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OPENSEQ.org
GH
Genes: A B A+B
Length: 140 170 291
Sequences: 1248 472 399
Seq/Len: 8.91 2.78 1.37
MirrorTree (Pazo et al. 2001) 0.65
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 0.08 0.01 1.20
2 0.09 0.01 1.20
5 0.09 0.01 1.28
10 0.09 0.01 1.28
20 0.09 0.01 1.29
100 0.09 0.01 1.29
∞ 0.13 0.03 1.31
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
117_I 4_R 1.60 0.89 0.28
49_L 25_V 1.53 0.86 0.24
92_I 25_V 1.49 0.84 0.22
8_T 7_T 1.31 0.71 0.13
117_I 39_Q 1.27 0.68 0.12
93_R 56_L 1.25 0.66 0.11
81_P 144_F 1.23 0.64 0.10
33_N 13_L 1.22 0.63 0.10
12_I 11_M 1.20 0.61 0.09
38_D 59_G 1.20 0.61 0.09
49_L 12_M 1.17 0.59 0.09
10_L 23_G 1.15 0.57 0.08
49_L 3_Q 1.14 0.56 0.08
35_E 70_R 1.12 0.53 0.07
24_S 13_L 1.10 0.52 0.07
41_K 139_G 1.10 0.52 0.07
52_A 12_M 1.07 0.48 0.06
46_L 26_M 1.06 0.47 0.06
71_Q 164_P 1.05 0.47 0.06
83_A 154_I 1.04 0.46 0.05
54_D 17_L 1.04 0.45 0.05
19_L 16_L 1.03 0.45 0.05
4_Q 3_Q 1.02 0.44 0.05
35_E 42_A 1.02 0.43 0.05
19_L 103_R 1.01 0.43 0.05
55_M 13_L 1.00 0.41 0.05
42_V 64_A 0.98 0.40 0.04
25_L 48_L 0.97 0.39 0.04
102_S 57_Q 0.97 0.39 0.04
77_P 7_T 0.97 0.39 0.04
60_N 146_L 0.97 0.38 0.04
74_V 80_E 0.96 0.38 0.04
26_V 162_S 0.96 0.38 0.04
72_A 12_M 0.96 0.38 0.04
132_I 4_R 0.95 0.37 0.04
34_K 59_G 0.94 0.36 0.04
26_V 63_G 0.94 0.35 0.04
7_F 6_F 0.93 0.35 0.04
118_F 16_L 0.93 0.35 0.04
130_D 13_L 0.93 0.35 0.04
31_M 38_A 0.92 0.34 0.03
37_A 44_F 0.91 0.34 0.03
12_I 15_L 0.91 0.33 0.03
114_Q 32_S 0.91 0.33 0.03
24_S 105_A 0.90 0.32 0.03
50_E 133_V 0.90 0.32 0.03
65_T 116_H 0.90 0.32 0.03
93_R 137_P 0.90 0.32 0.03
102_S 53_Q 0.90 0.32 0.03
103_D 67_H 0.89 0.32 0.03
10_L 98_P 0.88 0.31 0.03
55_M 16_L 0.88 0.30 0.03
34_K 27_L 0.88 0.30 0.03
4_Q 164_P 0.88 0.30 0.03
132_I 112_G 0.87 0.30 0.03
49_L 29_F 0.87 0.30 0.03
119_S 45_E 0.87 0.30 0.03
42_V 104_I 0.87 0.29 0.03
113_G 20_V 0.86 0.29 0.03
87_P 100_R 0.86 0.29 0.03
65_T 16_L 0.86 0.29 0.03
91_Y 59_G 0.86 0.29 0.03
1_M 1_M 0.86 0.29 0.03
78_S 53_Q 0.86 0.29 0.03
84_R 138_G 0.85 0.28 0.03
42_V 54_R 0.85 0.28 0.03
46_L 79_R 0.85 0.28 0.03
40_Q 40_A 0.85 0.28 0.03
68_Q 63_G 0.85 0.28 0.03
89_G 103_R 0.84 0.28 0.03
74_V 22_A 0.84 0.28 0.03
61_S 46_A 0.84 0.27 0.03
21_V 159_R 0.84 0.27 0.02
63_Y 12_M 0.84 0.27 0.02
35_E 44_F 0.84 0.27 0.02
31_M 30_P 0.83 0.27 0.02
63_Y 62_F 0.83 0.27 0.02
125_V 2_R 0.83 0.26 0.02
94_R 12_M 0.83 0.26 0.02
137_I 127_P 0.83 0.26 0.02
87_P 28_A 0.83 0.26 0.02
119_S 52_Q 0.82 0.26 0.02
75_S 111_A 0.82 0.26 0.02
71_Q 154_I 0.82 0.26 0.02
30_L 138_G 0.82 0.25 0.02
58_L 55_G 0.82 0.25 0.02
133_G 138_G 0.81 0.25 0.02
101_G 43_R 0.81 0.25 0.02
29_N 73_F 0.81 0.25 0.02
5_R 66_V 0.81 0.25 0.02
118_F 21_S 0.81 0.25 0.02
49_L 21_S 0.81 0.25 0.02
132_I 146_L 0.81 0.25 0.02
8_T 158_A 0.80 0.24 0.02
119_S 109_S 0.80 0.24 0.02
23_A 7_T 0.80 0.24 0.02
33_N 9_L 0.80 0.24 0.02
44_S 49_R 0.80 0.24 0.02
16_I 39_Q 0.80 0.24 0.02
53_L 22_A 0.80 0.24 0.02
90_G 53_Q 0.80 0.24 0.02
26_V 71_W 0.79 0.24 0.02
58_L 41_L 0.79 0.24 0.02
112_H 137_P 0.79 0.23 0.02
10_L 13_L 0.79 0.23 0.02
43_V 146_L 0.79 0.23 0.02
125_V 119_F 0.79 0.23 0.02
114_Q 121_Q 0.79 0.23 0.02
12_I 73_F 0.79 0.23 0.02
67_E 136_F 0.79 0.23 0.02
23_A 124_A 0.79 0.23 0.02
29_N 46_A 0.78 0.23 0.02
12_I 151_G 0.78 0.23 0.02
17_V 146_L 0.78 0.23 0.02
52_A 114_T 0.78 0.23 0.02
57_K 121_Q 0.78 0.23 0.02
65_T 101_A 0.78 0.22 0.02
103_D 22_A 0.77 0.22 0.02
46_L 149_G 0.77 0.22 0.02
134_N 131_P 0.77 0.22 0.02
101_G 15_L 0.77 0.22 0.02
103_D 107_S 0.77 0.22 0.02
42_V 102_G 0.77 0.22 0.02
111_Q 136_F 0.76 0.22 0.02
12_I 75_V 0.76 0.22 0.02
54_D 103_R 0.76 0.22 0.02
57_K 38_A 0.76 0.21 0.02
13_M 6_F 0.76 0.21 0.02
119_S 12_M 0.76 0.21 0.02
51_G 162_S 0.76 0.21 0.02
30_L 155_A 0.76 0.21 0.02
22_L 59_G 0.76 0.21 0.02
29_N 62_F 0.76 0.21 0.02
132_I 104_I 0.76 0.21 0.02
106_L 95_R 0.76 0.21 0.02
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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