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OPENSEQ.org
5202
Genes: A B A+B
Length: 97 164 245
Sequences: 689 10658 610
Seq/Len: 7.1 64.99 2.49
MirrorTree (Pazo et al. 2001) 0.70
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 0.03 2.34
2 0.01 0.05 2.35
5 0.01 0.06 2.35
10 0.02 0.08 2.36
20 0.03 0.09 2.36
100 0.05 0.14 2.38
∞ 0.10 0.20 2.53
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
87_M 106_R 1.85 0.99 0.94
89_T 102_R 1.81 0.98 0.94
80_N 141_G 1.71 0.98 0.91
82_A 139_R 1.66 0.97 0.89
92_P 103_A 1.52 0.94 0.83
74_D 44_F 1.44 0.92 0.78
59_F 62_S 1.42 0.91 0.77
71_N 49_T 1.42 0.91 0.77
74_D 42_R 1.20 0.79 0.58
27_D 87_G 1.16 0.76 0.54
86_T 127_H 1.15 0.75 0.53
86_T 106_R 1.11 0.71 0.48
40_F 88_R 1.11 0.71 0.48
94_E 19_S 1.10 0.69 0.46
94_E 106_R 1.08 0.68 0.45
69_F 64_V 1.08 0.67 0.44
62_D 131_D 1.06 0.66 0.42
94_E 15_T 1.06 0.65 0.42
41_V 85_V 1.05 0.64 0.41
64_D 147_V 1.04 0.64 0.40
85_K 139_R 1.04 0.63 0.40
69_F 15_T 1.02 0.62 0.38
25_L 30_Q 1.01 0.60 0.36
87_M 110_L 0.99 0.58 0.35
23_R 76_N 0.99 0.58 0.34
36_N 132_Q 0.98 0.57 0.34
34_G 31_R 0.98 0.56 0.33
76_P 44_F 0.97 0.55 0.32
67_Q 66_T 0.96 0.55 0.32
59_F 125_L 0.96 0.54 0.32
25_L 56_Y 0.96 0.54 0.31
34_G 78_P 0.95 0.53 0.30
88_Q 68_V 0.95 0.53 0.30
38_T 84_V 0.94 0.53 0.30
36_N 136_F 0.93 0.51 0.29
53_L 95_L 0.93 0.51 0.28
23_R 87_G 0.93 0.50 0.28
37_R 75_R 0.93 0.50 0.28
34_G 86_L 0.92 0.50 0.28
66_Y 66_T 0.92 0.49 0.27
62_D 147_V 0.90 0.47 0.26
43_E 64_V 0.90 0.47 0.25
26_I 76_N 0.90 0.47 0.25
52_A 67_Y 0.89 0.47 0.25
88_Q 135_E 0.89 0.46 0.25
65_D 87_G 0.89 0.45 0.24
69_F 83_V 0.88 0.45 0.24
61_I 153_M 0.88 0.45 0.24
73_L 55_A 0.88 0.45 0.23
87_M 68_V 0.88 0.44 0.23
57_R 100_I 0.87 0.44 0.23
59_F 151_I 0.87 0.43 0.22
38_T 121_I 0.86 0.42 0.22
9_A 22_E 0.85 0.41 0.21
30_A 101_G 0.84 0.40 0.20
69_F 123_G 0.84 0.40 0.20
67_Q 50_Y 0.83 0.40 0.20
61_I 123_G 0.83 0.39 0.19
11_R 56_Y 0.81 0.37 0.18
65_D 14_F 0.81 0.37 0.18
18_I 119_I 0.80 0.35 0.17
72_R 120_G 0.80 0.35 0.17
75_Q 143_E 0.79 0.35 0.17
39_E 98_Q 0.79 0.35 0.16
82_A 141_G 0.79 0.35 0.16
15_N 42_R 0.79 0.35 0.16
90_P 103_A 0.79 0.35 0.16
81_A 131_D 0.78 0.33 0.15
73_L 44_F 0.78 0.33 0.15
82_A 140_V 0.77 0.33 0.15
67_Q 143_E 0.77 0.33 0.15
21_A 57_Y 0.77 0.33 0.15
20_P 113_L 0.77 0.32 0.14
17_R 105_V 0.76 0.32 0.14
78_A 138_L 0.76 0.31 0.14
36_N 125_L 0.76 0.31 0.14
36_N 90_A 0.76 0.31 0.14
55_E 127_H 0.75 0.30 0.14
34_G 76_N 0.75 0.30 0.14
10_R 93_K 0.75 0.30 0.13
57_R 46_S 0.75 0.30 0.13
85_K 103_A 0.75 0.30 0.13
41_V 86_L 0.74 0.30 0.13
33_R 82_P 0.74 0.30 0.13
39_E 27_W 0.74 0.29 0.13
72_R 126_V 0.74 0.29 0.13
36_N 76_N 0.73 0.29 0.13
26_I 138_L 0.73 0.29 0.13
27_D 40_A 0.73 0.29 0.12
86_T 44_F 0.73 0.29 0.12
14_L 24_M 0.73 0.29 0.12
36_N 94_S 0.73 0.28 0.12
69_F 78_P 0.73 0.28 0.12
54_I 91_I 0.72 0.27 0.12
60_R 65_E 0.71 0.27 0.11
76_P 70_T 0.71 0.27 0.11
83_L 20_G 0.71 0.27 0.11
56_Q 69_A 0.71 0.27 0.11
77_P 122_R 0.71 0.27 0.11
23_R 27_W 0.71 0.27 0.11
26_I 25_D 0.71 0.27 0.11
26_I 41_S 0.71 0.26 0.11
81_A 91_I 0.71 0.26 0.11
37_R 89_L 0.70 0.26 0.11
16_L 130_S 0.70 0.26 0.11
93_W 76_N 0.70 0.26 0.11
21_A 58_S 0.70 0.26 0.11
82_A 138_L 0.70 0.26 0.11
26_I 31_R 0.70 0.26 0.11
59_F 127_H 0.70 0.26 0.10
38_T 118_V 0.70 0.26 0.10
59_F 59_L 0.70 0.26 0.10
86_T 102_R 0.70 0.26 0.10
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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