.41

1.29

0.58

2.21

II

Tglobosa

Sunisp

29.50

65.50

52.67

157.33

0.56

0.42

1.03

0.61

1.70

II

Tglobosa

Sexiguus

28.12

73.88

51.17

158.83

0.55

0.47

0.99

0.73

1.36

II

Tglobosa

Ctropicalis

32.25

72.75

52.67

157.33

0.61

0.46

1.27

0.72

1.77

II

Tglobosa

Scastelli

35.50

52.50

51.50

158.50

0.69

0.33

1.89

0.44

4.31

II

Tglobosa

Cglabrata

26.00

82.00

45.50

143.50

0.57

0.57

1.08

1.08

1.00

II

Tglobosa

Klactis

33.75

73.25

49.50

151.50

0.68

0.48

1.80

0.78

2.32

II

Tglobosa

Dhansenii

31.25

55.75

53.00

154.00

0.59

0.36

1.16

0.49

2.34

II

*Zbailli

Tpret

32.75

21.25

52.33

157.67

0.63

0.13

1.35

0.15

9.08

AI

*Zbailli

Zbisporus

30.62

33.38

48.50

152.50

0.63

0.22

1.38

0.26

5.35

AI

*Zbailli

Zrouxii

31.75

31.25

47.67

153.33

0.67

0.20

1.64

0.24

6.91

AI

*Zbailli

Kpolysp

30.75

65.25

47.50

162.50

0.65

0.40

1.49

0.57

2.59

AI

*Zbailli

Sdair

31.62

63.38

51.00

159.00

0.62

0.40

1.31

0.57

2.31

AI

*Zbailli

Sunisp

30.38

68.62

51.67

158.33

0.59

0.43

1.15

0.65

1.78

AI

*Zbailli

Sexiguus

29.00

73.00

50.17

159.83

0.58

0.46

1.10

0.70

1.57

AI

*Zbailli

Ctropicalis

35.75

74.25

51.67

158.33

0.69

0.47

1.92

0.74

2.61

AI

*Zbailli

Scastelli

31.25

53.75

50.50

159.50

0.62

0.34

1.31

0.45

2.92

AI

*Zbailli

Cglabrata

21.62

76.38

44.67

144.33

0.48

0.53

0.78

0.92

0.85

AI

*Zbailli

Klactis

28.88

71.12

48.67

152.33

0.59

0.47

1.17

0.73

1.61

AI

*Zbailli

Dhansenii

34.75

59.25

52.00

155.00

0.67

0.38

1.66

0.53

3.11

AI

Tpret

Zbisporus

28.38

36.62

50.00

151.00

0.57

0.24

1.06

0.29

3.62

II

Tpret

Zrouxii

26.00

37.00

49.17

151.83

0.53

0.24

0.92

0.29

3.11

II

Tpret

Kpolysp

27.38

59.62

48.83

161.17

0.56

0.37

1.03

0.51

2.02

II

Tpret

Sdair

27.62

62.38

52.33

157.67

0.53

0.40

0.91

0.56

1.62

II

Tpret

Sunisp

27.62

71.38

53.00

157.00

0.52

0.45

0.89

0.70

1.27

II

Tpret

Sexiguus

32.00

71.00

51.50

158.50

0.62

0.45

1.32

0.68

1.94

II

Tpret

Ctropicalis

30.62

65.38

53.00

157.00

0.58

0.42

1.10

0.61

1.82

II

Tpret

Scastelli

29.00

55.00

51.83

158.17

0.56

0.35

1.03

0.47

2.20

II

Tpret

Cglabrata

29.88

80.12

46.50

142.50

0.64

0.56

1.46

1.04

1.40

II

Tpret

Klactis

38.38

77.62

50.17

150.83

0.76

0.51

NA

0.87

NA

II

Tpret

Dhansenii

34.25

57.75

53.33

153.67

0.64

0.38

1.45

0.52

2.79

II

Zbisporus

Zrouxii

18.12

25.88

47.83

153.17

0.38

0.17

0.53

0.19

2.76

II

Zbisporus

Kpolysp

27.38

55.62

45.67

155.33

0.60

0.36

1.20

0.49

2.47

II

Zbisporus

Sdair

29.25

59.75

48.67

152.33

0.60

0.39

1.21

0.56

2.18

II

Zbisporus

Sunisp

27.38

61.62

49.00

152.00

0.56

0.41

1.02

0.58

1.76

II

Zbisporus

Sexiguus

19.25

62.75

48.50

152.50

0.40

0.41

0.57

0.60

0.95

II

Zbisporus

Ctropicalis

26.75

66.25

49.33

151.67

0.54

0.44

0.96

0.65

1.47

II

Zbisporus

Scastelli

30.50

55.50

48.33

152.67

0.63

0.36

1.38

0.50

2.78

II

Zbisporus

Cglabrata

24.88

71.12

44.50

144.50

0.56

0.49

1.03

0.80

1.28

II

Zbisporus

Klactis

33.38

76.62

48.83

152.17

0.68

0.50

1.82

0.83

2.18

II

Zbisporus

Dhansenii

29.88

58.12

50.33

150.67

0.59

0.39

1.18

0.54

2.17

II

Zrouxii

Kpolysp

24.00

58.00

44.83

156.17

0.54

0.37

0.94

0.51

1.83

II

Zrouxii

Sdair

28.50

63.50

47.83

153.17

0.60

0.41

1.19

0.60

1.97

II

Zrouxii

Sunisp

27.88

68.12

48.17

