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OPENSEQ.org
TA_one
Genes: A B A+B
Length: 111 154 251
Sequences: 555 144 105
Seq/Len: 5 0.94 0.42
MirrorTree (Pazo et al. 2001) 0.88
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 0.00 0.40
2 0.01 0.00 0.40
5 0.01 0.01 0.40
10 0.02 0.01 0.40
20 0.02 0.01 0.40
100 0.02 0.02 0.40
∞ 0.04 0.03 0.40
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
107_I 92_R 2.17 0.88 0.42
29_V 80_N 1.70 0.65 0.15
66_M 107_I 1.65 0.62 0.13
107_I 89_G 1.52 0.53 0.09
16_K 69_F 1.50 0.51 0.08
86_P 5_Q 1.38 0.42 0.06
101_V 67_P 1.37 0.41 0.05
41_S 68_A 1.37 0.41 0.05
20_R 92_R 1.36 0.41 0.05
110_D 107_I 1.35 0.40 0.05
107_I 119_T 1.33 0.39 0.05
44_Y 52_V 1.33 0.39 0.05
78_Q 103_E 1.29 0.36 0.04
105_D 77_S 1.29 0.36 0.04
20_R 93_Y 1.29 0.36 0.04
46_I 62_V 1.28 0.36 0.04
105_D 150_T 1.24 0.33 0.04
31_E 124_T 1.21 0.31 0.03
107_I 44_A 1.18 0.29 0.03
101_V 142_D 1.18 0.29 0.03
91_Q 14_A 1.18 0.29 0.03
107_I 52_V 1.17 0.28 0.03
38_G 121_G 1.17 0.28 0.03
107_I 91_G 1.17 0.28 0.03
47_L 80_N 1.16 0.27 0.03
74_D 69_F 1.16 0.27 0.03
17_V 119_T 1.15 0.27 0.02
16_K 57_E 1.14 0.27 0.02
55_C 132_K 1.14 0.27 0.02
93_K 138_H 1.14 0.27 0.02
93_K 142_D 1.14 0.26 0.02
91_Q 23_D 1.13 0.26 0.02
21_G 89_G 1.13 0.26 0.02
65_T 7_V 1.13 0.26 0.02
84_T 13_Y 1.11 0.25 0.02
99_M 107_I 1.10 0.25 0.02
25_I 150_T 1.08 0.23 0.02
23_T 18_F 1.08 0.23 0.02
37_P 17_C 1.07 0.23 0.02
23_T 126_A 1.06 0.22 0.02
31_E 101_E 1.06 0.22 0.02
81_P 120_Y 1.05 0.22 0.02
47_L 117_L 1.05 0.22 0.02
94_K 117_L 1.05 0.22 0.02
44_Y 93_Y 1.05 0.22 0.02
86_P 38_E 1.04 0.21 0.02
51_Q 12_L 1.04 0.21 0.02
81_P 29_V 1.04 0.21 0.02
78_Q 12_L 1.04 0.21 0.02
20_R 119_T 1.03 0.21 0.02
23_T 88_F 1.03 0.21 0.02
100_D 144_E 1.03 0.21 0.01
56_R 143_W 1.02 0.20 0.01
47_L 73_K 1.02 0.20 0.01
35_L 92_R 1.02 0.20 0.01
75_A 69_F 1.02 0.20 0.01
44_Y 28_E 1.02 0.20 0.01
53_F 56_I 1.01 0.20 0.01
23_T 49_L 1.01 0.20 0.01
105_D 115_N 1.01 0.20 0.01
34_K 33_K 1.01 0.20 0.01
99_M 79_K 1.01 0.20 0.01
64_H 74_S 1.00 0.20 0.01
64_H 82_D 1.00 0.19 0.01
57_L 65_S 1.00 0.19 0.01
49_G 132_K 1.00 0.19 0.01
44_Y 48_L 0.99 0.19 0.01
109_D 108_L 0.99 0.19 0.01
100_D 54_K 0.99 0.19 0.01
25_I 56_I 0.98 0.19 0.01
73_L 69_F 0.97 0.18 0.01
110_D 22_Y 0.97 0.18 0.01
21_G 48_L 0.96 0.18 0.01
109_D 40_Y 0.96 0.18 0.01
43_H 99_Y 0.96 0.18 0.01
85_R 104_K 0.96 0.18 0.01
37_P 92_R 0.96 0.17 0.01
81_P 126_A 0.96 0.17 0.01
47_L 55_V 0.96 0.17 0.01
41_S 58_E 0.96 0.17 0.01
92_G 150_T 0.95 0.17 0.01
96_V 4_P 0.95 0.17 0.01
42_I 67_P 0.94 0.17 0.01
91_Q 30_E 0.94 0.17 0.01
17_V 117_L 0.94 0.17 0.01
37_P 91_G 0.94 0.17 0.01
106_E 91_G 0.94 0.17 0.01
46_I 114_E 0.94 0.17 0.01
