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OPENSEQ.org
ParD-ParE
Genes: A B A+B
Length: 93 103 181
Sequences: 1097 3238 796
Seq/Len: 11.8 31.44 4.4
MirrorTree (Pazo et al. 2001) 0.65
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 4.06
2 0.00 0.01 4.06
5 0.01 0.01 4.10
10 0.01 0.02 4.13
20 0.02 0.04 4.15
100 0.04 0.06 4.29
∞ 0.10 0.13 4.66
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 2.93 1.00 1.00
74_F 7_W 2.32 1.00 0.99
80_E 16_I 2.26 1.00 0.99
62_E 10_T 2.03 1.00 0.99
60_W 72_L 1.99 1.00 0.99
77_L 12_K 1.71 0.99 0.96
63_G 91_R 1.67 0.99 0.96
63_G 90_V 1.62 0.99 0.95
78_R 38_E 1.61 0.99 0.95
70_E 9_P 1.22 0.91 0.78
64_K 74_E 1.21 0.91 0.77
84_K 20_V 1.17 0.89 0.74
66_S 9_P 1.13 0.86 0.70
72_V 9_P 1.08 0.83 0.66
78_R 35_D 1.07 0.82 0.64
82_R 31_D 1.05 0.80 0.62
71_P 9_P 1.04 0.80 0.62
56_L 93_V 1.04 0.80 0.62
82_R 38_E 1.03 0.79 0.61
39_V 73_Y 1.03 0.79 0.60
81_A 16_I 1.00 0.75 0.56
79_K 32_R 0.98 0.74 0.55
9_V 70_V 0.97 0.73 0.54
72_V 29_A 0.96 0.72 0.53
71_P 6_V 0.96 0.72 0.52
78_R 31_D 0.95 0.71 0.51
57_R 57_I 0.94 0.70 0.50
77_L 15_L 0.94 0.69 0.50
36_R 93_V 0.94 0.69 0.49
10_A 69_F 0.93 0.68 0.48
78_R 15_L 0.93 0.68 0.48
74_F 41_A 0.93 0.68 0.48
58_Q 39_A 0.90 0.64 0.44
84_K 16_I 0.89 0.63 0.43
22_A 98_D 0.87 0.61 0.41
59_L 91_R 0.86 0.59 0.39
72_V 7_W 0.86 0.59 0.39
72_V 19_Y 0.85 0.58 0.39
32_S 73_Y 0.85 0.57 0.38
75_D 38_E 0.83 0.56 0.36
73_D 31_D 0.83 0.55 0.36
79_K 39_A 0.83 0.55 0.36
11_V 88_E 0.82 0.54 0.34
17_A 20_V 0.81 0.53 0.34
43_L 22_I 0.81 0.52 0.33
73_D 7_W 0.81 0.52 0.33
64_K 90_V 0.80 0.51 0.32
65_A 73_Y 0.80 0.51 0.32
75_D 42_L 0.78 0.49 0.30
30_T 86_W 0.78 0.48 0.30
76_A 24_S 0.78 0.48 0.29
66_S 14_D 0.77 0.47 0.28
44_A 35_D 0.77 0.47 0.28
52_D 63_M 0.77 0.47 0.28
57_R 60_S 0.77 0.46 0.28
24_E 31_D 0.76 0.46 0.28
44_A 53_R 0.76 0.46 0.28
72_V 12_K 0.76 0.46 0.27
78_R 7_W 0.76 0.45 0.27
19_M 15_L 0.76 0.45 0.27
11_V 57_I 0.76 0.45 0.27
84_K 23_G 0.75 0.44 0.26
10_A 55_P 0.75 0.44 0.26
84_K 19_Y 0.75 0.44 0.26
25_A 46_D 0.74 0.43 0.25
54_R 46_D 0.74 0.43 0.25
27_E 73_Y 0.73 0.42 0.24
36_R 94_D 0.73 0.42 0.24
34_I 71_L 0.73 0.41 0.24
75_D 77_P 0.72 0.40 0.23
62_E 91_R 0.72 0.40 0.23
17_A 13_A 0.72 0.40 0.23
8_S 8_S 0.71 0.39 0.23
25_A 6_V 0.71 0.39 0.22
15_Q 69_F 0.71 0.39 0.22
61_D 59_P 0.71 0.39 0.22
66_S 10_T 0.71 0.39 0.22
11_V 74_E 0.71 0.39 0.22
6_K 14_D 0.71 0.39 0.22
13_P 69_F 0.71 0.39 0.22
13_P 59_P 0.71 0.38 0.22
35_V 38_E 0.70 0.38 0.22
30_T 63_M 0.70 0.37 0.21
62_E 39_A 0.70 0.37 0.21
19_M 41_A 0.69 0.37 0.21
56_L 72_L 0.69 0.36 0.20
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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