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OPENSEQ.org
1R6Q_AC
Genes: A B A+B
Length: 143 106 239
Sequences: 1229 1103 94
Seq/Len: 8.59 10.41 0.39
MirrorTree (Pazo et al. 2001) 0.74
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 0.01 0.06 0.36
2 0.01 0.06 0.37
5 0.01 0.06 0.38
10 0.01 0.06 0.38
20 0.01 0.06 0.38
100 0.02 0.06 0.45
∞ 0.08 0.09 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
83_S 79_E 1.69 0.62 0.00
100_R 79_E 1.68 0.62 0.00
116_Q 71_A 1.64 0.58 0.00
33_A 41_E 1.61 0.56 0.00
117_E 78_A 1.43 0.43 0.00
109_L 71_A 1.39 0.41 0.00
120_A 63_L 1.37 0.40 0.00
136_N 39_P 1.33 0.37 0.00
134_V 78_A 1.31 0.36 0.00
61_F 54_D 1.29 0.34 0.00
38_P 39_P 1.28 0.34 0.00
42_E 23_K 1.27 0.33 0.00
58_L 30_V 1.26 0.33 0.00
123_L 105_K 1.24 0.31 0.00
45_E 76_F 1.24 0.31 0.00
10_L 27_M 1.23 0.31 0.00
50_D 64_A 1.23 0.30 0.00
28_E 62_M 1.20 0.29 0.00
28_E 66_H 1.20 0.29 0.00
56_Q 75_V 1.20 0.29 0.00
112_I 101_C 1.20 0.28 0.00
7_E 41_E 1.19 0.28 0.00
129_V 80_V 1.18 0.28 0.00
13_A 28_Y 1.17 0.27 0.00
51_L 56_E 1.16 0.26 0.00
39_S 54_D 1.14 0.25 0.00
2_L 39_P 1.14 0.25 0.00
92_V 15_E 1.13 0.25 0.00
105_G 97_H 1.13 0.25 0.00
128_E 71_A 1.13 0.25 0.00
105_G 39_P 1.12 0.24 0.00
27_V 79_E 1.11 0.24 0.00
49_V 31_I 1.11 0.23 0.00
59_E 27_M 1.10 0.23 0.00
94_H 76_F 1.08 0.22 0.00
138_I 41_E 1.07 0.22 0.00
117_E 96_E 1.07 0.22 0.00
65_T 77_T 1.07 0.22 0.00
119_Q 101_C 1.07 0.21 0.00
30_L 39_P 1.07 0.21 0.00
139_S 75_V 1.06 0.21 0.00
58_L 76_F 1.06 0.21 0.00
119_Q 22_L 1.06 0.21 0.00
118_S 84_K 1.05 0.21 0.00
129_V 77_T 1.04 0.20 0.00
117_E 26_S 1.03 0.20 0.00
113_F 101_C 1.03 0.20 0.00
64_Q 17_K 1.00 0.18 0.00
30_L 97_H 1.00 0.18 0.00
10_L 85_V 0.99 0.18 0.00
9_S 39_P 0.99 0.18 0.00
109_L 46_V 0.99 0.18 0.00
9_S 19_R 0.98 0.18 0.00
137_F 19_R 0.98 0.17 0.00
26_T 42_F 0.97 0.17 0.00
117_E 105_K 0.97 0.17 0.00
38_P 85_V 0.97 0.17 0.00
80_P 101_C 0.96 0.17 0.00
107_N 37_Y 0.96 0.17 0.00
79_Q 48_Q 0.96 0.17 0.00
117_E 93_R 0.96 0.17 0.00
65_T 105_K 0.95 0.17 0.00
100_R 103_L 0.95 0.16 0.00
79_Q 79_E 0.94 0.16 0.00
86_R 97_H 0.94 0.16 0.00
