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OPENSEQ.org
Ayesha
Genes: A B A+B
Length: 128 116 229
Sequences: 88685 170 137
Seq/Len: 692.85 1.47 0.6
MirrorTree (Pazo et al. 2001) 0.21
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 0.11 0.06 0.05
2 0.13 0.06 0.08
5 0.16 0.06 0.24
10 0.19 0.06 0.43
20 0.23 0.06 0.56
100 0.32 0.07 0.75
∞ 0.34 0.08 0.81
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
95_I 12_D 1.66 0.73 0.01
123_F 12_D 1.32 0.48 0.00
41_A 89_Q 1.29 0.45 0.00
54_I 104_V 1.28 0.44 0.00
106_V 88_Q 1.23 0.40 0.00
97_A 33_M 1.19 0.37 0.00
80_L 23_R 1.19 0.37 0.00
122_I 46_L 1.17 0.36 0.00
124_E 19_L 1.12 0.32 0.00
35_A 44_T 1.10 0.30 0.00
59_M 61_N 1.08 0.29 0.00
38_G 99_R 1.05 0.27 0.00
104_G 57_L 1.01 0.25 0.00
6_K 90_I 0.99 0.24 0.00
67_L 68_R 0.99 0.23 0.00
62_M 37_G 0.94 0.21 0.00
67_L 56_K 0.94 0.21 0.00
8_L 20_L 0.92 0.20 0.00
12_D 49_L 0.92 0.20 0.00
41_A 79_T 0.92 0.20 0.00
123_F 25_I 0.91 0.20 0.00
51_G 25_I 0.91 0.19 0.00
62_M 71_S 0.91 0.19 0.00
34_E 24_L 0.90 0.19 0.00
119_L 38_I 0.90 0.19 0.00
32_V 50_T 0.89 0.18 0.00
44_K 97_S 0.89 0.18 0.00
38_G 64_V 0.89 0.18 0.00
60_P 61_N 0.89 0.18 0.00
84_M 98_T 0.88 0.18 0.00
37_D 30_A 0.88 0.18 0.00
57_W 31_S 0.88 0.18 0.00
24_L 91_H 0.87 0.17 0.00
26_E 32_A 0.87 0.17 0.00
38_G 53_Q 0.87 0.17 0.00
59_M 53_Q 0.86 0.17 0.00
41_A 32_A 0.86 0.17 0.00
71_I 43_A 0.86 0.17 0.00
103_S 12_D 0.84 0.16 0.00
86_T 78_L 0.83 0.16 0.00
43_N 60_T 0.83 0.16 0.00
65_L 31_S 0.83 0.16 0.00
67_L 37_G 0.82 0.15 0.00
101_G 14_N 0.81 0.15 0.00
101_G 17_Y 0.81 0.15 0.00
6_K 50_T 0.81 0.15 0.00
53_V 25_I 0.81 0.15 0.00
102_A 28_D 0.80 0.14 0.00
52_F 74_T 0.80 0.14 0.00
66_E 49_L 0.79 0.14 0.00
106_V 58_A 0.79 0.14 0.00
43_N 93_G 0.79 0.14 0.00
121_K 93_G 0.79 0.14 0.00
19_I 105_N 0.78 0.14 0.00
82_V 89_Q 0.78 0.14 0.00
10_V 1_M 0.78 0.14 0.00
45_L 9_H 0.78 0.14 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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