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OPENSEQ.org
1010
Genes: A B A+B
Length: 96 112 193
Sequences: 4246 2550 815
Seq/Len: 44.23 22.77 4.22
MirrorTree (Pazo et al. 2001) 0.73
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.02 3.92
2 0.02 0.02 3.97
5 0.02 0.03 4.02
10 0.03 0.04 4.07
20 0.04 0.04 4.17
100 0.06 0.07 4.53
∞ 0.11 0.12 6.02
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
7_D 34_Q 1.79 1.00 0.96
19_Q 24_Q 1.57 0.98 0.92
10_W 31_D 1.29 0.93 0.78
34_N 32_R 1.21 0.90 0.72
27_A 28_Y 1.21 0.90 0.72
55_Q 68_Y 1.19 0.89 0.70
9_V 7_F 1.13 0.85 0.64
13_V 23_R 1.12 0.85 0.64
6_F 30_L 1.09 0.83 0.60
16_T 23_R 1.07 0.81 0.58
84_H 91_Q 1.06 0.81 0.57
12_A 16_R 1.01 0.75 0.51
58_I 5_L 0.98 0.72 0.47
24_R 28_Y 0.97 0.72 0.47
28_E 37_L 0.97 0.71 0.46
33_I 68_Y 0.94 0.67 0.42
54_T 78_V 0.93 0.66 0.41
20_A 31_D 0.89 0.62 0.37
77_M 53_R 0.89 0.62 0.37
20_A 52_V 0.86 0.58 0.33
52_G 106_Q 0.86 0.57 0.33
59_S 22_S 0.84 0.56 0.32
47_A 50_P 0.83 0.55 0.30
71_I 91_Q 0.82 0.53 0.29
60_E 62_G 0.82 0.52 0.29
24_R 31_D 0.81 0.52 0.28
43_S 105_V 0.81 0.51 0.27
59_S 99_R 0.80 0.50 0.27
84_H 35_Q 0.80 0.50 0.27
62_A 56_R 0.78 0.47 0.25
46_Q 85_K 0.78 0.47 0.25
23_M 32_R 0.77 0.46 0.24
84_H 15_L 0.77 0.45 0.23
82_G 89_T 0.76 0.44 0.23
12_A 17_A 0.76 0.44 0.23
23_M 25_E 0.76 0.44 0.23
6_F 12_L 0.76 0.44 0.23
81_A 87_Q 0.76 0.44 0.22
7_D 110_N 0.75 0.43 0.22
78_M 60_A 0.75 0.43 0.22
49_S 50_P 0.75 0.43 0.22
31_T 32_R 0.75 0.43 0.22
80_H 26_I 0.75 0.43 0.22
21_E 59_D 0.75 0.42 0.21
70_S 68_Y 0.75 0.42 0.21
64_G 45_F 0.74 0.42 0.21
72_D 8_L 0.73 0.41 0.20
29_L 30_L 0.73 0.41 0.20
12_A 12_L 0.73 0.40 0.20
33_I 14_D 0.73 0.40 0.20
10_W 27_G 0.71 0.38 0.19
31_T 35_Q 0.71 0.38 0.18
26_R 66_V 0.71 0.38 0.18
17_P 20_E 0.71 0.38 0.18
44_Q 68_Y 0.71 0.38 0.18
59_S 100_R 0.70 0.37 0.18
33_I 26_I 0.70 0.37 0.18
37_I 56_R 0.70 0.36 0.17
81_A 55_I 0.70 0.36 0.17
56_P 68_Y 0.69 0.36 0.17
35_N 94_I 0.69 0.35 0.17
19_Q 20_E 0.68 0.34 0.16
19_Q 41_D 0.68 0.34 0.16
43_S 18_F 0.68 0.34 0.16
79_A 17_A 0.68 0.34 0.16
20_A 24_Q 0.68 0.34 0.16
69_F 68_Y 0.68 0.34 0.16
33_I 8_L 0.68 0.33 0.15
35_N 99_R 0.68 0.33 0.15
38_E 102_K 0.67 0.33 0.15
82_G 63_I 0.67 0.33 0.15
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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