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OPENSEQ.org
1015
Genes: A B A+B
Length: 94 161 240
Sequences: 686 14791 609
Seq/Len: 7.3 91.87 2.54
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 0.05 2.39
2 0.01 0.06 2.39
5 0.01 0.08 2.40
10 0.02 0.10 2.41
20 0.03 0.11 2.41
100 0.05 0.16 2.44
∞ 0.10 0.22 2.58
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
87_M 108_K 1.86 0.99 0.95
89_R 104_V 1.82 0.99 0.94
82_K 141_K 1.74 0.98 0.92
78_E 143_A 1.61 0.96 0.88
72_D 45_Y 1.50 0.94 0.83
92_P 105_A 1.48 0.94 0.82
57_F 64_G 1.32 0.87 0.70
25_D 89_G 1.30 0.86 0.68
72_D 43_R 1.25 0.83 0.64
34_S 78_N 1.23 0.82 0.62
67_F 16_A 1.18 0.78 0.57
67_F 66_I 1.15 0.75 0.53
86_L 129_H 1.13 0.74 0.52
14_I 132_D 1.13 0.73 0.51
94_E 16_A 1.12 0.72 0.50
86_L 108_K 1.11 0.71 0.49
38_F 90_R 1.11 0.71 0.49
94_E 20_C 1.10 0.71 0.48
57_F 127_I 1.05 0.65 0.42
85_A 141_K 1.03 0.63 0.41
41_D 66_I 1.02 0.62 0.39
60_D 133_D 1.02 0.62 0.39
88_N 137_N 1.01 0.61 0.38
65_D 68_R 1.01 0.61 0.38
34_S 138_F 1.00 0.59 0.36
50_I 69_N 0.98 0.57 0.34
21_R 89_G 0.96 0.55 0.32
13_N 81_E 0.95 0.54 0.32
87_M 112_Y 0.94 0.53 0.31
32_A 32_K 0.93 0.52 0.30
39_M 87_V 0.93 0.52 0.30
37_D 100_K 0.93 0.51 0.29
23_L 31_K 0.92 0.51 0.29
62_E 149_F 0.92 0.50 0.28
67_F 125_A 0.89 0.47 0.25
81_A 133_D 0.89 0.47 0.25
73_A 145_V 0.89 0.47 0.25
36_T 86_V 0.88 0.46 0.25
32_A 88_L 0.88 0.45 0.24
74_P 45_Y 0.87 0.45 0.24
57_F 129_H 0.86 0.43 0.23
82_K 142_Y 0.86 0.43 0.23
94_E 108_K 0.86 0.43 0.23
51_L 97_W 0.86 0.43 0.23
86_L 104_V 0.86 0.43 0.23
37_D 88_L 0.85 0.42 0.22
9_E 58_Y 0.85 0.42 0.22
34_S 134_S 0.85 0.42 0.22
82_K 143_A 0.85 0.42 0.22
63_Q 89_G 0.84 0.41 0.21
64_Y 68_R 0.84 0.41 0.21
89_R 105_A 0.84 0.41 0.21
71_L 57_G 0.83 0.40 0.20
21_R 78_N 0.83 0.39 0.20
55_R 102_L 0.83 0.39 0.20
23_L 58_Y 0.82 0.39 0.20
31_V 84_P 0.82 0.39 0.20
84_N 132_D 0.82 0.38 0.19
13_N 43_R 0.82 0.38 0.19
34_S 92_A 0.81 0.38 0.19
28_A 103_G 0.81 0.38 0.19
75_I 124_R 0.81 0.37 0.18
12_I 86_V 0.81 0.37 0.18
10_A 117_I 0.80 0.37 0.18
52_L 93_I 0.80 0.36 0.18
59_L 130_A 0.79 0.35 0.17
88_N 70_L 0.79 0.35 0.17
53_D 129_H 0.79 0.35 0.17
14_I 81_E 0.79 0.35 0.17
86_L 45_Y 0.79 0.35 0.17
18_A 115_M 0.79 0.35 0.17
39_M 84_P 0.78 0.34 0.16
35_R 77_R 0.78 0.34 0.16
24_I 140_L 0.78 0.34 0.16
87_M 70_L 0.78 0.34 0.16
24_I 121_V 0.78 0.34 0.16
35_R 91_L 0.77 0.33 0.15
93_W 78_N 0.76 0.32 0.15
50_I 59_Y 0.76 0.32 0.14
32_A 80_P 0.76 0.31 0.14
21_R 28_W 0.76 0.31 0.14
58_I 67_Q 0.76 0.31 0.14
7_S 114_T 0.75 0.31 0.14
67_F 148_P 0.75 0.31 0.14
67_F 85_V 0.75 0.31 0.14
70_A 128_V 0.74 0.30 0.14
57_F 147_S 0.74 0.30 0.14
29_N 126_L 0.74 0.30 0.14
39_M 88_L 0.74 0.30 0.13
71_L 45_Y 0.74 0.30 0.13
69_A 52_T 0.73 0.29 0.13
29_N 55_V 0.73 0.29 0.13
15_R 87_V 0.73 0.29 0.13
19_S 60_C 0.73 0.29 0.13
63_Q 15_L 0.73 0.29 0.13
15_R 107_L 0.73 0.29 0.13
51_L 69_N 0.73 0.29 0.13
65_D 145_V 0.73 0.28 0.13
37_D 28_W 0.72 0.28 0.12
66_A 109_D 0.71 0.28 0.12
71_L 107_L 0.71 0.27 0.12
12_I 25_M 0.71 0.27 0.12
19_S 59_Y 0.71 0.27 0.12
57_F 61_L 0.70 0.26 0.11
78_E 45_Y 0.70 0.26 0.11
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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