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OPENSEQ.org
E B
Genes: A B A+B
Length: 144 85 222
Sequences: 94 302 65
Seq/Len: 0.65 3.55 0.29
MirrorTree (Pazo et al. 2001) 0.76
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.28
2 0.00 0.00 0.28
5 0.00 0.00 0.28
10 0.01 0.01 0.28
20 0.02 0.01 0.28
100 0.03 0.02 0.28
∞ 0.11 0.04 0.28
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
132_M 23_E 1.56 0.44 0.00
55_R 61_L 1.50 0.41 0.00
79_Q 16_D 1.42 0.36 0.00
104_Q 16_D 1.39 0.34 0.00
23_A 74_L 1.36 0.32 0.00
115_A 55_L 1.33 0.30 0.00
87_L 43_R 1.33 0.30 0.00
61_S 43_R 1.32 0.30 0.00
24_A 80_A 1.31 0.30 0.00
101_V 14_T 1.31 0.29 0.00
38_R 70_V 1.29 0.28 0.00
114_V 66_V 1.28 0.28 0.00
118_P 74_L 1.26 0.27 0.00
82_V 65_R 1.26 0.26 0.00
43_L 29_W 1.23 0.25 0.00
40_R 23_E 1.23 0.25 0.00
103_T 35_G 1.21 0.24 0.00
2_S 18_M 1.19 0.23 0.00
73_A 19_V 1.19 0.23 0.00
31_L 14_T 1.19 0.23 0.00
101_V 34_T 1.17 0.22 0.00
25_V 59_F 1.17 0.22 0.00
44_S 25_T 1.16 0.22 0.00
74_G 77_L 1.14 0.21 0.00
64_A 73_L 1.14 0.21 0.00
101_V 28_Y 1.13 0.21 0.00
57_E 52_V 1.11 0.20 0.00
47_A 12_A 1.11 0.19 0.00
128_F 73_L 1.10 0.19 0.00
99_T 6_A 1.10 0.19 0.00
35_P 54_E 1.10 0.19 0.00
51_R 74_L 1.09 0.19 0.00
85_V 62_D 1.09 0.19 0.00
82_V 37_A 1.09 0.19 0.00
58_A 55_L 1.08 0.18 0.00
42_V 38_V 1.08 0.18 0.00
114_V 61_L 1.07 0.18 0.00
65_V 6_A 1.06 0.18 0.00
47_A 48_V 1.06 0.17 0.00
67_S 46_K 1.05 0.17 0.00
96_D 10_A 1.04 0.17 0.00
21_A 54_E 1.03 0.17 0.00
67_S 66_V 1.03 0.17 0.00
41_R 35_G 1.03 0.16 0.00
10_R 24_T 1.02 0.16 0.00
114_V 68_A 1.01 0.16 0.00
3_F 22_H 1.01 0.16 0.00
134_V 1_M 1.01 0.15 0.00
53_A 14_T 1.00 0.15 0.00
38_R 40_R 1.00 0.15 0.00
38_R 23_E 0.99 0.15 0.00
137_A 52_V 0.99 0.15 0.00
106_F 28_Y 0.99 0.15 0.00
121_E 28_Y 0.99 0.15 0.00
6_V 23_E 0.98 0.15 0.00
46_V 56_S 0.98 0.15 0.00
56_A 40_R 0.97 0.14 0.00
79_Q 60_S 0.97 0.14 0.00
22_R 39_V 0.96 0.14 0.00
26_T 68_A 0.96 0.14 0.00
86_L 77_L 0.96 0.14 0.00
21_A 46_K 0.96 0.14 0.00
108_A 9_V 0.96 0.14 0.00
117_C 10_A 0.96 0.14 0.00
73_A 41_S 0.96 0.14 0.00
6_V 78_T 0.95 0.14 0.00
130_T 81_G 0.94 0.14 0.00
89_R 21_L 0.94 0.14 0.00
