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OPENSEQ.org
2wDQ_CD
Genes: A B A+B
Length: 121 105 225
Sequences: 1325 819 794
Seq/Len: 10.95 7.8 3.53
MirrorTree (Pazo et al. 2001) 0.84
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.00 3.53
2 0.01 0.00 3.51
5 0.01 0.00 3.51
10 0.01 0.00 3.51
20 0.01 0.00 3.51
100 0.01 0.00 3.51
∞ 0.02 0.01 3.51
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
28_V 69_V 4.23 1.00 1.00
44_S 38_W 2.05 1.00 0.99
81_G 65_G 1.93 1.00 0.98
78_V 17_T 1.79 0.99 0.97
78_V 16_L 1.68 0.99 0.95
38_L 101_V 1.58 0.98 0.93
77_H 65_G 1.51 0.97 0.92
85_M 16_L 1.45 0.96 0.89
44_S 35_Y 1.45 0.96 0.89
85_M 13_A 1.37 0.94 0.86
27_G 65_G 1.37 0.94 0.86
42_G 97_Y 1.35 0.93 0.85
31_F 87_I 1.34 0.93 0.84
91_Y 50_F 1.22 0.88 0.76
44_S 104_G 1.21 0.87 0.75
77_H 61_H 1.16 0.84 0.70
23_H 10_R 1.15 0.83 0.70
49_E 36_E 1.11 0.80 0.66
38_L 98_G 1.11 0.80 0.66
106_S 6_F 1.09 0.79 0.64
84_H 64_I 1.05 0.75 0.60
111_V 1_N 1.04 0.73 0.58
48_P 46_F 1.01 0.71 0.55
81_G 61_H 0.98 0.67 0.51
51_F 38_W 0.98 0.67 0.51
27_G 61_H 0.96 0.66 0.49
55_S 52_L 0.95 0.64 0.48
37_L 99_F 0.95 0.64 0.47
99_G 55_L 0.94 0.62 0.45
51_F 23_M 0.93 0.62 0.45
41_L 19_Y 0.91 0.59 0.42
88_D 10_R 0.90 0.57 0.41
104_K 58_I 0.89 0.57 0.40
101_R 96_I 0.89 0.57 0.40
103_A 59_L 0.88 0.56 0.39
31_F 62_A 0.88 0.55 0.39
77_H 13_A 0.88 0.55 0.38
117_A 17_T 0.88 0.55 0.38
81_G 13_A 0.87 0.53 0.37
96_F 6_F 0.86 0.53 0.36
39_W 96_I 0.86 0.53 0.36
94_E 68_Q 0.86 0.53 0.36
16_T 20_I 0.86 0.52 0.36
14_P 16_L 0.85 0.51 0.35
75_A 24_V 0.85 0.51 0.34
5_N 71_T 0.84 0.50 0.34
17_A 87_I 0.84 0.49 0.33
23_H 9_V 0.84 0.49 0.33
61_F 31_G 0.83 0.49 0.33
98_A 96_I 0.83 0.49 0.33
103_A 48_K 0.83 0.48 0.32
81_G 10_R 0.82 0.48 0.32
82_I 17_T 0.82 0.48 0.32
5_N 67_W 0.82 0.47 0.32
34_V 95_V 0.82 0.47 0.31
45_L 38_W 0.82 0.47 0.31
31_F 66_M 0.82 0.47 0.31
115_L 97_Y 0.82 0.47 0.31
34_V 59_L 0.82 0.47 0.31
34_V 58_I 0.81 0.47 0.31
12_R 88_V 0.79 0.44 0.28
47_S 35_Y 0.79 0.44 0.28
85_M 65_G 0.79 0.43 0.28
74_L 20_I 0.79 0.43 0.28
109_I 29_T 0.78 0.42 0.27
112_V 7_I 0.78 0.42 0.27
29_I 58_I 0.77 0.41 0.26
48_P 35_Y 0.77 0.41 0.26
9_Q 86_V 0.77 0.41 0.26
97_E 102_V 0.77 0.41 0.26
76_Y 16_L 0.77 0.40 0.25
102_S 80_R 0.76 0.40 0.25
17_A 68_Q 0.76 0.40 0.25
29_I 89_V 0.76 0.39 0.24
68_W 49_V 0.76 0.39 0.24
49_E 53_L 0.75 0.38 0.23
116_L 36_E 0.74 0.38 0.23
13_F 68_Q 0.74 0.38 0.23
114_S 60_I 0.74 0.38 0.23
56_A 14_I 0.74 0.37 0.23
12_R 66_M 0.74 0.37 0.23
110_T 66_M 0.73 0.36 0.22
115_L 40_G 0.73 0.36 0.22
27_G 13_A 0.73 0.36 0.22
108_V 12_T 0.73 0.36 0.21
49_E 74_V 0.73 0.35 0.21
54_A 60_I 0.72 0.35 0.21
58_M 78_A 0.72 0.35 0.21
105_I 56_F 0.72 0.35 0.21
102_S 91_L 0.72 0.35 0.21
12_R 30_S 0.72 0.35 0.21
51_F 25_G 0.72 0.34 0.20
71_L 104_G 0.71 0.34 0.20
40_L 101_V 0.71 0.34 0.20
70_I 6_F 0.71 0.34 0.20
76_Y 55_L 0.71 0.34 0.20
65_F 82_M 0.71 0.33 0.20
96_F 62_A 0.71 0.33 0.20
121_V 105_V 0.71 0.33 0.19
87_M 18_L 0.70 0.33 0.19
32_V 93_V 0.70 0.33 0.19
31_F 63_W 0.70 0.33 0.19
38_L 94_Y 0.70 0.33 0.19
41_L 57_S 0.70 0.33 0.19
82_I 36_E 0.69 0.32 0.18
80_V 22_Y 0.69 0.31 0.18
17_A 16_L 0.69 0.31 0.18
109_I 100_V 0.69 0.31 0.18
1_Q 105_V 0.69 0.31 0.18
96_F 41_F 0.68 0.31 0.17
17_A 62_A 0.68 0.30 0.17
110_T 9_V 0.68 0.30 0.17
105_I 35_Y 0.68 0.30 0.17
72_T 67_W 0.68 0.30 0.17
41_L 51_T 0.68 0.30 0.17
115_L 35_Y 0.68 0.30 0.17
73_A 102_V 0.68 0.30 0.17
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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