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OPENSEQ.org
ParD-ParE
Genes: A B A+B
Length: 93 103 181
Sequences: 1252 2837 636
Seq/Len: 13.46 27.54 3.51
MirrorTree (Pazo et al. 2001) 0.60
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 0.00 0.00 3.24
2 0.00 0.00 3.25
5 0.00 0.01 3.30
10 0.01 0.02 3.34
20 0.01 0.03 3.37
100 0.02 0.05 3.49
∞ 0.07 0.10 3.99
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 2.74 1.00 1.00
80_E 12_K 2.37 1.00 0.99
60_W 61_A 1.99 1.00 0.98
64_K 61_A 1.97 1.00 0.98
62_E 10_T 1.95 1.00 0.98
61_D 58_R 1.89 1.00 0.98
63_G 91_R 1.77 0.99 0.96
60_W 72_L 1.62 0.98 0.94
63_G 90_V 1.51 0.97 0.91
82_R 31_D 1.50 0.97 0.91
78_R 35_D 1.49 0.97 0.91
67_G 8_S 1.40 0.95 0.87
84_K 20_V 1.37 0.94 0.85
17_A 20_V 1.19 0.86 0.73
82_R 38_E 1.13 0.81 0.67
70_E 9_P 1.12 0.81 0.67
64_K 74_E 1.10 0.79 0.64
70_E 12_K 1.09 0.78 0.63
81_A 20_V 1.04 0.74 0.58
59_L 91_R 1.00 0.70 0.54
57_R 60_S 0.99 0.68 0.51
84_K 16_I 0.98 0.67 0.50
71_P 6_V 0.97 0.66 0.49
78_R 31_D 0.95 0.64 0.47
8_S 99_L 0.93 0.61 0.44
78_R 38_E 0.86 0.52 0.35
37_E 48_P 0.85 0.52 0.35
75_D 31_D 0.85 0.51 0.34
57_R 57_I 0.85 0.51 0.34
35_V 64_L 0.82 0.48 0.32
74_F 41_A 0.81 0.46 0.30
43_L 91_R 0.81 0.46 0.30
17_A 87_V 0.81 0.46 0.29
74_F 7_W 0.80 0.45 0.29
56_L 72_L 0.78 0.42 0.26
77_L 15_L 0.78 0.41 0.26
45_K 37_L 0.77 0.41 0.25
39_V 44_L 0.77 0.40 0.25
82_R 35_D 0.76 0.40 0.24
72_V 19_Y 0.76 0.39 0.24
63_G 14_D 0.76 0.39 0.24
81_A 71_L 0.75 0.39 0.24
61_D 68_P 0.75 0.38 0.23
8_S 57_I 0.75 0.38 0.23
83_Q 20_V 0.75 0.38 0.23
56_L 93_V 0.74 0.37 0.22
38_A 50_M 0.73 0.36 0.21
22_A 98_D 0.73 0.35 0.21
63_G 72_L 0.73 0.35 0.21
8_S 19_Y 0.72 0.35 0.21
81_A 16_I 0.72 0.35 0.20
74_F 38_E 0.71 0.34 0.20
8_S 8_S 0.71 0.33 0.19
72_V 22_I 0.71 0.33 0.19
18_V 51_G 0.70 0.33 0.19
57_R 56_D 0.70 0.33 0.19
67_G 91_R 0.70 0.33 0.19
72_V 30_A 0.70 0.33 0.19
6_K 65_V 0.70 0.32 0.18
23_V 47_Q 0.69 0.31 0.18
38_A 43_Q 0.69 0.31 0.18
71_P 87_V 0.68 0.30 0.17
19_M 44_L 0.68 0.30 0.17
79_K 31_D 0.68 0.30 0.17
65_A 16_I 0.68 0.30 0.17
36_R 93_V 0.68 0.30 0.17
9_V 58_R 0.68 0.30 0.17
62_E 77_P 0.68 0.30 0.17
11_V 89_I 0.67 0.29 0.16
23_V 98_D 0.67 0.29 0.16
59_L 97_R 0.67 0.29 0.16
37_E 3_V 0.67 0.29 0.16
9_V 46_D 0.67 0.28 0.16
67_G 90_V 0.66 0.28 0.15
85_L 19_Y 0.66 0.28 0.15
78_R 19_Y 0.66 0.28 0.15
70_E 75_T 0.66 0.28 0.15
76_A 63_M 0.65 0.27 0.14
9_V 70_V 0.65 0.27 0.14
24_E 34_Y 0.65 0.27 0.14
64_K 90_V 0.64 0.26 0.14
60_W 58_R 0.64 0.26 0.14
30_T 56_D 0.64 0.26 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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