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OPENSEQ.org
parde
Genes: A B A+B
Length: 93 103 181
Sequences: 1283 3825 959
Seq/Len: 13.8 37.14 5.3
MirrorTree (Pazo et al. 2001) 0.55
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 2.53 1.00 1.00
80_E 12_K 2.52 1.00 1.00
62_E 10_T 2.21 1.00 0.99
61_D 58_R 2.01 1.00 0.99
84_K 20_V 1.71 1.00 0.97
60_W 61_A 1.69 1.00 0.96
64_K 61_A 1.68 0.99 0.96
78_R 35_D 1.57 0.99 0.94
82_R 31_D 1.57 0.99 0.94
60_W 72_L 1.54 0.99 0.94
63_G 91_R 1.44 0.98 0.91
64_K 74_E 1.35 0.97 0.87
67_G 8_S 1.28 0.95 0.83
74_F 38_E 1.26 0.95 0.82
78_R 38_E 1.20 0.93 0.78
63_G 90_V 1.11 0.89 0.70
84_K 16_I 1.08 0.87 0.67
81_A 20_V 0.99 0.80 0.58
59_L 91_R 0.94 0.74 0.51
81_A 16_I 0.94 0.74 0.50
71_P 9_P 0.93 0.74 0.50
78_R 31_D 0.93 0.73 0.50
56_L 72_L 0.89 0.69 0.45
69_P 88_E 0.89 0.68 0.44
70_E 9_P 0.85 0.63 0.39
64_K 90_V 0.83 0.61 0.37
74_F 41_A 0.82 0.60 0.36
38_A 43_Q 0.82 0.59 0.36
63_G 14_D 0.81 0.57 0.34
72_V 89_I 0.80 0.56 0.33
43_L 91_R 0.79 0.54 0.32
38_A 50_M 0.76 0.51 0.29
74_F 42_L 0.76 0.51 0.29
81_A 19_Y 0.76 0.50 0.28
17_A 20_V 0.75 0.50 0.28
70_E 12_K 0.74 0.47 0.26
22_A 98_D 0.74 0.47 0.26
74_F 7_W 0.71 0.44 0.23
57_R 59_P 0.71 0.43 0.23
15_Q 72_L 0.70 0.42 0.23
60_W 58_R 0.70 0.42 0.22
69_P 9_P 0.70 0.42 0.22
76_A 12_K 0.69 0.41 0.21
7_M 97_R 0.69 0.40 0.21
71_P 8_S 0.68 0.39 0.20
56_L 93_V 0.67 0.38 0.20
75_D 38_E 0.67 0.38 0.19
74_F 34_Y 0.66 0.37 0.19
85_L 19_Y 0.66 0.37 0.18
57_R 60_S 0.66 0.37 0.18
11_V 98_D 0.66 0.37 0.18
23_V 60_S 0.65 0.35 0.17
67_G 91_R 0.63 0.33 0.16
65_A 53_R 0.63 0.33 0.16
69_P 8_S 0.63 0.33 0.16
23_V 51_G 0.63 0.33 0.16
62_E 91_R 0.63 0.33 0.16
82_R 19_Y 0.63 0.32 0.16
68_R 9_P 0.62 0.32 0.15
57_R 53_R 0.62 0.32 0.15
11_V 67_A 0.62 0.32 0.15
53_I 56_D 0.62 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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