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OPENSEQ.org
Vi-Vc
Genes: A B A+B
Length: 77 128 199
Sequences: 9891 1255 262
Seq/Len: 128.45 9.8 1.32
MirrorTree (Pazo et al. 2001) 0.75
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 1.28
2 0.00 0.00 1.28
5 0.01 0.00 1.26
10 0.02 0.00 1.31
20 0.02 0.00 1.35
100 0.07 0.00 1.59
∞ 0.14 0.02 2.26
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
76_Y 13_I 1.47 0.82 0.06
66_Y 5_K 1.39 0.77 0.05
33_T 95_A 1.38 0.76 0.05
19_T 18_I 1.36 0.75 0.05
4_V 111_Y 1.34 0.72 0.04
70_R 45_Q 1.30 0.70 0.04
9_R 72_Q 1.29 0.69 0.04
50_V 13_I 1.28 0.68 0.04
39_Y 80_A 1.26 0.66 0.04
66_Y 18_I 1.25 0.65 0.04
20_H 80_A 1.24 0.65 0.03
67_I 62_Y 1.20 0.60 0.03
61_P 84_E 1.17 0.58 0.03
67_I 113_N 1.15 0.56 0.03
68_L 82_A 1.14 0.54 0.02
68_L 95_A 1.13 0.54 0.02
47_D 60_R 1.12 0.53 0.02
70_R 11_D 1.11 0.52 0.02
50_V 57_I 1.11 0.52 0.02
18_A 27_V 1.10 0.51 0.02
27_R 73_G 1.09 0.50 0.02
43_V 11_D 1.09 0.50 0.02
19_T 43_S 1.09 0.49 0.02
47_D 73_G 1.09 0.49 0.02
33_T 67_A 1.08 0.49 0.02
20_H 43_S 1.08 0.49 0.02
46_V 25_G 1.08 0.48 0.02
21_T 107_I 1.08 0.48 0.02
26_T 101_E 1.07 0.48 0.02
49_T 13_I 1.06 0.46 0.02
49_T 105_F 1.06 0.46 0.02
27_R 60_R 1.06 0.46 0.02
50_V 37_Q 1.02 0.42 0.02
3_E 29_I 1.02 0.42 0.02
57_I 99_E 1.02 0.42 0.02
37_Y 52_K 1.01 0.42 0.02
49_T 84_E 1.00 0.41 0.02
47_D 68_R 1.00 0.41 0.02
43_V 84_E 1.00 0.41 0.02
65_E 119_D 0.99 0.40 0.01
60_T 14_L 0.98 0.39 0.01
68_L 55_P 0.98 0.39 0.01
26_T 24_G 0.97 0.38 0.01
14_L 69_S 0.96 0.37 0.01
52_R 84_E 0.95 0.36 0.01
16_H 103_S 0.95 0.36 0.01
27_R 68_R 0.94 0.35 0.01
11_F 22_P 0.94 0.35 0.01
44_R 73_G 0.94 0.35 0.01
15_H 21_S 0.94 0.35 0.01
33_T 30_T 0.94 0.35 0.01
59_D 9_V 0.93 0.34 0.01
22_G 80_A 0.93 0.34 0.01
44_R 62_Y 0.93 0.34 0.01
73_V 24_G 0.93 0.34 0.01
58_E 66_K 0.92 0.34 0.01
19_T 98_E 0.92 0.33 0.01
12_E 66_K 0.92 0.33 0.01
38_D 6_M 0.91 0.33 0.01
73_V 94_W 0.91 0.33 0.01
66_Y 14_L 0.91 0.33 0.01
44_R 60_R 0.91 0.33 0.01
70_R 7_T 0.91 0.32 0.01
32_E 87_K 0.91 0.32 0.01
30_L 27_V 0.90 0.32 0.01
36_G 19_K 0.90 0.32 0.01
16_H 85_I 0.90 0.32 0.01
33_T 42_I 0.90 0.31 0.01
1_G 10_I 0.89 0.30 0.01
59_D 38_L 0.88 0.29 0.01
38_D 80_A 0.88 0.29 0.01
38_D 7_T 0.87 0.29 0.01
48_V 66_K 0.86 0.28 0.01
45_T 19_K 0.85 0.28 0.01
32_E 75_T 0.85 0.28 0.01
27_R 62_Y 0.85 0.27 0.01
65_E 114_D 0.85 0.27 0.01
3_E 90_K 0.85 0.27 0.01
40_F 50_P 0.85 0.27 0.01
47_D 62_Y 0.84 0.27 0.01
28_E 6_M 0.84 0.27 0.01
70_R 13_I 0.84 0.27 0.01
18_A 10_I 0.84 0.26 0.01
20_H 99_E 0.84 0.26 0.01
48_V 87_K 0.83 0.26 0.01
49_T 72_Q 0.83 0.26 0.01
43_V 82_A 0.83 0.26 0.01
37_Y 29_I 0.83 0.26 0.01
57_I 86_V 0.83 0.26 0.01
