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OPENSEQ.org
fliQfliPcamp
Genes: A B A+B
Length: 89 244 319
Sequences: 1330 1469 1138
Seq/Len: 14.94 6.02 3.57
MirrorTree (Pazo et al. 2001) 0.68
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 2.94
2 0.00 0.00 2.97
5 0.00 0.01 3.11
10 0.01 0.01 3.19
20 0.01 0.02 3.42
100 0.02 0.03 3.57
∞ 0.05 0.07 3.71
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
84_I 184_I 2.77 1.00 1.00
77_T 228_V 1.93 1.00 0.98
24_M 202_V 1.86 0.99 0.98
80_I 187_L 1.56 0.98 0.93
55_I 53_A 1.48 0.96 0.90
9_L 187_L 1.45 0.96 0.89
13_T 190_L 1.40 0.95 0.87
17_T 197_M 1.36 0.94 0.85
55_I 212_P 1.35 0.94 0.85
67_P 148_L 1.23 0.89 0.77
66_M 90_T 1.19 0.86 0.74
47_M 80_Q 1.19 0.86 0.73
81_L 228_V 1.16 0.84 0.71
36_S 215_M 1.10 0.79 0.65
66_M 223_L 1.09 0.79 0.64
43_Q 218_L 1.08 0.78 0.62
25_L 212_P 1.05 0.75 0.59
81_L 188_I 1.00 0.70 0.54
64_F 205_A 0.99 0.69 0.53
35_I 209_M 0.98 0.68 0.51
63_I 68_V 0.97 0.66 0.49
47_M 73_L 0.96 0.66 0.49
30_I 140_N 0.96 0.65 0.48
56_I 198_V 0.92 0.61 0.44
17_T 198_V 0.92 0.60 0.43
22_L 217_S 0.91 0.59 0.42
40_A 179_K 0.91 0.59 0.42
56_I 217_S 0.90 0.58 0.41
76_F 194_V 0.90 0.58 0.41
53_P 114_P 0.90 0.58 0.41
66_M 188_I 0.90 0.58 0.41
41_T 175_I 0.90 0.57 0.40
11_V 16_A 0.88 0.55 0.38
72_T 242_F 0.87 0.54 0.37
58_V 107_S 0.87 0.54 0.37
77_T 108_Y 0.85 0.51 0.34
20_L 198_V 0.84 0.50 0.33
84_I 199_V 0.83 0.49 0.32
38_F 119_K 0.83 0.48 0.32
6_L 190_L 0.83 0.48 0.32
60_V 128_K 0.82 0.48 0.32
81_L 241_S 0.82 0.48 0.31
57_L 88_L 0.82 0.48 0.31
12_Q 104_A 0.81 0.47 0.31
45_N 206_M 0.81 0.47 0.30
79_N 160_T 0.81 0.46 0.30
41_T 78_G 0.81 0.46 0.30
37_I 84_P 0.81 0.46 0.30
62_L 103_V 0.81 0.46 0.30
17_T 194_V 0.81 0.46 0.29
84_I 71_S 0.80 0.46 0.29
70_T 227_L 0.80 0.45 0.29
14_F 173_F 0.80 0.44 0.28
66_M 204_M 0.79 0.44 0.28
35_I 199_V 0.79 0.44 0.28
66_M 137_M 0.79 0.43 0.28
29_L 209_M 0.79 0.43 0.28
28_G 198_V 0.79 0.43 0.28
80_I 237_R 0.78 0.43 0.27
78_E 49_I 0.78 0.42 0.27
50_S 38_V 0.78 0.42 0.26
60_V 131_K 0.78 0.42 0.26
36_S 205_A 0.77 0.41 0.26
2_D 91_L 0.77 0.41 0.26
50_S 152_I 0.77 0.41 0.26
47_M 187_L 0.77 0.41 0.25
69_M 48_T 0.76 0.40 0.24
36_S 91_L 0.76 0.40 0.24
76_F 242_F 0.75 0.39 0.23
45_N 175_I 0.75 0.39 0.23
84_I 227_L 0.75 0.39 0.23
9_L 202_V 0.75 0.38 0.23
85_P 174_M 0.74 0.38 0.23
34_V 28_L 0.74 0.38 0.23
61_I 118_E 0.74 0.38 0.23
3_E 41_L 0.74 0.37 0.23
74_I 228_V 0.74 0.37 0.22
33_L 189_Y 0.73 0.37 0.22
57_L 205_A 0.73 0.36 0.22
59_V 197_M 0.73 0.36 0.22
6_L 216_I 0.73 0.36 0.22
47_M 209_M 0.73 0.36 0.21
20_L 151_R 0.73 0.36 0.21
43_Q 75_Q 0.72 0.35 0.21
69_M 95_L 0.72 0.35 0.21
43_Q 146_L 0.72 0.35 0.20
43_Q 72_F 0.72 0.34 0.20
18_L 81_S 0.72 0.34 0.20
48_T 99_I 0.72 0.34 0.20
84_I 63_F 0.71 0.34 0.20
35_I 239_V 0.71 0.33 0.19
3_E 194_V 0.70 0.33 0.19
47_M 90_T 0.70 0.33 0.19
75_D 153_R 0.70 0.33 0.19
62_L 41_L 0.70 0.32 0.19
78_E 68_V 0.70 0.32 0.19
52_V 209_M 0.70 0.32 0.19
33_L 181_A 0.69 0.32 0.18
65_L 172_A 0.69 0.32 0.18
6_L 227_L 0.69 0.32 0.18
41_T 179_K 0.69 0.32 0.18
50_S 52_L 0.69 0.32 0.18
76_F 178_L 0.69 0.32 0.18
26_L 106_K 0.69 0.32 0.18
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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