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OPENSEQ.org
2wdq_F_H
Genes: A B A+B
Length: 238 115 345
Sequences: 2049 821 518
Seq/Len: 8.61 7.14 1.5
MirrorTree (Pazo et al. 2001) 0.82
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 0.00 0.06
2 0.01 0.00 1.23
5 0.01 0.00 1.44
10 0.01 0.00 1.46
20 0.01 0.00 1.47
100 0.01 0.00 1.49
∞ 0.08 0.01 1.57
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
177_A 19_V 1.78 0.95 0.73
207_H 78_Q 1.54 0.88 0.55
202_S 9_G 1.29 0.72 0.32
133_H 16_F 1.26 0.70 0.30
207_H 74_I 1.24 0.68 0.28
117_I 106_I 1.21 0.65 0.26
191_D 7_A 1.19 0.63 0.24
168_K 90_R 1.18 0.62 0.24
156_S 74_I 1.17 0.61 0.23
39_L 21_A 1.16 0.60 0.22
107_M 33_M 1.12 0.56 0.20
126_Q 95_L 1.11 0.55 0.19
202_S 26_L 1.09 0.54 0.18
133_H 72_A 1.09 0.53 0.17
191_D 9_G 1.08 0.53 0.17
10_Y 41_G 1.07 0.51 0.16
141_E 24_I 1.06 0.50 0.16
20_M 48_W 1.06 0.50 0.16
168_K 84_V 1.04 0.49 0.15
114_Y 16_F 1.04 0.48 0.15
45_K 41_G 1.02 0.47 0.14
11_N 36_F 1.01 0.45 0.13
230_K 6_S 0.99 0.43 0.12
38_A 84_V 0.99 0.43 0.12
6_S 37_F 0.99 0.43 0.12
156_S 89_L 0.98 0.42 0.12
19_R 29_Y 0.98 0.42 0.12
116_K 81_T 0.98 0.42 0.12
82_L 79_V 0.98 0.42 0.12
100_I 44_T 0.97 0.41 0.11
179_Y 25_V 0.94 0.38 0.10
100_I 56_F 0.94 0.38 0.10
174_G 36_F 0.94 0.38 0.10
134_L 69_L 0.94 0.38 0.10
202_S 22_T 0.92 0.36 0.09
48_S 106_I 0.92 0.36 0.09
202_S 61_T 0.92 0.36 0.09
137_P 34_V 0.91 0.35 0.09
117_I 45_Y 0.91 0.35 0.09
196_G 16_F 0.90 0.34 0.09
69_G 16_F 0.90 0.34 0.08
201_F 81_T 0.90 0.34 0.08
141_E 99_V 0.89 0.34 0.08
156_S 100_A 0.89 0.33 0.08
7_I 64_A 0.89 0.33 0.08
48_S 84_V 0.89 0.33 0.08
59_V 51_F 0.89 0.33 0.08
91_I 24_I 0.89 0.33 0.08
234_L 26_L 0.87 0.32 0.07
4_E 22_T 0.86 0.31 0.07
139_Q 102_V 0.86 0.31 0.07
91_I 38_A 0.86 0.31 0.07
195_D 9_G 0.86 0.31 0.07
7_I 66_F 0.85 0.30 0.07
7_I 89_L 0.85 0.30 0.07
70_K 45_Y 0.85 0.30 0.07
82_L 96_V 0.85 0.30 0.07
136_M 84_V 0.85 0.29 0.07
139_Q 19_V 0.85 0.29 0.07
3_L 102_V 0.84 0.29 0.07
204_F 13_V 0.84 0.29 0.07
30_G 92_M 0.84 0.29 0.07
139_Q 58_K 0.84 0.29 0.07
24_T 96_V 0.84 0.29 0.07
117_I 100_A 0.84 0.29 0.06
89_I 84_V 0.83 0.28 0.06
1_M 109_F 0.83 0.28 0.06
116_K 77_W 0.83 0.28 0.06
70_K 108_G 0.82 0.28 0.06
183_I 18_L 0.82 0.27 0.06
121_L 103_V 0.82 0.27 0.06
201_F 78_Q 0.82 0.27 0.06
176_L 74_I 0.81 0.26 0.06
196_G 30_I 0.81 0.26 0.06
111_Y 10_R 0.80 0.26 0.06
116_K 8_L 0.80 0.26 0.05
114_Y 20_R 0.80 0.25 0.05
142_K 18_L 0.80 0.25 0.05
208_S 22_T 0.80 0.25 0.05
123_N 16_F 0.80 0.25 0.05
59_V 65_L 0.80 0.25 0.05
89_I 14_H 0.79 0.25 0.05
23_Y 63_L 0.79 0.25 0.05
90_V 108_G 0.79 0.25 0.05
23_Y 108_G 0.79 0.25 0.05
48_S 24_I 0.79 0.25 0.05
170_I 115_V 0.78 0.24 0.05
70_K 67_S 0.78 0.24 0.05
202_S 35_G 0.78 0.24 0.05
87_K 38_A 0.78 0.24 0.05
137_P 20_R 0.78 0.24 0.05
14_V 115_V 0.78 0.24 0.05
133_H 32_Y 0.77 0.23 0.05
109_Q 62_L 0.77 0.23 0.05
89_I 37_F 0.77 0.23 0.05
64_G 70_I 0.77 0.23 0.05
59_V 52_F 0.77 0.23 0.05
154_C 112_V 0.77 0.23 0.05
197_L 79_V 0.77 0.23 0.05
114_Y 68_I 0.77 0.23 0.05
38_A 98_V 0.76 0.23 0.04
233_L 13_V 0.76 0.22 0.04
183_I 30_I 0.76 0.22 0.04
207_H 80_L 0.76 0.22 0.04
158_S 105_V 0.76 0.22 0.04
185_S 111_V 0.75 0.22 0.04
27_A 97_I 0.75 0.22 0.04
115_E 90_R 0.75 0.22 0.04
59_V 10_R 0.75 0.22 0.04
104_V 85_K 0.75 0.22 0.04
232_M 112_V 0.75 0.22 0.04
230_K 107_Y 0.75 0.22 0.04
123_N 76_M 0.75 0.22 0.04
118_K 72_A 0.75 0.22 0.04
79_I 76_M 0.75 0.22 0.04
79_I 112_V 0.75 0.22 0.04
89_I 17_I 0.74 0.21 0.04
35_L 101_L 0.74 0.21 0.04
122_L 23_A 0.74 0.21 0.04
139_Q 65_L 0.74 0.21 0.04
162_F 29_Y 0.74 0.21 0.04
10_Y 17_I 0.74 0.21 0.04
156_S 98_V 0.74 0.21 0.04
24_T 37_F 0.74 0.21 0.04
126_Q 7_A 0.74 0.21 0.04
89_I 49_I 0.74 0.21 0.04
67_M 2_V 0.74 0.21 0.04
173_A 66_F 0.74 0.21 0.04
213_V 104_Y 0.73 0.21 0.04
89_I 64_A 0.73 0.21 0.04
122_L 95_L 0.73 0.21 0.04
20_M 91_L 0.73 0.21 0.04
214_S 114_G 0.73 0.20 0.04
181_F 78_Q 0.73 0.20 0.04
79_I 16_F 0.73 0.20 0.04
117_I 10_R 0.73 0.20 0.04
195_D 7_A 0.73 0.20 0.04
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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