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OPENSEQ.org
3rko_2_G_F
Genes: A B A+B
Length: 100 184 262
Sequences: 2614 2185 1765
Seq/Len: 26.14 11.88 6.74
MirrorTree (Pazo et al. 2001) 0.82
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.07 0.02 5.43
2 0.07 0.02 5.62
5 0.07 0.02 5.81
10 0.07 0.02 6.04
20 0.07 0.02 6.21
100 0.08 0.03 6.32
∞ 0.08 0.05 6.30
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
13_I 13_I 4.77 1.00 1.00
6_H 6_Y 2.94 1.00 1.00
17_L 17_L 2.77 1.00 1.00
14_L 16_T 2.50 1.00 1.00
33_I 19_V 2.20 1.00 0.99
10_L 42_V 2.19 1.00 0.99
67_S 144_A 2.07 1.00 0.99
17_L 16_T 2.07 1.00 0.99
44_L 39_I 2.02 1.00 0.99
81_L 159_G 1.75 1.00 0.97
33_I 29_L 1.71 1.00 0.97
60_V 129_V 1.67 1.00 0.96
21_G 20_I 1.67 1.00 0.96
40_N 55_E 1.56 0.99 0.94
75_I 147_L 1.44 0.99 0.91
44_L 43_F 1.40 0.99 0.90
32_L 73_M 1.34 0.98 0.88
10_L 9_G 1.29 0.97 0.85
73_A 130_G 1.29 0.97 0.85
37_I 35_S 1.27 0.97 0.84
31_M 28_A 1.26 0.97 0.83
34_G 19_V 1.26 0.97 0.83
19_L 57_I 1.20 0.95 0.79
48_V 46_L 1.18 0.95 0.78
40_N 43_F 1.18 0.95 0.78
6_H 2_E 1.15 0.94 0.76
33_I 18_R 1.14 0.94 0.75
98_M 4_A 1.13 0.93 0.73
82_Q 139_L 1.07 0.90 0.68
40_N 39_I 1.05 0.90 0.66
81_L 157_H 1.03 0.88 0.64
3_P 2_E 1.03 0.88 0.63
60_V 155_A 1.01 0.87 0.62
47_V 48_A 1.01 0.87 0.62
56_T 129_V 1.00 0.86 0.60
67_S 150_A 1.00 0.86 0.60
82_Q 158_V 0.97 0.83 0.56
7_G 42_V 0.96 0.83 0.56
97_E 28_A 0.96 0.82 0.55
14_L 71_V 0.96 0.82 0.55
48_V 48_A 0.95 0.82 0.54
50_G 75_N 0.94 0.81 0.53
11_A 40_S 0.94 0.81 0.53
64_L 140_A 0.93 0.80 0.52
24_I 153_V 0.93 0.80 0.52
82_Q 28_A 0.92 0.79 0.50
33_I 64_M 0.92 0.78 0.50
28_L 77_G 0.91 0.78 0.49
17_L 20_I 0.91 0.77 0.48
62_Y 43_F 0.91 0.77 0.48
7_G 5_F 0.90 0.77 0.48
86_R 142_E 0.90 0.77 0.48
78_A 67_F 0.90 0.77 0.48
22_L 36_L 0.90 0.76 0.47
63_I 140_A 0.89 0.76 0.47
95_V 33_I 0.89 0.75 0.46
68_L 24_N 0.89 0.75 0.46
73_A 25_P 0.89 0.75 0.46
82_Q 157_H 0.88 0.75 0.46
25_R 64_M 0.88 0.74 0.45
60_V 49_Y 0.87 0.73 0.44
90_L 66_L 0.87 0.73 0.44
66_I 145_S 0.87 0.73 0.44
46_F 81_I 0.87 0.73 0.44
99_R 154_V 0.87 0.73 0.44
18_G 154_V 0.86 0.72 0.42
10_L 39_I 0.86 0.71 0.42
38_M 46_L 0.85 0.71 0.42
66_I 55_E 0.85 0.71 0.41
17_L 24_N 0.85 0.71 0.41
41_A 73_M 0.84 0.69 0.40
45_A 71_V 0.83 0.69 0.39
66_I 144_A 0.83 0.68 0.39
18_G 55_E 0.83 0.68 0.39
