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OPENSEQ.org
5196
Genes: A B A+B
Length: 80 93 170
Sequences: 1610 3889 979
Seq/Len: 20.12 41.82 5.76
MirrorTree (Pazo et al. 2001) 0.56
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 5.66
2 0.02 0.03 5.69
5 0.02 0.04 5.73
10 0.03 0.05 5.79
20 0.03 0.06 5.87
100 0.05 0.08 6.06
∞ 0.10 0.14 6.81
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
73_E 9_V 2.91 1.00 1.00
56_E 7_K 2.47 1.00 1.00
73_E 13_R 2.46 1.00 1.00
58_L 58_V 2.12 1.00 0.99
57_G 81_R 1.83 1.00 0.98
75_K 29_D 1.81 1.00 0.98
54_V 58_V 1.70 1.00 0.96
71_A 33_D 1.55 0.99 0.94
77_K 17_D 1.53 0.99 0.94
54_V 69_Y 1.52 0.99 0.94
61_G 5_S 1.43 0.98 0.91
58_L 71_V 1.41 0.98 0.90
77_K 13_R 1.41 0.98 0.90
57_G 80_A 1.40 0.98 0.90
65_M 9_V 1.30 0.96 0.85
71_A 29_D 1.24 0.95 0.81
74_R 17_D 1.18 0.93 0.78
74_R 13_R 1.16 0.93 0.76
51_R 55_I 1.04 0.86 0.64
64_S 9_V 0.99 0.81 0.58
71_A 36_G 0.98 0.81 0.57
67_L 36_G 0.96 0.79 0.54
60_S 7_K 0.96 0.79 0.54
61_G 80_A 0.94 0.76 0.51
62_E 71_V 0.91 0.74 0.49
53_A 87_M 0.90 0.72 0.46
74_R 16_Y 0.89 0.71 0.46
68_R 36_G 0.86 0.67 0.41
53_A 81_R 0.82 0.62 0.37
66_T 16_Y 0.82 0.62 0.37
26_Y 75_D 0.81 0.61 0.36
6_S 89_P 0.81 0.60 0.35
65_M 16_Y 0.81 0.60 0.35
60_S 6_G 0.81 0.60 0.35
69_D 74_V 0.81 0.60 0.35
75_K 33_D 0.80 0.59 0.34
57_G 11_D 0.80 0.58 0.34
70_I 9_V 0.79 0.58 0.33
75_K 36_G 0.79 0.58 0.33
65_M 6_G 0.79 0.58 0.33
54_V 55_I 0.78 0.57 0.32
75_K 25_E 0.78 0.56 0.32
78_H 16_Y 0.75 0.52 0.29
20_M 23_F 0.75 0.52 0.28
15_S 17_D 0.75 0.51 0.28
71_A 16_Y 0.74 0.50 0.27
79_R 25_E 0.72 0.48 0.25
63_S 78_L 0.71 0.47 0.24
56_E 81_R 0.70 0.45 0.23
51_R 56_P 0.70 0.44 0.23
75_K 28_A 0.69 0.44 0.22
57_G 83_L 0.69 0.43 0.22
36_A 48_I 0.69 0.43 0.22
33_M 72_I 0.69 0.42 0.21
78_H 42_L 0.68 0.42 0.21
67_L 4_L 0.68 0.42 0.21
67_L 32_T 0.68 0.41 0.21
19_R 37_I 0.68 0.41 0.21
61_G 78_L 0.68 0.41 0.21
9_V 12_F 0.68 0.41 0.20
51_R 57_E 0.68 0.41 0.20
46_R 87_M 0.66 0.39 0.19
4_I 23_F 0.66 0.39 0.19
13_L 69_Y 0.66 0.39 0.19
50_V 69_Y 0.66 0.38 0.19
67_L 39_L 0.65 0.38 0.18
54_V 80_A 0.65 0.38 0.18
58_L 80_A 0.65 0.37 0.18
19_R 56_P 0.65 0.37 0.18
41_E 81_R 0.64 0.36 0.17
54_V 60_K 0.64 0.36 0.17
51_R 54_A 0.64 0.36 0.17
59_E 14_G 0.64 0.36 0.17
70_I 4_L 0.63 0.35 0.16
44_E 82_I 0.63 0.35 0.16
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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