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OPENSEQ.org
ParD-ParE
Genes: A B A+B
Length: 93 103 180
Sequences: 1097 3498 795
Seq/Len: 11.8 33.96 4.42
MirrorTree (Pazo et al. 2001) 0.64
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 4.07
5 0.01 0.02 4.10
10 0.01 0.03 4.15
20 0.02 0.04 4.18
100 0.04 0.08 4.31
∞ 0.10 0.15 4.67
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 2.96 1.00 1.00
74_F 7_W 2.31 1.00 0.99
80_E 16_I 2.17 1.00 0.99
60_W 72_L 1.97 1.00 0.98
62_E 10_T 1.95 1.00 0.98
78_R 38_E 1.83 1.00 0.98
77_L 12_K 1.73 0.99 0.97
63_G 91_R 1.68 0.99 0.96
63_G 90_V 1.55 0.98 0.94
84_K 20_V 1.36 0.96 0.87
70_E 9_P 1.20 0.90 0.77
79_K 32_R 1.18 0.90 0.76
64_K 74_E 1.16 0.88 0.74
66_S 9_P 1.14 0.87 0.71
75_D 38_E 1.13 0.87 0.71
78_R 35_D 1.09 0.84 0.68
71_P 9_P 1.07 0.83 0.65
82_R 38_E 1.05 0.80 0.62
72_V 9_P 1.04 0.80 0.61
56_L 93_V 1.02 0.78 0.60
81_A 16_I 1.02 0.78 0.60
9_V 70_V 1.02 0.78 0.59
71_P 6_V 0.99 0.74 0.55
77_L 15_L 0.98 0.74 0.54
39_V 73_Y 0.95 0.71 0.51
82_R 31_D 0.95 0.70 0.50
56_L 97_R 0.94 0.70 0.50
78_R 15_L 0.94 0.70 0.50
76_A 24_S 0.93 0.68 0.48
10_A 69_F 0.91 0.66 0.46
22_A 98_D 0.91 0.66 0.46
79_K 39_A 0.90 0.65 0.45
74_F 41_A 0.89 0.63 0.43
17_A 20_V 0.89 0.63 0.43
72_V 19_Y 0.87 0.60 0.40
84_K 16_I 0.86 0.59 0.40
59_L 91_R 0.86 0.59 0.39
36_R 93_V 0.86 0.59 0.39
72_V 7_W 0.84 0.57 0.37
73_D 31_D 0.83 0.56 0.36
64_K 90_V 0.83 0.55 0.36
55_R 50_M 0.83 0.55 0.35
34_I 37_L 0.83 0.55 0.35
84_K 23_G 0.82 0.54 0.35
62_E 16_I 0.82 0.53 0.34
72_V 29_A 0.82 0.53 0.34
78_R 34_Y 0.82 0.53 0.34
52_D 63_M 0.82 0.53 0.34
43_L 22_I 0.80 0.51 0.32
72_V 12_K 0.80 0.51 0.32
75_D 77_P 0.80 0.51 0.32
10_A 55_P 0.79 0.50 0.31
11_V 65_V 0.79 0.49 0.31
84_K 19_Y 0.79 0.49 0.31
39_V 30_A 0.79 0.49 0.30
75_D 5_L 0.78 0.49 0.30
17_A 13_A 0.78 0.48 0.30
65_A 73_Y 0.78 0.48 0.29
83_Q 77_P 0.78 0.48 0.29
78_R 31_D 0.77 0.47 0.29
58_Q 39_A 0.76 0.46 0.28
77_L 11_A 0.76 0.45 0.27
61_D 42_L 0.76 0.45 0.27
19_M 15_L 0.76 0.45 0.27
66_S 14_D 0.75 0.44 0.26
8_S 8_S 0.75 0.44 0.26
32_S 73_Y 0.75 0.44 0.26
13_P 34_Y 0.75 0.44 0.26
11_V 88_E 0.74 0.43 0.26
36_R 94_D 0.74 0.43 0.25
14_Q 92_V 0.74 0.42 0.25
62_E 91_R 0.74 0.42 0.25
30_T 63_M 0.74 0.42 0.25
44_A 35_D 0.73 0.42 0.24
31_A 64_L 0.72 0.41 0.24
25_A 6_V 0.72 0.41 0.23
24_E 31_D 0.72 0.41 0.23
66_S 10_T 0.72 0.40 0.23
13_P 69_F 0.72 0.40 0.23
41_D 50_M 0.72 0.40 0.23
73_D 7_W 0.71 0.39 0.22
40_R 87_V 0.71 0.39 0.22
27_E 73_Y 0.70 0.38 0.22
10_A 65_V 0.70 0.38 0.22
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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