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OPENSEQ.org
relBE
Genes: A B A+B
Length: 97 89 178
Sequences: 1401 982 81
Seq/Len: 14.44 11.03 0.46
MirrorTree (Pazo et al. 2001) 0.80
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 0.00 0.01 0.41
2 0.01 0.01 0.44
5 0.01 0.01 0.47
10 0.02 0.01 0.52
20 0.02 0.02 0.53
100 0.04 0.03 0.70
∞ 0.10 0.07 1.35
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
67_V 54_V 2.06 0.86 0.25
46_G 26_R 1.72 0.69 0.11
32_E 43_D 1.68 0.67 0.10
18_D 31_R 1.50 0.53 0.06
43_H 32_H 1.42 0.48 0.05
12_T 66_E 1.35 0.42 0.04
25_K 29_I 1.31 0.40 0.03
11_I 59_G 1.30 0.39 0.03
69_A 68_L 1.23 0.34 0.02
80_I 64_I 1.22 0.33 0.02
56_L 68_L 1.22 0.33 0.02
88_S 52_L 1.20 0.32 0.02
35_F 79_N 1.19 0.31 0.02
76_R 80_D 1.19 0.31 0.02
40_N 80_D 1.19 0.31 0.02
82_I 40_I 1.14 0.28 0.02
50_R 9_V 1.13 0.28 0.02
77_V 12_R 1.11 0.26 0.01
78_E 67_G 1.10 0.26 0.01
71_D 61_S 1.10 0.26 0.01
52_D 72_A 1.10 0.26 0.01
20_Q 78_S 1.09 0.25 0.01
76_R 82_I 1.08 0.25 0.01
27_A 24_H 1.07 0.24 0.01
88_S 66_E 1.06 0.24 0.01
80_I 5_P 1.06 0.24 0.01
30_C 87_T 1.06 0.24 0.01
79_I 47_S 1.05 0.23 0.01
16_A 28_T 1.03 0.22 0.01
22_L 40_I 1.02 0.21 0.01
58_S 54_V 1.01 0.21 0.01
12_T 72_A 1.01 0.21 0.01
12_T 52_L 1.00 0.20 0.01
79_I 27_I 0.99 0.20 0.01
88_S 81_E 0.99 0.20 0.01
9_V 81_E 0.99 0.20 0.01
36_G 38_V 0.99 0.20 0.01
91_M 11_N 0.99 0.20 0.01
47_K 50_E 0.99 0.20 0.01
82_I 80_D 0.99 0.20 0.01
34_V 52_L 0.98 0.20 0.01
9_V 69_A 0.98 0.20 0.01
51_N 64_I 0.98 0.19 0.01
81_H 47_S 0.98 0.19 0.01
19_L 80_D 0.97 0.19 0.01
72_D 17_V 0.97 0.19 0.01
12_T 3_V 0.96 0.19 0.01
34_V 85_R 0.96 0.19 0.01
9_V 19_E 0.96 0.18 0.01
77_V 76_F 0.96 0.18 0.01
36_G 35_P 0.95 0.18 0.01
57_H 58_P 0.95 0.18 0.01
29_A 30_T 0.95 0.18 0.01
14_T 42_A 0.94 0.18 0.01
39_L 56_R 0.93 0.17 0.01
14_T 70_D 0.93 0.17 0.01
87_A 20_V 0.93 0.17 0.01
31_V 67_G 0.93 0.17 0.01
35_F 25_E 0.93 0.17 0.01
33_F 1_M 0.93 0.17 0.01
30_C 5_P 0.92 0.17 0.01
68_Y 26_R 0.92 0.17 0.01
34_V 81_E 0.91 0.16 0.01
64_Y 25_E 0.91 0.16 0.01
78_E 77_V 0.91 0.16 0.01
10_A 56_R 0.91 0.16 0.01
73_G 27_I 0.90 0.16 0.01
36_G 70_D 0.90 0.16 0.01
13_A 59_G 0.90 0.16 0.01
54_E 39_L 0.89 0.16 0.01
51_N 86_Y 0.89 0.16 0.01
45_L 7_G 0.88 0.15 0.01
26_I 69_A 0.88 0.15 0.01
75_H 77_V 0.88 0.15 0.01
9_V 48_I 0.88 0.15 0.01
67_V 57_T 0.87 0.15 0.01
39_L 25_E 0.87 0.15 0.01
16_A 85_R 0.86 0.15 0.01
24_E 26_R 0.86 0.15 0.01
29_A 74_G 0.86 0.14 0.01
21_R 45_L 0.86 0.14 0.01
20_Q 64_I 0.86 0.14 0.01
67_V 60_A 0.86 0.14 0.01
71_D 84_N 0.85 0.14 0.01
66_V 13_L 0.85 0.14 0.01
57_H 9_V 0.85 0.14 0.01
23_P 24_H 0.85 0.14 0.01
52_D 70_D 0.85 0.14 0.01
87_A 15_E 0.85 0.14 0.01
55_G 18_A 0.84 0.14 0.01
55_G 52_L 0.84 0.14 0.01
85_R 50_E 0.84 0.14 0.01
81_H 82_I 0.84 0.14 0.01
83_A 7_G 0.84 0.14 0.01
10_A 43_D 0.84 0.14 0.01
46_G 32_H 0.83 0.13 0.01
52_D 9_V 0.83 0.13 0.01
81_H 54_V 0.83 0.13 0.01
29_A 14_S 0.82 0.13 0.01
84_R 55_L 0.82 0.13 0.01
55_G 20_V 0.82 0.13 0.01
67_V 47_S 0.82 0.13 0.01
11_I 34_H 0.82 0.13 0.01
69_A 67_G 0.81 0.13 0.01
40_N 46_A 0.81 0.13 0.01
9_V 25_E 0.81 0.12 0.01
26_I 82_I 0.81 0.12 0.01
88_S 85_R 0.80 0.12 0.01
82_I 84_N 0.80 0.12 0.01
71_D 77_V 0.80 0.12 0.00
68_Y 39_L 0.80 0.12 0.00
86_S 25_E 0.80 0.12 0.00
55_G 64_I 0.80 0.12 0.00
81_H 58_P 0.80 0.12 0.00
82_I 21_E 0.80 0.12 0.00
47_K 17_V 0.80 0.12 0.00
90_R 89_R 0.79 0.12 0.00
9_V 83_R 0.79 0.12 0.00
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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