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OPENSEQ.org
5195
Genes: A B A+B
Length: 85 121 197
Sequences: 1547 2565 566
Seq/Len: 18.2 21.2 2.87
MirrorTree (Pazo et al. 2001) 0.76
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 0.01 2.75
2 0.01 0.01 2.76
5 0.02 0.01 2.78
10 0.02 0.02 2.83
20 0.03 0.03 2.86
100 0.05 0.05 3.05
∞ 0.09 0.10 3.85
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
61_C 68_F 1.51 0.96 0.72
57_L 115_R 1.44 0.94 0.67
52_Y 114_G 1.38 0.92 0.62
55_A 43_A 1.29 0.88 0.54
58_L 68_F 1.27 0.87 0.52
58_L 66_A 1.27 0.87 0.51
76_D 89_R 1.26 0.86 0.51
82_Q 94_K 1.15 0.79 0.40
26_S 17_I 1.15 0.78 0.40
9_V 30_Q 1.13 0.77 0.38
14_M 59_G 1.11 0.75 0.36
19_P 53_V 1.07 0.70 0.32
14_M 52_V 1.01 0.65 0.27
21_L 60_G 0.99 0.62 0.25
78_P 23_D 0.98 0.61 0.24
60_Q 83_V 0.94 0.56 0.21
42_L 112_V 0.94 0.56 0.21
32_E 83_V 0.93 0.55 0.20
6_L 65_T 0.91 0.53 0.19
61_C 67_G 0.91 0.53 0.19
65_A 86_D 0.90 0.51 0.18
9_V 32_G 0.89 0.50 0.18
46_P 70_V 0.89 0.50 0.17
30_D 56_V 0.87 0.48 0.16
80_T 116_L 0.86 0.46 0.15
8_R 53_V 0.84 0.44 0.14
35_M 107_T 0.83 0.43 0.14
5_R 21_S 0.83 0.42 0.14
23_N 108_I 0.82 0.41 0.13
43_I 47_V 0.81 0.41 0.13
28_G 109_M 0.80 0.39 0.12
24_A 103_R 0.80 0.39 0.12
21_L 40_T 0.79 0.38 0.12
41_R 46_R 0.79 0.38 0.12
23_N 110_N 0.79 0.38 0.12
38_D 17_I 0.78 0.36 0.11
45_E 39_V 0.78 0.36 0.11
25_L 82_V 0.77 0.36 0.11
41_R 83_V 0.77 0.36 0.11
61_C 66_A 0.77 0.35 0.10
35_M 71_S 0.77 0.35 0.10
48_R 20_V 0.76 0.35 0.10
10_G 29_E 0.76 0.35 0.10
8_R 64_R 0.76 0.34 0.10
53_S 50_L 0.75 0.34 0.10
52_Y 111_E 0.75 0.34 0.10
42_L 18_W 0.75 0.34 0.10
36_V 103_R 0.75 0.34 0.10
14_M 81_G 0.75 0.34 0.10
58_L 67_G 0.75 0.33 0.10
7_K 48_T 0.75 0.33 0.10
68_S 37_L 0.75 0.33 0.10
16_T 86_D 0.74 0.33 0.09
6_L 12_M 0.74 0.32 0.09
23_N 44_F 0.73 0.32 0.09
9_V 68_F 0.73 0.32 0.09
65_A 66_A 0.73 0.32 0.09
35_M 43_A 0.73 0.31 0.09
56_E 108_I 0.73 0.31 0.09
1_M 83_V 0.73 0.31 0.09
24_A 32_G 0.72 0.31 0.09
33_V 13_E 0.72 0.31 0.09
61_C 48_T 0.72 0.31 0.09
6_L 58_S 0.72 0.30 0.09
44_V 109_M 0.72 0.30 0.08
40_G 26_A 0.72 0.30 0.08
21_L 106_E 0.71 0.30 0.08
66_E 58_S 0.71 0.30 0.08
10_G 55_P 0.71 0.29 0.08
36_V 90_T 0.71 0.29 0.08
16_T 84_R 0.70 0.29 0.08
35_M 37_L 0.70 0.29 0.08
33_V 14_R 0.70 0.29 0.08
3_T 101_L 0.70 0.29 0.08
32_E 37_L 0.70 0.28 0.08
58_L 85_C 0.70 0.28 0.08
12_S 30_Q 0.70 0.28 0.08
47_Y 104_V 0.70 0.28 0.08
9_V 15_G 0.69 0.28 0.07
3_T 18_W 0.69 0.28 0.07
60_Q 68_F 0.69 0.27 0.07
39_N 76_G 0.69 0.27 0.07
10_G 87_Q 0.69 0.27 0.07
12_S 83_V 0.68 0.27 0.07
67_I 44_F 0.68 0.26 0.07
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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