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OPENSEQ.org
fliRflhB
Genes: A B A+B
Length: 255 211 455
Sequences: 1842 1992 1494
Seq/Len: 7.22 9.44 3.28
MirrorTree (Pazo et al. 2001) 0.77
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 2.99
2 0.00 0.00 3.00
5 0.01 0.01 3.01
10 0.01 0.01 3.08
20 0.02 0.02 3.21
100 0.03 0.03 3.48
∞ 0.07 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
186_F 180_Q 3.14 1.00 1.00
190_G 184_L 2.24 1.00 0.99
198_I 158_A 1.59 0.98 0.93
16_M 31_D 1.42 0.95 0.87
194_L 191_L 1.24 0.87 0.76
189_L 13_T 1.23 0.87 0.75
202_L 123_L 1.22 0.87 0.75
75_E 28_K 1.20 0.85 0.73
12_V 40_I 1.18 0.83 0.71
101_A 19_D 1.16 0.82 0.69
152_L 111_G 1.16 0.82 0.69
35_N 132_L 1.15 0.82 0.69
80_M 119_I 1.14 0.81 0.67
24_G 125_K 1.14 0.81 0.67
192_S 31_D 1.13 0.80 0.66
211_L 209_L 1.12 0.79 0.65
212_L 131_G 1.09 0.76 0.62
204_K 134_N 1.03 0.71 0.56
197_V 104_L 1.03 0.71 0.55
190_G 180_Q 1.02 0.70 0.55
49_L 9_T 1.02 0.70 0.55
44_T 4_E 1.02 0.70 0.54
140_G 127_N 1.02 0.69 0.54
117_G 7_E 1.02 0.69 0.54
32_F 127_N 1.01 0.69 0.53
90_F 53_G 1.01 0.69 0.53
126_I 84_I 1.01 0.68 0.53
234_M 39_I 1.01 0.68 0.53
103_T 106_N 1.01 0.68 0.52
37_I 121_P 1.00 0.67 0.52
229_A 27_P 1.00 0.67 0.52
238_F 148_I 0.98 0.65 0.49
135_F 137_S 0.95 0.62 0.46
42_K 78_A 0.95 0.62 0.46
219_K 109_Q 0.95 0.61 0.45
190_G 169_L 0.94 0.61 0.45
46_V 60_Y 0.94 0.60 0.44
135_F 140_K 0.93 0.59 0.43
134_F 39_I 0.93 0.59 0.43
110_S 31_D 0.93 0.59 0.42
97_G 111_G 0.93 0.58 0.42
133_M 172_V 0.92 0.58 0.42
197_V 188_A 0.92 0.58 0.42
201_L 34_A 0.92 0.58 0.42
193_L 188_A 0.92 0.58 0.42
107_T 56_I 0.91 0.57 0.41
174_M 16_K 0.91 0.57 0.41
19_L 95_V 0.91 0.56 0.40
75_E 109_Q 0.90 0.56 0.40
229_A 141_I 0.90 0.56 0.40
221_A 153_I 0.90 0.56 0.40
206_M 122_N 0.90 0.56 0.40
226_V 102_G 0.90 0.55 0.39
77_I 92_A 0.90 0.55 0.39
212_L 143_E 0.90 0.55 0.39
157_L 79_I 0.90 0.55 0.39
225_V 125_K 0.89 0.54 0.38
49_L 152_G 0.89 0.54 0.38
204_K 170_P 0.89 0.54 0.38
148_L 103_V 0.89 0.54 0.38
209_F 45_T 0.89 0.53 0.38
150_H 177_M 0.89 0.53 0.38
204_K 16_K 0.88 0.53 0.37
136_L 129_L 0.88 0.52 0.36
160_F 198_A 0.87 0.52 0.36
72_L 185_R 0.87 0.52 0.36
226_V 48_M 0.87 0.51 0.35
48_F 52_M 0.86 0.51 0.35
204_K 119_I 0.86 0.51 0.35
27_V 45_T 0.86 0.51 0.35
165_N 200_L 0.86 0.50 0.35
87_Q 12_P 0.86 0.50 0.34
224_F 38_L 0.86 0.50 0.34
76_V 91_L 0.86 0.50 0.34
113_D 41_G 0.86 0.50 0.34
131_A 27_P 0.86 0.50 0.34
208_Q 209_L 0.85 0.49 0.34
103_T 76_I 0.85 0.49 0.34
82_A 23_E 0.85 0.49 0.34
202_L 191_L 0.85 0.49 0.34
75_E 110_F 0.85 0.49 0.33
191_I 12_P 0.85 0.49 0.33
103_T 210_V 0.85 0.49 0.33
204_K 173_E 0.85 0.48 0.33
211_L 150_K 0.85 0.48 0.33
231_L 13_T 0.84 0.48 0.32
76_V 204_V 0.84 0.48 0.32
243_L 104_L 0.84 0.47 0.32
128_N 122_N 0.84 0.47 0.32
188_I 52_M 0.84 0.47 0.32
75_E 183_W 0.83 0.47 0.32
105_G 93_P 0.83 0.47 0.31
230_I 71_F 0.83 0.46 0.30
119_S 34_A 0.82 0.46 0.30
152_L 28_K 0.82 0.45 0.30
144_M 96_L 0.82 0.45 0.30