14_L 39_I 0.83 0.68 0.39
76_G 60_A 0.82 0.67 0.38
84_H 50_F 0.82 0.67 0.38
95_V 143_L 0.82 0.67 0.37
19_L 32_L 0.82 0.66 0.37
52_Y 46_L 0.82 0.66 0.37
20_T 145_S 0.81 0.66 0.37
11_A 123_P 0.81 0.66 0.37
13_I 14_L 0.81 0.65 0.36
18_G 43_F 0.80 0.64 0.35
49_A 29_L 0.80 0.64 0.35
10_L 41_G 0.80 0.64 0.35
23_V 65_V 0.79 0.62 0.34
92_I 58_V 0.79 0.62 0.34
13_I 22_H 0.79 0.62 0.34
20_T 20_I 0.79 0.62 0.34
45_A 140_A 0.79 0.62 0.33
40_N 36_L 0.78 0.61 0.33
73_A 149_L 0.78 0.61 0.33
86_R 161_E 0.78 0.61 0.33
57_D 145_S 0.78 0.61 0.33
57_D 136_P 0.78 0.60 0.32
9_I 121_G 0.78 0.60 0.32
71_A 151_G 0.78 0.60 0.32
38_M 146_M 0.78 0.60 0.32
80_L 77_G 0.77 0.60 0.32
56_T 132_T 0.77 0.59 0.31
46_F 8_C 0.77 0.59 0.31
64_L 54_L 0.77 0.59 0.31
9_I 142_E 0.77 0.59 0.31
70_A 58_V 0.77 0.59 0.31
15_F 7_I 0.77 0.59 0.31
94_S 40_S 0.76 0.59 0.31
47_V 51_A 0.76 0.58 0.30
63_I 146_M 0.76 0.58 0.30
80_L 68_V 0.76 0.57 0.30
65_A 111_I 0.75 0.57 0.29
3_P 17_L 0.75 0.57 0.29
66_I 73_M 0.75 0.56 0.29
80_L 154_V 0.75 0.56 0.29
23_V 99_L 0.75 0.56 0.28
29_L 154_V 0.74 0.56 0.28
48_V 161_E 0.74 0.55 0.28
37_I 43_F 0.74 0.55 0.28
30_F 25_P 0.74 0.55 0.28
26_R 128_A 0.74 0.55 0.28
32_L 137_Y 0.74 0.54 0.27
91_N 52_G 0.73 0.54 0.27
42_S 23_T 0.73 0.54 0.27
75_I 74_L 0.73 0.54 0.27
20_T 57_I 0.73 0.54 0.27
11_A 3_F 0.73 0.54 0.27
98_M 83_Q 0.73 0.54 0.27
24_I 20_I 0.73 0.54 0.27
9_I 10_L 0.73 0.53 0.27
24_I 147_L 0.73 0.53 0.27
26_R 3_F 0.73 0.53 0.27
62_Y 51_A 0.73 0.53 0.27
85_R 145_S 0.73 0.53 0.26
40_N 53_A 0.73 0.53 0.26
37_I 15_A 0.73 0.53 0.26
47_V 158_V 0.73 0.53 0.26
65_A 9_G 0.72 0.53 0.26
92_I 52_G 0.72 0.52 0.26
57_D 132_T 0.72 0.52 0.26
62_Y 55_E 0.72 0.52 0.26
34_G 81_I 0.72 0.52 0.26
44_L 92_V 0.72 0.52 0.25
38_M 4_A 0.72 0.51 0.25
13_I 112_L 0.71 0.51 0.25
14_L 143_L 0.71 0.51 0.25
98_M 47_G 0.71 0.51 0.25
63_I 43_F 0.71 0.50 0.24
30_F 134_F 0.71 0.50 0.24
18_G 130_G 0.71 0.50 0.24
84_H 55_E 0.71 0.50 0.24
33_I 67_F 0.71 0.50 0.24
43_A 55_E 0.71 0.50 0.24
35_L 67_F 0.71 0.50 0.24
59_Q 72_M 0.71 0.50 0.24
89_N 51_A 0.70 0.49 0.24
12_A 138_V 0.70 0.49 0.24
9_I 6_Y 0.70 0.49 0.23
63_I 64_M 0.70 0.49 0.23
29_L 1_M 0.70 0.48 0.23
90_L 127_K 0.69 0.48 0.23
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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