50_V 50_P 0.83 0.26 0.01
60_T 106_T 0.82 0.25 0.01
7_T 64_V 0.82 0.25 0.01
41_G 25_G 0.81 0.25 0.01
45_T 110_P 0.81 0.25 0.01
33_T 38_L 0.81 0.25 0.01
8_H 13_I 0.81 0.25 0.01
7_T 63_R 0.81 0.24 0.01
3_E 100_G 0.81 0.24 0.01
60_T 88_Q 0.81 0.24 0.01
51_R 85_I 0.81 0.24 0.01
23_Q 82_A 0.81 0.24 0.01
25_M 53_D 0.80 0.24 0.01
73_V 103_S 0.80 0.24 0.01
60_T 52_K 0.80 0.23 0.01
8_H 84_E 0.79 0.23 0.01
40_F 82_A 0.79 0.23 0.01
27_R 70_R 0.79 0.23 0.01
33_T 103_S 0.79 0.23 0.01
44_R 68_R 0.79 0.23 0.01
57_I 96_N 0.79 0.23 0.01
33_T 119_D 0.79 0.23 0.01
4_V 71_A 0.78 0.22 0.01
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
5316 19.24 Vi-Vc Δgene:(1, 1) A:(1E-20, 2) B:(1E-20, 2) msa: Jackhmmer (2016_06b) 0.02 Done - Shared
5315 10.12 Vi-Vc Δgene:(1, 1) A:(1E-20, 4) B:(1E-40, 1) msa: HHblits (2015_06) 0.00 Done - Shared
5314 1.32 Vi-Vc Δgene:(1, 1) A:(1E-20, 4) B:(1E-40, 2) msa: Jackhmmer (2016_06b) 0.06 Done - Shared
5312 0.15 Vi-Vc Δgene:(1, 1) A:(1E-20, 2) B:(1E-40, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5311 0 Vi-Vc Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 4) msa: HHblits (2015_06) Killed - Shared
5309 35.47 Vi-Vc Δgene:(1, 1) A:(1E-20, 4) B:(1E-20, 2) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5308 0.08 Vi-Vc Δgene:(1, 1) A:(1E-20, 1) B:(1E-40, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5307 0 Vi-Vc Δgene:(1, 1) A:(1E-40, 4) B:(1E-40, 2) msa: HHblits (2015_06) Killed - Shared
5301 0 Vi-Vc Δgene:(1, 1) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed - Shared
5300 0.17 Vi-Vc Δgene:(1, 1) A:(1E-20, 4) B:(1E-40, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5298 0 Vi-Vc Δgene:(1, 1) A:(1E-60, 4) B:(1E-60, 4) msa: HHblits (2015_06) Killed - Shared
5297 0.07 Vi-Vc Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5289 22.37 Vi-Vc Δgene:(1, 1) A:(1E-10, 4) B:(1E-40, 4) msa: HHblits (2015_06) 0.00 Done - Shared
5288 22.35 Vi-Vc Δgene:(1, 1) A:(1E-20, 4) B:(1E-40, 4) msa: HHblits (2015_06) 0.00 Done - Shared
5286 26.12 Vi-Vc Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5285 22.35 Vi-Vc Δgene:(1, 1) A:(1E-20, 8) B:(1E-40, 4) msa: HHblits (2015_06) 0.00 Done - Shared
5272 26.53 Vi-Vc Δgene:(1, 1) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5271 73.84 Vi-Vc Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5259 22.35 Vi-Vc Δgene:(1, 1) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5258 25.07 Vi-Vc Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
5257 0.17 Vi-Vc Δgene:(1, 1) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) Killed - Shared
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