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OPENSEQ.org
3G5O_AB
Genes: A B A+B
Length: 93 87 171
Sequences: 1501 3077 623
Seq/Len: 16.14 35.37 3.64
MirrorTree (Pazo et al. 2001) 0.78
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 3.46
2 0.00 0.01 3.50
5 0.01 0.02 3.59
10 0.01 0.03 3.66
20 0.02 0.03 3.74
100 0.10 0.07 4.04
∞ 0.14 0.12 4.92
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
67_A 8_T 2.73 1.00 1.00
66_E 10_T 2.02 1.00 0.99
68_D 52_T 1.88 1.00 0.98
72_A 65_R 1.84 0.99 0.97
79_E 7_F 1.83 0.99 0.97
70_D 8_T 1.83 0.99 0.97
76_T 8_T 1.70 0.99 0.96
76_T 6_R 1.47 0.97 0.90
78_G 4_T 1.39 0.95 0.87
70_D 9_T 1.38 0.95 0.86
65_A 48_E 1.24 0.89 0.77
71_I 8_T 1.23 0.89 0.77
79_E 5_V 1.09 0.79 0.64
9_I 38_P 1.06 0.77 0.61
68_D 65_R 1.05 0.76 0.59
63_S 77_R 1.05 0.75 0.59
72_A 20_P 0.99 0.70 0.53
63_S 13_R 0.99 0.70 0.53
70_D 10_T 0.98 0.69 0.52
72_A 52_T 0.97 0.67 0.50
54_W 63_L 0.96 0.66 0.49
75_R 9_T 0.94 0.64 0.47
26_Q 42_G 0.93 0.63 0.45
13_L 56_R 0.92 0.60 0.43
27_I 63_L 0.91 0.59 0.42
3_I 34_L 0.90 0.59 0.41
51_T 54_S 0.90 0.59 0.41
24_Q 66_I 0.90 0.58 0.41
56_A 47_R 0.89 0.57 0.39
43_D 21_R 0.87 0.55 0.37
61_R 48_E 0.85 0.52 0.35
8_T 5_V 0.82 0.49 0.32
16_F 25_A 0.81 0.46 0.30
52_L 47_R 0.80 0.46 0.29
71_I 72_T 0.80 0.46 0.29
74_G 8_T 0.80 0.46 0.29
71_I 52_T 0.80 0.45 0.29
55_L 49_L 0.79 0.44 0.28
10_K 64_Y 0.79 0.44 0.28
59_G 66_I 0.78 0.43 0.27
11_G 21_R 0.78 0.42 0.27
77_Y 9_T 0.78 0.42 0.27
10_K 56_R 0.77 0.42 0.26
71_I 74_V 0.77 0.41 0.26
50_E 43_K 0.77 0.41 0.26
39_L 51_G 0.76 0.40 0.25
40_V 5_V 0.76 0.40 0.24
71_I 7_F 0.75 0.39 0.24
13_L 38_P 0.75 0.39 0.23
83_R 31_F 0.74 0.37 0.22
67_A 52_T 0.73 0.37 0.22
25_D 84_I 0.72 0.36 0.21
67_A 77_R 0.72 0.36 0.21
48_L 40_R 0.72 0.35 0.21
44_E 47_R 0.72 0.35 0.20
10_K 82_A 0.71 0.35 0.20
54_W 54_S 0.70 0.34 0.19
8_T 75_I 0.70 0.33 0.19
56_A 30_A 0.70 0.33 0.19
50_E 54_S 0.69 0.33 0.19
79_E 12_R 0.69 0.32 0.18
47_S 45_L 0.68 0.31 0.18
29_I 67_D 0.68 0.31 0.17
67_A 54_S 0.68 0.31 0.17
78_G 6_R 0.68 0.31 0.17
3_I 37_E 0.68 0.31 0.17
8_T 72_T 0.68 0.30 0.17
79_E 27_V 0.68 0.30 0.17
72_A 28_E 0.68 0.30 0.17
52_L 50_A 0.67 0.30 0.17
50_E 45_L 0.67 0.29 0.16
34_A 38_P 0.66 0.29 0.16
15_E 49_L 0.66 0.28 0.15
48_L 10_T 0.65 0.28 0.15
5_P 76_L 0.65 0.28 0.15
55_L 5_V 0.65 0.28 0.15
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)
ID Seq/Len Name Options I_Prob Status
0726 4.64 3G5O_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done
0152 3.64 3G5O_AB Δgene:(1, 1) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0151 5.09 3G5O_AB Δgene:(1, ∞) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 0.95 Done
0150 0.3 3G5O_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
0149 3.89 3G5O_AB Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0148 0.22 3G5O_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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