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OPENSEQ.org
1016
Genes: A B A+B
Length: 88 175 249
Sequences: 690 37553 145
Seq/Len: 7.84 214.59 0.58
MirrorTree (Pazo et al. 2001) 0.74
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 0.07 0.55
2 0.01 0.09 0.57
5 0.01 0.11 0.60
10 0.02 0.13 0.65
20 0.03 0.15 0.73
100 0.05 0.21 1.02
∞ 0.10 0.25 1.82
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
81_A 134_E 1.61 0.69 0.00
77_K 98_I 1.55 0.64 0.00
9_I 61_Y 1.44 0.56 0.00
57_N 138_E 1.40 0.53 0.00
83_K 100_R 1.31 0.46 0.00
75_G 148_G 1.31 0.46 0.00
67_A 133_V 1.28 0.43 0.00
60_S 37_R 1.26 0.42 0.00
60_S 30_F 1.25 0.41 0.00
15_D 120_W 1.23 0.40 0.00
81_A 113_A 1.22 0.39 0.00
9_I 145_K 1.22 0.39 0.00
48_I 122_A 1.17 0.35 0.00
35_F 95_R 1.17 0.35 0.00
31_S 143_F 1.14 0.33 0.00
68_L 64_L 1.14 0.33 0.00
26_A 22_C 1.10 0.30 0.00
12_R 112_V 1.08 0.29 0.00
79_K 116_M 1.08 0.29 0.00
85_L 39_H 1.07 0.28 0.00
57_N 37_R 1.07 0.28 0.00
82_A 113_A 1.07 0.28 0.00
64_V 92_T 1.07 0.28 0.00
54_V 152_L 1.05 0.27 0.00
37_L 29_L 1.05 0.27 0.00
56_L 30_F 1.04 0.26 0.00
33_S 56_R 1.04 0.26 0.00
25_A 111_L 1.03 0.26 0.00
61_W 71_R 1.03 0.26 0.00
60_S 152_L 1.02 0.25 0.00
51_H 93_L 1.02 0.25 0.00
81_A 90_S 1.02 0.25 0.00
32_V 119_V 1.02 0.25 0.00
27_I 88_I 1.02 0.25 0.00
72_P 150_I 1.02 0.25 0.00
74_P 134_E 1.01 0.24 0.00
67_A 30_F 1.01 0.24 0.00
31_S 61_Y 1.01 0.24 0.00
77_K 146_S 1.01 0.24 0.00
38_N 69_F 1.00 0.24 0.00
51_H 107_W 1.00 0.24 0.00
47_V 137_N 1.00 0.23 0.00
20_M 107_W 0.99 0.23 0.00
33_S 130_G 0.99 0.23 0.00
21_I 58_V 0.98 0.23 0.00
36_M 127_G 0.98 0.22 0.00
85_L 69_F 0.97 0.22 0.00
66_D 138_E 0.97 0.22 0.00
56_L 135_A 0.97 0.22 0.00
21_I 82_K 0.97 0.22 0.00
13_L 51_R 0.96 0.22 0.00
54_V 74_L 0.96 0.22 0.00
35_F 64_L 0.96 0.21 0.00
21_I 24_E 0.96 0.21 0.00
9_I 98_I 0.96 0.21 0.00
43_R 44_L 0.95 0.21 0.00
35_F 103_Q 0.95 0.21 0.00
6_K 52_N 0.95 0.21 0.00
31_S 17_L 0.95 0.21 0.00
42_Q 128_I 0.94 0.20 0.00
77_K 145_K 0.94 0.20 0.00
62_T 151_P 0.94 0.20 0.00
18_K 59_L 0.93 0.20 0.00
40_A 78_S 0.93 0.20 0.00
83_K 61_Y 0.92 0.20 0.00
26_A 75_P 0.91 0.19 0.00
68_L 47_Y 0.91 0.19 0.00
80_R 148_G 0.90 0.19 0.00
47_V 24_E 0.90 0.19 0.00
21_I 28_N 0.90 0.19 0.00
82_A 109_A 0.90 0.19 0.00
48_I 108_G 0.90 0.18 0.00
19_S 72_A 0.90 0.18 0.00
44_A 135_A 0.90 0.18 0.00
78_L 28_N 0.89 0.18 0.00
26_A 65_C 0.89 0.18 0.00
51_H 74_L 0.89 0.18 0.00
67_A 135_A 0.89 0.18 0.00
51_H 59_L 0.89 0.18 0.00
22_E 94_G 0.88 0.18 0.00
47_V 32_T 0.88 0.18 0.00
52_R 107_W 0.88 0.17 0.00
36_M 106_G 0.88 0.17 0.00
64_V 38_Q 0.88 0.17 0.00
47_V 102_L 0.88 0.17 0.00
31_S 42_K 0.88 0.17 0.00
64_V 130_G 0.88 0.17 0.00
32_V 109_A 0.88 0.17 0.00
25_A 63_T 0.88 0.17 0.00
85_L 79_K 0.87 0.17 0.00
81_A 152_L 0.87 0.17 0.00
25_A 127_G 0.87 0.17 0.00
34_Q 28_N 0.87 0.17 0.00
72_P 63_T 0.87 0.17 0.00
10_D 140_A 0.87 0.17 0.00
81_A 74_L 0.87 0.17 0.00
71_P 47_Y 0.86 0.17 0.00
18_K 30_F 0.86 0.17 0.00
25_A 99_D 0.86 0.17 0.00
14_T 28_N 0.86 0.17 0.00
21_I 43_I 0.86 0.17 0.00
86_Q 134_E 0.86 0.16 0.00
59_E 76_S 0.85 0.16 0.00
9_I 128_I 0.85 0.16 0.00
71_P 64_L 0.85 0.16 0.00
31_S 132_F 0.84 0.16 0.00
50_Q 69_F 0.84 0.16 0.00
46_E 145_K 0.84 0.16 0.00
40_A 143_F 0.84 0.15 0.00
59_E 154_G 0.84 0.15 0.00
54_V 67_S 0.83 0.15 0.00
62_T 55_E 0.82 0.15 0.00
66_D 51_R 0.82 0.15 0.00
59_E 120_W 0.82 0.15 0.00
84_R 23_G 0.82 0.15 0.00
38_N 88_I 0.82 0.15 0.00
57_N 134_E 0.82 0.15 0.00
9_I 62_Y 0.82 0.15 0.00
14_T 104_G 0.81 0.15 0.00
84_R 109_A 0.81 0.15 0.00
81_A 38_Q 0.81 0.14 0.00
13_L 92_T 0.81 0.14 0.00
11_L 83_I 0.81 0.14 0.00
48_I 85_Y 0.81 0.14 0.00
60_S 94_G 0.81 0.14 0.00
33_S 93_L 0.81 0.14 0.00
33_S 121_S 0.80 0.14 0.00
32_V 147_L 0.80 0.14 0.00
22_E 65_C 0.80 0.14 0.00
84_R 126_V 0.79 0.14 0.00
64_V 156_N 0.79 0.14 0.00
37_L 19_R 0.79 0.14 0.00
46_E 33_T 0.79 0.14 0.00
61_W 59_L 0.79 0.14 0.00
33_S 34_H 0.79 0.14 0.00
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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