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OPENSEQ.org
2qan_F_R
Genes: A B A+B
Length: 135 74 184
Sequences: 651 1407 479
Seq/Len: 4.82 19.01 2.6
MirrorTree (Pazo et al. 2001) 0.86
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 0.07 0.09 1.82
2 0.07 0.09 2.32
5 0.07 0.09 2.29
10 0.07 0.09 2.29
20 0.07 0.09 2.29
100 0.07 0.09 2.30
∞ 0.07 0.10 2.40
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
7_V 64_L 2.39 1.00 0.99
9_M 65_S 2.39 1.00 0.99
88_M 64_L 1.77 0.98 0.95
57_A 65_S 1.69 0.98 0.94
59_Y 65_S 1.49 0.94 0.87
79_R 39_V 1.41 0.91 0.83
79_R 20_I 1.38 0.90 0.81
86_R 64_L 1.35 0.89 0.79
91_R 5_R 1.33 0.88 0.78
6_I 31_Y 1.29 0.86 0.75
57_A 72_R 1.17 0.77 0.63
76_T 35_S 1.17 0.77 0.63
9_M 31_Y 1.14 0.75 0.61
51_I 64_L 1.14 0.74 0.60
94_H 35_S 1.13 0.73 0.59
55_H 30_N 1.11 0.72 0.57
88_M 63_Y 1.11 0.72 0.57
90_M 60_R 1.04 0.64 0.48
53_K 43_I 1.03 0.64 0.48
86_R 57_A 1.03 0.64 0.48
105_A 65_S 0.97 0.57 0.41
61_L 57_A 0.97 0.57 0.41
60_V 48_A 0.96 0.55 0.39
80_F 35_S 0.92 0.51 0.35
68_Q 43_I 0.91 0.50 0.34
23_E 4_F 0.91 0.50 0.34
52_N 32_I 0.91 0.49 0.33
71_I 56_R 0.90 0.48 0.32
87_S 58_I 0.90 0.48 0.32
2_R 45_G 0.89 0.47 0.32
38_R 19_E 0.89 0.47 0.31
2_R 11_R 0.89 0.47 0.31
86_R 63_Y 0.88 0.46 0.30
55_H 24_D 0.87 0.45 0.29
64_V 41_S 0.85 0.43 0.27
51_I 44_T 0.85 0.43 0.27
12_P 11_R 0.85 0.42 0.27
113_R 56_R 0.85 0.42 0.27
7_V 67_L 0.83 0.41 0.25
8_F 10_C 0.83 0.40 0.25
8_F 32_I 0.82 0.39 0.24
51_I 65_S 0.82 0.39 0.24
44_R 44_T 0.81 0.39 0.23
78_F 45_G 0.81 0.38 0.23
59_Y 69_Y 0.81 0.37 0.23
42_W 66_L 0.80 0.37 0.22
37_H 31_Y 0.80 0.37 0.22
41_D 28_L 0.80 0.37 0.22
60_V 10_C 0.80 0.37 0.22
86_R 21_D 0.80 0.37 0.22
45_R 12_F 0.80 0.36 0.22
18_V 64_L 0.79 0.36 0.21
92_T 31_Y 0.79 0.35 0.21
50_P 8_K 0.79 0.35 0.21
68_Q 32_I 0.79 0.35 0.21
52_N 55_A 0.78 0.35 0.20
29_I 53_Q 0.78 0.34 0.20
90_M 31_Y 0.78 0.34 0.20
96_V 19_E 0.77 0.34 0.19
17_Q 47_R 0.77 0.34 0.19
28_A 30_N 0.77 0.34 0.19
88_M 60_R 0.77 0.33 0.19
100_S 54_L 0.77 0.33 0.19
86_R 18_Q 0.77 0.33 0.19
77_T 35_S 0.76 0.33 0.19
98_E 31_Y 0.76 0.32 0.18
36_I 22_Y 0.76 0.32 0.18
55_H 58_I 0.75 0.32 0.18
3_H 50_Y 0.75 0.32 0.18
90_M 37_K 0.75 0.31 0.18
71_I 63_Y 0.75 0.31 0.18
71_I 43_I 0.74 0.31 0.17
61_L 12_F 0.74 0.31 0.17
25_Y 32_I 0.74 0.30 0.17
61_L 54_L 0.74 0.30 0.17
114_D 56_R 0.74 0.30 0.17
9_M 34_E 0.73 0.30 0.17
8_F 34_E 0.73 0.30 0.16
70_V 41_S 0.73 0.30 0.16
107_D 41_S 0.73 0.30 0.16
52_N 26_A 0.73 0.29 0.16
39_L 29_K 0.73 0.29 0.16
46_Q 9_F 0.72 0.29 0.16
42_W 52_R 0.72 0.29 0.16
31_G 64_L 0.72 0.28 0.15
28_A 66_L 0.72 0.28 0.15
54_L 46_T 0.72 0.28 0.15
56_K 41_S 0.72 0.28 0.15
82_D 12_F 0.72 0.28 0.15
32_A 72_R 0.72 0.28 0.15
67_P 72_R 0.71 0.28 0.15
84_V 67_L 0.71 0.28 0.15
27_A 32_I 0.71 0.28 0.15
39_L 70_T 0.71 0.28 0.15
73_E 43_I 0.71 0.28 0.15
33_E 32_I 0.71 0.28 0.15
33_E 59_K 0.71 0.27 0.15
91_R 3_Y 0.71 0.27 0.14
87_S 52_R 0.71 0.27 0.14
99_A 33_T 0.70 0.27 0.14
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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