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OPENSEQ.org
ParD-ParE
Genes: A B A+B
Length: 93 103 184
Sequences: 752 2462 588
Seq/Len: 8.09 23.9 3.2
MirrorTree (Pazo et al. 2001) 0.61
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 2.93
2 0.00 0.00 2.96
5 0.01 0.02 2.97
10 0.01 0.02 2.98
20 0.01 0.03 3.00
100 0.03 0.05 3.07
∞ 0.08 0.12 3.29
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 2.90 1.00 1.00
60_W 61_A 2.62 1.00 1.00
62_E 10_T 2.34 1.00 0.99
80_E 16_I 2.05 1.00 0.99
84_K 16_I 1.70 0.99 0.95
64_K 61_A 1.64 0.98 0.94
60_W 72_L 1.63 0.98 0.94
61_D 58_R 1.43 0.95 0.88
82_R 31_D 1.42 0.94 0.87
11_V 15_L 1.38 0.93 0.85
84_K 20_V 1.36 0.93 0.84
78_R 35_D 1.35 0.92 0.84
64_K 74_E 1.33 0.92 0.82
63_G 91_R 1.33 0.92 0.82
64_K 58_R 1.26 0.88 0.78
78_R 31_D 1.25 0.87 0.76
82_R 38_E 1.23 0.87 0.75
82_R 35_D 1.09 0.76 0.62
69_P 9_P 1.08 0.75 0.60
38_A 43_Q 1.08 0.75 0.60
78_R 38_E 1.07 0.74 0.59
48_L 100_N 0.98 0.64 0.48
60_W 58_R 0.95 0.61 0.45
76_A 92_V 0.94 0.59 0.43
17_A 87_V 0.92 0.57 0.41
7_M 97_R 0.91 0.55 0.39
83_Q 13_A 0.89 0.53 0.37
21_E 59_P 0.89 0.53 0.37
57_R 26_N 0.89 0.53 0.37
33_E 48_P 0.87 0.50 0.35
85_L 19_Y 0.86 0.50 0.34
63_G 14_D 0.86 0.49 0.34
81_A 20_V 0.85 0.48 0.33
68_R 9_P 0.85 0.48 0.33
55_R 21_M 0.84 0.47 0.32
58_Q 71_L 0.84 0.47 0.32
78_R 34_Y 0.83 0.45 0.30
62_E 91_R 0.82 0.45 0.30
63_G 90_V 0.82 0.44 0.29
86_T 27_I 0.81 0.44 0.29
35_V 56_D 0.81 0.43 0.28
66_S 10_T 0.81 0.43 0.28
74_F 34_Y 0.81 0.43 0.28
33_E 86_W 0.80 0.42 0.27
52_D 52_V 0.79 0.41 0.26
67_G 91_R 0.79 0.41 0.26
35_V 42_L 0.79 0.40 0.26
87_E 89_I 0.78 0.39 0.25
9_V 55_P 0.78 0.39 0.24
67_G 8_S 0.77 0.38 0.24
58_Q 8_S 0.77 0.38 0.24
20_R 54_R 0.77 0.38 0.23
85_L 2_A 0.76 0.38 0.23
38_A 50_M 0.76 0.37 0.23
59_L 91_R 0.76 0.37 0.23
81_A 71_L 0.75 0.36 0.22
28_Y 35_D 0.75 0.35 0.21
20_R 48_P 0.74 0.35 0.21
74_F 16_I 0.74 0.35 0.21
35_V 87_V 0.74 0.35 0.21
58_Q 39_A 0.74 0.34 0.21
61_D 68_P 0.73 0.33 0.20
55_R 53_R 0.72 0.33 0.20
38_A 90_V 0.72 0.33 0.19
60_W 66_E 0.72 0.33 0.19
20_R 36_Q 0.72 0.32 0.19
71_P 9_P 0.72 0.32 0.19
25_A 37_L 0.71 0.32 0.19
75_D 38_E 0.71 0.32 0.18
54_R 17_D 0.71 0.32 0.18
74_F 2_A 0.71 0.32 0.18
89_P 28_R 0.71 0.31 0.18
73_D 45_A 0.70 0.31 0.18
37_E 4_R 0.70 0.31 0.18
64_K 90_V 0.70 0.31 0.18
21_E 102_L 0.70 0.30 0.17
69_P 8_S 0.70 0.30 0.17
78_R 7_W 0.70 0.30 0.17
28_Y 28_R 0.69 0.30 0.17
79_K 35_D 0.69 0.29 0.17
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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