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OPENSEQ.org
5200
Genes: A B A+B
Length: 83 98 178
Sequences: 1477 3943 981
Seq/Len: 17.8 40.23 5.51
MirrorTree (Pazo et al. 2001) 0.58
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 0.02 0.02 5.42
2 0.02 0.03 5.46
5 0.03 0.04 5.52
10 0.04 0.05 5.57
20 0.04 0.06 5.62
100 0.06 0.09 5.77
∞ 0.12 0.14 6.24
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
76_K 11_N 2.95 1.00 1.00
76_K 15_E 2.79 1.00 1.00
58_E 9_K 2.25 1.00 0.99
60_L 60_I 1.99 1.00 0.99
57_A 57_G 1.86 1.00 0.98
56_L 60_I 1.76 1.00 0.97
78_K 31_D 1.74 1.00 0.97
74_L 35_E 1.72 1.00 0.97
59_G 83_R 1.71 1.00 0.97
63_G 7_M 1.69 1.00 0.96
56_L 71_Y 1.50 0.99 0.93
80_G 19_Y 1.47 0.99 0.92
59_G 82_I 1.47 0.98 0.92
60_L 73_L 1.42 0.98 0.90
66_Q 11_N 1.28 0.96 0.84
80_G 15_E 1.25 0.95 0.82
74_L 31_D 1.24 0.95 0.81
77_V 19_Y 1.20 0.94 0.79
67_P 8_P 1.15 0.92 0.75
74_L 38_S 1.08 0.88 0.68
70_K 38_S 1.07 0.87 0.67
62_S 9_K 1.01 0.82 0.60
64_E 73_L 0.90 0.71 0.47
60_L 57_G 0.88 0.68 0.44
70_K 34_V 0.87 0.68 0.43
77_V 18_W 0.85 0.65 0.41
59_G 13_D 0.85 0.65 0.40
82_R 27_E 0.84 0.63 0.39
71_D 38_S 0.82 0.60 0.36
55_M 89_Q 0.81 0.60 0.36
78_K 38_S 0.81 0.60 0.36
77_V 15_E 0.80 0.58 0.34
15_E 19_Y 0.80 0.57 0.33
55_M 83_R 0.79 0.56 0.33
81_I 44_L 0.79 0.56 0.32
41_R 83_R 0.78 0.55 0.32
17_I 41_L 0.77 0.54 0.31
63_G 82_I 0.77 0.53 0.30
49_L 55_E 0.77 0.53 0.30
66_Q 8_P 0.77 0.53 0.30
26_Y 77_E 0.76 0.53 0.30
78_K 27_E 0.74 0.49 0.27
52_L 71_Y 0.73 0.47 0.26
53_R 59_G 0.73 0.47 0.26
56_L 56_L 0.73 0.47 0.25
65_A 80_I 0.72 0.47 0.25
6_T 91_A 0.71 0.45 0.24
73_F 11_N 0.71 0.45 0.24
60_L 82_I 0.71 0.45 0.24
33_I 74_Q 0.71 0.44 0.23
47_S 66_E 0.70 0.44 0.23
36_S 43_I 0.70 0.44 0.23
74_L 34_V 0.70 0.43 0.23
36_S 49_I 0.70 0.43 0.22
70_K 41_L 0.70 0.43 0.22
20_L 25_F 0.70 0.43 0.22
81_I 18_W 0.69 0.42 0.22
78_K 35_E 0.69 0.41 0.21
53_R 58_E 0.68 0.41 0.21
77_V 81_V 0.68 0.40 0.21
37_L 91_A 0.67 0.39 0.20
74_L 18_W 0.67 0.39 0.20
19_S 58_E 0.67 0.39 0.20
9_L 14_L 0.67 0.39 0.19
56_L 65_F 0.65 0.37 0.18
17_I 44_L 0.64 0.35 0.17
58_E 83_R 0.64 0.35 0.17
72_A 70_I 0.64 0.35 0.17
35_E 47_N 0.64 0.35 0.17
9_L 66_E 0.64 0.34 0.17
19_S 39_D 0.63 0.34 0.17
64_E 79_I 0.63 0.34 0.16
13_L 71_Y 0.63 0.33 0.16
28_T 21_S 0.63 0.33 0.16
63_G 80_I 0.62 0.33 0.16
78_K 18_W 0.62 0.33 0.16
18_E 26_G 0.62 0.32 0.15
50_Q 12_E 0.62 0.32 0.15
59_G 85_L 0.62 0.32 0.15
65_A 8_P 0.61 0.31 0.15
73_F 14_L 0.61 0.31 0.15
70_K 6_L 0.61 0.31 0.14
21_I 90_Y 0.60 0.30 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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