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OPENSEQ.org
5205
Genes: A B A+B
Length: 98 105 198
Sequences: 2539 813 414
Seq/Len: 25.91 7.74 2.09
MirrorTree (Pazo et al. 2001) 0.68
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.00 2.04
2 0.01 0.00 2.03
5 0.02 0.01 2.05
10 0.02 0.01 2.05
20 0.02 0.01 2.08
100 0.04 0.03 2.15
∞ 0.09 0.07 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
10_L 100_L 2.26 1.00 0.99
3_D 93_Q 1.61 0.95 0.88
10_L 96_A 1.59 0.94 0.87
65_K 47_R 1.39 0.87 0.75
49_R 46_F 1.36 0.85 0.73
11_A 12_K 1.35 0.85 0.73
63_L 47_R 1.26 0.79 0.64
78_P 18_L 1.22 0.76 0.61
86_Q 28_E 1.21 0.75 0.59
70_K 81_Y 1.19 0.73 0.57
51_Q 28_E 1.15 0.69 0.53
13_A 93_Q 1.14 0.69 0.52
33_T 58_K 1.10 0.65 0.47
49_R 41_A 1.09 0.63 0.46
79_R 93_Q 1.07 0.62 0.44
57_V 53_R 1.06 0.61 0.43
63_L 46_F 1.04 0.58 0.40
34_F 61_G 1.04 0.58 0.40
12_S 79_L 1.02 0.56 0.38
62_D 18_L 1.01 0.55 0.36
15_E 61_G 1.01 0.54 0.36
4_E 93_Q 1.00 0.54 0.36
61_Y 38_D 1.00 0.54 0.36
49_R 20_D 1.00 0.54 0.36
54_A 10_F 0.99 0.53 0.35
32_H 2_F 0.99 0.53 0.35
60_S 76_Y 0.99 0.53 0.35
39_V 92_E 0.99 0.52 0.34
12_S 45_S 0.99 0.52 0.34
41_A 52_N 0.99 0.52 0.34
63_L 34_P 0.98 0.52 0.34
94_Q 42_G 0.98 0.52 0.34
57_V 40_I 0.97 0.51 0.33
23_E 59_R 0.97 0.51 0.33
50_Q 80_I 0.97 0.51 0.33
83_L 61_G 0.97 0.51 0.33
6_F 67_Y 0.96 0.50 0.32
15_E 78_A 0.96 0.49 0.31
80_K 97_L 0.95 0.48 0.31
13_A 101_S 0.95 0.48 0.31
8_D 12_K 0.95 0.48 0.30
83_L 67_Y 0.95 0.48 0.30
93_N 42_G 0.95 0.48 0.30
78_P 8_Q 0.95 0.47 0.30
60_S 4_F 0.94 0.47 0.30
78_P 46_F 0.94 0.47 0.29
65_K 30_L 0.94 0.46 0.29
65_K 67_Y 0.94 0.46 0.29
24_E 33_D 0.94 0.46 0.29
35_S 70_T 0.93 0.46 0.29
42_I 41_A 0.93 0.46 0.28
42_I 80_I 0.93 0.46 0.28
73_Q 38_D 0.93 0.45 0.28
6_F 97_L 0.92 0.45 0.27
2_K 85_E 0.92 0.45 0.27
25_T 98_K 0.92 0.44 0.27
92_I 33_D 0.91 0.44 0.26
9_L 64_I 0.91 0.44 0.26
37_I 11_S 0.90 0.42 0.25
33_T 11_S 0.89 0.42 0.25
13_A 100_L 0.89 0.42 0.25
15_E 8_Q 0.89 0.41 0.24
13_A 102_E 0.89 0.41 0.24
45_A 21_D 0.89 0.41 0.24
20_E 74_R 0.88 0.41 0.24
72_R 17_L 0.88 0.41 0.24
18_R 45_S 0.88 0.40 0.23
16_M 12_K 0.88 0.40 0.23
69_T 47_R 0.88 0.40 0.23
40_K 54_S 0.88 0.40 0.23
47_G 29_L 0.87 0.39 0.22
8_D 62_T 0.87 0.39 0.22
39_V 100_L 0.86 0.39 0.22
8_D 9_G 0.86 0.38 0.22
72_R 14_R 0.86 0.38 0.21
17_V 39_I 0.86 0.38 0.21
92_I 41_A 0.85 0.37 0.21
59_V 52_N 0.85 0.37 0.21
79_R 18_L 0.85 0.37 0.20
56_A 98_K 0.85 0.37 0.20
50_Q 94_R 0.84 0.36 0.20
53_F 61_G 0.84 0.36 0.20
80_K 68_N 0.84 0.36 0.20
33_T 3_T 0.84 0.36 0.20
77_A 18_L 0.83 0.35 0.19
49_R 71_R 0.83 0.35 0.19
92_I 15_Q 0.83 0.35 0.19
72_R 75_I 0.83 0.35 0.19
40_K 77_L 0.83 0.35 0.19
49_R 10_F 0.83 0.35 0.19
38_D 4_F 0.83 0.34 0.19
41_A 45_S 0.82 0.34 0.19
32_H 65_I 0.82 0.34 0.18
34_F 31_I 0.81 0.33 0.18
59_V 60_G 0.81 0.33 0.17
5_L 4_F 0.81 0.33 0.17
2_K 42_G 0.81 0.33 0.17
62_D 67_Y 0.81 0.33 0.17
84_L 76_Y 0.80 0.32 0.16
76_G 78_A 0.80 0.32 0.16
50_Q 42_G 0.80 0.31 0.16
57_V 10_F 0.79 0.31 0.16
36_E 18_L 0.79 0.31 0.16
66_S 47_R 0.79 0.31 0.16
93_N 73_G 0.79 0.31 0.16
20_E 59_R 0.79 0.31 0.16
90_F 26_F 0.79 0.31 0.16
41_A 21_D 0.79 0.30 0.16
60_S 10_F 0.78 0.30 0.15
66_S 66_Y 0.78 0.30 0.15
64_V 67_Y 0.77 0.29 0.15
79_R 68_N 0.77 0.29 0.14
13_A 42_G 0.77 0.28 0.14
69_T 68_N 0.77 0.28 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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