112_I 85_V 0.93 0.16 0.00
115_E 88_V 0.93 0.16 0.00
142_T 96_E 0.93 0.16 0.00
117_E 28_Y 0.93 0.16 0.00
29_H 74_G 0.93 0.15 0.00
24_F 16_E 0.93 0.15 0.00
70_P 76_F 0.93 0.15 0.00
12_M 33_V 0.92 0.15 0.00
73_E 37_Y 0.92 0.15 0.00
85_Q 36_D 0.92 0.15 0.00
110_V 69_G 0.92 0.15 0.00
60_A 75_V 0.92 0.15 0.00
52_V 32_L 0.91 0.15 0.00
48_S 24_P 0.90 0.14 0.00
120_A 84_K 0.90 0.14 0.00
50_D 86_A 0.90 0.14 0.00
12_M 46_V 0.89 0.14 0.00
118_S 58_A 0.89 0.14 0.00
32_L 33_V 0.89 0.14 0.00
35_L 80_V 0.89 0.14 0.00
74_E 27_M 0.89 0.14 0.00
107_N 97_H 0.88 0.14 0.00
137_F 56_E 0.88 0.14 0.00
99_G 65_V 0.88 0.14 0.00
104_T 57_R 0.88 0.14 0.00
55_R 37_Y 0.87 0.14 0.00
34_L 84_K 0.87 0.14 0.00
86_R 82_E 0.86 0.13 0.00
35_L 94_E 0.86 0.13 0.00
129_V 78_A 0.86 0.13 0.00
24_F 56_E 0.86 0.13 0.00
101_N 79_E 0.86 0.13 0.00
27_V 73_C 0.85 0.13 0.00
103_V 101_C 0.85 0.13 0.00
12_M 41_E 0.85 0.13 0.00
85_Q 69_G 0.85 0.13 0.00
46_A 39_P 0.85 0.13 0.00
32_L 39_P 0.84 0.13 0.00
35_L 45_D 0.84 0.13 0.00
31_L 62_M 0.84 0.12 0.00
31_L 66_H 0.84 0.12 0.00
141_G 88_V 0.84 0.12 0.00
101_N 61_L 0.84 0.12 0.00
81_T 83_T 0.84 0.12 0.00
58_L 63_L 0.84 0.12 0.00
27_V 97_H 0.84 0.12 0.00
88_L 77_T 0.83 0.12 0.00
72_S 60_Q 0.83 0.12 0.00
93_F 100_L 0.83 0.12 0.00
119_Q 103_L 0.83 0.12 0.00
62_I 100_L 0.83 0.12 0.00
127_H 63_L 0.83 0.12 0.00
2_L 79_E 0.83 0.12 0.00
55_R 23_K 0.82 0.12 0.00
35_L 27_M 0.82 0.12 0.00
38_P 53_Y 0.82 0.12 0.00
85_Q 101_C 0.82 0.12 0.00
31_L 58_A 0.82 0.12 0.00
76_R 106_A 0.82 0.12 0.00
110_V 56_E 0.82 0.12 0.00
44_L 30_V 0.82 0.12 0.00
31_L 74_G 0.82 0.12 0.00
80_P 39_P 0.82 0.12 0.00
9_S 21_A 0.82 0.12 0.00
4_Q 106_A 0.81 0.12 0.00
37_N 24_P 0.81 0.12 0.00
30_L 58_A 0.81 0.12 0.00
142_T 75_V 0.81 0.12 0.00
60_A 45_D 0.81 0.12 0.00
95_V 28_Y 0.81 0.11 0.00
23_E 94_E 0.81 0.11 0.00
125_R 95_N 0.81 0.11 0.00
80_P 73_C 0.80 0.11 0.00
138_I 42_F 0.80 0.11 0.00
40_A 48_Q 0.80 0.11 0.00
2_L 102_T 0.79 0.11 0.00
34_L 88_V 0.79 0.11 0.00
27_V 16_E 0.79 0.11 0.00
121_A 15_E 0.79 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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