58_G 46_T 0.94 0.17 0.01
38_G 101_E 0.94 0.17 0.01
19_I 48_L 0.94 0.17 0.01
80_N 80_N 0.94 0.17 0.01
27_A 89_G 0.93 0.16 0.01
62_E 58_E 0.93 0.16 0.01
20_R 28_E 0.93 0.16 0.01
50_G 18_F 0.93 0.16 0.01
38_G 56_I 0.93 0.16 0.01
48_P 102_K 0.93 0.16 0.01
65_T 116_T 0.92 0.16 0.01
107_I 48_L 0.92 0.16 0.01
20_R 52_V 0.92 0.16 0.01
72_F 46_T 0.92 0.16 0.01
93_K 128_T 0.92 0.16 0.01
54_M 131_S 0.92 0.16 0.01
72_F 124_T 0.92 0.16 0.01
29_V 16_P 0.91 0.16 0.01
77_I 151_E 0.91 0.16 0.01
20_R 43_K 0.90 0.15 0.01
67_N 86_V 0.90 0.15 0.01
20_R 45_A 0.90 0.15 0.01
41_S 59_H 0.90 0.15 0.01
78_Q 20_E 0.90 0.15 0.01
16_K 132_K 0.90 0.15 0.01
105_D 84_S 0.90 0.15 0.01
16_K 73_K 0.90 0.15 0.01
93_K 104_K 0.90 0.15 0.01
81_P 88_F 0.90 0.15 0.01
41_S 57_E 0.89 0.15 0.01
109_D 80_N 0.89 0.15 0.01
101_V 31_T 0.89 0.15 0.01
38_G 117_L 0.88 0.14 0.01
100_D 34_G 0.88 0.14 0.01
72_F 54_K 0.88 0.14 0.01
94_K 149_E 0.88 0.14 0.01
34_K 28_E 0.88 0.14 0.01
21_G 28_E 0.88 0.14 0.01
78_Q 11_A 0.88 0.14 0.01
71_R 153_T 0.88 0.14 0.01
73_L 129_V 0.87 0.14 0.01
40_D 91_G 0.87 0.14 0.01
91_Q 108_L 0.87 0.14 0.01
104_D 104_K 0.87 0.14 0.01
36_K 105_V 0.87 0.14 0.01
106_E 92_R 0.87 0.14 0.01
45_E 132_K 0.86 0.14 0.01
89_I 34_G 0.86 0.14 0.01
40_D 14_A 0.86 0.14 0.01
59_D 138_H 0.86 0.14 0.01
32_A 143_W 0.86 0.14 0.01
79_N 36_D 0.86 0.14 0.01
53_F 128_T 0.86 0.14 0.01
28_P 65_S 0.86 0.14 0.01
40_D 93_Y 0.86 0.14 0.01
66_M 93_Y 0.85 0.14 0.01
25_I 122_K 0.85 0.13 0.01
81_P 49_L 0.85 0.13 0.01
27_A 55_V 0.85 0.13 0.01
74_D 114_E 0.85 0.13 0.01
76_D 109_G 0.85 0.13 0.01
89_I 149_E 0.84 0.13 0.01
94_K 150_T 0.84 0.13 0.01
97_A 46_T 0.84 0.13 0.01
86_P 23_D 0.84 0.13 0.01
54_M 33_K 0.84 0.13 0.01
96_V 135_K 0.84 0.13 0.01
23_T 50_A 0.84 0.13 0.01
56_R 40_Y 0.84 0.13 0.01
37_P 89_G 0.84 0.13 0.01
38_G 100_S 0.83 0.13 0.01
45_E 12_L 0.83 0.13 0.01
13_T 28_E 0.83 0.13 0.01
104_D 81_K 0.83 0.13 0.01
32_A 80_N 0.83 0.13 0.01
38_G 22_Y 0.83 0.13 0.01
17_V 122_K 0.83 0.13 0.01
108_G 44_A 0.83 0.13 0.01
12_T 46_T 0.83 0.13 0.01
20_R 89_G 0.83 0.13 0.01
19_I 119_T 0.83 0.13 0.01
62_E 24_A 0.82 0.12 0.01
16_K 61_T 0.82 0.12 0.01
53_F 59_H 0.82 0.12 0.01
83_K 27_A 0.82 0.12 0.01
104_D 145_T 0.82 0.12 0.01
21_G 93_Y 0.82 0.12 0.01
40_D 48_L 0.82 0.12 0.01
40_D 89_G 0.82 0.12 0.01
17_V 52_V 0.81 0.12 0.01
99_M 91_G 0.81 0.12 0.01
27_A 44_A 0.81 0.12 0.01
41_S 89_G 0.81 0.12 0.01
73_L 142_D 0.81 0.12 0.01
86_P 34_G 0.81 0.12 0.01
79_N 39_N 0.80 0.12 0.01
23_T 120_Y 0.80 0.12 0.01
71_R 42_R 0.80 0.12 0.01
55_C 34_G 0.80 0.12 0.01
21_G 117_L 0.80 0.12 0.01
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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