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OPENSEQ.org
1FM0-2
Genes: A B A+B
Length: 81 149 214
Sequences: 1868 1759 975
Seq/Len: 23.06 11.81 4.56
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 0.01 3.92
2 0.01 0.01 4.11
5 0.01 0.01 4.18
10 0.01 0.02 4.23
20 0.01 0.02 4.24
100 0.01 0.02 4.31
∞ 0.03 0.02 4.87
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
11_R 52_E 2.22 1.00 0.99
58_T 60_K 1.84 1.00 0.98
78_V 58_T 1.20 0.91 0.77
57_Q 60_K 1.12 0.87 0.69
78_V 37_V 1.12 0.87 0.69
59_L 61_A 1.09 0.84 0.66
57_Q 54_Y 1.08 0.84 0.66
79_T 53_H 1.06 0.82 0.63
57_Q 56_G 1.02 0.79 0.58
75_F 57_M 1.02 0.79 0.58
9_Q 36_K 1.01 0.78 0.58
2_I 73_W 1.00 0.77 0.56
54_A 57_M 1.00 0.77 0.56
58_T 64_E 0.88 0.63 0.41
75_F 93_I 0.83 0.56 0.34
75_F 51_L 0.83 0.56 0.34
57_Q 57_M 0.82 0.55 0.34
72_V 75_L 0.82 0.55 0.34
46_L 100_S 0.82 0.55 0.34
60_V 136_V 0.82 0.55 0.33
51_L 110_G 0.80 0.52 0.31
1_M 64_E 0.79 0.51 0.30
7_F 54_Y 0.79 0.50 0.30
33_Q 132_G 0.78 0.49 0.29
3_K 73_W 0.77 0.48 0.28
54_A 122_P 0.77 0.48 0.28
78_V 84_I 0.77 0.48 0.28
71_E 57_M 0.77 0.48 0.28
2_I 70_R 0.76 0.47 0.27
50_K 91_D 0.76 0.47 0.27
73_A 54_Y 0.76 0.46 0.27
8_A 62_L 0.76 0.46 0.26
10_V 93_I 0.76 0.46 0.26
47_E 58_T 0.75 0.45 0.26
4_V 88_W 0.75 0.45 0.26
24_D 91_D 0.75 0.45 0.25
53_A 78_V 0.74 0.43 0.24
15_G 80_V 0.73 0.43 0.24
30_A 13_S 0.73 0.42 0.24
79_T 69_A 0.72 0.41 0.23
59_L 7_V 0.72 0.41 0.23
29_E 10_Q 0.72 0.41 0.22
58_T 49_L 0.71 0.40 0.22
10_V 61_A 0.70 0.39 0.21
3_K 11_P 0.70 0.38 0.21
12_E 126_R 0.69 0.38 0.20
30_A 19_P 0.69 0.37 0.20
67_T 49_L 0.68 0.36 0.19
35_M 135_W 0.68 0.36 0.19
54_A 80_V 0.68 0.35 0.19
18_A 126_R 0.68 0.35 0.18
5_L 104_S 0.67 0.35 0.18
10_V 36_K 0.67 0.34 0.18
19_T 27_D 0.66 0.34 0.17
52_L 46_V 0.66 0.33 0.17
13_L 66_V 0.66 0.33 0.17
12_E 57_M 0.65 0.32 0.17
79_T 7_V 0.64 0.31 0.15
79_T 87_L 0.64 0.31 0.15
10_V 57_M 0.64 0.31 0.15
54_A 33_F 0.63 0.30 0.15
59_L 58_T 0.63 0.30 0.15
5_L 49_L 0.63 0.29 0.14
62_F 19_P 0.63 0.29 0.14
5_L 98_V 0.63 0.29 0.14
65_P 6_V 0.62 0.29 0.14
51_L 108_E 0.62 0.29 0.14
78_V 87_L 0.62 0.29 0.14
66_L 5_I 0.62 0.29 0.14
17_D 133_D 0.62 0.29 0.14
8_A 83_R 0.62 0.29 0.14
55_V 3_T 0.62 0.29 0.14
78_V 73_W 0.62 0.28 0.14
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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