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OPENSEQ.org
fliPfliR
Genes: A B A+B
Length: 215 255 458
Sequences: 1428 1842 1459
Seq/Len: 6.64 7.22 3.19
MirrorTree (Pazo et al. 2001) 0.80
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 0.08
2 0.00 0.00 2.66
5 0.01 0.01 2.74
10 0.01 0.01 2.97
20 0.02 0.02 3.10
100 0.03 0.03 3.27
∞ 0.07 0.07 3.41
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
115_A 139_D 1.61 0.98 0.87
48_L 185_S 1.54 0.97 0.83
182_V 200_G 1.40 0.94 0.75
11_S 90_F 1.26 0.88 0.63
187_I 191_I 1.22 0.86 0.59
122_R 146_L 1.20 0.85 0.57
195_L 192_S 1.17 0.82 0.54
61_G 84_L 1.17 0.82 0.53
50_T 93_I 1.14 0.80 0.50
150_K 139_D 1.12 0.79 0.49
30_M 44_T 1.09 0.76 0.46
46_N 101_A 1.09 0.76 0.45
29_L 124_S 1.09 0.76 0.45
39_I 169_Y 1.08 0.75 0.44
145_V 41_I 1.05 0.72 0.41
20_S 80_M 1.00 0.67 0.36
50_T 119_S 1.00 0.67 0.36
168_L 119_S 0.99 0.65 0.34
183_P 183_T 0.98 0.64 0.34
128_P 181_G 0.98 0.64 0.34
183_P 206_M 0.97 0.64 0.33
159_I 198_I 0.97 0.63 0.33
63_A 84_L 0.97 0.63 0.32
41_F 247_T 0.97 0.63 0.32
213_F 101_A 0.95 0.61 0.31
209_L 37_I 0.95 0.61 0.31
173_V 223_G 0.95 0.61 0.31
116_D 142_H 0.95 0.60 0.30
117_L 96_A 0.94 0.60 0.30
183_P 210_N 0.94 0.59 0.29
43_L 36_S 0.93 0.58 0.29
175_M 106_F 0.92 0.57 0.28
165_I 191_I 0.92 0.57 0.28
169_V 145_L 0.92 0.57 0.28
80_V 45_I 0.92 0.57 0.27
22_T 38_P 0.92 0.57 0.27
48_L 93_I 0.91 0.56 0.27
198_L 109_A 0.91 0.56 0.27
206_M 105_G 0.91 0.56 0.27
168_L 203_M 0.91 0.55 0.26
49_G 115_S 0.90 0.55 0.26
124_A 20_A 0.90 0.55 0.26
176_A 20_A 0.90 0.55 0.26
18_I 208_Q 0.89 0.53 0.25
114_E 222_L 0.89 0.53 0.24
63_A 95_M 0.89 0.53 0.24
160_F 178_F 0.89 0.53 0.24
30_M 194_L 0.89 0.53 0.24
52_S 125_Q 0.88 0.53 0.24
187_I 216_Y 0.88 0.52 0.24
17_F 229_A 0.88 0.52 0.24
141_L 48_F 0.88 0.52 0.24
81_D 85_M 0.88 0.52 0.24
46_N 90_F 0.88 0.52 0.24
11_S 205_T 0.88 0.52 0.24
39_I 105_G 0.88 0.52 0.24
55_P 91_A 0.88 0.52 0.24
70_I 237_Y 0.88 0.52 0.24
59_L 116_S 0.88 0.51 0.24
36_R 101_A 0.88 0.51 0.24
36_R 104_M 0.88 0.51 0.24
36_R 106_F 0.87 0.50 0.23
60_L 85_M 0.87 0.50 0.23
194_M 101_A 0.86 0.50 0.23
111_Q 55_P 0.86 0.50 0.22
119_L 145_L 0.86 0.50 0.22
207_G 101_A 0.86 0.49 0.22
147_S 82_A 0.86 0.49 0.22
165_I 174_M 0.85 0.49 0.22
84_Q 197_V 0.85 0.48 0.22
169_V 165_N 0.85 0.48 0.21
29_L 104_M 0.85 0.48 0.21
78_I 249_M 0.85 0.48 0.21
146_T 142_H 0.85 0.48 0.21
177_L 191_I 0.85 0.48 0.21
95_E 164_E 0.85 0.48 0.21
105_R 190_G 0.85 0.48 0.21
176_A 95_M 0.84 0.47 0.21
15_L 215_G 0.84 0.47 0.21
14_T 112_L 0.84 0.47 0.21
74_V 184_M 0.84 0.47 0.21
89_Q 16_M 0.84 0.47 0.21
150_K 141_H 0.84 0.47 0.20
182_V 9_D 0.83 0.46 0.20
10_L 101_A 0.83 0.46 0.20
131_G 46_V 0.83 0.46 0.20
46_N 196_D 0.83 0.46 0.20
125_N 218_I 0.83 0.46 0.20
47_A 99_Q 0.83 0.46 0.20
105_R 70_L 0.82 0.45 0.19
176_A 137_A 0.82 0.45 0.19
