Skip to main content

Table 6 Protein structure modelling of associated genes

From: Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes

Protein haplotypes

P-value

uGDT (GDT)

uSeqId (SeqId)

Score

Domain/motif

Literature

CBF-A3_1

3.03E−4

71 (62)

30 (26)

51

2gcc (AP2)

[28]

CBF-A3_2

1.52E−4

71 (61)

29 (25)

51

2gcc (AP2)

[28]

CBF-A5_1

3.22E−4

69 (67)

30 (29)

51

2gcc (AP2)

[28]

CBF-A5_2

5.75E−4

56 (54)

30 (29)

54

2gcc (AP2)

[28]

CBF-A5_3

9.71E−4

57 (56)

29 (28)

56

2gcc (AP2)

[28]

CBF-A10_1

2.78E−4

70 (66)

31 (29)

51

2gcc (AP2)

[28]

CBF-A10_2

2.88E−4

71 (67)

31 (29)

50

2gcc (AP2)

[28]

CBF-A13_1

4.79E−4

51 (38)

15 (11)

36

2gcc (AP2)

[28]

CBF-A13_2

n.a.

n.a.

n.a.

n.a.

n.a.

n.a.

CBF-A14_1

1.97E−4

71 (69)

29 (28)

52

2gcc (AP2)

[28]

CBF-A14_2

1.97E−4

71 (69)

29 (28)

52

2gcc (AP2)

[28]

CBF-A15_1

3.80E−4

70 (66)

29 (27)

50

2gcc (AP2)

[28]

CBF-A15_2

2.95E−4

70 (70)

29 (29)

49

2gcc (AP2)

[28]

CBF-A18_1

1.33E−3

55 (49)

29 (26)

52

2gcc (AP2)

[28]

CBF-A18_2

8.72E− 4

55 (49)

29 (26)

54

2gcc (AP2)

[28]

PPD-B1

1.24E− 4

105(62)

32(19)

130

3t6k (putative response regulator domain)

n.a.

 

8.74E−5

101(60)

27(16)

134

3jte (response regulator receiver domain)

[111]

PPD-B2

1.21E−4

104(61)

32(19)

129

3t6k (putative response regulator domain)

n.a.

 

8.12E−5

101(59)

27(16)

134

3jte (response regulator receiver domain)

[111]

PPD-B3

1.06E−4

103(60)

31(18)

129

3t6k (putative response regulator domain)

n.a.

 

7.21E−5

102(59)

27(16)

134

3jte (response regulator receiver domain)

[111]

PPD-B4

1.28E−4

104(61)

32(19)

130

3t6k (putative response regulator domain)

n.a.

 

8.98E−5

102(59)

27(16)

134

3jte (response regulator receiver domain)

[111]

PPD-D1_1

1.05E−4

104 (47)

32 (15)

131

3t6k (putative response regulator domain)

n.a.

 

7.11E−5

102 (46)

27 (12)

136

3jte (response regulator receiver domain)

[111]

PPD-D1_2

1.14E−4

105 (63)

32 (19)

130

3t6k (putative response regulator domain)

n.a.

PPD-D1_3

1.16E−4

104(62)

32 (19)

129

3t6k (putative response regulator domain)

n.a.

 

8.07E−5

101 (60)

27 (16)

134

3jte (response regulator receiver domain)

[111]

VRN-A1_1

8.02E− 3

84 (83)

39 (39)

84

4ox0 (K domain)

[110]

 

1.02E−4

78 (103)

38 (50)

53

3kov (MADS domain/I domain)

[112]

 

1.30E−4

75 (98)

38 (50)

52

1egw (MADS domain/I domain)

[113]

VRN-A1_2

8.47E−3

83 (82)

39 (39)

84

4ox0 (K domain)

[110]

 

7.90E−5

73 (103)

38 (50)

54

3kov (MADS domain/I domain)

[112]

 

9.11E−5

74 (98)

38 (50)

53

1egw (MADS domain/I domain)

[113]

VRN-A1_3

7.95E−3

84 (83)

38 (38)

84

4ox0 (K domain)

[110]

 

7.06E−5

78 (103)

38 (50)

54

3kov (MADS domain/I domain)

[112]

 

1.08E−4

75 (99)

38 (50)

53

1egw (MADS domain/I domain)

[113]

VRN-B3_1

7.92E-13

154 (87)

147 (83)

166

3axy (Hd3A protein)

[104]

VRN-B3_2

1.66E-12

154 (87)

148 (84)

168

3axy (Hd3A protein)

[104]

  1. P: probability, uGDT: unnormalized GDT (Global Distance Test) score, GDT: calculated as uGDT divided by the protein (or domain) length and multiplied by a 100, uSeqID: number of identical residues in the alignment, SeqID: uSeqID normalized by the protein (or domain) sequence length and multiplied by 100, n.a.: not available
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us