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OPENSEQ.org
1733
Genes: A B A+B
Length: 94 91 175
Sequences: 1093 3970 511
Seq/Len: 11.63 43.63 2.92
MirrorTree (Pazo et al. 2001) 0.79
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 2.76
2 0.01 0.03 2.81
5 0.02 0.04 2.86
10 0.02 0.05 2.85
20 0.03 0.06 2.90
100 0.04 0.08 3.08
∞ 0.09 0.14 3.82
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
84_L 17_Y 2.70 1.00 1.00
62_A 82_L 2.65 1.00 1.00
65_D 8_K 2.59 1.00 1.00
77_V 10_L 2.22 1.00 0.99
80_W 10_L 1.93 0.99 0.98
74_H 5_W 1.93 0.99 0.98
58_L 83_R 1.79 0.99 0.96
70_Q 7_S 1.79 0.99 0.96
78_Q 36_T 1.78 0.99 0.96
75_Q 40_V 1.61 0.97 0.93
78_Q 40_V 1.45 0.94 0.87
59_T 71_R 1.44 0.94 0.87
65_D 6_S 1.42 0.94 0.86
84_L 18_D 1.39 0.92 0.84
72_I 10_L 1.33 0.90 0.81
71_V 4_K 1.32 0.89 0.80
18_V 43_L 1.24 0.85 0.74
15_T 82_L 1.23 0.85 0.73
76_A 7_S 1.16 0.80 0.66
66_V 82_L 1.14 0.78 0.64
71_V 6_S 1.12 0.76 0.62
67_T 73_E 1.11 0.76 0.62
66_V 73_E 1.11 0.75 0.61
85_S 32_V 1.10 0.75 0.60
62_A 6_S 1.10 0.74 0.60
58_L 85_W 1.10 0.74 0.60
26_V 13_L 1.09 0.73 0.59
41_I 20_L 1.06 0.71 0.56
15_T 23_A 1.02 0.66 0.51
66_V 80_Y 1.01 0.65 0.50
80_W 14_A 0.99 0.62 0.47
18_V 65_A 0.97 0.61 0.45
11_T 46_P 0.96 0.60 0.44
73_D 4_K 0.92 0.55 0.39
87_D 17_Y 0.90 0.52 0.37
81_A 35_L 0.87 0.49 0.33
49_L 1_M 0.87 0.48 0.33
15_T 38_A 0.86 0.47 0.32
18_V 75_N 0.86 0.47 0.32
66_V 6_S 0.86 0.47 0.32
69_G 6_S 0.86 0.47 0.31
82_D 36_T 0.86 0.46 0.31
62_A 20_L 0.84 0.44 0.29
30_A 49_G 0.82 0.42 0.28
45_L 32_V 0.82 0.42 0.28
62_A 16_L 0.82 0.42 0.27
80_W 89_E 0.81 0.41 0.27
72_I 45_H 0.81 0.41 0.26
45_L 13_L 0.81 0.41 0.26
81_A 32_V 0.81 0.41 0.26
83_S 14_A 0.81 0.41 0.26
80_W 19_F 0.81 0.40 0.26
75_Q 2_E 0.80 0.39 0.24
81_A 21_V 0.79 0.39 0.24
84_L 16_L 0.78 0.37 0.23
52_E 27_A 0.77 0.36 0.22
72_I 43_L 0.77 0.36 0.22
75_Q 30_R 0.76 0.35 0.21
71_V 73_E 0.76 0.35 0.21
50_A 70_I 0.76 0.35 0.21
48_W 62_R 0.75 0.34 0.20
17_H 83_R 0.75 0.34 0.20
80_W 15_R 0.75 0.34 0.20
36_S 67_E 0.75 0.34 0.20
35_R 86_H 0.75 0.33 0.20
57_R 81_V 0.74 0.33 0.20
54_E 23_A 0.74 0.33 0.19
29_M 63_I 0.74 0.33 0.19
24_D 37_Q 0.74 0.33 0.19
42_K 13_L 0.73 0.32 0.19
40_V 70_I 0.73 0.32 0.18
23_A 45_H 0.73 0.32 0.18
38_G 20_L 0.73 0.32 0.18
21_P 4_K 0.72 0.31 0.18
70_Q 6_S 0.72 0.31 0.18
67_T 30_R 0.72 0.31 0.18
85_S 17_Y 0.72 0.31 0.18
66_V 4_K 0.72 0.31 0.18
28_Q 6_S 0.71 0.30 0.17
49_L 16_L 0.71 0.30 0.17
76_A 55_F 0.71 0.29 0.17
19_P 26_P 0.70 0.29 0.16
44_A 13_L 0.70 0.29 0.16
31_A 27_A 0.70 0.29 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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