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OPENSEQ.org
3sfs_J_C
Genes: A B A+B
Length: 103 233 314
Sequences: 1166 2210 958
Seq/Len: 11.32 9.48 3.05
MirrorTree (Pazo et al. 2001) 0.82
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 0.09 0.09 0.00
2 0.09 0.09 0.02
5 0.09 0.09 0.10
10 0.09 0.09 2.80
20 0.09 0.09 2.85
100 0.09 0.09 3.04
∞ 0.09 0.09 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
26_V 66_V 1.43 0.94 0.61
69_T 23_F 1.33 0.91 0.52
67_I 29_F 1.26 0.87 0.45
69_T 24_A 1.25 0.86 0.44
24_E 80_K 1.22 0.85 0.41
36_V 129_M 1.16 0.81 0.36
76_I 72_R 1.16 0.80 0.35
4_Q 112_D 1.13 0.78 0.33
27_E 153_V 1.13 0.78 0.33
63_D 129_M 1.12 0.77 0.32
65_Y 35_S 1.10 0.75 0.30
33_G 77_I 1.10 0.75 0.30
46_K 75_I 1.08 0.73 0.28
18_I 126_R 1.07 0.73 0.28
54_S 172_R 1.05 0.70 0.26
29_A 126_R 1.04 0.70 0.26
79_P 17_P 1.04 0.70 0.26
14_D 187_S 1.04 0.69 0.25
98_V 80_K 1.03 0.69 0.25
56_H 149_I 1.01 0.66 0.23
88_M 149_I 1.00 0.65 0.23
9_R 139_Q 1.00 0.65 0.22
14_D 20_S 0.99 0.64 0.22
18_I 98_P 0.97 0.62 0.20
94_A 82_E 0.97 0.62 0.20
13_F 33_L 0.97 0.61 0.20
91_D 161_E 0.96 0.60 0.20
86_A 77_I 0.95 0.60 0.19
98_V 108_K 0.95 0.59 0.19
18_I 129_M 0.94 0.58 0.18
58_N 172_R 0.94 0.58 0.18
55_P 172_R 0.92 0.56 0.17
31_R 108_K 0.87 0.50 0.14
36_V 186_T 0.87 0.49 0.14
91_D 60_P 0.87 0.49 0.14
78_E 6_H 0.86 0.48 0.14
91_D 83_D 0.86 0.48 0.14
57_V 147_K 0.86 0.48 0.13
61_A 129_M 0.86 0.48 0.13
18_I 15_V 0.86 0.48 0.13
73_L 6_H 0.84 0.46 0.13
60_D 169_R 0.84 0.46 0.12
12_A 202_I 0.84 0.46 0.12
67_I 141_A 0.84 0.45 0.12
9_R 209_G 0.84 0.45 0.12
46_K 17_P 0.84 0.45 0.12
8_I 79_K 0.83 0.45 0.12
98_V 172_R 0.82 0.44 0.12
101_S 198_V 0.82 0.44 0.12
65_Y 129_M 0.82 0.43 0.12
99_Q 87_L 0.82 0.43 0.11
81_E 104_A 0.82 0.43 0.11
27_E 140_N 0.81 0.43 0.11
58_N 192_T 0.81 0.42 0.11
47_E 29_F 0.81 0.42 0.11
81_E 158_G 0.81 0.42 0.11
22_T 101_I 0.81 0.42 0.11
19_D 58_E 0.80 0.41 0.11
94_A 19_N 0.80 0.41 0.11
81_E 33_L 0.80 0.41 0.11
94_A 185_N 0.80 0.41 0.11
13_F 162_I 0.80 0.41 0.10
51_V 29_F 0.80 0.41 0.10
48_R 140_N 0.80 0.41 0.10
51_V 12_L 0.80 0.41 0.10
98_V 209_G 0.80 0.41 0.10