130_T 76_R 0.94 0.13 0.00
124_D 62_D 0.94 0.13 0.00
84_T 31_L 0.93 0.13 0.00
16_A 71_D 0.93 0.13 0.00
131_L 73_L 0.92 0.13 0.00
7_P 63_I 0.92 0.13 0.00
115_A 63_I 0.92 0.13 0.00
31_L 34_T 0.92 0.13 0.00
99_T 61_L 0.92 0.13 0.00
96_D 15_D 0.91 0.13 0.00
58_A 33_T 0.91 0.12 0.00
67_S 41_S 0.91 0.12 0.00
2_S 50_E 0.91 0.12 0.00
82_V 76_R 0.90 0.12 0.00
127_Y 16_D 0.90 0.12 0.00
84_T 39_V 0.90 0.12 0.00
108_A 1_M 0.90 0.12 0.00
120_G 8_H 0.89 0.12 0.00
13_V 12_A 0.88 0.12 0.00
117_C 8_H 0.87 0.12 0.00
88_C 29_W 0.87 0.11 0.00
138_T 64_T 0.87 0.11 0.00
82_V 83_V 0.87 0.11 0.00
20_L 55_L 0.87 0.11 0.00
39_L 22_H 0.87 0.11 0.00
128_F 59_F 0.87 0.11 0.00
24_A 61_L 0.87 0.11 0.00
14_P 23_E 0.86 0.11 0.00
99_T 58_R 0.86 0.11 0.00
32_I 30_M 0.86 0.11 0.00
7_P 71_D 0.86 0.11 0.00
114_V 8_H 0.85 0.11 0.00
9_R 72_A 0.85 0.11 0.00
124_D 33_T 0.85 0.11 0.00
64_A 19_V 0.85 0.11 0.00
38_R 66_V 0.85 0.11 0.00
26_T 80_A 0.85 0.11 0.00
122_G 63_I 0.85 0.11 0.00
4_P 82_L 0.85 0.11 0.00
131_L 58_R 0.85 0.11 0.00
38_R 43_R 0.85 0.11 0.00
48_R 55_L 0.84 0.11 0.00
13_V 27_R 0.84 0.11 0.00
98_C 35_G 0.84 0.11 0.00
66_V 56_S 0.84 0.11 0.00
107_R 10_A 0.84 0.10 0.00
58_A 19_V 0.84 0.10 0.00
12_H 59_F 0.84 0.10 0.00
114_V 60_S 0.84 0.10 0.00
49_G 29_W 0.83 0.10 0.00
129_Q 18_M 0.83 0.10 0.00
67_S 35_G 0.83 0.10 0.00
114_V 49_A 0.83 0.10 0.00
62_R 45_G 0.83 0.10 0.00
132_M 59_F 0.83 0.10 0.00
58_A 51_I 0.83 0.10 0.00
132_M 6_A 0.83 0.10 0.00
102_R 31_L 0.83 0.10 0.00
62_R 43_R 0.83 0.10 0.00
85_V 39_V 0.83 0.10 0.00
119_V 23_E 0.82 0.10 0.00
120_G 70_V 0.82 0.10 0.00
96_D 66_V 0.82 0.10 0.00
33_R 19_V 0.81 0.10 0.00
104_Q 41_S 0.81 0.10 0.00
60_R 1_M 0.81 0.10 0.00
113_E 81_G 0.81 0.10 0.00
73_A 65_R 0.81 0.10 0.00
33_R 5_L 0.81 0.10 0.00
96_D 4_S 0.81 0.10 0.00
16_A 25_T 0.81 0.10 0.00
40_R 78_T 0.81 0.10 0.00
57_E 68_A 0.80 0.10 0.00
39_L 76_R 0.80 0.10 0.00
72_C 77_L 0.80 0.10 0.00
51_R 4_S 0.80 0.10 0.00
138_T 49_A 0.79 0.10 0.00
90_A 63_I 0.79 0.10 0.00
125_V 52_V 0.79 0.09 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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