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OPENSEQ.org
PxR
Genes: A B A+B
Length: 244 255 476
Sequences: 1471 1848 1544
Seq/Len: 6.03 7.25 3.24
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 0.07
2 0.00 0.00 2.53
5 0.01 0.01 2.58
10 0.01 0.01 2.81
20 0.02 0.02 2.95
100 0.03 0.03 3.09
∞ 0.07 0.07 3.23
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
144_K 139_D 1.95 1.00 0.98
211_L 200_G 1.52 0.97 0.89
90_T 84_L 1.27 0.89 0.75
77_M 185_S 1.26 0.88 0.74
79_T 93_I 1.24 0.87 0.72
40_T 90_F 1.22 0.86 0.71
179_K 139_D 1.21 0.85 0.69
216_I 191_I 1.18 0.83 0.67
151_R 146_L 1.17 0.83 0.66
222_L 99_Q 1.16 0.82 0.65
224_I 192_S 1.15 0.81 0.64
58_F 124_S 1.14 0.81 0.63
174_M 41_I 1.13 0.80 0.62
212_P 206_M 1.06 0.74 0.54
145_D 142_H 1.05 0.72 0.53
204_M 106_F 1.05 0.72 0.53
157_N 181_G 1.05 0.72 0.52
217_S 68_F 1.04 0.71 0.51
79_T 119_S 1.02 0.69 0.50
162_D 226_V 1.02 0.69 0.49
59_V 44_T 1.01 0.69 0.49
88_L 116_S 1.00 0.67 0.47
194_V 191_I 0.99 0.66 0.46
170_V 48_F 0.99 0.66 0.46
242_F 101_A 0.99 0.66 0.46
75_Q 101_A 0.99 0.66 0.45
70_F 247_T 0.97 0.64 0.44
41_L 46_V 0.97 0.63 0.43
110_E 85_M 0.97 0.63 0.43
109_N 45_I 0.96 0.63 0.42
205_A 20_A 0.96 0.62 0.42
153_R 20_A 0.96 0.62 0.42
81_S 125_Q 0.95 0.61 0.41
51_A 38_P 0.95 0.61 0.41
68_V 169_Y 0.95 0.61 0.40
212_P 210_N 0.94 0.60 0.40
75_Q 90_F 0.94 0.60 0.40
113_K 229_A 0.94 0.60 0.40
236_Q 101_A 0.93 0.59 0.39
194_V 152_L 0.93 0.59 0.39
113_K 197_V 0.93 0.59 0.39
146_L 96_A 0.92 0.58 0.38
189_Y 139_D 0.92 0.58 0.38
72_F 36_S 0.92 0.58 0.38
79_T 116_S 0.92 0.57 0.37
204_M 220_I 0.92 0.57 0.37
77_M 93_I 0.91 0.57 0.36
189_Y 178_F 0.91 0.57 0.36
68_V 105_G 0.91 0.56 0.36
58_F 104_M 0.91 0.56 0.36
78_G 115_S 0.91 0.56 0.36
239_V 204_K 0.91 0.56 0.36
134_K 70_L 0.91 0.56 0.36
216_I 204_K 0.91 0.56 0.36
92_A 95_M 0.90 0.55 0.35
73_L 193_L 0.89 0.54 0.34
209_M 152_L 0.89 0.54 0.34
243_V 49_L 0.88 0.53 0.33
197_M 224_F 0.88 0.52 0.33
223_L 106_F 0.88 0.52 0.33
175_I 108_M 0.88 0.52 0.33
49_I 80_M 0.88 0.52 0.33
227_L 109_A 0.88 0.52 0.32
76_A 99_Q 0.88 0.52 0.32
173_F 42_K 0.87 0.52 0.32
133_F 252_L 0.87 0.51 0.32
216_I 216_Y 0.87 0.51 0.32
202_V 223_G 0.87 0.51 0.32
92_A 84_L 0.87 0.51 0.32
84_P 91_A 0.87 0.51 0.31
211_L 113_D 0.86 0.50 0.30
88_L 238_F 0.85 0.49 0.29
124_E 164_E 0.85 0.48 0.29
200_S 63_H 0.84 0.47 0.28
227_L 42_K 0.84 0.47 0.28
197_M 203_M 0.84 0.47 0.28
97_F 197_V 0.84 0.47 0.28
117_A 69_V 0.83 0.46 0.27
91_L 174_M 0.83 0.46 0.27
65_R 104_M 0.83 0.46 0.27
151_R 222_L 0.83 0.46 0.27
65_R 106_F 0.83 0.46 0.27
179_K 141_H 0.83 0.46 0.27
157_N 47_L 0.82 0.45 0.27
129_G 95_M 0.82 0.45 0.27
178_L 221_A 0.82 0.45 0.26
58_F 206_M 0.82 0.44 0.26
