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OPENSEQ.org
fliQflhB
Genes: A B A+B
Length: 89 211 296
Sequences: 1330 1992 1252
Seq/Len: 14.94 9.44 4.23
MirrorTree (Pazo et al. 2001) 0.69
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 0.20
2 0.00 0.00 3.74
5 0.00 0.01 3.83
10 0.01 0.01 4.03
20 0.01 0.02 4.17
100 0.02 0.03 4.69
∞ 0.05 0.07 5.10
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
45_N 30_Q 1.41 0.96 0.69
45_N 110_F 1.37 0.96 0.66
41_T 144_S 1.34 0.95 0.63
45_N 28_K 1.30 0.94 0.60
41_T 132_L 1.22 0.91 0.52
47_M 35_I 1.16 0.88 0.46
43_Q 113_I 1.11 0.85 0.41
43_Q 137_S 1.08 0.82 0.39
88_I 8_K 1.03 0.77 0.33
45_N 109_Q 1.01 0.76 0.31
12_Q 42_V 1.01 0.75 0.31
26_L 85_F 1.00 0.74 0.30
41_T 126_I 1.00 0.74 0.30
18_L 38_L 0.99 0.73 0.29
40_A 126_I 0.98 0.72 0.28
6_L 195_V 0.95 0.69 0.26
6_L 7_E 0.93 0.66 0.24
47_M 151_V 0.92 0.66 0.24
23_P 109_Q 0.92 0.65 0.23
36_S 199_F 0.91 0.65 0.23
29_L 96_L 0.90 0.63 0.22
24_M 12_P 0.89 0.62 0.21
28_G 46_L 0.89 0.61 0.21
68_W 111_G 0.88 0.61 0.21
63_I 26_V 0.88 0.61 0.21
54_K 109_Q 0.87 0.60 0.20
35_I 125_K 0.87 0.60 0.20
28_G 7_E 0.87 0.59 0.20
28_G 199_F 0.87 0.59 0.19
67_P 181_L 0.86 0.58 0.19
73_M 18_E 0.86 0.58 0.19
59_V 188_A 0.86 0.58 0.19
19_L 164_K 0.86 0.58 0.19
36_S 38_L 0.85 0.57 0.18
60_V 65_S 0.85 0.57 0.18
2_D 148_I 0.85 0.56 0.18
84_I 94_I 0.85 0.56 0.18
76_F 168_E 0.85 0.56 0.18
14_F 60_Y 0.84 0.56 0.18
25_L 5_D 0.84 0.56 0.18
72_T 157_I 0.84 0.55 0.17
29_L 18_E 0.83 0.55 0.17
20_L 55_R 0.83 0.54 0.17
47_M 210_V 0.83 0.54 0.17
22_L 126_I 0.82 0.53 0.17
43_Q 14_S 0.82 0.53 0.16
67_P 125_K 0.82 0.53 0.16
21_S 60_Y 0.82 0.53 0.16
24_M 82_K 0.82 0.52 0.16
33_L 35_I 0.81 0.51 0.16
44_I 38_L 0.81 0.51 0.15
40_A 140_K 0.80 0.50 0.15
55_I 154_V 0.80 0.49 0.15
82_N 100_I 0.80 0.49 0.15
31_A 34_A 0.79 0.49 0.14
51_F 7_E 0.79 0.49 0.14
64_F 80_M 0.79 0.48 0.14
8_A 203_A 0.79 0.48 0.14
65_L 129_L 0.79 0.48 0.14
68_W 137_S 0.79 0.48 0.14
15_K 16_K 0.79 0.48 0.14
35_I 119_I 0.78 0.48 0.14
87_F 17_I 0.78 0.47 0.14
69_M 114_F 0.77 0.46 0.13
38_F 135_L 0.77 0.45 0.13
46_E 146_K 0.76 0.45 0.13
6_L 51_F 0.76 0.45 0.13
12_Q 100_I 0.76 0.44 0.12
85_P 37_T 0.76 0.44 0.12
83_Q 137_S 0.75 0.43 0.12
47_M 199_F 0.75 0.43 0.12
61_I 135_L 0.74 0.42 0.12
38_F 151_V 0.74 0.42 0.12
22_L 88_L 0.74 0.42 0.12
6_L 80_M 0.73 0.41 0.11
12_Q 119_I 0.73 0.41 0.11
2_D 39_I 0.73 0.40 0.11
28_G 194_I 0.73 0.40 0.11
30_I 152_G 0.73 0.40 0.11
29_L 110_F 0.73 0.40 0.11
13_T 101_A 0.72 0.40 0.11
60_V 169_L 0.72 0.39 0.11
70_T 144_S 0.72 0.39 0.11
58_V 127_N 0.72 0.39 0.10
35_I 122_N 0.72 0.39 0.10
46_E 134_N 0.72 0.39 0.10
70_T 143_E 0.71 0.38 0.10
64_F 70_E 0.71 0.38 0.10
66_M 131_G 0.71 0.38 0.10
58_V 191_L 0.71 0.38 0.10
52_V 99_M 0.71 0.38 0.10
36_S 112_F 0.71 0.38 0.10
78_E 103_V 0.71 0.38 0.10
31_A 177_M 0.71 0.37 0.10
45_N 25_N 0.71 0.37 0.10
35_I 194_I 0.71 0.37 0.10
54_K 208_F 0.70 0.37 0.10
40_A 210_V 0.70 0.37 0.10
4_S 12_P 0.70 0.37 0.10
76_F 151_V 0.70 0.37 0.10
81_L 151_V 0.70 0.36 0.10
14_F 121_P 0.70 0.36 0.10
72_T 45_T 0.70 0.36 0.10
22_L 115_T 0.70 0.36 0.10
86_T 13_T 0.70 0.36 0.09
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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