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OPENSEQ.org
2803
Genes: A B A+B
Length: 94 90 179
Sequences: 14800 2139 743
Seq/Len: 157.45 23.77 4.15
MirrorTree (Pazo et al. 2001) 0.71
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 0.04 0.01 4.04
2 0.05 0.01 4.09
5 0.06 0.02 4.20
10 0.08 0.02 4.30
20 0.09 0.03 4.42
100 0.14 0.04 5.15
∞ 0.19 0.09 6.98
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
69_N 37_A 2.95 1.00 1.00
63_S 43_D 2.60 1.00 1.00
7_P 33_A 2.28 1.00 0.99
73_A 36_D 2.12 1.00 0.99
73_A 37_A 1.95 1.00 0.98
12_I 34_V 1.66 0.99 0.95
65_Q 39_C 1.61 0.99 0.95
11_D 26_K 1.60 0.99 0.94
66_M 34_V 1.54 0.98 0.93
69_N 39_C 1.43 0.97 0.90
77_A 33_A 1.40 0.96 0.88
15_E 30_H 1.26 0.92 0.81
20_L 47_P 1.26 0.92 0.81
70_L 37_A 1.22 0.91 0.78
16_S 31_R 1.07 0.81 0.65
19_E 31_R 1.05 0.79 0.61
62_S 43_D 1.04 0.78 0.60
71_Q 66_V 1.03 0.77 0.59
12_I 30_H 1.02 0.77 0.59
70_L 34_V 1.02 0.77 0.59
63_S 40_C 1.02 0.76 0.58
16_S 49_Y 0.94 0.68 0.49
59_V 8_L 0.94 0.67 0.49
37_T 52_H 0.91 0.64 0.45
16_S 46_M 0.89 0.61 0.42
11_D 30_H 0.88 0.60 0.41
16_S 48_G 0.85 0.57 0.38
61_G 46_M 0.84 0.55 0.37
66_M 43_D 0.84 0.54 0.36
15_E 31_R 0.83 0.53 0.35
4_A 29_R 0.83 0.53 0.34
22_V 77_V 0.82 0.52 0.34
19_E 48_G 0.78 0.47 0.29
51_E 38_A 0.76 0.44 0.27
91_L 50_R 0.76 0.44 0.27
23_S 36_D 0.76 0.43 0.26
50_P 66_V 0.76 0.43 0.26
38_A 21_I 0.73 0.40 0.24
76_L 48_G 0.73 0.40 0.23
79_A 36_D 0.71 0.37 0.22
68_L 9_R 0.71 0.37 0.21
34_A 53_P 0.70 0.37 0.21
46_A 8_L 0.70 0.36 0.21
70_L 33_A 0.70 0.36 0.21
64_P 36_D 0.69 0.35 0.20
18_D 30_H 0.69 0.34 0.19
4_A 33_A 0.68 0.34 0.19
7_P 29_R 0.68 0.34 0.19
15_E 57_D 0.68 0.34 0.19
80_E 10_D 0.67 0.32 0.17
18_D 55_S 0.67 0.32 0.17
81_K 14_L 0.66 0.32 0.17
7_P 26_K 0.65 0.30 0.16
40_R 19_G 0.64 0.29 0.15
67_W 76_F 0.63 0.28 0.14
74_W 20_V 0.63 0.28 0.14
18_D 7_G 0.63 0.28 0.14
46_A 63_A 0.61 0.26 0.13
56_L 38_A 0.61 0.26 0.13
69_N 36_D 0.61 0.25 0.13
89_R 55_S 0.61 0.25 0.13
62_S 37_A 0.60 0.25 0.13
73_A 33_A 0.60 0.25 0.13
40_R 86_Y 0.60 0.25 0.12
50_P 7_G 0.60 0.25 0.12
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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