33_G 116_V 0.80 0.40 0.10
69_T 131_R 0.79 0.40 0.10
17_L 153_V 0.79 0.40 0.10
56_H 193_Y 0.79 0.40 0.10
11_K 42_Y 0.79 0.39 0.10
22_T 128_V 0.79 0.39 0.10
60_D 140_N 0.78 0.39 0.10
91_D 61_A 0.78 0.39 0.10
58_N 161_E 0.78 0.38 0.10
65_Y 10_I 0.78 0.38 0.10
16_R 37_F 0.77 0.38 0.09
86_A 52_V 0.77 0.38 0.09
33_G 123_Q 0.77 0.37 0.09
56_H 3_Q 0.77 0.37 0.09
21_A 72_R 0.77 0.37 0.09
63_D 9_G 0.77 0.37 0.09
50_T 6_H 0.77 0.37 0.09
13_F 25_N 0.77 0.37 0.09
61_A 178_L 0.77 0.37 0.09
5_R 196_I 0.76 0.36 0.09
60_D 182_I 0.76 0.36 0.09
48_R 136_R 0.76 0.35 0.09
63_D 104_A 0.75 0.35 0.09
56_H 130_F 0.75 0.35 0.09
37_R 136_R 0.75 0.35 0.09
22_T 119_S 0.75 0.35 0.08
40_I 5_V 0.75 0.35 0.08
3_N 66_V 0.75 0.34 0.08
98_V 140_N 0.75 0.34 0.08
11_K 168_Y 0.74 0.34 0.08
25_I 182_I 0.74 0.34 0.08
49_F 12_L 0.74 0.34 0.08
57_V 103_I 0.74 0.34 0.08
82_K 15_V 0.74 0.34 0.08
98_V 72_R 0.74 0.33 0.08
82_K 152_E 0.74 0.33 0.08
22_T 15_V 0.74 0.33 0.08
55_P 67_T 0.74 0.33 0.08
26_V 192_T 0.73 0.33 0.08
24_E 108_K 0.73 0.33 0.08
14_D 75_I 0.72 0.32 0.07
23_A 80_K 0.72 0.32 0.07
71_L 116_V 0.72 0.32 0.07
51_V 106_V 0.72 0.32 0.07
74_V 158_G 0.72 0.32 0.07
73_L 137_A 0.72 0.32 0.07
58_N 190_H 0.72 0.32 0.07
74_V 203_F 0.72 0.31 0.07
49_F 176_H 0.72 0.31 0.07
90_L 142_M 0.72 0.31 0.07
84_V 102_N 0.72 0.31 0.07
94_A 118_D 0.72 0.31 0.07
17_L 154_S 0.71 0.31 0.07
69_T 188_E 0.71 0.30 0.07
84_V 54_R 0.71 0.30 0.07
16_R 76_V 0.71 0.30 0.07
15_H 10_I 0.71 0.30 0.07
12_A 120_I 0.71 0.30 0.07
56_H 168_Y 0.70 0.29 0.07
45_R 195_V 0.70 0.29 0.07
98_V 6_H 0.70 0.29 0.07
78_E 210_G 0.70 0.29 0.07
35_Q 138_V 0.70 0.29 0.07
80_T 131_R 0.70 0.29 0.07
89_R 104_A 0.70 0.29 0.07
34_A 74_G 0.69 0.29 0.07
15_H 104_A 0.69 0.29 0.07
68_R 131_R 0.69 0.29 0.07
25_I 105_E 0.69 0.28 0.06
18_I 104_A 0.69 0.28 0.06
20_Q 103_I 0.69 0.28 0.06
90_L 176_H 0.69 0.28 0.06
82_K 63_S 0.69 0.28 0.06
36_V 114_K 0.69 0.28 0.06
94_A 110_E 0.68 0.28 0.06
49_F 6_H 0.68 0.28 0.06
18_I 55_I 0.68 0.28 0.06
55_P 167_W 0.68 0.27 0.06
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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