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OPENSEQ.org
a9_1-93_md2
Genes: A B A+B
Length: 92 160 210
Sequences: 8071 531 81
Seq/Len: 87.73 3.32 0.39
MirrorTree (Pazo et al. 2001) 0.12
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 0.07 0.05 0.01
2 0.07 0.06 0.01
5 0.08 0.06 0.01
10 0.09 0.06 0.02
20 0.09 0.06 0.03
100 0.14 0.07 0.12
∞ 0.20 0.10 0.32
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
16_I 93_V 1.86 0.73 0.02
32_L 34_Y 1.39 0.41 0.01
19_F 106_R 1.38 0.40 0.01
10_R 93_V 1.31 0.36 0.00
79_F 106_R 1.21 0.29 0.00
22_Y 66_I 1.20 0.29 0.00
36_E 142_P 1.17 0.27 0.00
27_G 44_I 1.16 0.26 0.00
67_D 95_C 1.15 0.26 0.00
72_K 95_C 1.14 0.25 0.00
23_S 148_C 1.10 0.23 0.00
72_K 105_C 1.08 0.22 0.00
76_F 59_G 1.07 0.22 0.00
30_D 52_I 1.07 0.21 0.00
80_I 122_K 1.05 0.21 0.00
35_G 124_I 1.03 0.20 0.00
80_I 124_I 1.03 0.20 0.00
36_E 135_V 1.02 0.19 0.00
31_T 63_I 0.99 0.18 0.00
23_S 127_S 0.99 0.18 0.00
30_D 127_S 0.97 0.17 0.00
67_D 93_V 0.95 0.17 0.00
80_I 117_I 0.94 0.16 0.00
66_L 74_L 0.94 0.16 0.00
70_A 118_S 0.94 0.16 0.00
32_L 117_I 0.94 0.16 0.00
74_L 68_R 0.94 0.16 0.00
56_E 132_K 0.94 0.16 0.00
71_D 132_K 0.94 0.16 0.00
74_L 58_K 0.93 0.15 0.00
32_L 74_L 0.92 0.15 0.00
78_E 80_I 0.92 0.15 0.00
74_L 125_K 0.91 0.15 0.00
27_G 60_L 0.89 0.14 0.00
46_Q 52_I 0.89 0.14 0.00
71_D 46_I 0.88 0.14 0.00
14_T 142_P 0.87 0.14 0.00
81_M 73_Q 0.87 0.14 0.00
76_F 64_F 0.87 0.13 0.00
36_E 147_F 0.87 0.13 0.00
23_S 106_R 0.86 0.13 0.00
37_F 49_N 0.86 0.13 0.00
82_L 49_N 0.85 0.13 0.00
67_D 131_Y 0.85 0.13 0.00
33_N 147_F 0.85 0.13 0.00
81_M 53_E 0.83 0.12 0.00
32_L 118_S 0.83 0.12 0.00
78_E 82_V 0.83 0.12 0.00
65_D 45_S 0.83 0.12 0.00
75_S 93_V 0.82 0.12 0.00
77_E 48_V 0.82 0.12 0.00
25_K 85_M 0.82 0.12 0.00
30_D 140_G 0.82 0.12 0.00
32_L 152_V 0.82 0.12 0.00
31_T 146_L 0.82 0.12 0.00
24_V 117_I 0.82 0.12 0.00
41_V 122_K 0.81 0.12 0.00
66_L 102_Y 0.81 0.12 0.00
19_F 110_G 0.81 0.12 0.00
23_S 78_L 0.81 0.12 0.00
74_L 49_N 0.81 0.11 0.00
72_K 93_V 0.81 0.11 0.00
9_E 146_L 0.80 0.11 0.00
37_F 86_N 0.80 0.11 0.00
29_P 153_I 0.80 0.11 0.00
39_E 80_I 0.80 0.11 0.00
60_E 142_P 0.80 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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