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OPENSEQ.org
ExQ
Genes: A B A+B
Length: 98 89 179
Sequences: 888 1330 634
Seq/Len: 9.06 14.94 3.54
MirrorTree (Pazo et al. 2001) 0.60
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 0.00 0.00 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.03
10 0.00 0.01 0.24
20 0.00 0.01 3.20
100 0.01 0.02 3.39
∞ 0.01 0.05 3.84
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
81_E 22_L 1.62 0.98 0.89
36_E 12_Q 1.49 0.97 0.83
36_E 47_M 1.39 0.95 0.77
95_R 45_N 1.36 0.94 0.75
45_E 9_L 1.28 0.91 0.69
74_S 47_M 1.26 0.90 0.67
76_M 55_I 1.22 0.88 0.64
80_L 52_V 1.15 0.83 0.56
70_T 16_I 1.12 0.81 0.53
76_M 84_I 1.11 0.80 0.51
17_N 76_F 1.08 0.78 0.49
37_I 20_L 1.08 0.78 0.49
94_T 66_M 1.07 0.77 0.47
20_Q 60_V 1.05 0.75 0.46
41_N 26_L 1.04 0.74 0.45
62_L 37_I 1.04 0.74 0.45
92_E 88_I 1.04 0.74 0.44
32_M 62_L 1.04 0.74 0.44
85_K 28_G 1.01 0.70 0.41
28_E 83_Q 1.00 0.70 0.40
91_K 6_L 1.00 0.70 0.40
81_E 36_S 1.00 0.70 0.40
19_S 35_I 0.99 0.69 0.39
47_G 19_L 0.99 0.68 0.38
81_E 63_I 0.98 0.68 0.38
75_S 88_I 0.98 0.67 0.37
70_T 13_T 0.98 0.67 0.37
28_E 34_V 0.96 0.65 0.35
74_S 80_I 0.95 0.63 0.34
38_N 31_A 0.94 0.63 0.34
76_M 66_M 0.94 0.62 0.33
84_N 21_S 0.94 0.62 0.33
72_A 69_M 0.93 0.62 0.32
47_G 81_L 0.93 0.61 0.32
92_E 86_T 0.92 0.60 0.31
76_M 41_T 0.92 0.59 0.31
13_I 20_L 0.89 0.57 0.28
61_D 59_V 0.89 0.56 0.28
26_G 64_F 0.89 0.56 0.28
36_E 52_V 0.89 0.56 0.28
40_L 14_F 0.88 0.56 0.27
76_M 43_Q 0.88 0.56 0.27
44_Q 35_I 0.87 0.54 0.27
72_A 48_T 0.87 0.54 0.26
23_T 34_V 0.87 0.54 0.26
39_D 61_I 0.87 0.54 0.26
93_I 72_T 0.86 0.53 0.26
55_A 41_T 0.86 0.53 0.25
38_N 60_V 0.86 0.53 0.25
88_S 56_I 0.86 0.52 0.25
37_I 12_Q 0.85 0.51 0.24
91_K 14_F 0.84 0.50 0.24
51_M 66_M 0.84 0.49 0.23
97_Q 57_L 0.84 0.49 0.23
54_I 65_L 0.84 0.49 0.23
48_E 88_I 0.83 0.49 0.23
19_S 80_I 0.83 0.48 0.22
69_I 43_Q 0.82 0.48 0.22
97_Q 45_N 0.82 0.48 0.22
81_E 45_N 0.82 0.47 0.21
35_N 65_L 0.82 0.47 0.21
38_N 28_G 0.81 0.46 0.20
85_K 18_L 0.81 0.46 0.20
40_L 55_I 0.81 0.46 0.20
82_V 52_V 0.80 0.44 0.20
16_T 22_L 0.79 0.44 0.19
27_D 35_I 0.79 0.43 0.19
79_M 37_I 0.78 0.42 0.18
13_I 34_V 0.78 0.42 0.18
58_Q 31_A 0.78 0.42 0.18
38_N 5_T 0.77 0.41 0.18
74_S 6_L 0.77 0.41 0.18
77_K 49_L 0.77 0.41 0.18
85_K 37_I 0.77 0.40 0.17
79_M 43_Q 0.77 0.40 0.17
32_M 77_T 0.76 0.40 0.17
72_A 2_D 0.76 0.40 0.17
36_E 76_F 0.76 0.40 0.17
97_Q 27_A 0.76 0.39 0.17
20_Q 84_I 0.75 0.38 0.16
31_K 34_V 0.75 0.38 0.16
77_K 31_A 0.75 0.38 0.16
98_I 88_I 0.75 0.38 0.16
33_L 4_S 0.74 0.38 0.16
63_H 43_Q 0.74 0.37 0.15
64_Q 31_A 0.74 0.37 0.15
67_I 50_S 0.74 0.37 0.15
83_R 85_P 0.73 0.36 0.15
98_I 3_E 0.73 0.35 0.14
59_V 20_L 0.72 0.35 0.14
41_N 57_L 0.72 0.35 0.14
92_E 18_L 0.72 0.35 0.14
59_V 7_V 0.72 0.35 0.14
71_K 83_Q 0.72 0.35 0.14
88_S 77_T 0.72 0.34 0.14
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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