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OPENSEQ.org
ParD-ParE
Genes: A B A+B
Length: 93 103 179
Sequences: 689 3238 483
Seq/Len: 7.41 31.44 2.7
MirrorTree (Pazo et al. 2001) 0.62
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 2.46
2 0.00 0.01 2.46
5 0.01 0.01 2.48
10 0.01 0.02 2.53
20 0.01 0.04 2.56
100 0.02 0.06 2.69
∞ 0.09 0.13 2.98
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
63_G 90_V 2.13 1.00 0.98
60_W 72_L 2.09 1.00 0.98
62_E 10_T 1.87 0.99 0.96
63_G 91_R 1.78 0.99 0.95
80_E 12_K 1.62 0.97 0.91
78_R 31_D 1.23 0.83 0.69
79_K 32_R 1.23 0.82 0.68
59_L 91_R 1.20 0.81 0.66
80_E 16_I 1.17 0.79 0.63
22_A 98_D 1.13 0.75 0.59
74_F 41_A 1.13 0.75 0.58
60_W 61_A 1.13 0.75 0.58
74_F 7_W 1.08 0.70 0.53
9_V 70_V 1.05 0.67 0.50
38_A 90_V 1.04 0.66 0.48
57_R 57_I 1.03 0.65 0.48
82_R 31_D 1.01 0.62 0.44
56_L 93_V 1.00 0.61 0.43
71_P 9_P 1.00 0.61 0.43
8_S 8_S 0.99 0.60 0.42
64_K 90_V 0.98 0.59 0.41
80_E 87_V 0.97 0.58 0.41
36_R 93_V 0.97 0.58 0.40
78_R 38_E 0.97 0.58 0.40
17_A 20_V 0.95 0.56 0.38
82_R 90_V 0.95 0.55 0.37
78_R 35_D 0.95 0.55 0.37
19_M 8_S 0.94 0.54 0.36
75_D 77_P 0.92 0.52 0.34
24_E 89_I 0.90 0.50 0.32
56_L 97_R 0.90 0.49 0.32
75_D 12_K 0.90 0.49 0.32
24_E 31_D 0.89 0.48 0.31
72_V 19_Y 0.89 0.48 0.30
79_K 31_D 0.87 0.46 0.29
8_S 57_I 0.87 0.46 0.29
64_K 74_E 0.87 0.46 0.29
61_D 58_R 0.87 0.46 0.28
38_A 50_M 0.87 0.46 0.28
72_V 9_P 0.86 0.44 0.27
71_P 6_V 0.85 0.44 0.27
82_R 38_E 0.84 0.43 0.26
55_R 96_R 0.84 0.42 0.26
55_R 18_I 0.84 0.42 0.25
65_A 15_L 0.83 0.42 0.25
84_K 20_V 0.83 0.41 0.25
81_A 16_I 0.82 0.41 0.24
34_I 71_L 0.82 0.40 0.24
30_T 22_I 0.82 0.40 0.24
40_R 33_Y 0.82 0.40 0.24
52_D 63_M 0.82 0.40 0.23
67_G 9_P 0.81 0.39 0.23
30_T 63_M 0.81 0.39 0.23
64_K 61_A 0.81 0.39 0.22
78_R 23_G 0.81 0.38 0.22
53_I 90_V 0.80 0.38 0.22
39_V 51_G 0.79 0.37 0.21
84_K 35_D 0.79 0.36 0.20
23_V 6_V 0.78 0.35 0.20
70_E 12_K 0.77 0.35 0.19
65_A 73_Y 0.77 0.35 0.19
6_K 56_D 0.77 0.34 0.19
63_G 72_L 0.76 0.34 0.19
43_L 73_Y 0.76 0.34 0.18
66_S 91_R 0.76 0.33 0.18
10_A 69_F 0.76 0.33 0.18
58_Q 71_L 0.76 0.33 0.18
81_A 20_V 0.75 0.33 0.18
60_W 29_A 0.75 0.32 0.17
33_E 33_Y 0.75 0.32 0.17
78_R 15_L 0.75 0.32 0.17
55_R 50_M 0.75 0.32 0.17
41_D 18_I 0.74 0.32 0.17
12_T 57_I 0.74 0.32 0.17
63_G 94_D 0.74 0.31 0.16
13_P 69_F 0.73 0.30 0.16
77_L 12_K 0.72 0.29 0.15
59_L 19_Y 0.72 0.29 0.15
38_A 98_D 0.72 0.29 0.15
28_Y 32_R 0.71 0.28 0.15
10_A 99_L 0.70 0.28 0.14
57_R 38_E 0.70 0.28 0.14
17_A 39_A 0.70 0.28 0.14
85_L 26_N 0.70 0.28 0.14
68_R 8_S 0.70 0.28 0.14
62_E 91_R 0.70 0.27 0.14
63_G 70_V 0.70 0.27 0.14
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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