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OPENSEQ.org
6150
Genes: A B A+B
Length: 73 126 195
Sequences: 2720 5696 73
Seq/Len: 37.26 45.21 0.37
MirrorTree (Pazo et al. 2001) 0.81
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 0.37
2 0.02 0.02 0.47
5 0.03 0.04 0.61
10 0.03 0.04 0.77
20 0.04 0.05 0.97
100 0.06 0.07 2.00
∞ 0.12 0.12 4.71
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
28_I 22_G 1.73 0.64 0.00
5_N 17_I 1.57 0.53 0.00
13_L 76_A 1.33 0.36 0.00
9_A 13_H 1.26 0.31 0.00
44_F 62_T 1.25 0.30 0.00
28_I 13_H 1.24 0.30 0.00
54_A 34_A 1.23 0.29 0.00
58_S 9_L 1.22 0.29 0.00
35_P 61_A 1.20 0.28 0.00
38_I 36_I 1.18 0.27 0.00
50_A 14_D 1.18 0.26 0.00
1_M 63_A 1.16 0.25 0.00
43_T 4_I 1.15 0.25 0.00
5_N 5_S 1.13 0.24 0.00
54_A 39_V 1.13 0.24 0.00
45_E 110_S 1.12 0.23 0.00
2_Q 5_S 1.11 0.23 0.00
48_K 96_E 1.10 0.22 0.00
7_R 91_V 1.10 0.22 0.00
24_E 75_T 1.08 0.21 0.00
60_F 14_D 1.07 0.21 0.00
59_L 85_R 1.07 0.21 0.00
6_F 71_A 1.07 0.21 0.00
4_I 91_V 1.06 0.21 0.00
21_E 76_A 1.06 0.21 0.00
22_A 99_D 1.04 0.20 0.00
4_I 36_I 1.03 0.19 0.00
30_R 104_A 1.03 0.19 0.00
44_F 90_Q 1.02 0.19 0.00
39_V 12_L 1.02 0.19 0.00
25_E 88_G 1.01 0.18 0.00
29_T 75_T 1.00 0.18 0.00
13_L 3_H 0.99 0.18 0.00
24_E 106_T 0.99 0.17 0.00
18_N 80_A 0.99 0.17 0.00
18_N 55_S 0.99 0.17 0.00
39_V 104_A 0.99 0.17 0.00
23_G 88_G 0.99 0.17 0.00
30_R 76_A 0.99 0.17 0.00
50_A 30_G 0.98 0.17 0.00
38_I 9_L 0.97 0.17 0.00
29_T 33_E 0.97 0.17 0.00
26_V 107_G 0.97 0.17 0.00
7_R 15_A 0.96 0.16 0.00
46_A 23_L 0.96 0.16 0.00
7_R 97_L 0.96 0.16 0.00
72_N 71_A 0.96 0.16 0.00
55_E 12_L 0.96 0.16 0.00
63_L 110_S 0.95 0.16 0.00
66_T 77_L 0.94 0.15 0.00
31_R 104_A 0.93 0.15 0.00
20_V 48_I 0.93 0.15 0.00
5_N 41_A 0.93 0.15 0.00
8_T 27_S 0.93 0.15 0.00
9_A 89_V 0.92 0.15 0.00
37_V 17_I 0.92 0.15 0.00
30_R 80_A 0.92 0.15 0.00
31_R 80_A 0.91 0.14 0.00
44_F 41_A 0.91 0.14 0.00
9_A 87_N 0.90 0.14 0.00
32_G 76_A 0.90 0.14 0.00
42_A 75_T 0.90 0.14 0.00
30_R 13_H 0.90 0.14 0.00
40_S 52_F 0.90 0.14 0.00
28_I 89_V 0.90 0.14 0.00
36_A 34_A 0.90 0.14 0.00
54_A 9_L 0.89 0.14 0.00
10_R 76_A 0.89 0.14 0.00
20_V 80_A 0.89 0.14 0.00
28_I 84_L 0.89 0.14 0.00
25_E 17_I 0.89 0.14 0.00
37_V 11_A 0.88 0.13 0.00
48_K 24_P 0.88 0.13 0.00
11_G 57_T 0.88 0.13 0.00
20_V 13_H 0.87 0.13 0.00
10_R 104_A 0.87 0.13 0.00
30_R 54_V 0.87 0.13 0.00
11_G 13_H 0.86 0.13 0.00
4_I 93_D 0.86 0.13 0.00
11_G 43_V 0.86 0.13 0.00
10_R 59_L 0.86 0.13 0.00
10_R 12_L 0.86 0.13 0.00
7_R 114_V 0.86 0.13 0.00
15_E 59_L 0.86 0.13 0.00
57_A 85_R 0.86 0.13 0.00
7_R 77_L 0.86 0.13 0.00
53_D 5_S 0.86 0.13 0.00
27_E 45_Y 0.85 0.12 0.00
5_N 43_V 0.85 0.12 0.00
4_I 34_A 0.85 0.12 0.00
58_S 16_N 0.85 0.12 0.00
13_L 12_L 0.85 0.12 0.00
43_T 28_D 0.85 0.12 0.00
31_R 59_L 0.85 0.12 0.00
18_N 8_E 0.84 0.12 0.00
10_R 38_R 0.84 0.12 0.00
44_F 99_D 0.84 0.12 0.00
17_L 71_A 0.84 0.12 0.00
4_I 18_N 0.84 0.12 0.00
6_F 98_A 0.84 0.12 0.00
6_F 3_H 0.84 0.12 0.00
56_F 56_A 0.84 0.12 0.00
48_K 86_R 0.83 0.12 0.00
28_I 28_D 0.83 0.12 0.00
20_V 82_L 0.83 0.12 0.00
1_M 45_Y 0.83 0.12 0.00
59_L 61_A 0.83 0.12 0.00
24_E 58_Y 0.82 0.12 0.00
67_N 59_L 0.82 0.12 0.00
25_E 55_S 0.81 0.11 0.00
37_V 68_F 0.81 0.11 0.00
37_V 25_G 0.81 0.11 0.00
58_S 99_D 0.81 0.11 0.00
38_I 69_N 0.81 0.11 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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