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OPENSEQ.org
1008
Genes: A B A+B
Length: 75 92 154
Sequences: 313 3929 231
Seq/Len: 4.17 42.71 1.5
MirrorTree (Pazo et al. 2001) 0.70
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.02 1.38
2 0.01 0.03 1.41
5 0.01 0.04 1.41
10 0.01 0.05 1.41
20 0.02 0.06 1.44
100 0.02 0.08 1.51
∞ 0.04 0.14 1.62
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
60_R 11_D 2.58 1.00 0.99
57_V 11_D 2.40 1.00 0.99
44_S 82_V 2.06 0.98 0.96
60_R 15_D 2.05 0.98 0.96
37_L 85_I 1.88 0.97 0.93
44_S 83_N 1.87 0.97 0.92
40_K 83_N 1.78 0.95 0.90
33_Y 85_I 1.71 0.94 0.87
47_D 9_S 1.61 0.91 0.82
34_N 17_I 1.41 0.81 0.67
64_R 19_S 1.41 0.81 0.67
40_K 85_I 1.39 0.80 0.66
63_E 26_I 1.36 0.78 0.64
18_S 50_Y 1.32 0.75 0.59
52_I 11_D 1.27 0.71 0.54
69_R 30_E 1.26 0.70 0.53
65_F 33_W 1.25 0.69 0.52
62_A 33_W 1.24 0.68 0.50
58_E 37_R 1.22 0.66 0.48
36_W 63_V 1.21 0.65 0.47
45_L 73_R 1.21 0.65 0.47
53_P 79_V 1.19 0.63 0.45
52_I 34_Q 1.19 0.63 0.45
54_H 66_P 1.14 0.58 0.40
65_F 14_L 1.13 0.57 0.38
51_A 5_L 1.12 0.56 0.37
71_E 77_S 1.09 0.53 0.34
47_D 12_T 1.07 0.52 0.33
38_R 21_I 1.07 0.52 0.33
35_E 36_L 1.06 0.51 0.32
30_E 81_V 1.06 0.50 0.31
25_E 89_R 1.06 0.50 0.31
41_V 58_G 1.06 0.50 0.31
30_E 51_P 1.05 0.49 0.30
67_K 8_E 1.05 0.49 0.30
56_E 57_P 1.04 0.48 0.29
58_E 14_L 1.02 0.46 0.28
40_K 13_D 1.01 0.46 0.27
47_D 7_L 1.01 0.45 0.26
61_M 91_F 1.00 0.45 0.26
58_E 41_L 1.00 0.44 0.26
37_L 54_D 1.00 0.44 0.26
31_N 69_I 0.99 0.43 0.24
40_K 39_C 0.97 0.41 0.23
61_M 18_T 0.97 0.41 0.23
48_P 73_R 0.96 0.40 0.22
37_L 89_R 0.96 0.40 0.22
32_S 12_T 0.95 0.39 0.21
61_M 33_W 0.95 0.39 0.21
54_H 4_V 0.94 0.38 0.20
30_E 71_L 0.94 0.38 0.20
48_P 80_E 0.94 0.38 0.20
63_E 5_L 0.92 0.36 0.18
63_E 36_L 0.91 0.35 0.18
47_D 73_R 0.90 0.34 0.17
36_W 69_I 0.90 0.34 0.17
36_W 64_A 0.89 0.34 0.17
34_N 54_D 0.88 0.32 0.16
56_E 23_R 0.87 0.31 0.15
70_K 23_R 0.86 0.31 0.15
33_Y 25_D 0.86 0.31 0.14
38_R 55_R 0.86 0.31 0.14
59_R 40_V 0.86 0.30 0.14
69_R 49_L 0.85 0.30 0.14
44_S 85_I 0.84 0.29 0.13
60_R 16_D 0.84 0.29 0.13
46_A 83_N 0.84 0.29 0.13
25_E 23_R 0.83 0.28 0.12
35_E 56_V 0.82 0.27 0.12
37_L 59_L 0.81 0.27 0.12
18_S 3_P 0.80 0.26 0.11
54_H 79_V 0.80 0.25 0.11
65_F 91_F 0.80 0.25 0.11
52_I 79_V 0.79 0.25 0.10
20_M 35_R 0.79 0.25 0.10
69_R 44_S 0.79 0.24 0.10
29_Q 76_T 0.78 0.24 0.10
54_H 6_W 0.78 0.24 0.10
57_V 10_A 0.77 0.24 0.10
41_V 71_L 0.77 0.23 0.10
58_E 33_W 0.77 0.23 0.10
36_W 86_H 0.77 0.23 0.09
61_M 14_L 0.77 0.23 0.09
59_R 36_L 0.76 0.23 0.09
55_D 77_S 0.76 0.23 0.09
34_N 20_Y 0.74 0.21 0.08
62_A 37_R 0.74 0.21 0.08
25_E 88_R 0.74 0.21 0.08
44_S 7_L 0.74 0.21 0.08
32_S 85_I 0.73 0.20 0.08
41_V 39_C 0.73 0.20 0.08
36_W 55_R 0.73 0.20 0.07
56_E 38_G 0.72 0.20 0.07
40_K 69_I 0.72 0.20 0.07
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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