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OPENSEQ.org
ParD-ParE
Genes: A B A+B
Length: 93 103 180
Sequences: 594 3238 423
Seq/Len: 6.39 31.44 2.35
MirrorTree (Pazo et al. 2001) 0.56
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 2.07
2 0.00 0.01 2.07
5 0.01 0.01 2.10
10 0.01 0.02 2.13
20 0.01 0.04 2.16
100 0.02 0.06 2.29
∞ 0.09 0.13 2.58
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
60_W 72_L 2.05 0.99 0.97
63_G 91_R 2.04 0.99 0.97
62_E 10_T 1.60 0.96 0.88
63_G 90_V 1.54 0.94 0.86
80_E 12_K 1.47 0.92 0.82
9_V 70_V 1.42 0.91 0.79
80_E 16_I 1.37 0.88 0.76
60_W 61_A 1.26 0.82 0.67
74_F 41_A 1.25 0.81 0.65
78_R 31_D 1.18 0.76 0.58
78_R 35_D 1.03 0.61 0.41
72_V 19_Y 1.01 0.58 0.39
22_A 98_D 0.99 0.56 0.37
79_K 32_R 0.99 0.56 0.36
81_A 20_V 0.99 0.56 0.36
17_A 20_V 0.99 0.56 0.36
82_R 31_D 0.97 0.54 0.35
38_A 90_V 0.97 0.54 0.34
78_R 38_E 0.96 0.53 0.33
28_Y 32_R 0.95 0.52 0.32
80_E 87_V 0.95 0.52 0.32
30_T 86_W 0.95 0.51 0.32
65_A 47_Q 0.95 0.51 0.32
13_P 69_F 0.94 0.50 0.31
70_E 12_K 0.90 0.46 0.27
30_T 63_M 0.87 0.42 0.24
64_K 90_V 0.86 0.42 0.24
58_Q 89_I 0.86 0.41 0.23
84_K 20_V 0.85 0.40 0.23
5_E 69_F 0.84 0.39 0.22
59_L 91_R 0.84 0.39 0.22
75_D 12_K 0.84 0.39 0.22
61_D 58_R 0.83 0.38 0.21
71_P 9_P 0.83 0.38 0.21
53_I 46_D 0.83 0.38 0.21
36_R 93_V 0.83 0.38 0.21
71_P 6_V 0.83 0.38 0.20
82_R 38_E 0.83 0.38 0.20
60_W 57_I 0.83 0.37 0.20
8_S 57_I 0.82 0.37 0.20
41_D 72_L 0.82 0.37 0.20
59_L 19_Y 0.82 0.36 0.20
64_K 74_E 0.82 0.36 0.20
81_A 16_I 0.81 0.36 0.19
23_V 6_V 0.81 0.36 0.19
60_W 50_M 0.81 0.36 0.19
28_Y 55_P 0.80 0.34 0.18
57_R 57_I 0.79 0.33 0.17
61_D 42_L 0.79 0.33 0.17
52_D 63_M 0.79 0.33 0.17
64_K 61_A 0.78 0.33 0.17
31_A 64_L 0.78 0.33 0.17
8_S 8_S 0.78 0.33 0.17
28_Y 85_E 0.78 0.32 0.16
58_Q 71_L 0.78 0.32 0.16
30_T 65_V 0.78 0.32 0.16
82_R 42_L 0.78 0.32 0.16
43_L 91_R 0.76 0.31 0.15
29_A 13_A 0.75 0.29 0.14
26_G 89_I 0.75 0.29 0.14
36_R 94_D 0.75 0.29 0.14
59_L 89_I 0.75 0.29 0.14
38_A 50_M 0.75 0.29 0.14
70_E 9_P 0.74 0.28 0.14
47_E 89_I 0.73 0.28 0.13
56_L 93_V 0.73 0.28 0.13
75_D 38_E 0.73 0.28 0.13
67_G 9_P 0.73 0.28 0.13
28_Y 97_R 0.73 0.27 0.13
27_E 8_S 0.73 0.27 0.13
43_L 73_Y 0.72 0.27 0.12
81_A 71_L 0.72 0.27 0.12
63_G 14_D 0.72 0.26 0.12
69_P 5_L 0.72 0.26 0.12
35_V 101_R 0.72 0.26 0.12
23_V 51_G 0.71 0.26 0.12
23_V 67_A 0.71 0.26 0.12
78_R 19_Y 0.71 0.26 0.12
79_K 59_P 0.71 0.26 0.12
25_A 6_V 0.71 0.25 0.12
6_K 56_D 0.71 0.25 0.12
43_L 22_I 0.70 0.25 0.11
79_K 39_A 0.70 0.25 0.11
59_L 63_M 0.70 0.25 0.11
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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