69_V 95_V 0.81 0.45 0.29
56_L 152_G 0.81 0.44 0.29
95_M 186_D 0.81 0.44 0.29
252_L 96_L 0.81 0.44 0.28
130_L 36_V 0.80 0.43 0.28
151_S 161_V 0.80 0.43 0.28
136_L 10_E 0.80 0.43 0.28
104_M 16_K 0.80 0.43 0.28
188_I 12_P 0.80 0.43 0.28
148_L 156_T 0.80 0.42 0.27
77_I 107_I 0.80 0.42 0.27
81_I 116_T 0.79 0.42 0.27
198_I 203_A 0.79 0.42 0.27
242_I 18_E 0.79 0.41 0.27
105_G 137_S 0.79 0.41 0.27
110_S 203_A 0.79 0.41 0.27
51_M 132_L 0.79 0.41 0.27
121_P 162_L 0.79 0.41 0.26
231_L 127_N 0.79 0.41 0.26
126_I 134_N 0.79 0.41 0.26
168_H 88_L 0.79 0.41 0.26
124_S 207_V 0.78 0.41 0.26
37_I 68_G 0.78 0.41 0.26
54_Y 103_V 0.78 0.40 0.26
64_L 88_L 0.78 0.40 0.26
50_T 204_V 0.78 0.40 0.26
61_S 160_I 0.78 0.40 0.25
62_L 104_L 0.78 0.40 0.25
106_F 197_V 0.78 0.40 0.25
182_F 53_G 0.78 0.40 0.25
215_G 28_K 0.77 0.39 0.25
107_T 41_G 0.77 0.39 0.25
124_S 200_L 0.77 0.39 0.25
75_E 139_K 0.77 0.39 0.25
105_G 134_N 0.77 0.39 0.24
144_M 105_G 0.77 0.39 0.24
52_Y 115_T 0.77 0.39 0.24
198_I 56_I 0.77 0.39 0.24
99_Q 83_S 0.77 0.39 0.24
106_F 140_K 0.77 0.38 0.24
214_I 151_V 0.76 0.38 0.24
60_E 103_V 0.76 0.38 0.24
139_D 41_G 0.76 0.38 0.23
143_L 124_G 0.76 0.38 0.23
193_L 204_V 0.76 0.38 0.23
214_I 133_K 0.76 0.38 0.23
201_L 202_I 0.76 0.37 0.23
206_M 102_G 0.76 0.37 0.23
209_F 30_Q 0.76 0.37 0.23
80_M 100_I 0.76 0.37 0.23
101_A 22_K 0.76 0.37 0.23
43_S 132_L 0.75 0.37 0.23
101_A 11_E 0.75 0.37 0.23
48_F 182_A 0.75 0.37 0.23
181_G 51_F 0.75 0.37 0.23
139_D 124_G 0.75 0.36 0.22
153_G 96_L 0.75 0.36 0.22
212_L 15_K 0.75 0.36 0.22
26_I 127_N 0.75 0.36 0.22
204_K 143_E 0.75 0.36 0.22
82_A 26_V 0.74 0.36 0.22
177_I 194_I 0.74 0.36 0.22
13_V 12_P 0.74 0.36 0.22
183_T 177_M 0.74 0.36 0.22
72_L 201_I 0.74 0.36 0.22
47_L 20_A 0.74 0.36 0.22
69_V 200_L 0.74 0.35 0.21
166_L 114_F 0.74 0.35 0.21
24_G 196_I 0.74 0.35 0.21
107_T 37_T 0.74 0.35 0.21
205_T 199_F 0.74 0.35 0.21
148_L 145_I 0.73 0.35 0.21
208_Q 137_S 0.73 0.35 0.21
123_T 3_G 0.73 0.35 0.21
123_T 181_L 0.73 0.35 0.21
108_M 117_K 0.73 0.34 0.21
56_L 132_L 0.73 0.34 0.21
193_L 94_I 0.73 0.34 0.21
68_F 70_E 0.73 0.34 0.20
42_K 160_I 0.73 0.34 0.20
45_I 126_I 0.73 0.34 0.20
75_E 15_K 0.73 0.34 0.20
125_Q 158_A 0.73 0.34 0.20
125_Q 7_E 0.73 0.34 0.20
31_F 137_S 0.73 0.34 0.20
107_T 8_K 0.73 0.34 0.20
194_L 153_I 0.72 0.34 0.20
230_I 125_K 0.72 0.34 0.20
185_S 165_F 0.72 0.34 0.20
211_L 101_A 0.72 0.34 0.20
68_F 109_Q 0.72 0.33 0.20
192_S 25_N 0.72 0.33 0.20
187_P 93_P 0.72 0.33 0.20
202_L 16_K 0.72 0.33 0.20
57_A 103_V 0.72 0.33 0.20
160_F 65_S 0.72 0.33 0.20
47_L 171_R 0.72 0.33 0.20
204_K 34_A 0.72 0.33 0.20
61_S 100_I 0.72 0.33 0.19
167_M 186_D 0.72 0.33 0.19
73_I 104_L 0.72 0.33 0.19
28_F 100_I 0.72 0.33 0.19
53_L 37_T 0.72 0.33 0.19
102_F 184_L 0.71 0.33 0.19
198_I 117_K 0.71 0.33 0.19
93_I 143_E 0.71 0.32 0.19
23_S 137_S 0.71 0.32 0.19
243_L 58_N 0.71 0.32 0.19
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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