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OPENSEQ.org
parde
Genes: A B A+B
Length: 93 103 181
Sequences: 1283 3825 930
Seq/Len: 13.8 37.14 5.14
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 4.74
2 0.02 0.03 4.77
5 0.03 0.04 4.81
10 0.03 0.05 4.84
20 0.04 0.06 4.89
100 0.05 0.08 5.02
∞ 0.11 0.14 5.39
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 16_I 2.66 1.00 1.00
80_E 12_K 2.60 1.00 1.00
62_E 10_T 2.27 1.00 0.99
61_D 58_R 2.12 1.00 0.99
64_K 61_A 1.78 1.00 0.97
82_R 31_D 1.77 1.00 0.97
60_W 61_A 1.75 1.00 0.97
84_K 20_V 1.69 0.99 0.96
78_R 35_D 1.64 0.99 0.95
63_G 91_R 1.59 0.99 0.95
60_W 72_L 1.49 0.98 0.92
74_F 38_E 1.45 0.98 0.91
64_K 74_E 1.30 0.96 0.84
63_G 90_V 1.29 0.95 0.84
67_G 8_S 1.22 0.94 0.80
84_K 16_I 1.14 0.90 0.73
78_R 38_E 1.13 0.89 0.72
81_A 20_V 1.07 0.86 0.67
71_P 9_P 0.98 0.78 0.56
59_L 91_R 0.98 0.78 0.56
56_L 72_L 0.97 0.77 0.55
78_R 31_D 0.97 0.77 0.55
70_E 12_K 0.93 0.73 0.50
70_E 9_P 0.92 0.71 0.48
69_P 88_E 0.91 0.70 0.47
81_A 16_I 0.90 0.69 0.46
63_G 14_D 0.88 0.66 0.43
22_A 98_D 0.85 0.63 0.40
81_A 19_Y 0.85 0.62 0.40
38_A 43_Q 0.84 0.62 0.39
74_F 41_A 0.84 0.61 0.38
64_K 90_V 0.83 0.60 0.37
57_R 59_P 0.82 0.59 0.36
17_A 20_V 0.82 0.58 0.35
74_F 42_L 0.79 0.54 0.32
53_I 56_D 0.77 0.51 0.29
69_P 9_P 0.75 0.48 0.27
75_D 38_E 0.74 0.47 0.27
38_A 50_M 0.74 0.47 0.26
60_W 58_R 0.74 0.47 0.26
82_R 19_Y 0.74 0.47 0.26
7_M 97_R 0.73 0.46 0.26
56_L 93_V 0.73 0.45 0.25
15_Q 72_L 0.72 0.45 0.25
43_L 91_R 0.72 0.44 0.24
69_P 8_S 0.71 0.43 0.23
67_G 91_R 0.71 0.43 0.23
30_T 56_D 0.70 0.41 0.22
23_V 51_G 0.70 0.41 0.22
11_V 15_L 0.69 0.40 0.21
74_F 7_W 0.69 0.39 0.21
17_A 77_P 0.68 0.39 0.20
71_P 8_S 0.67 0.38 0.20
74_F 34_Y 0.67 0.37 0.19
65_A 53_R 0.66 0.36 0.18
56_L 40_R 0.66 0.35 0.18
19_M 95_G 0.66 0.35 0.18
72_V 19_Y 0.65 0.35 0.17
76_A 12_K 0.65 0.34 0.17
73_D 19_Y 0.65 0.34 0.17
57_R 53_R 0.64 0.34 0.17
8_S 99_L 0.64 0.34 0.17
19_M 41_A 0.64 0.34 0.17
65_A 16_I 0.64 0.34 0.17
47_E 13_A 0.64 0.33 0.17
9_V 47_Q 0.63 0.32 0.16
15_Q 63_M 0.63 0.32 0.16
82_R 27_I 0.63 0.32 0.16
20_R 36_Q 0.63 0.32 0.16
24_E 34_Y 0.63 0.32 0.16
35_V 75_T 0.63 0.32 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
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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