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OPENSEQ.org
3HI2-3
Genes: A B A+B
Length: 76 94 169
Sequences: 144 140 113
Seq/Len: 1.89 1.49 0.67
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 0.66
2 0.01 0.00 0.66
5 0.01 0.00 0.66
10 0.01 0.00 0.66
20 0.01 0.00 0.66
100 0.01 0.00 0.66
∞ 0.01 0.01 0.66
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
58_K 32_D 2.08 0.93 0.60
54_M 64_T 1.46 0.62 0.16
48_E 49_S 1.41 0.58 0.14
50_S 36_L 1.35 0.54 0.12
43_S 88_D 1.31 0.50 0.10
5_V 64_T 1.31 0.50 0.10
31_G 44_V 1.29 0.48 0.10
58_K 23_T 1.25 0.45 0.08
75_V 17_N 1.24 0.44 0.08
3_C 48_L 1.23 0.43 0.08
23_R 5_P 1.21 0.42 0.07
47_K 31_A 1.18 0.39 0.06
16_K 93_S 1.17 0.39 0.06
41_E 26_S 1.15 0.37 0.06
37_C 69_V 1.15 0.37 0.06
38_V 35_G 1.13 0.35 0.05
48_E 51_S 1.12 0.35 0.05
57_V 32_D 1.10 0.33 0.05
73_F 5_P 1.08 0.32 0.04
54_M 28_L 1.07 0.31 0.04
67_E 51_S 1.07 0.31 0.04
19_P 91_I 1.07 0.31 0.04
50_S 25_R 1.06 0.30 0.04
31_G 84_T 1.05 0.30 0.04
1_M 52_D 1.05 0.29 0.04
43_S 71_R 1.05 0.29 0.04
51_D 42_C 1.05 0.29 0.04
44_I 86_I 1.05 0.29 0.04
42_E 30_N 1.03 0.28 0.04
27_T 13_K 1.03 0.28 0.04
52_A 84_T 1.02 0.28 0.04
59_A 65_I 1.02 0.27 0.03
36_Y 21_V 1.02 0.27 0.03
13_S 45_I 1.01 0.27 0.03
10_E 43_N 1.01 0.27 0.03
26_K 30_N 1.01 0.27 0.03
31_G 45_I 1.01 0.27 0.03
30_K 12_V 1.00 0.26 0.03
53_F 41_M 1.00 0.26 0.03
40_C 69_V 0.99 0.26 0.03
21_T 10_S 0.99 0.25 0.03
26_K 16_V 0.98 0.25 0.03
37_C 57_M 0.97 0.24 0.03
6_C 48_L 0.97 0.24 0.03
62_A 45_I 0.96 0.24 0.03
26_K 73_R 0.96 0.24 0.03
71_P 31_A 0.96 0.24 0.03
14_G 81_L 0.95 0.23 0.03
53_F 16_V 0.95 0.23 0.03
18_I 28_L 0.95 0.23 0.03
52_A 6_H 0.94 0.23 0.03
14_G 26_S 0.94 0.23 0.03
58_K 4_T 0.94 0.23 0.03
57_V 28_L 0.94 0.22 0.02
47_K 42_C 0.94 0.22 0.02
8_Q 26_S 0.93 0.22 0.02
25_R 53_F 0.93 0.22 0.02
60_F 83_I 0.92 0.21 0.02
57_V 29_L 0.92 0.21 0.02
66_A 40_G 0.92 0.21 0.02
5_V 72_P 0.91 0.21 0.02
68_T 45_I 0.91 0.21 0.02
36_Y 88_D 0.91 0.21 0.02
37_C 54_Y 0.91 0.21 0.02
72_E 3_R 0.91 0.21 0.02
15_I 49_S 0.91 0.21 0.02
50_S 13_K 0.90 0.20 0.02
47_K 49_S 0.90 0.20 0.02
56_Q 65_I 0.90 0.20 0.02
35_L 60_Y 0.90 0.20 0.02
57_V 35_G 0.90 0.20 0.02
15_I 54_Y 0.90 0.20 0.02
15_I 34_L 0.89 0.20 0.02
40_C 57_M 0.89 0.20 0.02
22_F 53_F 0.89 0.20 0.02
75_V 10_S 0.88 0.19 0.02
39_H 81_L 0.88 0.19 0.02
63_S 14_K 0.88 0.19 0.02
59_A 32_D 0.88 0.19 0.02
73_F 7_T 0.88 0.19 0.02
10_E 35_G 0.88 0.19 0.02
43_S 78_Q 0.87 0.19 0.02
56_Q 23_T 0.87 0.19 0.02
20_Y 34_L 0.87 0.19 0.02
38_V 59_T 0.87 0.19 0.02
31_G 61_S 0.87 0.18 0.02
18_I 25_R 0.86 0.18 0.02
12_V 91_I 0.86 0.18 0.02
70_A 25_R 0.86 0.18 0.02
18_I 29_L 0.85 0.18 0.02
39_H 14_K 0.85 0.18 0.02
24_G 34_L 0.85 0.18 0.02
45_M 40_G 0.85 0.17 0.02
69_V 40_G 0.85 0.17 0.02
3_C 69_V 0.84 0.17 0.02
23_R 93_S 0.84 0.17 0.02
61_R 36_L 0.84 0.17 0.01
61_R 90_L 0.83 0.17 0.01
17_D 44_V 0.83 0.17 0.01
41_E 65_I 0.83 0.17 0.01
52_A 91_I 0.83 0.17 0.01
34_G 47_G 0.82 0.17 0.01
26_K 28_L 0.82 0.16 0.01
45_M 7_T 0.82 0.16 0.01
72_E 1_E 0.82 0.16 0.01
16_K 41_M 0.81 0.16 0.01
71_P 92_V 0.81 0.16 0.01
45_M 64_T 0.81 0.16 0.01
21_T 44_V 0.80 0.15 0.01
19_P 88_D 0.80 0.15 0.01
36_Y 31_A 0.80 0.15 0.01
53_F 36_L 0.80 0.15 0.01
3_C 92_V 0.79 0.15 0.01
13_S 46_I 0.79 0.15 0.01
17_D 61_S 0.79 0.15 0.01
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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