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OPENSEQ.org
fliPfliQ
Genes: A B A+B
Length: 215 89 299
Sequences: 1428 1330 1114
Seq/Len: 6.64 14.94 3.73
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 3.17
2 0.00 0.00 3.20
5 0.01 0.00 3.34
10 0.01 0.01 3.41
20 0.02 0.01 3.66
100 0.03 0.02 3.82
∞ 0.07 0.05 3.98
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
155_I 84_I 2.50 1.00 1.00
199_V 77_T 1.89 1.00 0.98
173_V 24_M 1.83 0.99 0.97
158_T 80_I 1.54 0.98 0.92
24_L 55_I 1.50 0.97 0.91
158_T 9_L 1.50 0.97 0.91
183_P 55_I 1.34 0.94 0.84
161_I 13_T 1.31 0.93 0.82
51_P 47_M 1.22 0.89 0.76
168_L 17_T 1.20 0.88 0.75
199_V 81_L 1.11 0.81 0.66
180_M 35_I 1.10 0.81 0.66
176_A 64_F 1.10 0.81 0.65
183_P 25_L 1.08 0.79 0.63
186_T 36_S 1.07 0.78 0.62
119_L 67_P 1.03 0.74 0.57
194_M 66_M 1.02 0.74 0.57
61_G 66_M 1.02 0.73 0.56
169_V 56_I 1.01 0.72 0.55
189_L 43_Q 0.99 0.70 0.52
78_I 58_V 0.96 0.66 0.48
44_L 47_M 0.96 0.66 0.48
123_L 50_S 0.95 0.66 0.48
165_I 76_F 0.95 0.65 0.47
111_Q 30_I 0.93 0.63 0.45
175_M 66_M 0.93 0.63 0.45
213_F 72_T 0.92 0.62 0.44
188_A 56_I 0.92 0.62 0.44
208_S 80_I 0.92 0.62 0.44
144_Y 14_F 0.91 0.61 0.43
169_V 20_L 0.91 0.60 0.42
159_I 81_L 0.89 0.58 0.40
49_G 41_T 0.89 0.58 0.40
188_A 22_L 0.89 0.57 0.40
150_K 40_A 0.88 0.57 0.39
169_V 17_T 0.87 0.55 0.38
169_V 28_G 0.86 0.54 0.36
20_S 78_E 0.85 0.53 0.35
170_I 84_I 0.84 0.52 0.34
159_I 66_M 0.83 0.51 0.33
146_T 41_T 0.83 0.50 0.33
99_K 60_V 0.83 0.50 0.33
212_S 81_L 0.83 0.50 0.33
12_V 4_S 0.83 0.50 0.32
104_L 62_L 0.82 0.48 0.31
62_L 36_S 0.82 0.48 0.31
180_M 29_L 0.81 0.47 0.30
19_T 69_M 0.81 0.47 0.30
160_F 11_V 0.80 0.46 0.29
79_Y 77_T 0.80 0.46 0.29
170_I 35_I 0.79 0.45 0.28
42_G 84_I 0.79 0.45 0.28
126_S 73_M 0.79 0.45 0.28
180_M 47_M 0.79 0.44 0.28
155_I 17_T 0.79 0.44 0.28
63_A 82_N 0.78 0.43 0.27
62_L 2_D 0.78 0.43 0.27
66_L 19_L 0.78 0.43 0.27
49_G 43_Q 0.78 0.43 0.27
66_L 69_M 0.77 0.42 0.26
168_L 59_V 0.77 0.42 0.26
140_L 28_G 0.76 0.41 0.25
12_V 62_L 0.76 0.41 0.25
9_S 50_S 0.76 0.41 0.25
38_I 80_I 0.76 0.40 0.24
170_I 57_L 0.76 0.40 0.24
176_A 36_S 0.75 0.40 0.24
146_T 45_N 0.75 0.40 0.24
74_V 62_L 0.75 0.40 0.24
193_L 72_T 0.75 0.40 0.24
177_L 45_N 0.75 0.40 0.24
7_S 26_L 0.75 0.40 0.24
180_M 52_V 0.74 0.39 0.23
122_R 20_L 0.74 0.39 0.23
187_I 12_Q 0.74 0.38 0.23
55_P 37_I 0.74 0.38 0.23
70_I 48_T 0.73 0.38 0.22
145_V 85_P 0.73 0.38 0.22
143_A 65_L 0.73 0.38 0.22
118_A 64_F 0.73 0.37 0.22
108_M 66_M 0.72 0.36 0.21
39_I 63_I 0.72 0.36 0.21
34_F 84_I 0.72 0.36 0.21
46_N 43_Q 0.72 0.36 0.21
43_L 43_Q 0.72 0.36 0.21
75_I 12_Q 0.72 0.36 0.21
210_A 35_I 0.72 0.36 0.21
59_L 57_L 0.72 0.36 0.21
189_L 7_V 0.72 0.35 0.21
158_T 47_M 0.71 0.35 0.20
149_L 76_F 0.71 0.35 0.20
20_S 88_I 0.71 0.35 0.20
12_V 3_E 0.71 0.34 0.20
176_A 57_L 0.71 0.34 0.20
160_F 33_L 0.71 0.34 0.20
52_S 40_A 0.70 0.34 0.20
127_G 64_F 0.70 0.34 0.19
173_V 9_L 0.70 0.34 0.19
198_L 3_E 0.70 0.34 0.19
152_A 33_L 0.70 0.34 0.19
198_L 6_L 0.69 0.33 0.18
110_R 56_I 0.69 0.33 0.18
97_L 34_V 0.69 0.32 0.18
8_W 31_A 0.69 0.32 0.18
112_T 69_M 0.68 0.32 0.18
61_G 47_M 0.68 0.32 0.17
8_W 55_I 0.68 0.32 0.17
198_L 84_I 0.68 0.31 0.17
165_I 17_T 0.68 0.31 0.17
165_I 47_M 0.68 0.31 0.17
199_V 74_I 0.68 0.31 0.17
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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