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OPENSEQ.org
3i1o_S_N
Genes: A B A+B
Length: 92 101 192
Sequences: 2140 1732 698
Seq/Len: 23.26 17.15 3.64
MirrorTree (Pazo et al. 2001) 0.77
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 0.09 0.09 0.01
2 0.09 0.09 0.03
5 0.09 0.09 0.23
10 0.09 0.09 3.23
20 0.09 0.09 3.62
100 0.09 0.09 4.49
∞ 0.09 0.09 5.61
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
44_M 87_A 1.42 0.96 0.67
58_V 29_A 1.35 0.94 0.60
52_H 9_R 1.19 0.87 0.45
49_I 92_E 1.14 0.83 0.41
65_E 80_S 1.14 0.83 0.40
57_H 89_M 1.13 0.83 0.40
44_M 93_I 1.12 0.81 0.38
13_L 50_T 1.11 0.81 0.37
65_E 71_H 1.10 0.80 0.37
78_R 81_R 1.09 0.79 0.35
60_V 25_A 1.07 0.78 0.34
65_E 93_I 1.06 0.76 0.33
84_A 26_E 1.03 0.74 0.30
37_R 76_K 1.02 0.72 0.29
74_F 101_W 1.01 0.71 0.28
2_P 17_A 1.00 0.71 0.28
47_L 44_A 1.00 0.70 0.28
44_M 79_L 1.00 0.70 0.27
17_K 23_K 0.96 0.66 0.24
50_A 26_E 0.96 0.66 0.24
81_R 9_R 0.95 0.65 0.23
5_L 42_W 0.93 0.62 0.21
57_H 58_S 0.92 0.61 0.21
75_A 38_D 0.90 0.58 0.19
5_L 43_N 0.89 0.57 0.19
44_M 82_I 0.88 0.55 0.18
21_K 73_F 0.87 0.55 0.18
61_F 74_L 0.86 0.53 0.17
57_H 3_K 0.85 0.52 0.16
45_I 87_A 0.85 0.52 0.16
67_V 31_I 0.84 0.51 0.16
22_A 47_K 0.84 0.51 0.16
39_T 56_S 0.84 0.51 0.16
62_V 21_F 0.83 0.49 0.15
30_P 89_M 0.82 0.48 0.14
31_L 15_A 0.81 0.47 0.14
33_T 72_G 0.80 0.46 0.13
5_L 7_K 0.80 0.46 0.13
65_E 77_F 0.80 0.45 0.13
8_G 81_R 0.80 0.45 0.13
58_V 91_G 0.80 0.45 0.13
21_K 29_A 0.79 0.44 0.12
47_L 30_I 0.79 0.44 0.12
62_V 82_I 0.79 0.44 0.12
76_P 80_S 0.78 0.43 0.12
49_I 89_M 0.78 0.42 0.12
17_K 47_K 0.77 0.41 0.12
86_D 61_R 0.76 0.40 0.11
49_I 60_Q 0.76 0.40 0.11
33_T 97_K 0.76 0.40 0.11
11_I 18_D 0.75 0.40 0.11
19_V 26_E 0.75 0.40 0.11
55_R 8_A 0.75 0.39 0.11
86_D 71_H 0.75 0.39 0.11
6_K 34_V 0.75 0.39 0.10
6_K 49_Q 0.74 0.39 0.10
87_K 89_M 0.74 0.39 0.10
75_A 40_D 0.74 0.38 0.10
32_R 20_Y 0.74 0.38 0.10
18_K 39_E 0.74 0.37 0.10
52_H 57_P 0.73 0.37 0.10
45_I 15_A 0.72 0.36 0.10
6_K 37_S 0.72 0.36 0.09
50_A 2_A 0.72 0.35 0.09
2_P 56_S 0.71 0.35 0.09
56_Q 61_R 0.71 0.35 0.09
12_D 76_K 0.71 0.35 0.09
61_F 56_S 0.71 0.34 0.09
55_R 66_Q 0.71 0.34 0.09
20_E 37_S 0.71 0.34 0.09
49_I 10_E 0.71 0.34 0.09
46_G 52_P 0.71 0.34 0.09
57_H 54_D 0.70 0.33 0.09
53_N 100_S 0.70 0.33 0.08
22_A 44_A 0.70 0.33 0.08
84_A 21_F 0.70 0.33 0.08
69_H 99_A 0.69 0.32 0.08
13_L 41_R 0.69 0.32 0.08
28_K 97_K 0.69 0.32 0.08
60_V 21_F 0.69 0.32 0.08
48_T 77_F 0.68 0.31 0.08
35_S 51_L 0.68 0.31 0.08
13_L 49_Q 0.68 0.30 0.07
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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