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OPENSEQ.org
4489
Genes: A B A+B
Length: 92 84 167
Sequences: 1738 3131 726
Seq/Len: 18.89 37.27 4.35
MirrorTree (Pazo et al. 2001) 0.75
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 0.01 0.01 4.12
2 0.01 0.02 4.16
5 0.01 0.03 4.27
10 0.02 0.04 4.30
20 0.02 0.04 4.36
100 0.04 0.06 4.59
∞ 0.09 0.11 5.32
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
75_D 8_E 2.95 1.00 1.00
76_S 6_S 2.71 1.00 1.00
79_S 6_S 2.30 1.00 0.99
79_S 7_E 2.25 1.00 0.99
66_S 82_Y 2.06 1.00 0.99
81_K 69_A 2.05 1.00 0.99
77_I 55_F 1.99 1.00 0.99
87_E 2_K 1.83 1.00 0.98
72_R 79_A 1.70 0.99 0.96
85_G 6_S 1.59 0.99 0.94
74_M 51_N 1.58 0.99 0.94
72_R 11_D 1.53 0.98 0.93
65_R 82_Y 1.46 0.97 0.91
88_K 5_W 1.46 0.97 0.91
80_L 78_A 1.42 0.97 0.89
80_L 76_L 1.38 0.96 0.88
69_N 82_Y 1.28 0.93 0.82
77_I 78_A 1.26 0.93 0.81
81_K 55_F 1.21 0.91 0.77
63_L 67_V 1.14 0.87 0.71
80_L 6_S 1.05 0.80 0.63
74_M 52_L 1.02 0.78 0.60
61_A 50_H 1.02 0.77 0.59
85_G 4_I 0.88 0.62 0.42
85_G 76_L 0.88 0.62 0.42
79_S 8_E 0.86 0.59 0.40
64_L 52_L 0.85 0.58 0.39
78_D 75_L 0.85 0.58 0.38
73_L 55_F 0.84 0.56 0.36
77_I 69_A 0.83 0.55 0.35
53_E 62_E 0.83 0.54 0.35
48_L 29_E 0.82 0.54 0.34
76_S 55_F 0.81 0.52 0.33
72_R 12_D 0.80 0.50 0.32
29_A 82_Y 0.79 0.49 0.30
89_D 5_W 0.76 0.44 0.27
65_R 50_H 0.74 0.43 0.26
80_L 55_F 0.73 0.41 0.24
92_E 32_K 0.73 0.41 0.24
76_S 78_A 0.70 0.38 0.21
18_A 5_W 0.69 0.36 0.20
63_L 81_R 0.69 0.36 0.20
54_Y 9_S 0.69 0.35 0.20
22_L 52_L 0.68 0.34 0.19
91_I 23_I 0.67 0.34 0.19
27_M 24_V 0.67 0.34 0.18
88_K 7_E 0.67 0.33 0.18
44_E 79_A 0.67 0.33 0.18
30_V 26_K 0.66 0.32 0.17
62_Y 61_I 0.66 0.32 0.17
75_D 6_S 0.66 0.32 0.17
29_A 29_E 0.65 0.30 0.16
25_T 50_H 0.63 0.29 0.15
86_T 7_E 0.63 0.29 0.15
65_R 62_E 0.63 0.29 0.15
63_L 82_Y 0.63 0.29 0.15
70_A 51_N 0.63 0.28 0.15
41_Q 22_R 0.62 0.27 0.14
28_K 14_L 0.62 0.27 0.14
53_E 74_S 0.61 0.27 0.14
47_V 52_L 0.61 0.27 0.13
53_E 63_E 0.60 0.26 0.13
18_A 38_P 0.60 0.25 0.13
85_G 78_A 0.60 0.25 0.13
64_L 10_W 0.60 0.25 0.12
50_S 14_L 0.59 0.25 0.12
58_E 66_L 0.59 0.24 0.12
17_E 2_K 0.58 0.23 0.11
91_I 73_D 0.58 0.23 0.11
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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