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OPENSEQ.org
1r6o_D_A
Genes: A B A+B
Length: 106 143 239
Sequences: 1103 1229 94
Seq/Len: 10.41 8.59 0.39
MirrorTree (Pazo et al. 2001) 0.75
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 0.06 0.01 0.36
2 0.06 0.01 0.37
5 0.06 0.01 0.38
10 0.06 0.01 0.38
20 0.06 0.01 0.38
100 0.06 0.02 0.45
∞ 0.09 0.08 1.29
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
79_E 83_S 1.85 0.72 0.01
79_E 100_R 1.81 0.70 0.01
71_A 116_Q 1.53 0.51 0.01
78_A 117_E 1.53 0.51 0.01
41_E 33_A 1.49 0.48 0.01
64_A 50_D 1.45 0.46 0.01
71_A 109_L 1.35 0.38 0.00
39_P 2_L 1.34 0.38 0.00
41_E 138_I 1.33 0.37 0.00
78_A 134_V 1.33 0.37 0.00
39_P 136_N 1.32 0.36 0.00
101_C 112_I 1.30 0.35 0.00
63_L 120_A 1.29 0.34 0.00
75_V 56_Q 1.29 0.34 0.00
27_M 10_L 1.28 0.34 0.00
105_K 123_L 1.25 0.32 0.00
80_V 35_L 1.24 0.31 0.00
28_Y 13_A 1.23 0.30 0.00
27_M 59_E 1.22 0.30 0.00
86_A 50_D 1.21 0.29 0.00
41_E 7_E 1.21 0.29 0.00
76_F 45_E 1.20 0.29 0.00
54_D 61_F 1.19 0.28 0.00
30_V 58_L 1.17 0.27 0.00
80_V 129_V 1.16 0.27 0.00
101_C 119_Q 1.16 0.27 0.00
15_E 92_V 1.16 0.26 0.00
26_S 117_E 1.16 0.26 0.00
76_F 94_H 1.14 0.25 0.00
79_E 27_V 1.13 0.25 0.00
39_P 105_G 1.11 0.24 0.00
39_P 38_P 1.10 0.23 0.00
85_V 10_L 1.09 0.23 0.00
101_C 113_F 1.08 0.22 0.00
97_H 105_G 1.08 0.22 0.00
39_P 9_S 1.07 0.22 0.00
77_T 129_V 1.07 0.22 0.00
75_V 139_S 1.06 0.21 0.00
71_A 128_E 1.06 0.21 0.00
39_P 30_L 1.05 0.21 0.00
62_M 28_E 1.03 0.20 0.00
66_H 28_E 1.03 0.20 0.00
76_F 58_L 1.02 0.19 0.00
37_Y 107_N 1.02 0.19 0.00
93_R 117_E 1.02 0.19 0.00
19_R 137_F 1.01 0.19 0.00
79_E 79_Q 1.00 0.18 0.00
84_K 118_S 0.99 0.18 0.00
75_V 142_T 0.99 0.18 0.00
85_V 112_I 0.99 0.18 0.00
96_E 117_E 0.99 0.18 0.00
45_D 35_L 0.99 0.18 0.00
19_R 9_S 0.99 0.18 0.00
48_Q 79_Q 0.98 0.18 0.00
56_E 51_L 0.98 0.18 0.00
56_E 110_V 0.98 0.18 0.00
97_H 86_R 0.98 0.17 0.00
28_Y 117_E 0.97 0.17 0.00
39_P 46_A 0.97 0.17 0.00
97_H 30_L 0.97 0.17 0.00
46_V 12_M 0.96 0.17 0.00
16_E 24_F 0.96 0.17 0.00
85_V 38_P 0.95 0.16 0.00
105_K 117_E 0.94 0.16 0.00
101_C 80_P 0.93 0.16 0.00
39_P 32_L 0.93 0.15 0.00
23_K 42_E 0.93 0.15 0.00
31_I 137_F 0.93 0.15 0.00
33_V 32_L 0.93 0.15 0.00
