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OPENSEQ.org
2800
Genes: A B A+B
Length: 77 104 175
Sequences: 309 292 248
Seq/Len: 4.01 2.81 1.42
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 0.00 0.00 1.37
2 0.00 0.00 1.37
5 0.00 0.00 1.37
10 0.01 0.00 1.37
20 0.01 0.01 1.37
100 0.02 0.02 1.37
∞ 0.03 0.03 1.37
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_C 73_T 1.99 0.98 0.90
74_Y 75_P 1.95 0.97 0.89
61_N 30_N 1.44 0.82 0.56
70_F 2_Q 1.43 0.81 0.55
60_L 69_H 1.39 0.78 0.51
72_D 2_Q 1.30 0.71 0.42
50_R 27_G 1.22 0.65 0.35
26_G 69_H 1.21 0.64 0.34
29_M 102_D 1.21 0.63 0.34
60_L 70_E 1.17 0.59 0.30
45_A 26_I 1.16 0.59 0.29
41_L 30_N 1.14 0.57 0.28
17_E 3_F 1.14 0.56 0.27
61_N 29_I 1.13 0.56 0.27
60_L 90_R 1.12 0.55 0.26
60_L 30_N 1.11 0.54 0.25
37_L 17_F 1.07 0.50 0.22
16_R 84_C 1.07 0.49 0.22
13_T 86_A 1.05 0.48 0.21
63_L 64_Y 1.05 0.47 0.20
7_T 17_F 1.04 0.47 0.20
70_F 15_F 1.02 0.45 0.18
35_V 97_L 1.02 0.45 0.18
23_R 92_L 1.02 0.44 0.18
56_A 49_P 1.00 0.43 0.17
73_E 10_G 1.00 0.42 0.17
11_T 82_K 0.99 0.41 0.16
77_F 72_A 0.97 0.40 0.15
59_A 14_A 0.96 0.39 0.14
16_R 3_F 0.95 0.37 0.14
74_Y 74_V 0.94 0.37 0.13
26_G 71_T 0.94 0.37 0.13
19_V 65_V 0.94 0.37 0.13
44_H 3_F 0.93 0.36 0.13
30_S 54_P 0.93 0.36 0.13
31_A 101_L 0.93 0.36 0.13
58_A 60_D 0.93 0.36 0.13
24_D 80_G 0.93 0.35 0.12
52_E 63_E 0.92 0.35 0.12
70_F 73_T 0.92 0.35 0.12
63_L 48_P 0.91 0.34 0.12
71_S 73_T 0.91 0.34 0.12
32_T 23_S 0.91 0.34 0.12
36_A 103_G 0.89 0.32 0.11
56_A 48_P 0.89 0.32 0.11
52_E 71_T 0.89 0.32 0.11
48_R 21_V 0.87 0.30 0.10
45_A 95_G 0.87 0.30 0.10
24_D 3_F 0.86 0.29 0.09
20_N 61_G 0.86 0.29 0.09
70_F 8_S 0.86 0.29 0.09
34_T 69_H 0.85 0.29 0.09
71_S 2_Q 0.84 0.28 0.09
18_L 38_T 0.84 0.28 0.09
14_V 17_F 0.84 0.28 0.09
14_V 43_F 0.84 0.28 0.09
36_A 2_Q 0.84 0.28 0.09
74_Y 73_T 0.83 0.27 0.08
28_N 54_P 0.83 0.27 0.08
30_S 6_Y 0.82 0.27 0.08
31_A 15_F 0.82 0.27 0.08
51_E 60_D 0.82 0.26 0.08
37_L 98_D 0.82 0.26 0.08
16_R 17_F 0.82 0.26 0.08
19_V 49_P 0.82 0.26 0.08
72_D 8_S 0.81 0.25 0.07
77_F 90_R 0.81 0.25 0.07
61_N 16_P 0.80 0.25 0.07
64_A 70_E 0.80 0.25 0.07
33_L 67_M 0.80 0.25 0.07
39_A 10_G 0.80 0.25 0.07
10_V 102_D 0.80 0.24 0.07
39_A 97_L 0.80 0.24 0.07
14_V 10_G 0.79 0.24 0.07
33_L 2_Q 0.79 0.24 0.07
14_V 101_L 0.78 0.23 0.06
46_A 99_F 0.78 0.23 0.06
23_R 87_S 0.78 0.23 0.06
49_W 103_G 0.77 0.23 0.06
70_F 70_E 0.77 0.22 0.06
59_A 77_N 0.76 0.22 0.06
52_E 50_E 0.76 0.22 0.06
45_A 66_L 0.76 0.22 0.06
58_A 5_V 0.76 0.22 0.06
23_R 17_F 0.76 0.21 0.06
52_E 59_V 0.76 0.21 0.06
40_E 35_I 0.75 0.21 0.06
43_K 58_L 0.75 0.21 0.06
40_E 21_V 0.75 0.21 0.06
9_S 77_N 0.75 0.21 0.05
8_Q 29_I 0.75 0.21 0.05
27_L 28_E 0.74 0.21 0.05
71_S 15_F 0.74 0.21 0.05
65_D 3_F 0.74 0.21 0.05
18_L 102_D 0.74 0.21 0.05
11_T 22_T 0.74 0.21 0.05
19_V 8_S 0.74 0.21 0.05
31_A 4_T 0.74 0.21 0.05
41_L 81_T 0.74 0.20 0.05
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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