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OPENSEQ.org
1or7_F_B
Genes: A B A+B
Length: 90 194 272
Sequences: 385 24658 255
Seq/Len: 4.28 127.1 0.94
MirrorTree (Pazo et al. 2001) 0.65
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 0.00 0.01 0.89
2 0.00 0.01 0.90
5 0.00 0.03 0.90
10 0.00 0.06 0.90
20 0.00 0.09 0.90
100 0.00 0.17 0.90
∞ 0.00 0.23 0.92
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
35_S 185_D 1.96 0.94 0.67
43_M 138_I 1.61 0.82 0.39
37_H 64_L 1.58 0.80 0.36
21_N 143_E 1.53 0.77 0.33
66_E 22_Q 1.34 0.63 0.19
62_A 170_V 1.24 0.53 0.14
55_I 144_D 1.21 0.51 0.13
13_E 35_K 1.20 0.50 0.12
23_L 149_I 1.18 0.48 0.11
71_P 19_K 1.17 0.48 0.11
4_E 85_A 1.15 0.46 0.10
5_Q 23_K 1.11 0.42 0.09
53_F 184_I 1.10 0.41 0.09
6_L 88_Y 1.10 0.41 0.08
67_P 41_S 1.08 0.39 0.08
41_D 77_L 1.06 0.38 0.07
40_R 38_S 1.03 0.35 0.06
45_G 91_A 1.02 0.35 0.06
62_A 137_T 1.02 0.34 0.06
33_W 84_T 1.02 0.34 0.06
60_M 26_N 1.01 0.33 0.06
87_K 161_E 1.01 0.33 0.06
55_I 114_A 1.01 0.33 0.06
23_L 18_Q 1.00 0.33 0.06
34_E 191_L 0.99 0.32 0.06
39_I 155_D 0.99 0.32 0.06
37_H 39_L 0.98 0.31 0.05
63_I 35_K 0.98 0.31 0.05
5_Q 92_Q 0.97 0.31 0.05
59_V 26_N 0.97 0.30 0.05
60_M 125_M 0.96 0.30 0.05
12_G 143_E 0.96 0.30 0.05
66_E 139_E 0.96 0.30 0.05
8_A 85_A 0.96 0.30 0.05
44_R 82_V 0.95 0.29 0.05
89_P 63_A 0.95 0.29 0.05
6_L 110_E 0.95 0.29 0.05
55_I 170_V 0.95 0.29 0.05
5_Q 35_K 0.93 0.28 0.04
23_L 103_A 0.93 0.28 0.04
23_L 134_V 0.93 0.27 0.04
19_L 36_V 0.93 0.27 0.04
40_R 31_R 0.92 0.27 0.04
45_G 64_L 0.92 0.26 0.04
9_L 144_D 0.91 0.26 0.04
12_G 182_E 0.91 0.26 0.04
56_S 91_A 0.90 0.25 0.04
69_R 65_D 0.90 0.25 0.04
38_L 154_L 0.89 0.25 0.04
26_N 27_L 0.88 0.24 0.03
23_L 23_K 0.86 0.23 0.03
67_P 72_A 0.85 0.22 0.03
44_R 154_L 0.85 0.22 0.03
70_Q 19_K 0.85 0.22 0.03
5_Q 127_S 0.84 0.21 0.03
56_S 30_V 0.84 0.21 0.03
22_E 133_I 0.84 0.21 0.03
10_M 133_I 0.83 0.21 0.03
33_W 11_Q 0.83 0.21 0.03
28_E 136_R 0.83 0.21 0.03
21_N 130_L 0.82 0.20 0.03
59_V 66_S 0.82 0.20 0.03
35_S 43_Y 0.81 0.20 0.03
58_R 41_S 0.81 0.19 0.02
18_E 22_Q 0.80 0.19 0.02
64_E 129_E 0.80 0.19 0.02
45_G 49_V 0.80 0.19 0.02
14_T 146_R 0.80 0.19 0.02
45_G 26_N 0.80 0.19 0.02
18_E 149_I 0.80 0.19 0.02
50_V 89_L 0.79 0.18 0.02
55_I 127_S 0.79 0.18 0.02
60_M 91_A 0.79 0.18 0.02
31_K 35_K 0.79 0.18 0.02
35_S 26_N 0.78 0.18 0.02
35_S 160_E 0.78 0.18 0.02
64_E 154_L 0.78 0.18 0.02
1_M 31_R 0.78 0.18 0.02
20_L 63_A 0.78 0.18 0.02
56_S 59_K 0.78 0.18 0.02
46_D 82_V 0.78 0.18 0.02
68_V 90_V 0.78 0.18 0.02
86_Q 84_T 0.78 0.18 0.02
67_P 191_L 0.78 0.18 0.02
69_R 19_K 0.78 0.18 0.02
56_S 185_D 0.78 0.18 0.02
68_V 188_V 0.78 0.18 0.02
70_Q 71_S 0.77 0.17 0.02
17_S 93_G 0.77 0.17 0.02
17_S 91_A 0.77 0.17 0.02
21_N 77_L 0.77 0.17 0.02
42_S 150_T 0.77 0.17 0.02
34_E 147_M 0.77 0.17 0.02
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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