152.83

0.58

0.45

1.11

0.68

1.64

II

Zrouxii

Sexiguus

24.50

64.50

47.67

153.33

0.51

0.42

0.87

0.62

1.40

II

Zrouxii

Ctropicalis

25.88

66.12

48.50

152.50

0.53

0.43

0.93

0.65

1.44

II

Zrouxii

Scastelli

24.50

56.50

47.50

153.50

0.52

0.37

0.87

0.51

1.72

II

Zrouxii

Cglabrata

29.38

79.62

44.33

144.67

0.66

0.55

1.61

0.99

1.62

II

Zrouxii

Klactis

31.38

76.62

48.00

153.00

0.65

0.50

1.54

0.83

1.86

II

Zrouxii

Dhansenii

29.75

55.25

49.50

151.50

0.60

0.36

1.21

0.50

2.43

II

Kpolysp

Sdair

19.25

69.75

48.33

164.67

0.40

0.42

0.57

0.62

0.91

II

Kpolysp

Sunisp

19.88

77.12

49.17

163.83

0.40

0.47

0.58

0.74

0.78

II

Kpolysp

Sexiguus

21.12

74.88

47.67

165.33

0.44

0.45

0.67

0.69

0.97

II

Kpolysp

Ctropicalis

20.25

78.75

49.00

164.00

0.41

0.48

0.60

0.77

0.78

II

Kpolysp

Scastelli

28.50

71.50

47.67

165.33

0.60

0.43

1.20

0.64

1.86

II

Kpolysp

Cglabrata

20.12

70.88

42.50

146.50

0.47

0.48

0.75

0.78

0.96

II

Kpolysp

Klactis

28.38

80.62

45.83

155.17

0.62

0.52

1.31

0.89

1.48

II

Kpolysp

Dhansenii

30.12

70.88

48.67

158.33

0.62

0.45

1.31

0.68

1.92

II

Sdair

Sunisp

19.25

48.75

53.50

165.50

0.36

0.29

0.49

0.37

1.31

II

Sdair

Sexiguus

21.62

59.38

52.00

167.00

0.42

0.36

0.61

0.48

1.26

II

Sdair

Ctropicalis

26.12

48.88

52.67

163.33

0.50

0.30

0.81

0.38

2.13

II

Sdair

Scastelli

30.38

25.62

51.00

162.00

0.60

0.16

1.19

0.18

6.67

II

Sdair

Cglabrata

23.75

76.25

44.67

144.33

0.53

0.53

0.93

0.91

1.01

II

Sdair

Klactis

29.25

75.75

48.83

152.17

0.60

0.50

1.20

0.82

1.47

II

Sdair

Dhansenii

30.38

55.62

52.00

155.00

0.58

0.36

1.13

0.49

2.32

II

Sunisp

Sexiguus

17.12

61.88

53.17

165.83

0.32

0.37

0.42

0.52

0.82

II

Sunisp

Ctropicalis

21.50

59.50

53.50

162.50

0.40

0.37

0.58

0.50

1.15

II

Sunisp

Scastelli

29.88

57.12

51.83

161.17

0.58

0.35

1.10

0.48

2.29

II

Sunisp

Cglabrata

23.00

65.00

45.00

144.00

0.51

0.45

0.86

0.69

1.24

II

Sunisp

Klactis

27.88

67.12

49.17

151.83

0.57

0.44

1.06

0.67

1.58

II

Sunisp

Dhansenii

28.50

69.50

52.67

154.33

0.54

0.45

0.96

0.69

1.39

II

Sexiguus

Ctropicalis

21.25

65.75

52.33

163.67

0.41

0.40

0.58

0.58

1.02

II

Sexiguus

Scastelli

35.00

55.00

50.33

162.67

0.70

0.34

1.96

0.45

4.37

II

Sexiguus

Cglabrata

17.88

73.12

44.83

144.17

0.40

0.51

0.57

0.85

0.67

II

Sexiguus

Klactis

29.12

81.88

48.67

152.33

0.60

0.54

1.20

0.95

1.27

II

Sexiguus

Dhansenii

25.50

65.50

51.50

155.50

0.50

0.42

0.81

0.62

1.31

II

Ctropicalis

Scastelli

36.25

55.75

51.67

161.33

0.70

0.35

2.06

0.46

4.44

II

Ctropicalis

Cglabrata

29.38

74.62

45.50

143.50

0.65

0.52

1.48

0.89

1.67

II

Ctropicalis

Klactis

32.25

78.75

49.50

151.50

0.65

0.52

1.52

0.89

1.72

II

Ctropicalis

Dhansenii

32.00

66.00

52.67

154.33

0.61

0.43

1.25

0.63

1.97

II

Scastelli

Cglabrata

27.88

83.12

44.83

144.17

0.62

0.58

1.32

1.10

1.21

II

Scastelli

Klactis

31.50

78.50

48.50

152.50

0.65

0.51

1.51

0.87

1.73

II

Scastelli

Dhansenii

33.38

53.62

51.83

155.17

0.64

0.35

1.47

0.46

3.17

II

Cglabrata

Klactis

26.38

61.62

44.83

144.17

0.59

0.43

1.15

0.63

1.82

II

Cglabrata

Dhansenii

22.75

81.25

46.50

142.50

0.49

0.57

0.79

1.07

0.74

II

Klactis

Dhansenii

34.12

71.88

50.50

150.50

0.68

0.48

1.73

0.76

2.28

II