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OPENSEQ.org
3TCJ
Genes: A B A+B
Length: 72 105 175
Sequences: 319 1191 249
Seq/Len: 4.43 11.34 1.42
MirrorTree (Pazo et al. 2001) 0.67
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 0.00 0.00 1.41
2 0.00 0.00 1.41
5 0.00 0.00 1.41
10 0.01 0.01 1.41
20 0.01 0.01 1.41
100 0.02 0.03 1.41
∞ 0.04 0.06 1.42
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
64_S 74_S 1.85 0.96 0.79
69_N 76_P 1.84 0.96 0.79
56_A 33_N 1.40 0.79 0.44
55_V 70_Q 1.35 0.76 0.39
45_K 30_D 1.33 0.74 0.38
12_D 4_F 1.27 0.69 0.32
65_F 3_Q 1.20 0.63 0.26
24_I 103_T 1.18 0.60 0.24
55_V 71_Q 1.15 0.57 0.22
67_D 3_Q 1.14 0.56 0.21
43_R 24_V 1.12 0.55 0.20
21_D 70_Q 1.11 0.54 0.20
56_A 32_L 1.11 0.54 0.20
55_V 33_N 1.07 0.50 0.17
6_T 83_P 1.06 0.49 0.17
32_M 20_Y 1.03 0.46 0.15
11_S 4_F 1.03 0.45 0.15
67_D 9_N 1.03 0.45 0.15
40_R 29_L 1.02 0.45 0.14
36_A 33_N 1.02 0.44 0.14
68_E 12_K 1.01 0.44 0.14
19_A 81_S 1.01 0.44 0.14
55_V 91_R 1.01 0.43 0.13
8_T 87_L 1.00 0.43 0.13
58_F 65_F 1.00 0.43 0.13
51_G 51_P 0.98 0.41 0.12
9_V 20_Y 0.98 0.41 0.12
6_T 1_M 0.98 0.41 0.12
30_T 98_I 0.98 0.40 0.12
11_S 85_N 0.97 0.40 0.12
14_Y 66_I 0.97 0.40 0.12
31_T 104_G 0.97 0.39 0.12
68_E 11_D 0.96 0.39 0.11
38_R 59_H 0.95 0.38 0.11
28_V 3_Q 0.94 0.37 0.10
18_K 93_E 0.94 0.37 0.10
69_N 75_V 0.94 0.37 0.10
44_W 104_G 0.93 0.36 0.10
47_E 42_P 0.93 0.35 0.10
66_A 74_S 0.92 0.35 0.10
19_A 4_F 0.92 0.35 0.10
18_K 13_S 0.90 0.33 0.09
25_S 56_P 0.89 0.33 0.09
53_A 61_D 0.89 0.32 0.08
11_S 20_Y 0.89 0.32 0.08
2_K 20_Y 0.89 0.32 0.08
26_G 102_I 0.89 0.32 0.08
15_Q 62_E 0.89 0.32 0.08
27_L 26_S 0.88 0.31 0.08
65_F 18_Y 0.88 0.31 0.08
5_I 103_T 0.88 0.31 0.08
39_L 4_F 0.87 0.30 0.08
18_K 20_Y 0.86 0.29 0.07
65_F 74_S 0.85 0.28 0.07
69_N 74_S 0.84 0.28 0.07
14_Y 51_P 0.84 0.28 0.07
32_M 19_P 0.83 0.28 0.07
36_A 82_E 0.83 0.27 0.06
28_V 68_L 0.82 0.27 0.06
47_E 60_I 0.82 0.27 0.06
18_K 36_L 0.82 0.26 0.06
35_E 38_I 0.82 0.26 0.06
34_N 98_I 0.81 0.26 0.06
61_M 67_M 0.81 0.26 0.06
5_I 30_D 0.81 0.26 0.06
21_D 72_M 0.81 0.26 0.06
53_A 6_L 0.81 0.25 0.06
37_R 65_F 0.81 0.25 0.06
60_E 63_G 0.80 0.25 0.06
9_V 102_I 0.80 0.25 0.06
40_R 67_M 0.79 0.24 0.05
29_S 70_Q 0.78 0.23 0.05
37_R 104_G 0.78 0.23 0.05
31_T 3_Q 0.78 0.23 0.05
67_D 79_I 0.78 0.23 0.05
23_N 56_P 0.78 0.23 0.05
44_W 29_L 0.77 0.23 0.05
47_E 72_M 0.77 0.22 0.05
49_Q 60_I 0.77 0.22 0.05
21_D 48_K 0.77 0.22 0.05
65_F 9_N 0.76 0.22 0.05
46_A 61_D 0.76 0.22 0.05
48_N 104_G 0.76 0.22 0.05
11_S 95_I 0.76 0.22 0.04
13_S 103_T 0.76 0.22 0.04
66_A 73_T 0.76 0.22 0.04
45_K 2_S 0.75 0.21 0.04
3_Q 32_L 0.75 0.21 0.04
25_S 7_Y 0.75 0.21 0.04
52_M 46_L 0.75 0.21 0.04
41_A 77_V 0.75 0.21 0.04
57_R 61_D 0.75 0.21 0.04
26_G 5_T 0.75 0.21 0.04
47_E 64_D 0.75 0.21 0.04
34_N 11_D 0.75 0.21 0.04
8_T 11_D 0.75 0.21 0.04
47_E 52_S 0.74 0.21 0.04
22_V 102_I 0.74 0.21 0.04
22_V 104_G 0.74 0.20 0.04
43_R 92_N 0.74 0.20 0.04
50_E 79_I 0.74 0.20 0.04
10_D 28_L 0.74 0.20 0.04
65_F 71_Q 0.73 0.20 0.04
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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