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OPENSEQ.org
fliQfliR
Genes: A B A+B
Length: 89 255 335
Sequences: 1330 1842 1435
Seq/Len: 14.94 7.22 4.28
MirrorTree (Pazo et al. 2001) 0.76
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 3.77
2 0.00 0.00 3.93
5 0.00 0.01 4.00
10 0.01 0.01 4.13
20 0.01 0.02 4.17
100 0.02 0.03 4.19
∞ 0.05 0.07 4.35
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
10_G 126_I 1.51 0.98 0.83
13_T 126_I 1.49 0.98 0.82
14_F 224_F 1.20 0.90 0.60
36_S 103_T 1.18 0.89 0.58
14_F 227_L 1.18 0.89 0.57
18_L 208_Q 1.17 0.88 0.56
8_A 209_F 1.16 0.88 0.55
62_L 20_A 1.14 0.86 0.53
25_L 214_I 1.14 0.86 0.53
10_G 130_L 1.12 0.86 0.52
43_Q 196_D 1.12 0.85 0.51
24_M 104_M 1.12 0.85 0.51
47_M 214_I 1.09 0.83 0.48
47_M 101_A 1.09 0.83 0.48
6_L 119_S 1.07 0.82 0.46
44_I 107_T 1.07 0.81 0.46
76_F 224_F 1.07 0.81 0.46
71_T 100_I 1.05 0.80 0.44
28_G 178_F 1.05 0.80 0.43
76_F 68_F 1.05 0.80 0.43
18_L 225_V 1.04 0.79 0.43
17_T 185_S 1.03 0.78 0.41
43_Q 211_L 1.02 0.78 0.41
22_L 221_A 1.02 0.77 0.40
35_I 55_P 0.98 0.72 0.36
45_N 196_D 0.96 0.71 0.34
30_I 234_M 0.96 0.71 0.34
14_F 33_S 0.96 0.71 0.34
76_F 145_L 0.96 0.71 0.34
50_S 213_V 0.96 0.71 0.34
38_F 180_I 0.96 0.70 0.34
50_S 108_M 0.95 0.70 0.33
29_L 80_M 0.94 0.69 0.32
88_I 89_I 0.94 0.68 0.32
45_N 101_A 0.94 0.68 0.32
20_L 182_F 0.93 0.67 0.31
76_F 85_M 0.93 0.67 0.31
60_V 81_I 0.92 0.66 0.30
26_L 194_L 0.92 0.66 0.30
23_P 176_N 0.92 0.65 0.29
76_F 146_L 0.90 0.64 0.28
43_Q 189_L 0.90 0.64 0.28
46_E 113_D 0.90 0.64 0.28
73_M 59_L 0.90 0.63 0.28
40_A 83_G 0.90 0.63 0.28
66_M 215_G 0.89 0.62 0.27
40_A 211_L 0.88 0.60 0.26
55_I 206_M 0.88 0.60 0.26
85_P 152_L 0.87 0.60 0.26
22_L 61_S 0.87 0.60 0.25
8_A 63_H 0.87 0.60 0.25
33_L 198_I 0.87 0.59 0.25
44_I 208_Q 0.86 0.59 0.25
23_P 187_P 0.86 0.59 0.25
29_L 141_H 0.86 0.59 0.25
15_K 43_S 0.86 0.59 0.25
18_L 50_T 0.86 0.58 0.24
52_V 186_F 0.85 0.58 0.24
4_S 78_F 0.85 0.57 0.24
24_M 230_I 0.85 0.57 0.24
71_T 88_I 0.85 0.57 0.24
6_L 137_A 0.85 0.57 0.23
6_L 178_F 0.85 0.57 0.23
13_T 132_L 0.85 0.56 0.23
20_L 189_L 0.84 0.56 0.23
6_L 249_M 0.84 0.56 0.23
75_D 47_L 0.84 0.56 0.23
72_T 82_A 0.84 0.56 0.23
35_I 180_I 0.84 0.56 0.23
60_V 197_V 0.84 0.55 0.23
51_F 200_G 0.84 0.55 0.23
54_K 238_F 0.84 0.55 0.22
45_N 219_K 0.83 0.55 0.22
56_I 72_L 0.83 0.55 0.22
73_M 185_S 0.83 0.54 0.22
25_L 32_F 0.83 0.54 0.22
26_L 153_G 0.83 0.54 0.22
13_T 190_G 0.83 0.54 0.22
78_E 82_A 0.83 0.54 0.21
77_T 225_V 0.82 0.53 0.21
64_F 243_L 0.82 0.53 0.21
53_P 207_P 0.82 0.52 0.21
47_M 206_M 0.81 0.52 0.20
21_S 221_A 0.81 0.52 0.20
53_P 106_F 0.81 0.52 0.20
17_T 224_F 0.81 0.52 0.20
77_T 196_D 0.81 0.52 0.20
80_I 150_H 0.81 0.51 0.20
67_P 182_F 0.81 0.51 0.20
33_L 47_L 0.81 0.51 0.20
69_M 20_A 0.80 0.51 0.20
41_T 215_G 0.80 0.50 0.19
85_P 140_G 0.80 0.50 0.19
53_P 220_I 0.80 0.50 0.19
55_I 220_I 0.80 0.50 0.19
28_G 121_P 0.79 0.49 0.18
59_V 203_M 0.79 0.49 0.18
75_D 223_G 0.79 0.48 0.18
47_M 174_M 0.79 0.48 0.18
82_N 24_G 0.78 0.48 0.18
33_L 60_E 0.78 0.48 0.18
41_T 113_D 0.78 0.47 0.18
36_S 202_L 0.78 0.47 0.18
28_G 174_M 0.78 0.47 0.17
83_Q 52_Y 0.77 0.47 0.17
20_L 168_H 0.77 0.47 0.17
36_S 199_F 0.77 0.46 0.17
14_F 204_K 0.77 0.46 0.17
70_T 122_I 0.77 0.46 0.17
43_Q 190_G 0.76 0.45 0.17
76_F 14_T 0.76 0.45 0.17
34_V 96_A 0.76 0.45 0.17
87_F 230_I 0.76 0.45 0.16
5_T 185_S 0.76 0.44 0.16
26_L 51_M 0.76 0.44 0.16
85_P 145_L 0.76 0.44 0.16
45_N 193_L 0.76 0.44 0.16
57_L 94_M 0.75 0.44 0.16
76_F 38_P 0.75 0.44 0.16
63_I 226_V 0.75 0.43 0.16
81_L 51_M 0.75 0.43 0.15
35_I 252_L 0.75 0.43 0.15
55_I 200_G 0.75 0.43 0.15
52_V 234_M 0.75 0.43 0.15
53_P 141_H 0.75 0.43 0.15
50_S 120_M 0.74 0.42 0.15
78_E 171_N 0.74 0.42 0.15
40_A 117_G 0.74 0.42 0.15
36_S 112_L 0.74 0.42 0.15
22_L 195_A 0.74 0.42 0.15
50_S 49_L 0.74 0.42 0.15
62_L 99_Q 0.74 0.41 0.15
37_I 70_L 0.74 0.41 0.15
37_I 62_L 0.73 0.41 0.15
81_L 83_G 0.73 0.41 0.15
79_N 145_L 0.73 0.41 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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