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OPENSEQ.org
TA verification
Genes: A B A+B
Length: 93 103 182
Sequences: 1742 3856 855
Seq/Len: 18.73 37.44 4.7
MirrorTree (Pazo et al. 2001) 0.60
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 0.02 4.36
2 0.01 0.03 4.40
5 0.02 0.04 4.43
10 0.03 0.05 4.48
20 0.03 0.06 4.53
100 0.04 0.08 4.70
∞ 0.10 0.14 5.47
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
80_E 12_K 2.87 1.00 1.00
62_E 10_T 2.57 1.00 1.00
80_E 16_I 2.45 1.00 1.00
61_D 58_R 2.11 1.00 0.99
64_K 61_A 2.05 1.00 0.99
60_W 61_A 1.86 1.00 0.98
63_G 91_R 1.80 1.00 0.97
84_K 16_I 1.64 0.99 0.95
82_R 31_D 1.61 0.99 0.95
78_R 35_D 1.59 0.99 0.95
63_G 90_V 1.56 0.99 0.94
84_K 20_V 1.55 0.99 0.94
67_G 8_S 1.48 0.98 0.92
60_W 72_L 1.40 0.97 0.89
81_A 16_I 1.20 0.92 0.78
78_R 31_D 1.16 0.90 0.74
64_K 74_E 1.13 0.88 0.72
81_A 20_V 1.10 0.86 0.68
70_E 12_K 1.04 0.81 0.62
78_R 38_E 0.99 0.77 0.56
85_L 19_Y 0.97 0.75 0.54
77_L 12_K 0.95 0.72 0.51
82_R 38_E 0.94 0.71 0.50
67_G 91_R 0.93 0.70 0.49
30_T 56_D 0.91 0.68 0.47
17_A 20_V 0.90 0.66 0.45
38_A 43_Q 0.89 0.65 0.44
11_V 15_L 0.88 0.64 0.43
69_P 9_P 0.87 0.63 0.41
74_F 38_E 0.87 0.63 0.41
56_L 93_V 0.86 0.61 0.40
69_P 88_E 0.84 0.58 0.37
8_S 99_L 0.79 0.51 0.31
60_W 58_R 0.79 0.51 0.31
59_L 91_R 0.79 0.51 0.31
38_A 50_M 0.78 0.49 0.30
71_P 71_L 0.77 0.49 0.29
53_I 87_V 0.77 0.48 0.29
74_F 7_W 0.77 0.48 0.29
78_R 19_Y 0.77 0.48 0.29
72_V 9_P 0.76 0.48 0.28
82_R 35_D 0.76 0.48 0.28
56_L 72_L 0.76 0.47 0.28
63_G 14_D 0.76 0.47 0.28
78_R 34_Y 0.76 0.47 0.27
12_T 77_P 0.75 0.46 0.27
11_V 67_A 0.74 0.44 0.26
67_G 90_V 0.74 0.44 0.25
82_R 27_I 0.73 0.44 0.25
7_M 97_R 0.73 0.43 0.25
22_A 98_D 0.72 0.42 0.24
81_A 71_L 0.71 0.40 0.23
21_E 59_P 0.71 0.40 0.23
53_I 56_D 0.71 0.40 0.23
85_L 26_N 0.70 0.39 0.22
45_K 37_L 0.69 0.38 0.21
79_K 59_P 0.69 0.38 0.21
12_T 66_E 0.69 0.38 0.20
81_A 41_A 0.68 0.37 0.20
66_S 10_T 0.68 0.37 0.20
35_V 64_L 0.68 0.37 0.20
65_A 16_I 0.68 0.36 0.20
74_F 34_Y 0.68 0.36 0.20
17_A 87_V 0.68 0.36 0.19
76_A 88_E 0.68 0.36 0.19
35_V 75_T 0.67 0.35 0.19
15_Q 63_M 0.67 0.35 0.18
82_R 19_Y 0.67 0.34 0.18
88_V 23_G 0.66 0.34 0.18
71_P 9_P 0.66 0.34 0.18
38_A 73_Y 0.66 0.34 0.18
83_Q 28_R 0.66 0.33 0.17
74_F 41_A 0.65 0.32 0.17
57_R 59_P 0.64 0.32 0.16
23_V 98_D 0.64 0.32 0.16
69_P 8_S 0.64 0.31 0.16
72_V 30_A 0.64 0.31 0.16
43_L 91_R 0.64 0.31 0.16
36_R 33_Y 0.63 0.31 0.16
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
4775 4.7 TA verification Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared
3677 3.2 ParD-ParE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
3676 0.27 ParD-ParE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
2849 5.14 parde Δgene:(1, 1) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2015_06) 1.00 Done
2848 5.3 parde Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2015_06) 1.00 Done - Shared
0641 3.53 ParD-ParE Δgene:(1, 1) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done
0640 3.51 ParD-ParE Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done
0639 4.42 ParD-ParE Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 1.00 Done
0638 4.4 ParD-ParE Δgene:(1, 1) A:(1E-04, 8) B:(1E-06, 4) msa: HHblits (2013_03) 1.00 Done
0637 2.7 ParD-ParE Δgene:(1, 1) A:(1E-04, 4) B:(1E-06, 4) msa: HHblits (2013_03) 0.98 Done
0636 2.35 ParD-ParE Δgene:(1, 20) A:(1E-06, 4) B:(1E-06, 4) msa: HHblits (2013_03) 0.97 Done
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