143_A 52_Y 0.82 0.45 0.19
182_V 113_D 0.82 0.45 0.19
188_A 150_H 0.82 0.44 0.19
9_S 46_V 0.81 0.44 0.19
90_K 63_H 0.81 0.44 0.18
188_A 119_S 0.81 0.43 0.18
62_L 111_I 0.81 0.43 0.18
102_Q 12_V 0.81 0.43 0.18
39_I 133_M 0.81 0.43 0.18
172_S 97_G 0.81 0.43 0.18
168_L 224_F 0.81 0.43 0.18
183_P 237_Y 0.81 0.43 0.18
44_L 135_F 0.81 0.43 0.18
90_K 69_V 0.81 0.43 0.18
165_I 202_L 0.81 0.43 0.18
150_K 130_L 0.81 0.43 0.18
144_Y 42_K 0.81 0.43 0.18
208_S 221_A 0.81 0.42 0.18
44_L 193_L 0.81 0.42 0.18
9_S 177_I 0.80 0.42 0.18
16_V 82_A 0.80 0.42 0.18
17_F 73_I 0.80 0.42 0.18
88_E 67_F 0.80 0.42 0.17
23_F 57_A 0.80 0.42 0.17
84_Q 202_L 0.80 0.41 0.17
91_I 158_G 0.80 0.41 0.17
199_V 196_D 0.80 0.41 0.17
79_Y 219_K 0.79 0.41 0.17
50_T 116_S 0.79 0.41 0.17
187_I 204_K 0.79 0.41 0.17
188_A 123_T 0.79 0.41 0.17
77_K 148_L 0.79 0.41 0.17
104_L 252_L 0.79 0.41 0.17
12_V 176_N 0.79 0.40 0.17
144_Y 12_V 0.79 0.40 0.17
175_M 220_I 0.79 0.40 0.17
193_L 99_Q 0.78 0.40 0.16
173_V 92_I 0.78 0.40 0.16
63_A 252_L 0.78 0.40 0.16
141_L 249_M 0.78 0.40 0.16
146_T 108_M 0.78 0.40 0.16
159_I 176_N 0.78 0.39 0.16
164_L 168_H 0.78 0.39 0.16
159_I 197_V 0.78 0.39 0.16
193_L 213_V 0.78 0.39 0.16
170_I 207_P 0.78 0.39 0.16
210_A 149_S 0.78 0.39 0.16
168_L 210_N 0.78 0.39 0.16
165_I 67_F 0.77 0.39 0.15
62_L 174_M 0.77 0.38 0.15
165_I 36_S 0.77 0.38 0.15
104_L 161_Y 0.77 0.38 0.15
43_L 78_F 0.77 0.38 0.15
46_N 103_T 0.77 0.38 0.15
188_A 68_F 0.76 0.38 0.15
175_M 24_G 0.76 0.37 0.15
149_L 221_A 0.76 0.37 0.15
134_A 159_G 0.76 0.37 0.15
70_I 232_L 0.76 0.37 0.15
96_A 141_H 0.76 0.37 0.15
70_I 49_L 0.76 0.37 0.15
186_T 108_M 0.76 0.37 0.14
188_A 242_I 0.76 0.36 0.14
146_T 213_V 0.76 0.36 0.14
23_F 111_I 0.75 0.36 0.14
59_L 238_F 0.75 0.36 0.14
46_N 231_L 0.75 0.36 0.14
128_P 47_L 0.75 0.36 0.14
24_L 92_I 0.75 0.36 0.14
181_M 212_L 0.75 0.36 0.14
189_L 181_G 0.75 0.36 0.14
24_L 66_S 0.75 0.36 0.14
100_G 95_M 0.75 0.36 0.14
173_V 29_F 0.75 0.35 0.14
80_V 63_H 0.74 0.35 0.14
193_L 203_M 0.74 0.35 0.14
52_S 190_G 0.74 0.35 0.14
203_Q 172_M 0.74 0.35 0.14
164_L 116_S 0.74 0.35 0.14
141_L 177_I 0.74 0.35 0.14
29_L 19_L 0.74 0.35 0.14
177_L 111_I 0.74 0.35 0.14
18_I 197_V 0.74 0.35 0.13
74_V 163_H 0.74 0.35 0.13
165_I 62_L 0.74 0.35 0.13
12_V 86_L 0.74 0.34 0.13
110_R 246_F 0.74 0.34 0.13
143_A 56_L 0.74 0.34 0.13
17_F 165_N 0.74 0.34 0.13
194_M 210_N 0.73 0.34 0.13
38_I 76_V 0.73 0.34 0.13
214_Y 49_L 0.73 0.34 0.13
161_I 217_P 0.73 0.34 0.13
205_L 249_M 0.73 0.34 0.13
112_T 32_F 0.73 0.33 0.13
187_I 188_I 0.73 0.33 0.13
165_I 152_L 0.73 0.33 0.13
189_L 22_M 0.73 0.33 0.13
154_Q 142_H 0.73 0.33 0.13
146_T 15_F 0.72 0.33 0.12
100_G 15_F 0.72 0.33 0.12
106_A 61_S 0.72 0.33 0.12
181_M 210_N 0.72 0.33 0.12
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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