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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