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OPENSEQ.org
MazEF9_GREMLIN
Genes: A B A+B
Length: 76 118 186
Sequences: 967 2047 213
Seq/Len: 12.72 17.35 1.15
MirrorTree (Pazo et al. 2001) 0.74
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 0.12 0.01 1.02
2 0.12 0.01 1.03
5 0.13 0.01 1.05
10 0.13 0.01 1.08
20 0.13 0.02 1.10
100 0.14 0.04 1.22
∞ 0.19 0.10 1.76
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
58_G 28_V 1.46 0.77 0.02
28_S 4_R 1.37 0.71 0.02
50_A 84_R 1.34 0.69 0.02
59_D 60_P 1.28 0.64 0.01
35_I 27_V 1.21 0.57 0.01
13_A 27_V 1.17 0.54 0.01
15_L 27_V 1.16 0.52 0.01
15_L 46_I 1.15 0.51 0.01
32_Q 53_S 1.14 0.51 0.01
16_D 110_L 1.14 0.50 0.01
4_S 79_Q 1.11 0.47 0.01
20_K 93_R 1.10 0.47 0.01
47_Y 58_V 1.10 0.47 0.01
49_N 73_Q 1.09 0.46 0.01
64_E 84_R 1.08 0.45 0.01
71_V 52_T 1.08 0.44 0.01
28_S 35_N 1.06 0.43 0.01
47_Y 30_S 1.05 0.42 0.01
31_L 25_P 1.05 0.42 0.01
61_D 99_S 1.05 0.41 0.01
61_D 49_V 1.02 0.40 0.01
21_R 12_L 1.02 0.39 0.01
57_A 103_L 1.01 0.38 0.01
36_R 70_T 1.01 0.38 0.01
5_V 16_R 1.00 0.38 0.01
6_S 8_W 1.00 0.37 0.01
74_A 74_V 0.99 0.37 0.01
46_D 29_V 0.98 0.35 0.01
3_L 87_A 0.97 0.35 0.01
11_D 34_A 0.97 0.35 0.01
28_S 22_N 0.97 0.34 0.01
13_A 57_K 0.97 0.34 0.01
31_L 90_R 0.97 0.34 0.01
32_Q 78_A 0.97 0.34 0.01
69_D 85_S 0.96 0.33 0.01
27_R 47_T 0.95 0.33 0.01
59_D 57_K 0.95 0.33 0.01
46_D 116_L 0.95 0.33 0.01
4_S 59_Y 0.94 0.32 0.01
62_A 94_P 0.94 0.32 0.01
59_D 6_E 0.94 0.32 0.01
59_D 98_V 0.94 0.32 0.01
39_R 64_L 0.93 0.31 0.01
12_V 94_P 0.93 0.31 0.01
74_A 3_R 0.92 0.31 0.01
29_A 86_I 0.92 0.30 0.01
25_P 98_V 0.92 0.30 0.01
31_L 91_L 0.91 0.30 0.01
64_E 17_G 0.91 0.29 0.01
3_L 30_S 0.91 0.29 0.01
41_P 31_N 0.91 0.29 0.01
17_A 48_V 0.91 0.29 0.01
35_I 101_A 0.91 0.29 0.01
33_H 28_V 0.90 0.29 0.01
35_I 110_L 0.89 0.28 0.01
13_A 104_A 0.87 0.27 0.00
60_T 28_V 0.87 0.26 0.00
3_L 51_V 0.86 0.26 0.00
10_D 97_R 0.86 0.26 0.00
23_G 112_L 0.86 0.26 0.00
51_W 8_W 0.85 0.25 0.00
15_L 105_Q 0.85 0.25 0.00
8_S 9_Q 0.85 0.25 0.00
61_D 91_L 0.85 0.25 0.00
42_T 10_V 0.85 0.25 0.00
34_A 21_N 0.84 0.24 0.00
2_K 4_R 0.84 0.24 0.00
15_L 88_T 0.84 0.24 0.00
61_D 28_V 0.83 0.24 0.00
21_R 32_D 0.83 0.24 0.00
52_Q 74_V 0.83 0.24 0.00
34_A 79_Q 0.83 0.24 0.00
19_V 102_E 0.83 0.23 0.00
41_P 93_R 0.83 0.23 0.00
9_D 102_E 0.82 0.23 0.00
42_T 65_L 0.82 0.23 0.00
65_Q 28_V 0.82 0.23 0.00
53_E 82_Q 0.81 0.23 0.00
72_G 87_A 0.81 0.22 0.00
44_E 87_A 0.81 0.22 0.00
47_Y 59_Y 0.81 0.22 0.00
23_G 28_V 0.81 0.22 0.00
20_K 52_T 0.81 0.22 0.00
56_A 76_C 0.81 0.22 0.00
8_S 99_S 0.80 0.22 0.00
7_L 75_D 0.80 0.22 0.00
1_M 16_R 0.80 0.22 0.00
25_P 7_I 0.80 0.22 0.00
59_D 23_Q 0.80 0.21 0.00
62_A 115_D 0.80 0.21 0.00
8_S 13_D 0.80 0.21 0.00
8_S 33_R 0.80 0.21 0.00
68_G 23_Q 0.79 0.21 0.00
69_D 84_R 0.79 0.21 0.00
50_A 60_P 0.79 0.21 0.00
64_E 90_R 0.79 0.21 0.00
34_A 113_H 0.79 0.21 0.00
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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