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OPENSEQ.org
3RRL_A_B
Genes: A B A+B
Length: 235 207 425
Sequences: 2546 2567 1615
Seq/Len: 10.83 12.4 3.8
MirrorTree (Pazo et al. 2001) 0.94
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.01 3.55
2 0.01 0.01 3.61
5 0.01 0.01 3.64
10 0.01 0.01 3.65
20 0.02 0.02 3.65
100 0.04 0.04 3.65
∞ 0.12 0.13 3.66
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
172_K 78_F 1.92 1.00 0.98
115_A 86_A 1.90 1.00 0.97
173_T 46_L 1.75 0.99 0.96
180_L 80_N 1.65 0.99 0.94
180_L 82_A 1.33 0.94 0.81
173_T 72_V 1.25 0.91 0.76
214_Q 92_H 1.16 0.86 0.68
171_R 61_D 1.14 0.84 0.66
212_Y 87_M 1.14 0.84 0.66
143_E 161_K 1.13 0.84 0.65
130_I 122_M 1.12 0.83 0.64
212_Y 83_D 1.11 0.82 0.63
211_I 18_Y 1.09 0.81 0.61
183_M 83_D 1.08 0.79 0.59
173_T 49_I 1.04 0.76 0.55
172_K 62_L 0.95 0.66 0.44
129_L 113_M 0.93 0.64 0.42
217_Y 102_E 0.90 0.60 0.39
211_I 93_I 0.90 0.60 0.38
164_T 37_N 0.90 0.59 0.38
158_K 61_D 0.89 0.59 0.37
165_L 39_V 0.87 0.56 0.34
56_N 67_K 0.84 0.53 0.32
124_T 127_D 0.84 0.52 0.31
138_E 197_E 0.83 0.50 0.30
24_I 118_L 0.82 0.50 0.29
218_K 102_E 0.79 0.45 0.25
48_K 174_F 0.78 0.44 0.25
18_L 174_F 0.77 0.43 0.24
210_G 18_Y 0.77 0.43 0.24
81_V 122_M 0.77 0.43 0.24
124_T 130_H 0.77 0.43 0.24
136_S 155_S 0.77 0.43 0.24
82_G 122_M 0.75 0.40 0.22
119_A 201_A 0.74 0.39 0.21
83_E 120_K 0.73 0.38 0.20
88_E 33_V 0.72 0.37 0.20
138_E 15_E 0.72 0.37 0.20
210_G 77_S 0.70 0.35 0.18
211_I 87_M 0.70 0.34 0.17
93_N 193_D 0.70 0.34 0.17
40_D 193_D 0.69 0.33 0.17
165_L 37_N 0.68 0.31 0.16
137_R 181_M 0.67 0.30 0.15
100_L 132_A 0.67 0.30 0.15
158_K 1_M 0.67 0.30 0.15
139_F 130_H 0.66 0.30 0.15
210_G 109_L 0.66 0.29 0.14
201_L 181_M 0.65 0.29 0.14
63_G 149_K 0.65 0.28 0.14
123_P 92_H 0.65 0.28 0.13
190_A 147_E 0.64 0.28 0.13
172_K 59_D 0.64 0.28 0.13
219_G 200_E 0.63 0.26 0.12
93_N 197_E 0.63 0.26 0.12
16_S 197_E 0.62 0.26 0.12
80_Y 120_K 0.62 0.26 0.12
202_D 78_F 0.62 0.26 0.12
216_I 171_L 0.62 0.25 0.12
124_T 131_G 0.62 0.25 0.12
196_V 144_K 0.62 0.25 0.12
82_G 121_G 0.62 0.25 0.12
123_P 5_I 0.62 0.25 0.12
79_S 98_L 0.62 0.25 0.12
120_Y 77_S 0.62 0.25 0.12
201_L 151_K 0.62 0.25 0.11
122_T 127_D 0.61 0.25 0.11
184_A 94_D 0.61 0.25 0.11
127_G 127_D 0.61 0.24 0.11
86_I 6_I 0.61 0.24 0.11
107_A 84_S 0.61 0.24 0.11
10_D 148_S 0.60 0.24 0.11
58_G 59_D 0.60 0.24 0.11
161_K 144_K 0.60 0.24 0.11
117_I 76_A 0.60 0.23 0.10
22_D 93_I 0.60 0.23 0.10
172_K 72_V 0.60 0.23 0.10
15_L 39_V 0.60 0.23 0.10
18_L 200_E 0.60 0.23 0.10
150_I 141_H 0.60 0.23 0.10
80_Y 67_K 0.60 0.23 0.10
82_G 116_K 0.60 0.23 0.10
78_A 100_G 0.60 0.23 0.10
45_K 206_R 0.60 0.23 0.10
105_T 141_H 0.59 0.23 0.10
10_D 197_E 0.59 0.23 0.10
100_L 70_I 0.59 0.23 0.10
200_E 202_E 0.59 0.23 0.10
186_K 153_E 0.59 0.23 0.10
193_E 61_D 0.59 0.22 0.10
136_S 144_K 0.59 0.22 0.10
44_K 148_S 0.59 0.22 0.10
173_T 76_A 0.59 0.22 0.10
189_V 198_K 0.59 0.22 0.10
188_C 104_S 0.59 0.22 0.10
141_G 92_H 0.58 0.22 0.10
177_F 27_T 0.58 0.22 0.10
98_V 93_I 0.58 0.22 0.10
104_G 85_F 0.58 0.22 0.09
55_N 128_L 0.58 0.22 0.09
26_V 136_I 0.58 0.22 0.09
21_G 51_A 0.58 0.21 0.09
135_E 160_G 0.58 0.21 0.09
13_K 186_L 0.58 0.21 0.09
79_S 85_F 0.58 0.21 0.09
186_K 28_L 0.58 0.21 0.09
62_F 145_Y 0.58 0.21 0.09
13_K 153_E 0.57 0.21 0.09
176_N 81_S 0.57 0.21 0.09
172_K 83_D 0.57 0.21 0.09
102_P 127_D 0.57 0.21 0.09
129_L 60_A 0.57 0.21 0.09
29_F 123_G 0.57 0.20 0.09
111_H 90_G 0.57 0.20 0.09
92_L 100_G 0.57 0.20 0.09
179_P 109_L 0.57 0.20 0.09
8_I 40_F 0.56 0.20 0.09
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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