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OPENSEQ.org
2WDQ_C_D
Genes: A B A+B
Length: 129 115 239
Sequences: 1314 821 788
Seq/Len: 10.19 7.14 3.3
MirrorTree (Pazo et al. 2001) 0.85
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 3.24
2 0.01 0.00 3.23
5 0.01 0.00 3.23
10 0.01 0.00 3.23
20 0.01 0.00 3.23
100 0.02 0.00 3.23
∞ 0.02 0.01 3.23
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
35_V 79_V 4.28 1.00 1.00
51_S 48_W 2.10 1.00 0.99
88_G 75_G 1.96 1.00 0.98
85_V 27_T 1.86 0.99 0.97
85_V 26_L 1.79 0.99 0.97
45_L 111_V 1.59 0.98 0.93
84_H 75_G 1.52 0.97 0.91
51_S 45_Y 1.50 0.96 0.91
34_G 75_G 1.42 0.95 0.88
38_F 97_I 1.38 0.94 0.85
92_M 26_L 1.33 0.92 0.83
49_G 107_Y 1.29 0.90 0.80
30_H 20_R 1.26 0.89 0.78
51_S 114_G 1.25 0.88 0.77
92_M 23_A 1.22 0.87 0.75
113_S 16_F 1.20 0.85 0.73
98_Y 60_F 1.15 0.82 0.68
84_H 71_H 1.15 0.81 0.68
118_V 11_N 1.14 0.81 0.68
45_L 108_G 1.14 0.81 0.68
56_E 46_E 1.14 0.81 0.68
91_H 74_I 1.13 0.80 0.66
44_L 109_F 1.09 0.76 0.62
58_F 48_W 1.04 0.71 0.56
88_G 71_H 1.03 0.71 0.56
106_G 65_L 1.02 0.70 0.54
34_G 71_H 1.01 0.68 0.53
21_P 26_L 0.94 0.61 0.45
55_P 56_F 0.94 0.60 0.44
111_K 68_I 0.93 0.59 0.43
95_D 20_R 0.92 0.58 0.42
62_S 62_L 0.92 0.58 0.42
110_A 58_K 0.90 0.56 0.40
38_F 72_A 0.89 0.55 0.39
103_F 16_F 0.89 0.54 0.38
54_S 45_Y 0.88 0.53 0.37
88_G 23_A 0.88 0.53 0.37
84_H 23_A 0.87 0.52 0.36
46_W 106_I 0.87 0.52 0.36
41_V 68_I 0.87 0.52 0.36
58_F 33_M 0.86 0.51 0.35
88_G 20_R 0.86 0.50 0.35
108_R 106_I 0.85 0.50 0.34
24_A 97_I 0.85 0.50 0.34
23_T 30_I 0.84 0.48 0.32
68_F 41_G 0.84 0.48 0.32
41_V 69_L 0.84 0.48 0.32
112_I 84_V 0.84 0.47 0.32
30_H 19_V 0.83 0.46 0.31
55_P 45_Y 0.83 0.46 0.31
52_L 48_W 0.82 0.46 0.30
36_I 99_V 0.82 0.45 0.30
89_I 27_T 0.82 0.45 0.30
19_R 98_V 0.81 0.45 0.29
38_F 76_M 0.81 0.44 0.29
122_L 107_Y 0.81 0.44 0.29
41_V 105_V 0.81 0.44 0.29
75_W 59_V 0.81 0.44 0.28
105_A 106_I 0.80 0.43 0.28
92_M 75_G 0.79 0.42 0.27
119_V 42_E 0.79 0.42 0.27
83_Y 26_L 0.79 0.41 0.27
82_A 34_V 0.79 0.41 0.27
63_A 24_I 0.79 0.41 0.26
123_L 46_E 0.79 0.41 0.26
61_A 22_T 0.78 0.41 0.26
101_E 78_Q 0.78 0.40 0.26
34_G 23_A 0.78 0.40 0.26
12_N 81_T 0.77 0.39 0.25
109_S 90_R 0.77 0.39 0.24
128_V 115_V 0.77 0.39 0.24
119_V 17_I 0.76 0.38 0.24
102_T 66_F 0.76 0.38 0.23
115_V 63_L 0.76 0.38 0.23
29_L 93_L 0.76 0.37 0.23
24_A 72_A 0.75 0.37 0.23
12_N 77_W 0.75 0.37 0.23
124_A 27_T 0.75 0.37 0.23
81_L 30_I 0.75 0.37 0.23
20_F 9_G 0.75 0.36 0.22
115_V 18_L 0.75 0.36 0.22
39_V 103_V 0.75 0.36 0.22
112_I 66_F 0.74 0.36 0.22
81_L 6_S 0.74 0.36 0.22
103_F 51_F 0.74 0.35 0.21
16_Q 96_V 0.74 0.35 0.21
110_A 69_L 0.74 0.35 0.21
48_L 29_Y 0.73 0.35 0.21
109_S 101_L 0.73 0.35 0.21
103_F 72_A 0.73 0.35 0.21
38_F 73_W 0.73 0.34 0.21
58_F 35_G 0.73 0.34 0.20
72_F 92_M 0.72 0.33 0.20
73_I 92_M 0.71 0.33 0.19
19_R 76_M 0.71 0.33 0.19
43_I 112_V 0.71 0.32 0.19
77_I 16_F 0.71 0.32 0.18
47_L 111_V 0.71 0.32 0.18
95_D 71_H 0.70 0.32 0.18
45_L 104_Y 0.70 0.31 0.18
16_Q 85_K 0.70 0.31 0.18
24_A 78_Q 0.69 0.30 0.17
36_I 68_I 0.69 0.30 0.17
122_L 33_M 0.69 0.30 0.17
24_A 26_L 0.69 0.30 0.17
23_T 70_I 0.69 0.29 0.17
115_V 22_T 0.68 0.29 0.17
20_F 96_V 0.68 0.29 0.16
61_A 70_I 0.68 0.29 0.16
78_L 114_G 0.68 0.29 0.16
59_E 66_F 0.68 0.29 0.16
48_L 67_S 0.68 0.29 0.16
93_M 45_Y 0.68 0.29 0.16
116_I 110_V 0.68 0.28 0.16
68_F 67_S 0.67 0.28 0.16
20_F 78_Q 0.67 0.28 0.16
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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