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OPENSEQ.org
5206
Genes: A B A+B
Length: 107 117 217
Sequences: 1370 562 202
Seq/Len: 12.8 4.8 0.93
MirrorTree (Pazo et al. 2001) 0.76
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 0.00 0.00 0.90
2 0.01 0.00 0.92
5 0.01 0.01 0.92
10 0.01 0.01 0.92
20 0.01 0.01 0.92
100 0.02 0.02 0.94
∞ 0.04 0.06 1.03
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
21_G 107_E 3.20 1.00 1.00
11_A 84_F 2.48 0.99 0.98
19_A 87_L 1.92 0.93 0.88
27_A 94_L 1.71 0.86 0.77
15_I 84_F 1.71 0.86 0.76
28_I 94_L 1.54 0.78 0.63
78_Q 43_K 1.54 0.77 0.63
18_A 91_Y 1.53 0.77 0.62
78_Q 41_F 1.51 0.75 0.60
88_N 111_I 1.44 0.70 0.53
2_T 114_D 1.43 0.69 0.52
14_A 6_W 1.42 0.69 0.51
10_P 66_F 1.38 0.66 0.47
69_Y 69_A 1.36 0.64 0.45
76_T 43_K 1.25 0.54 0.34
53_K 43_K 1.24 0.53 0.33
58_K 40_V 1.19 0.49 0.29
35_T 86_E 1.19 0.48 0.28
90_I 20_E 1.18 0.48 0.28
90_I 95_T 1.13 0.44 0.23
66_F 11_A 1.13 0.43 0.23
39_A 28_T 1.12 0.42 0.22
39_A 27_E 1.11 0.42 0.22
71_N 88_A 1.11 0.42 0.21
93_K 84_F 1.10 0.41 0.21
22_L 80_E 1.10 0.41 0.20
49_P 53_I 1.09 0.40 0.20
87_P 7_F 1.06 0.38 0.18
30_A 103_I 1.06 0.37 0.18
35_T 108_L 1.04 0.36 0.17
76_T 10_E 1.04 0.36 0.17
23_S 17_T 1.04 0.36 0.16
15_I 87_L 1.04 0.35 0.16
21_G 72_D 1.04 0.35 0.16
14_A 66_F 1.03 0.35 0.16
12_F 83_G 1.02 0.34 0.15
27_A 77_N 1.02 0.34 0.15
11_A 28_T 1.01 0.34 0.15
50_V 111_I 1.00 0.33 0.14
82_S 43_K 1.00 0.32 0.14
37_D 69_A 1.00 0.32 0.14
86_R 53_I 0.99 0.32 0.14
22_L 92_A 0.98 0.31 0.13
65_V 7_F 0.98 0.31 0.13
27_A 102_M 0.98 0.31 0.13
28_I 18_D 0.97 0.30 0.12
47_L 49_R 0.96 0.29 0.12
83_G 75_N 0.96 0.29 0.12
78_Q 28_T 0.95 0.29 0.12
78_Q 10_E 0.95 0.29 0.11
32_T 14_H 0.95 0.29 0.11
79_K 41_F 0.95 0.29 0.11
10_P 102_M 0.95 0.28 0.11
82_S 10_E 0.95 0.28 0.11
29_S 74_S 0.95 0.28 0.11
82_S 41_F 0.94 0.28 0.11
70_L 73_M 0.94 0.28 0.11
18_A 68_Y 0.94 0.28 0.11
86_R 99_L 0.93 0.27 0.10
34_R 68_Y 0.93 0.27 0.10
33_M 33_A 0.92 0.27 0.10
36_F 75_N 0.92 0.27 0.10
55_L 40_V 0.92 0.26 0.10
69_Y 5_K 0.91 0.26 0.09
35_T 105_T 0.91 0.26 0.09
79_K 91_Y 0.90 0.25 0.09
44_V 40_V 0.89 0.25 0.09
14_A 79_Q 0.89 0.24 0.09
24_S 100_T 0.89 0.24 0.09
57_E 103_I 0.88 0.23 0.08
74_V 41_F 0.87 0.23 0.08
3_A 115_C 0.87 0.23 0.08
13_E 27_E 0.87 0.23 0.08
66_F 69_A 0.87 0.23 0.08
78_Q 55_L 0.87 0.23 0.08
71_N 4_T 0.86 0.22 0.07
91_S 50_E 0.86 0.22 0.07
4_K 115_C 0.86 0.22 0.07
82_S 56_A 0.86 0.22 0.07
19_A 9_R 0.86 0.22 0.07
35_T 60_S 0.85 0.22 0.07
24_S 19_E 0.85 0.22 0.07
19_A 88_A 0.85 0.22 0.07
75_S 10_E 0.85 0.22 0.07
2_T 32_K 0.84 0.21 0.07
75_S 43_K 0.84 0.21 0.07
17_S 59_G 0.84 0.21 0.07
85_K 62_W 0.84 0.21 0.07
34_R 69_A 0.84 0.21 0.07
20_A 17_T 0.84 0.21 0.07
85_K 54_I 0.83 0.21 0.07
91_S 89_K 0.83 0.21 0.07
33_M 39_G 0.83 0.21 0.07
72_T 43_K 0.83 0.21 0.07
93_K 78_S 0.83 0.21 0.06
2_T 46_H 0.83 0.20 0.06
83_G 68_Y 0.82 0.20 0.06
75_S 55_L 0.82 0.20 0.06
53_K 57_K 0.82 0.20 0.06
78_Q 62_W 0.82 0.20 0.06
51_E 96_K 0.82 0.20 0.06
51_E 85_R 0.81 0.20 0.06
72_T 62_W 0.81 0.19 0.06
49_P 84_F 0.80 0.19 0.06
74_V 68_Y 0.80 0.19 0.06
22_L 94_L 0.80 0.19 0.06
76_T 27_E 0.80 0.19 0.06
24_S 85_R 0.80 0.19 0.06
3_A 15_A 0.79 0.18 0.05
24_S 78_S 0.79 0.18 0.05
57_E 104_N 0.79 0.18 0.05
64_P 83_G 0.79 0.18 0.05
19_A 57_K 0.79 0.18 0.05
26_D 32_K 0.79 0.18 0.05
14_A 65_T 0.78 0.18 0.05
91_S 76_I 0.78 0.18 0.05
50_V 8_A 0.78 0.18 0.05
72_T 68_Y 0.78 0.18 0.05
64_P 78_S 0.78 0.18 0.05
55_L 113_Y 0.78 0.17 0.05
52_I 7_F 0.78 0.17 0.05
98_V 108_L 0.77 0.17 0.05
39_A 83_G 0.77 0.17 0.05
22_L 36_L 0.77 0.17 0.05
59_L 92_A 0.77 0.17 0.05
86_R 22_C 0.77 0.17 0.05
49_P 86_E 0.76 0.17 0.04
23_S 111_I 0.76 0.17 0.04
20_A 102_M 0.76 0.17 0.04
54_A 106_K 0.76 0.17 0.04
15_I 78_S 0.76 0.17 0.04
89_G 76_I 0.76 0.17 0.04
25_V 3_K 0.76 0.17 0.04
59_L 9_R 0.76 0.17 0.04
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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