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OPENSEQ.org
3hi2_C_D
Genes: A B A+B
Length: 76 101 173
Sequences: 144 141 112
Seq/Len: 1.89 1.4 0.65
MirrorTree (Pazo et al. 2001) 0.83
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 0.00 0.63
2 0.01 0.00 0.63
5 0.01 0.00 0.63
10 0.01 0.00 0.63
20 0.01 0.00 0.63
100 0.01 0.00 0.63
∞ 0.01 0.02 0.63
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
58_K 36_D 2.02 0.91 0.44
54_M 68_T 1.46 0.61 0.12
48_E 53_S 1.34 0.51 0.08
5_V 68_T 1.32 0.50 0.08
50_S 40_L 1.32 0.50 0.08
43_S 92_D 1.30 0.48 0.07
47_K 35_A 1.27 0.45 0.06
3_C 52_L 1.26 0.45 0.06
23_R 9_P 1.24 0.43 0.06
58_K 27_T 1.24 0.43 0.06
31_G 48_V 1.23 0.43 0.06
16_K 97_S 1.23 0.43 0.06
74_I 57_F 1.18 0.38 0.05
75_V 21_N 1.17 0.38 0.04
41_E 30_S 1.17 0.38 0.04
43_S 75_R 1.15 0.36 0.04
44_I 90_I 1.12 0.34 0.04
67_E 55_S 1.10 0.33 0.04
31_G 49_I 1.10 0.33 0.03
52_A 88_T 1.09 0.32 0.03
57_V 36_D 1.08 0.31 0.03
38_V 39_G 1.08 0.31 0.03
1_M 56_D 1.06 0.30 0.03
31_G 88_T 1.05 0.29 0.03
52_A 10_H 1.05 0.29 0.03
21_T 14_S 1.05 0.29 0.03
27_T 17_K 1.04 0.28 0.03
50_S 29_R 1.04 0.28 0.03
48_E 55_S 1.04 0.28 0.03
37_C 73_V 1.04 0.28 0.03
73_F 9_P 1.04 0.28 0.03
51_D 46_C 1.04 0.28 0.03
42_E 34_N 1.03 0.28 0.03
54_M 32_L 1.03 0.27 0.03
6_C 52_L 1.02 0.27 0.03
53_F 20_V 1.01 0.27 0.02
30_K 16_V 1.01 0.27 0.02
19_P 95_I 1.01 0.26 0.02
36_Y 25_V 0.99 0.25 0.02
10_E 47_N 0.99 0.25 0.02
53_F 45_M 0.99 0.25 0.02
62_A 49_I 0.98 0.24 0.02
25_R 57_F 0.97 0.24 0.02
14_G 85_L 0.95 0.23 0.02
37_C 58_Y 0.95 0.23 0.02
68_T 49_I 0.95 0.23 0.02
40_C 4_M 0.95 0.23 0.02
8_Q 30_S 0.95 0.23 0.02
13_S 101_K 0.95 0.22 0.02
59_A 69_I 0.95 0.22 0.02
18_I 32_L 0.94 0.22 0.02
23_R 97_S 0.94 0.22 0.02
22_F 57_F 0.94 0.22 0.02
69_V 44_G 0.93 0.22 0.02
60_F 87_I 0.93 0.21 0.02
13_S 49_I 0.93 0.21 0.02
50_S 17_K 0.93 0.21 0.02
19_P 92_D 0.92 0.21 0.02
15_I 53_S 0.92 0.21 0.02
14_G 30_S 0.92 0.21 0.02
71_P 35_A 0.92 0.21 0.02
26_K 32_L 0.91 0.20 0.02
56_Q 69_I 0.91 0.20 0.02
40_C 73_V 0.91 0.20 0.02
26_K 77_R 0.91 0.20 0.02
66_A 44_G 0.90 0.20 0.01
58_K 8_T 0.89 0.19 0.01
71_P 96_V 0.89 0.19 0.01
39_H 18_K 0.89 0.19 0.01
34_G 51_G 0.88 0.19 0.01
26_K 34_N 0.88 0.19 0.01
18_I 29_R 0.88 0.19 0.01
57_V 33_L 0.87 0.18 0.01
73_F 11_T 0.87 0.18 0.01
61_R 94_L 0.87 0.18 0.01
56_Q 27_T 0.87 0.18 0.01
72_E 7_R 0.87 0.18 0.01
38_V 63_T 0.87 0.18 0.01
5_V 76_P 0.86 0.18 0.01
47_K 46_C 0.86 0.18 0.01
36_Y 92_D 0.86 0.18 0.01
17_D 49_I 0.86 0.18 0.01
37_C 61_M 0.85 0.17 0.01
15_I 38_L 0.85 0.17 0.01
63_S 18_K 0.84 0.17 0.01
45_M 44_G 0.84 0.17 0.01
54_M 29_R 0.84 0.17 0.01
26_K 20_V 0.84 0.17 0.01
70_A 29_R 0.84 0.17 0.01
43_S 82_Q 0.84 0.17 0.01
16_K 100_E 0.84 0.17 0.01
52_A 95_I 0.84 0.17 0.01
8_Q 29_R 0.83 0.17 0.01
61_R 40_L 0.83 0.17 0.01
72_E 5_E 0.83 0.17 0.01
36_Y 35_A 0.83 0.16 0.01
47_K 53_S 0.83 0.16 0.01
20_Y 94_L 0.83 0.16 0.01
57_V 39_G 0.83 0.16 0.01
17_D 48_V 0.83 0.16 0.01
75_V 14_S 0.82 0.16 0.01
75_V 7_R 0.82 0.16 0.01
41_E 69_I 0.82 0.16 0.01
39_H 85_L 0.82 0.16 0.01
61_R 36_D 0.82 0.16 0.01
53_F 40_L 0.82 0.16 0.01
15_I 58_Y 0.82 0.16 0.01
24_G 38_L 0.82 0.16 0.01
9_G 19_L 0.82 0.16 0.01
18_I 33_L 0.81 0.16 0.01
17_D 65_S 0.81 0.16 0.01
3_C 96_V 0.81 0.16 0.01
31_G 65_S 0.81 0.16 0.01
16_K 45_M 0.81 0.16 0.01
40_C 61_M 0.81 0.15 0.01
12_V 95_I 0.81 0.15 0.01
60_F 96_V 0.81 0.15 0.01
40_C 52_L 0.80 0.15 0.01
35_L 64_Y 0.80 0.15 0.01
27_T 22_A 0.80 0.15 0.01
57_V 32_L 0.80 0.15 0.01
39_H 71_Q 0.80 0.15 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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