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OPENSEQ.org
ParD-ParE
Genes: A B A+B
Length: 93 103 190
Sequences: 92 100 51
Seq/Len: 0.99 0.97 0.27
MirrorTree (Pazo et al. 2001) 0.76
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 0.25
2 0.00 0.00 0.26
5 0.00 0.00 0.26
10 0.00 0.00 0.26
20 0.00 0.00 0.26
100 0.01 0.00 0.26
∞ 0.06 0.05 0.27
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
39_V 23_G 2.03 0.72 0.04
78_R 35_D 1.75 0.55 0.02
14_Q 74_E 1.69 0.51 0.02
60_W 72_L 1.63 0.47 0.01
44_A 72_L 1.49 0.38 0.01
78_R 7_W 1.44 0.35 0.01
73_D 70_V 1.43 0.35 0.01
22_A 72_L 1.41 0.33 0.01
25_A 86_W 1.37 0.31 0.01
46_R 56_D 1.31 0.28 0.01
69_P 45_A 1.30 0.27 0.01
30_T 82_G 1.30 0.27 0.01
70_E 37_L 1.29 0.27 0.01
77_L 92_V 1.25 0.25 0.01
81_A 7_W 1.24 0.24 0.01
78_R 25_E 1.23 0.24 0.01
13_P 85_E 1.20 0.23 0.00
76_A 6_V 1.17 0.21 0.00
21_E 16_I 1.17 0.21 0.00
33_E 48_P 1.16 0.21 0.00
49_R 8_S 1.16 0.20 0.00
38_A 18_I 1.15 0.20 0.00
76_A 5_L 1.13 0.20 0.00
49_R 74_E 1.12 0.19 0.00
80_E 59_P 1.12 0.19 0.00
82_R 99_L 1.09 0.18 0.00
68_R 87_V 1.08 0.18 0.00
34_I 82_G 1.08 0.17 0.00
45_K 25_E 1.06 0.17 0.00
10_A 56_D 1.06 0.17 0.00
65_A 66_E 1.06 0.17 0.00
19_M 41_A 1.05 0.16 0.00
49_R 9_P 1.05 0.16 0.00
8_S 91_R 1.04 0.16 0.00
53_I 49_R 1.04 0.16 0.00
29_A 26_N 1.03 0.16 0.00
19_M 66_E 1.03 0.16 0.00
73_D 87_V 1.02 0.15 0.00
62_E 10_T 1.02 0.15 0.00
58_Q 65_V 1.01 0.15 0.00
14_Q 56_D 1.01 0.15 0.00
21_E 34_Y 1.00 0.15 0.00
36_R 48_P 0.99 0.14 0.00
37_E 103_F 0.99 0.14 0.00
10_A 93_V 0.99 0.14 0.00
41_D 75_T 0.99 0.14 0.00
14_Q 70_V 0.99 0.14 0.00
9_V 34_Y 0.98 0.14 0.00
73_D 28_R 0.98 0.14 0.00
71_P 4_R 0.97 0.14 0.00
3_N 26_N 0.96 0.14 0.00
44_A 93_V 0.96 0.14 0.00
39_V 83_P 0.96 0.14 0.00
70_E 94_D 0.96 0.13 0.00
8_S 56_D 0.95 0.13 0.00
11_V 84_V 0.95 0.13 0.00
11_V 14_D 0.95 0.13 0.00
54_R 40_R 0.95 0.13 0.00
69_P 27_I 0.95 0.13 0.00
16_A 47_Q 0.95 0.13 0.00
20_R 90_V 0.95 0.13 0.00
81_A 35_D 0.95 0.13 0.00
42_W 72_L 0.94 0.13 0.00
61_D 58_R 0.94 0.13 0.00
64_K 74_E 0.94 0.13 0.00
84_K 42_L 0.94 0.13 0.00
57_R 72_L 0.94 0.13 0.00
46_R 72_L 0.93 0.12 0.00
39_V 19_Y 0.93 0.12 0.00
82_R 5_L 0.93 0.12 0.00
77_L 47_Q 0.93 0.12 0.00
86_T 10_T 0.92 0.12 0.00
8_S 72_L 0.92 0.12 0.00
9_V 50_M 0.92 0.12 0.00
57_R 91_R 0.92 0.12 0.00
60_W 99_L 0.92 0.12 0.00
25_A 63_M 0.91 0.12 0.00
16_A 46_D 0.90 0.12 0.00
61_D 66_E 0.90 0.12 0.00
58_Q 88_E 0.90 0.12 0.00
48_L 87_V 0.90 0.12 0.00
29_A 29_A 0.89 0.12 0.00
82_R 35_D 0.89 0.11 0.00
81_A 44_L 0.89 0.11 0.00
30_T 81_D 0.89 0.11 0.00
76_A 4_R 0.89 0.11 0.00
62_E 70_V 0.89 0.11 0.00
8_S 44_L 0.89 0.11 0.00
12_T 50_M 0.88 0.11 0.00
64_K 66_E 0.88 0.11 0.00
25_A 22_I 0.88 0.11 0.00
30_T 90_V 0.87 0.11 0.00
87_E 53_R 0.87 0.11 0.00
53_I 6_V 0.87 0.11 0.00
24_E 74_E 0.86 0.11 0.00
56_L 18_I 0.86 0.11 0.00
1_M 5_L 0.86 0.11 0.00
57_R 99_L 0.86 0.11 0.00
35_V 47_Q 0.86 0.11 0.00
39_V 31_D 0.85 0.10 0.00
27_E 56_D 0.85 0.10 0.00
52_D 63_M 0.85 0.10 0.00
14_Q 78_D 0.85 0.10 0.00
35_V 49_R 0.84 0.10 0.00
82_R 7_W 0.84 0.10 0.00
30_T 23_G 0.84 0.10 0.00
4_V 16_I 0.84 0.10 0.00
1_M 56_D 0.84 0.10 0.00
85_L 20_V 0.84 0.10 0.00
41_D 5_L 0.83 0.10 0.00
21_E 71_L 0.83 0.10 0.00
19_M 26_N 0.83 0.10 0.00
84_K 35_D 0.83 0.10 0.00
22_A 93_V 0.83 0.10 0.00
62_E 49_R 0.83 0.10 0.00
55_R 21_M 0.83 0.10 0.00
78_R 45_A 0.83 0.10 0.00
24_E 73_Y 0.82 0.10 0.00
84_K 74_E 0.82 0.10 0.00
13_P 69_F 0.82 0.10 0.00
37_E 91_R 0.82 0.10 0.00
74_F 94_D 0.81 0.10 0.00
30_T 69_F 0.81 0.10 0.00
35_V 43_Q 0.81 0.09 0.00
70_E 28_R 0.80 0.09 0.00
30_T 67_A 0.80 0.09 0.00
24_E 71_L 0.80 0.09 0.00
3_N 39_A 0.80 0.09 0.00
64_K 96_R 0.79 0.09 0.00
70_E 9_P 0.79 0.09 0.00
71_P 71_L 0.79 0.09 0.00
6_K 57_I 0.79 0.09 0.00
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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