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OPENSEQ.org
3G5O_AB
Genes: A B A+B
Length: 93 87 174
Sequences: 1501 3077 886
Seq/Len: 16.14 35.37 5.09
MirrorTree (Pazo et al. 2001) 0.56
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 1.71 1.00 0.95
66_E 10_T 1.58 0.99 0.92
68_D 52_T 1.46 0.98 0.88
72_A 65_R 1.33 0.96 0.81
79_E 7_F 1.25 0.94 0.76
76_T 6_R 1.07 0.85 0.58
79_E 5_V 1.07 0.85 0.58
65_A 48_E 0.99 0.79 0.50
70_D 8_T 0.99 0.79 0.49
71_I 8_T 0.94 0.73 0.43
26_Q 42_G 0.91 0.69 0.39
63_S 77_R 0.90 0.69 0.39
76_T 8_T 0.86 0.63 0.33
71_I 7_F 0.83 0.59 0.30
70_D 9_T 0.83 0.59 0.30
78_G 4_T 0.83 0.59 0.30
13_L 38_P 0.77 0.50 0.24
48_L 69_E 0.73 0.46 0.21
8_T 5_V 0.72 0.44 0.20
75_R 9_T 0.72 0.43 0.19
48_L 40_R 0.69 0.39 0.17
54_W 63_L 0.68 0.38 0.16
54_W 54_S 0.68 0.38 0.16
56_A 22_I 0.67 0.38 0.16
7_S 13_R 0.65 0.34 0.14
63_S 13_R 0.64 0.33 0.13
9_I 74_V 0.64 0.33 0.13
71_I 74_V 0.64 0.33 0.13
5_P 76_L 0.64 0.33 0.13
60_I 77_R 0.64 0.33 0.13
72_A 28_E 0.63 0.32 0.13
71_I 72_T 0.63 0.32 0.13
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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