194_V 174_M 0.82 0.44 0.26
103_V 184_M 0.81 0.44 0.26
150_Y 200_G 0.81 0.44 0.26
235_V 105_G 0.81 0.44 0.26
202_V 92_I 0.81 0.44 0.26
73_L 135_F 0.81 0.44 0.25
222_L 213_V 0.81 0.44 0.25
216_I 194_L 0.81 0.43 0.25
205_A 137_A 0.80 0.43 0.25
108_Y 219_K 0.80 0.43 0.25
117_A 67_F 0.80 0.43 0.24
45_I 168_H 0.80 0.42 0.24
52_L 57_A 0.80 0.42 0.24
96_T 95_M 0.80 0.42 0.24
42_N 157_L 0.80 0.42 0.24
234_L 237_Y 0.79 0.41 0.23
134_K 190_G 0.79 0.41 0.23
39_T 101_A 0.79 0.41 0.23
101_E 216_Y 0.79 0.41 0.23
81_S 190_G 0.79 0.41 0.23
77_M 98_E 0.79 0.41 0.23
189_Y 124_S 0.79 0.41 0.23
44_V 215_G 0.78 0.40 0.23
201_S 97_G 0.78 0.40 0.22
223_L 101_A 0.78 0.40 0.22
40_T 205_T 0.78 0.40 0.22
75_Q 103_T 0.78 0.40 0.22
222_L 203_M 0.78 0.40 0.22
211_L 9_D 0.78 0.39 0.22
238_L 37_I 0.78 0.39 0.22
218_L 22_M 0.77 0.39 0.22
163_D 76_V 0.77 0.39 0.22
89_V 85_M 0.77 0.39 0.22
176_S 82_A 0.77 0.39 0.22
173_F 12_V 0.77 0.39 0.21
46_V 165_N 0.77 0.38 0.21
127_I 250_Q 0.77 0.38 0.21
198_V 165_N 0.77 0.38 0.21
59_V 194_L 0.76 0.38 0.21
170_V 249_M 0.76 0.38 0.21
212_P 183_T 0.76 0.38 0.21
172_A 52_Y 0.76 0.38 0.21
175_I 142_H 0.76 0.38 0.21
95_L 10_K 0.76 0.38 0.21
154_N 239_K 0.76 0.37 0.20
106_K 148_L 0.76 0.37 0.20
194_V 184_M 0.76 0.37 0.20
223_L 210_N 0.76 0.37 0.20
34_P 206_M 0.76 0.37 0.20
181_A 210_N 0.76 0.37 0.20
193_L 116_S 0.76 0.37 0.20
92_A 252_L 0.75 0.37 0.20
91_L 213_V 0.75 0.37 0.20
228_V 196_D 0.75 0.36 0.20
105_T 44_T 0.75 0.36 0.20
215_M 108_M 0.75 0.36 0.20
41_L 176_N 0.75 0.36 0.20
236_Q 196_D 0.75 0.36 0.20
143_E 78_F 0.75 0.36 0.20
46_V 73_I 0.75 0.36 0.19
190_L 35_N 0.75 0.36 0.19
90_T 127_L 0.75 0.36 0.19
135_D 61_S 0.74 0.36 0.19
179_K 130_L 0.74 0.36 0.19
193_L 147_F 0.74 0.36 0.19
172_A 200_G 0.74 0.36 0.19
143_E 222_L 0.74 0.35 0.19
217_S 119_S 0.74 0.35 0.19
199_V 207_P 0.74 0.35 0.19
40_T 136_L 0.74 0.35 0.19
99_I 237_Y 0.74 0.35 0.18
234_L 219_K 0.73 0.34 0.18
117_A 181_G 0.73 0.34 0.18
187_L 103_T 0.73 0.34 0.18
70_F 235_M 0.73 0.34 0.18
45_I 22_M 0.73 0.34 0.18
47_L 123_T 0.73 0.34 0.18
70_F 167_M 0.73 0.34 0.18
43_I 112_L 0.73 0.34 0.18
128_K 232_L 0.73 0.34 0.18
220_F 200_G 0.73 0.34 0.18
175_I 15_F 0.73 0.34 0.18
218_L 181_G 0.72 0.33 0.17
52_L 111_I 0.72 0.33 0.17
153_R 69_V 0.72 0.33 0.17
210_M 212_L 0.72 0.33 0.17
220_F 103_T 0.72 0.33 0.17
65_R 101_A 0.72 0.33 0.17
205_A 95_M 0.72 0.33 0.17
38_V 177_I 0.72 0.33 0.17
134_K 196_D 0.72 0.33 0.17
70_F 174_M 0.72 0.33 0.17
197_M 210_N 0.72 0.32 0.17
223_L 196_D 0.72 0.32 0.17
188_I 176_N 0.72 0.32 0.17
79_T 174_M 0.71 0.32 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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