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OPENSEQ.org
sphing_172v171
Genes: A B A+B
Length: 78 103 164
Sequences: 177 276 69
Seq/Len: 2.27 2.68 0.42
MirrorTree (Pazo et al. 2001) 0.72
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 0.38
2 0.01 0.01 0.38
5 0.01 0.01 0.38
10 0.01 0.01 0.38
20 0.01 0.01 0.38
100 0.02 0.03 0.38
∞ 0.11 0.09 0.41
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
35_R 38_D 2.34 0.93 0.73
32_W 30_W 1.77 0.69 0.31
13_D 4_L 1.47 0.49 0.14
26_A 32_M 1.46 0.48 0.13
39_Y 77_L 1.43 0.46 0.12
60_A 47_G 1.37 0.41 0.10
51_E 40_L 1.35 0.40 0.09
58_A 4_L 1.29 0.36 0.07
65_H 21_H 1.28 0.35 0.07
32_W 84_L 1.27 0.35 0.07
25_R 52_Q 1.26 0.34 0.07
61_R 4_L 1.25 0.33 0.06
42_A 52_Q 1.20 0.30 0.05
30_W 55_G 1.20 0.30 0.05
70_P 98_G 1.18 0.29 0.05
30_W 38_D 1.17 0.28 0.05
66_A 49_I 1.15 0.27 0.04
14_S 17_S 1.15 0.27 0.04
43_A 15_R 1.15 0.27 0.04
13_D 13_L 1.14 0.26 0.04
61_R 50_A 1.13 0.26 0.04
32_W 26_R 1.13 0.26 0.04
40_R 63_W 1.13 0.26 0.04
18_A 53_L 1.13 0.26 0.04
20_L 30_W 1.11 0.25 0.04
65_H 51_E 1.10 0.25 0.04
21_A 94_Q 1.10 0.24 0.04
56_H 69_D 1.08 0.23 0.03
54_S 52_Q 1.08 0.23 0.03
9_P 26_R 1.07 0.23 0.03
17_Y 90_R 1.06 0.22 0.03
16_A 39_A 1.05 0.22 0.03
28_F 33_Q 1.04 0.21 0.03
17_Y 38_D 1.04 0.21 0.03
32_W 81_A 1.03 0.21 0.03
63_G 35_R 1.03 0.21 0.03
29_A 93_L 1.03 0.21 0.03
53_G 59_Q 1.02 0.20 0.03
39_Y 94_Q 1.00 0.20 0.02
19_A 72_A 0.99 0.19 0.02
67_F 58_G 0.98 0.18 0.02
19_A 64_R 0.98 0.18 0.02
51_E 4_L 0.96 0.18 0.02
25_R 64_R 0.96 0.18 0.02
17_Y 55_G 0.96 0.17 0.02
36_D 89_Y 0.96 0.17 0.02
30_W 25_A 0.96 0.17 0.02
60_A 9_A 0.94 0.17 0.02
14_S 51_E 0.94 0.17 0.02
17_Y 35_R 0.93 0.16 0.02
72_L 47_G 0.93 0.16 0.02
10_D 53_L 0.93 0.16 0.02
39_Y 6_R 0.93 0.16 0.02
6_S 67_H 0.93 0.16 0.02
67_F 67_H 0.93 0.16 0.02
48_A 11_W 0.93 0.16 0.02
17_Y 8_V 0.92 0.16 0.02
45_E 82_R 0.92 0.16 0.02
6_S 31_I 0.92 0.16 0.02
65_H 11_W 0.92 0.16 0.02
23_M 84_L 0.92 0.16 0.02
59_A 43_G 0.92 0.16 0.02
42_A 36_A 0.91 0.16 0.02
7_D 19_R 0.91 0.16 0.02
51_E 79_R 0.91 0.15 0.02
54_S 40_L 0.91 0.15 0.02
41_S 28_P 0.91 0.15 0.01
28_F 73_R 0.90 0.15 0.01
17_Y 49_I 0.89 0.15 0.01
30_W 39_A 0.89 0.15 0.01
17_Y 46_Q 0.88 0.14 0.01
38_E 35_R 0.88 0.14 0.01
27_G 45_S 0.87 0.14 0.01
9_P 96_H 0.87 0.14 0.01
45_E 43_G 0.87 0.14 0.01
37_E 13_L 0.87 0.14 0.01
37_E 30_W 0.87 0.14 0.01
67_F 68_P 0.87 0.14 0.01
58_A 63_W 0.85 0.13 0.01
43_A 6_R 0.85 0.13 0.01
34_R 71_R 0.85 0.13 0.01
60_A 13_L 0.85 0.13 0.01
11_W 88_G 0.85 0.13 0.01
58_A 2_L 0.84 0.13 0.01
26_A 90_R 0.84 0.13 0.01
72_L 30_W 0.84 0.13 0.01
17_Y 39_A 0.84 0.13 0.01
28_F 21_H 0.83 0.13 0.01
30_W 75_Q 0.83 0.13 0.01
23_M 12_K 0.83 0.13 0.01
30_W 46_Q 0.82 0.12 0.01
38_E 86_R 0.82 0.12 0.01
56_H 90_R 0.82 0.12 0.01
20_L 90_R 0.82 0.12 0.01
28_F 17_S 0.82 0.12 0.01
43_A 70_A 0.81 0.12 0.01
13_D 39_A 0.81 0.12 0.01
16_A 54_L 0.81 0.12 0.01
12_R 65_I 0.81 0.12 0.01
60_A 48_E 0.81 0.12 0.01
10_D 76_R 0.81 0.12 0.01
56_H 87_G 0.80 0.12 0.01
28_F 23_V 0.80 0.12 0.01
10_D 35_R 0.80 0.12 0.01
37_E 54_L 0.80 0.12 0.01
57_S 81_A 0.80 0.12 0.01
55_F 48_E 0.80 0.12 0.01
71_D 67_H 0.80 0.12 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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