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OPENSEQ.org
1C17
Genes: A B A+B
Length: 79 177 239
Sequences: 1098 3494 1299
Seq/Len: 13.9 19.74 5.44
MirrorTree (Pazo et al. 2001) 0.72
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.08 0.04 4.93
2 0.08 0.04 5.05
5 0.08 0.04 5.06
10 0.08 0.04 5.07
20 0.08 0.04 5.07
100 0.08 0.04 5.12
∞ 0.09 0.04 5.21
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
65_M 119_G 2.60 1.00 1.00
42_Q 110_P 1.48 0.99 0.92
66_I 112_S 1.39 0.98 0.89
54_F 168_V 1.32 0.96 0.86
71_G 52_D 1.31 0.96 0.85
11_M 73_K 1.20 0.93 0.78
62_A 169_Y 1.15 0.91 0.74
26_I 156_T 1.14 0.91 0.73
33_G 13_T 1.05 0.86 0.65
14_A 103_G 1.00 0.81 0.58
55_I 60_A 0.99 0.80 0.58
24_A 106_L 0.98 0.79 0.56
62_A 112_S 0.97 0.78 0.55
28_I 151_H 0.97 0.78 0.55
20_A 169_Y 0.95 0.76 0.53
42_Q 57_L 0.94 0.75 0.51
23_G 153_L 0.93 0.74 0.50
62_A 119_G 0.93 0.74 0.49
63_I 102_E 0.92 0.73 0.49
9_L 161_I 0.92 0.73 0.49
17_M 105_S 0.92 0.73 0.49
25_A 70_Y 0.90 0.70 0.46
66_I 154_I 0.89 0.70 0.46
44_D 136_P 0.88 0.68 0.44
39_A 128_F 0.88 0.68 0.43
42_Q 102_E 0.88 0.68 0.43
69_G 115_L 0.87 0.67 0.42
11_M 72_I 0.86 0.66 0.41
24_A 51_A 0.83 0.62 0.38
57_M 123_A 0.83 0.62 0.38
21_A 24_M 0.83 0.61 0.37
57_M 113_L 0.82 0.60 0.36
27_G 110_P 0.82 0.60 0.36
24_A 154_I 0.82 0.60 0.36
58_G 89_F 0.81 0.58 0.34
36_L 12_L 0.81 0.58 0.34
58_G 98_N 0.80 0.57 0.34
29_G 107_L 0.80 0.57 0.34
27_G 56_T 0.80 0.57 0.33
49_L 88_P 0.80 0.57 0.33
64_P 124_G 0.79 0.56 0.33
29_G 58_S 0.79 0.56 0.32
59_L 114_G 0.78 0.55 0.32
72_L 133_G 0.78 0.55 0.32
40_A 126_L 0.76 0.52 0.29
19_L 58_S 0.76 0.52 0.29
31_L 49_P 0.76 0.51 0.28
63_I 124_G 0.75 0.50 0.28
28_I 124_G 0.75 0.50 0.27
20_A 110_P 0.74 0.49 0.27
54_F 25_D 0.74 0.48 0.26
44_D 152_I 0.73 0.47 0.25
72_L 115_L 0.72 0.46 0.25
59_L 161_I 0.72 0.46 0.25
53_F 154_I 0.72 0.46 0.24
69_G 101_L 0.72 0.45 0.24
59_L 157_L 0.72 0.45 0.24
30_I 114_G 0.71 0.45 0.24
42_Q 105_S 0.71 0.45 0.24
55_I 101_L 0.71 0.45 0.24
69_G 169_Y 0.71 0.44 0.23
16_M 80_F 0.71 0.44 0.23
69_G 100_I 0.71 0.44 0.23
73_Y 131_I 0.71 0.44 0.23
11_M 21_M 0.70 0.43 0.23
62_A 123_A 0.70 0.43 0.22
77_A 122_Y 0.70 0.43 0.22
18_G 87_Q 0.70 0.42 0.22
49_L 16_V 0.70 0.42 0.22
22_I 123_A 0.70 0.42 0.22
64_P 105_S 0.69 0.42 0.22
58_G 146_P 0.69 0.42 0.22
36_L 153_L 0.69 0.42 0.22
30_I 50_S 0.68 0.40 0.20
51_T 12_L 0.68 0.40 0.20
70_L 107_L 0.68 0.40 0.20
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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