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OPENSEQ.org
4CHG
Genes: A B A+B
Length: 80 132 194
Sequences: 542 9209 369
Seq/Len: 6.78 69.77 1.9
MirrorTree (Pazo et al. 2001) 0.78
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 0.04 1.74
2 0.01 0.05 1.76
5 0.01 0.08 1.78
10 0.01 0.10 1.82
20 0.01 0.11 1.87
100 0.02 0.15 2.03
∞ 0.08 0.20 2.35
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
55_Q 24_A 1.83 0.97 0.89
57_S 47_K 1.56 0.92 0.75
57_S 56_R 1.49 0.90 0.70
54_L 5_T 1.41 0.86 0.63
32_S 2_I 1.39 0.85 0.62
10_N 116_D 1.28 0.78 0.51
52_L 24_A 1.27 0.77 0.50
61_F 93_S 1.21 0.72 0.44
59_F 82_R 1.20 0.72 0.43
54_L 88_G 1.19 0.70 0.42
14_D 112_H 1.18 0.69 0.40
44_E 31_S 1.15 0.67 0.38
59_F 93_S 1.15 0.66 0.37
54_L 46_G 1.14 0.66 0.37
67_E 93_S 1.12 0.64 0.35
7_S 7_V 1.12 0.63 0.34
38_L 6_S 1.11 0.62 0.34
16_E 122_T 1.11 0.62 0.34
66_I 93_S 1.09 0.60 0.32
51_A 6_S 1.08 0.60 0.31
39_R 43_L 1.07 0.59 0.30
66_I 117_Y 1.06 0.57 0.29
13_I 69_A 1.04 0.55 0.27
16_E 54_A 1.04 0.55 0.27
42_V 39_V 1.02 0.53 0.25
55_Q 11_Y 1.02 0.53 0.25
20_A 25_D 1.01 0.52 0.25
32_S 78_A 0.98 0.49 0.22
23_R 98_Q 0.94 0.45 0.19
62_S 99_V 0.94 0.44 0.19
49_D 63_F 0.94 0.44 0.19
16_E 108_V 0.94 0.44 0.19
61_F 33_V 0.93 0.43 0.18
28_D 91_V 0.92 0.42 0.17
25_Y 9_I 0.92 0.42 0.17
21_A 60_L 0.91 0.41 0.17
42_V 99_V 0.91 0.41 0.17
8_R 100_A 0.90 0.40 0.16
48_R 6_S 0.90 0.40 0.16
68_S 1_M 0.90 0.40 0.16
69_F 12_L 0.90 0.40 0.16
34_V 16_E 0.90 0.40 0.16
63_N 93_S 0.90 0.40 0.16
32_S 118_E 0.89 0.39 0.16
29_S 98_Q 0.88 0.38 0.15
18_V 101_A 0.88 0.38 0.15
37_A 75_E 0.88 0.37 0.15
56_G 46_G 0.86 0.36 0.14
15_D 54_A 0.85 0.35 0.13
58_G 13_S 0.84 0.34 0.13
8_R 9_I 0.84 0.34 0.13
25_Y 45_I 0.84 0.34 0.12
62_S 117_Y 0.84 0.34 0.12
37_A 101_A 0.83 0.33 0.12
13_I 23_L 0.83 0.33 0.12
44_E 84_C 0.83 0.33 0.12
52_L 27_I 0.83 0.32 0.12
32_S 64_A 0.82 0.32 0.12
34_V 109_A 0.82 0.32 0.12
17_L 23_L 0.82 0.32 0.12
28_D 59_L 0.82 0.32 0.11
16_E 71_V 0.81 0.31 0.11
39_R 79_A 0.81 0.31 0.11
69_F 101_A 0.81 0.30 0.11
44_E 48_T 0.80 0.30 0.11
16_E 79_A 0.80 0.30 0.10
11_I 17_S 0.80 0.29 0.10
53_A 69_A 0.79 0.29 0.10
37_A 121_R 0.79 0.29 0.10
64_D 6_S 0.79 0.29 0.10
36_L 27_I 0.79 0.29 0.10
10_N 78_A 0.78 0.28 0.10
48_R 31_S 0.78 0.28 0.10
67_E 9_I 0.78 0.28 0.10
20_A 118_E 0.78 0.28 0.10
47_G 65_I 0.78 0.28 0.10
48_R 21_R 0.78 0.28 0.10
41_L 47_K 0.78 0.28 0.09
44_E 43_L 0.78 0.28 0.09
62_S 17_S 0.78 0.28 0.09
63_N 43_L 0.78 0.28 0.09
45_P 35_V 0.77 0.27 0.09
27_L 98_Q 0.77 0.27 0.09
31_R 116_D 0.76 0.27 0.09
35_D 36_P 0.76 0.27 0.09
61_F 82_R 0.76 0.27 0.09
14_D 116_D 0.76 0.26 0.09
53_A 59_L 0.76 0.26 0.09
55_Q 21_R 0.76 0.26 0.09
14_D 109_A 0.76 0.26 0.09
28_D 103_A 0.75 0.26 0.08
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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