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OPENSEQ.org
4MCT
Genes: A B A+B
Length: 104 92 183
Sequences: 10472 1883 348
Seq/Len: 100.69 20.47 1.9
MirrorTree (Pazo et al. 2001) 0.70
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 0.03 0.01 1.78
2 0.04 0.01 1.81
5 0.06 0.01 1.87
10 0.07 0.02 1.95
20 0.09 0.02 2.02
100 0.13 0.04 2.54
∞ 0.17 0.09 4.12
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
69_R 39_T 2.85 1.00 1.00
63_T 45_E 2.53 1.00 0.99
73_N 39_T 2.21 0.99 0.98
7_S 35_Q 1.63 0.94 0.89
15_R 32_D 1.58 0.93 0.87
20_M 49_Q 1.43 0.87 0.78
11_E 28_D 1.34 0.82 0.71
12_M 36_A 1.31 0.80 0.68
82_Q 62_G 1.29 0.79 0.66
16_D 33_R 1.17 0.68 0.54
15_R 28_D 1.13 0.64 0.49
69_R 41_T 1.13 0.64 0.49
16_D 51_Y 1.12 0.64 0.48
71_Q 68_V 1.11 0.63 0.48
62_S 45_E 1.11 0.63 0.47
65_E 41_T 1.06 0.58 0.42
15_R 33_R 1.05 0.56 0.40
17_L 32_D 1.05 0.56 0.40
59_A 10_L 1.04 0.55 0.39
42_L 6_K 1.00 0.51 0.35
79_L 80_N 0.99 0.50 0.33
74_Y 22_V 0.98 0.48 0.32
76_L 50_I 0.97 0.47 0.31
50_P 50_I 0.93 0.43 0.27
80_E 12_L 0.93 0.43 0.27
46_T 10_L 0.93 0.43 0.27
41_L 13_L 0.91 0.41 0.25
88_I 13_L 0.91 0.41 0.25
70_L 39_T 0.90 0.40 0.25
43_A 72_W 0.90 0.40 0.24
79_L 38_D 0.89 0.39 0.24
21_G 25_Q 0.89 0.39 0.23
43_A 35_Q 0.89 0.39 0.23
50_P 68_V 0.88 0.38 0.23
54_I 50_I 0.88 0.38 0.22
11_E 32_D 0.88 0.38 0.22
70_L 36_A 0.88 0.38 0.22
13_I 4_S 0.88 0.37 0.22
61_G 57_K 0.87 0.36 0.21
66_F 45_E 0.86 0.36 0.21
16_D 54_H 0.86 0.36 0.21
60_L 19_T 0.86 0.36 0.20
73_N 38_D 0.86 0.35 0.20
49_T 12_L 0.86 0.35 0.20
28_A 62_G 0.85 0.35 0.20
37_T 54_H 0.85 0.34 0.19
19_D 51_Y 0.84 0.34 0.19
69_R 25_Q 0.84 0.34 0.19
50_P 9_G 0.84 0.34 0.19
61_G 44_G 0.83 0.33 0.18
15_R 48_R 0.82 0.32 0.18
16_D 48_R 0.82 0.32 0.17
13_I 57_K 0.82 0.32 0.17
45_K 12_L 0.81 0.31 0.17
19_D 32_D 0.81 0.31 0.17
19_D 33_R 0.81 0.31 0.16
54_I 76_F 0.81 0.30 0.16
80_E 64_W 0.80 0.30 0.16
66_F 33_R 0.80 0.30 0.16
77_R 22_V 0.80 0.29 0.15
51_S 46_L 0.79 0.29 0.15
55_R 91_Y 0.79 0.29 0.15
37_T 75_T 0.79 0.29 0.15
23_S 3_K 0.79 0.29 0.15
18_E 40_A 0.79 0.29 0.15
66_F 36_A 0.78 0.28 0.15
61_G 62_G 0.77 0.28 0.14
33_V 62_G 0.77 0.27 0.14
16_D 69_R 0.77 0.27 0.14
20_M 68_V 0.77 0.27 0.13
7_S 31_N 0.76 0.27 0.13
14_A 86_L 0.76 0.26 0.13
62_S 40_A 0.76 0.26 0.13
45_K 59_D 0.75 0.26 0.13
22_V 48_R 0.75 0.26 0.12
16_D 50_I 0.75 0.25 0.12
69_R 38_D 0.75 0.25 0.12
86_S 61_E 0.75 0.25 0.12
18_E 11_K 0.75 0.25 0.12
77_R 35_Q 0.74 0.25 0.12
43_A 85_I 0.74 0.25 0.12
55_R 92_H 0.74 0.25 0.12
88_I 23_P 0.74 0.25 0.12
13_I 46_L 0.74 0.25 0.12
47_A 57_K 0.74 0.24 0.12
64_P 37_I 0.73 0.24 0.11
42_L 27_V 0.72 0.23 0.11
13_I 25_Q 0.72 0.23 0.11
64_P 23_P 0.71 0.23 0.10
42_L 23_P 0.71 0.23 0.10
79_L 72_W 0.71 0.22 0.10
49_T 42_E 0.71 0.22 0.10
38_V 51_Y 0.71 0.22 0.10
13_I 44_G 0.70 0.22 0.10
55_R 2_I 0.70 0.22 0.10
29_H 40_A 0.70 0.22 0.10
17_L 68_V 0.70 0.22 0.10
22_V 39_T 0.70 0.22 0.10
64_P 38_D 0.70 0.21 0.10
19_D 66_I 0.70 0.21 0.10
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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