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OPENSEQ.org
1006
Genes: A B A+B
Length: 63 95 149
Sequences: 344 3947 246
Seq/Len: 5.46 41.55 1.65
MirrorTree (Pazo et al. 2001) 0.70
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 1.56
2 0.01 0.03 1.62
5 0.01 0.04 1.63
10 0.01 0.05 1.62
20 0.02 0.06 1.65
100 0.03 0.08 1.71
∞ 0.05 0.14 1.89
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
48_E 11_R 2.79 1.00 1.00
45_V 11_R 2.45 1.00 0.99
48_E 15_R 2.15 0.99 0.97
25_L 85_T 2.01 0.98 0.96
35_D 9_S 1.97 0.98 0.95
32_S 82_V 1.86 0.97 0.94
28_K 83_S 1.65 0.93 0.87
28_K 13_D 1.56 0.90 0.82
28_K 85_T 1.50 0.88 0.79
57_A 30_R 1.35 0.80 0.67
32_S 83_S 1.34 0.79 0.66
52_L 19_T 1.27 0.74 0.59
50_E 33_K 1.27 0.74 0.59
18_E 71_L 1.24 0.71 0.55
53_I 33_K 1.23 0.70 0.55
18_E 51_P 1.23 0.70 0.54
46_M 37_E 1.20 0.67 0.51
33_L 73_R 1.16 0.63 0.47
21_Y 85_T 1.14 0.62 0.45
24_W 63_V 1.14 0.62 0.45
44_E 23_K 1.11 0.59 0.41
40_I 11_R 1.10 0.57 0.40
55_Q 8_P 1.09 0.57 0.40
43_D 46_H 1.09 0.57 0.39
23_E 36_I 1.07 0.54 0.37
45_V 22_A 1.07 0.54 0.36
20_S 12_D 1.06 0.53 0.35
21_Y 68_Y 1.02 0.49 0.32
40_I 34_I 1.00 0.47 0.30
42_H 4_I 1.00 0.47 0.29
24_W 69_I 0.99 0.46 0.29
42_H 66_P 0.97 0.44 0.27
34_A 31_R 0.97 0.43 0.26
36_T 80_E 0.95 0.42 0.25
22_N 17_I 0.94 0.40 0.23
13_E 89_R 0.92 0.39 0.22
52_L 18_I 0.92 0.38 0.22
20_S 90_Q 0.91 0.37 0.21
33_L 50_Y 0.91 0.37 0.21
26_R 21_I 0.90 0.36 0.20
25_L 54_E 0.90 0.36 0.20
49_M 18_I 0.90 0.36 0.20
51_N 26_P 0.90 0.36 0.20
35_D 12_D 0.89 0.36 0.20
46_M 14_L 0.89 0.36 0.20
24_W 64_T 0.89 0.36 0.19
56_I 22_A 0.88 0.34 0.18
22_N 54_E 0.88 0.34 0.18
43_D 16_Q 0.88 0.34 0.18
18_E 81_I 0.86 0.33 0.17
57_A 44_S 0.86 0.33 0.17
6_S 50_Y 0.86 0.33 0.17
7_P 91_F 0.86 0.33 0.17
39_A 81_I 0.86 0.33 0.17
53_I 14_L 0.85 0.32 0.16
21_Y 62_I 0.84 0.31 0.16
42_H 79_I 0.84 0.31 0.16
17_Q 90_Q 0.84 0.31 0.16
48_E 16_Q 0.84 0.31 0.15
39_A 7_L 0.84 0.31 0.15
57_A 49_L 0.83 0.30 0.15
19_N 69_I 0.82 0.29 0.14
29_V 58_G 0.81 0.28 0.14
35_D 7_L 0.81 0.28 0.14
33_L 81_I 0.81 0.28 0.13
42_H 6_W 0.81 0.28 0.13
12_F 65_H 0.80 0.28 0.13
28_K 9_S 0.80 0.27 0.13
21_Y 61_E 0.80 0.27 0.13
36_T 73_R 0.80 0.27 0.13
49_M 33_K 0.79 0.26 0.12
39_A 5_L 0.79 0.26 0.12
18_E 63_V 0.79 0.26 0.12
22_N 71_L 0.78 0.26 0.12
50_E 19_T 0.78 0.26 0.12
6_S 14_L 0.78 0.26 0.12
50_E 30_R 0.78 0.26 0.12
49_M 91_F 0.78 0.26 0.12
14_T 65_H 0.78 0.26 0.12
25_L 89_R 0.77 0.25 0.11
28_K 33_K 0.77 0.25 0.11
17_Q 76_A 0.77 0.25 0.11
25_L 71_L 0.76 0.24 0.11
13_E 20_Y 0.76 0.24 0.11
44_E 57_S 0.76 0.24 0.11
46_M 65_H 0.76 0.24 0.10
55_Q 37_E 0.76 0.24 0.10
46_M 33_K 0.75 0.23 0.10
23_E 77_S 0.74 0.23 0.10
7_P 14_L 0.74 0.23 0.10
34_A 74_V 0.74 0.23 0.10
26_R 55_R 0.74 0.23 0.10
24_W 55_R 0.74 0.22 0.10
57_A 87_S 0.73 0.22 0.09
9_V 50_Y 0.73 0.22 0.09
33_L 82_V 0.73 0.22 0.09
31_S 40_V 0.73 0.22 0.09
31_S 56_V 0.72 0.21 0.09
19_N 78_S 0.72 0.21 0.09
58_V 35_R 0.72 0.21 0.09
11_E 20_Y 0.72 0.21 0.09
51_N 34_I 0.72 0.21 0.09
17_Q 89_R 0.71 0.21 0.08
8_I 63_V 0.71 0.20 0.08
32_S 85_T 0.71 0.20 0.08
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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