96_E 142_T 0.92 0.15 0.00
37_Y 73_E 0.92 0.15 0.00
56_E 24_F 0.92 0.15 0.00
65_V 99_G 0.92 0.15 0.00
46_V 109_L 0.92 0.15 0.00
16_E 27_V 0.92 0.15 0.00
23_K 55_R 0.91 0.15 0.00
54_D 39_S 0.91 0.15 0.00
76_F 61_F 0.90 0.15 0.00
77_T 65_T 0.90 0.14 0.00
69_G 110_V 0.90 0.14 0.00
36_D 85_Q 0.90 0.14 0.00
88_V 141_G 0.90 0.14 0.00
78_A 137_F 0.90 0.14 0.00
42_F 26_T 0.89 0.14 0.00
22_L 119_Q 0.89 0.14 0.00
31_I 49_V 0.89 0.14 0.00
53_Y 101_N 0.89 0.14 0.00
100_L 62_I 0.89 0.14 0.00
78_A 129_V 0.89 0.14 0.00
97_H 107_N 0.88 0.14 0.00
105_K 65_T 0.88 0.14 0.00
39_P 80_P 0.88 0.14 0.00
37_Y 55_R 0.88 0.14 0.00
76_F 70_P 0.88 0.14 0.00
28_Y 95_V 0.88 0.14 0.00
101_C 103_V 0.87 0.14 0.00
59_T 33_A 0.87 0.13 0.00
95_N 125_R 0.87 0.13 0.00
37_Y 139_S 0.87 0.13 0.00
24_P 48_S 0.86 0.13 0.00
97_H 27_V 0.86 0.13 0.00
27_M 74_E 0.86 0.13 0.00
24_P 37_N 0.86 0.13 0.00
79_E 2_L 0.86 0.13 0.00
61_L 101_N 0.85 0.13 0.00
83_T 81_T 0.85 0.13 0.00
31_I 98_S 0.85 0.13 0.00
28_Y 126_K 0.85 0.13 0.00
79_E 101_N 0.85 0.13 0.00
33_V 12_M 0.85 0.13 0.00
58_A 118_S 0.85 0.13 0.00
67_Y 123_L 0.85 0.13 0.00
17_K 64_Q 0.84 0.12 0.00
82_E 86_R 0.84 0.12 0.00
65_V 98_S 0.84 0.12 0.00
57_R 104_T 0.83 0.12 0.00
76_F 117_E 0.83 0.12 0.00
77_T 88_L 0.83 0.12 0.00
100_L 93_F 0.83 0.12 0.00
48_Q 42_E 0.83 0.12 0.00
101_C 85_Q 0.83 0.12 0.00
32_L 52_V 0.83 0.12 0.00
74_G 29_H 0.82 0.12 0.00
32_L 112_I 0.82 0.12 0.00
97_H 81_T 0.82 0.12 0.00
41_E 109_L 0.82 0.12 0.00
48_Q 136_N 0.82 0.12 0.00
100_L 2_L 0.82 0.12 0.00
105_K 39_S 0.81 0.12 0.00
27_M 35_L 0.81 0.12 0.00
88_V 86_R 0.81 0.12 0.00
21_A 9_S 0.81 0.12 0.00
53_Y 2_L 0.81 0.12 0.00
63_L 127_H 0.81 0.12 0.00
94_E 23_E 0.81 0.11 0.00
46_V 51_L 0.81 0.11 0.00
84_K 120_A 0.80 0.11 0.00
56_E 137_F 0.80 0.11 0.00
79_E 68_V 0.80 0.11 0.00
103_L 119_Q 0.80 0.11 0.00
84_K 34_L 0.80 0.11 0.00
15_E 121_A 0.80 0.11 0.00
79_E 16_R 0.79 0.11 0.00
104_E 99_G 0.79 0.11 0.00
96_E 88_L 0.79 0.11 0.00
60_Q 72_S 0.79 0.11 0.00
69_G 85_Q 0.79 0.11 0.00
102_T 2_L 0.78 0.11 0.00
73_C 27_V 0.78 0.11 0.00
79_E 19_E 0.78 0.11 0.00
101_C 122_Y 0.78 0.11 0.00
75_V 14_F 0.78 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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