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OPENSEQ.org
Vi-Vc
Genes: A B A+B
Length: 77 128 192
Sequences: 15224 3428 1943
Seq/Len: 197.71 26.78 10.12
MirrorTree (Pazo et al. 2001) 0.49
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 0.01 0.00 9.48
2 0.01 0.00 9.68
5 0.02 0.00 9.79
10 0.04 0.00 10.24
20 0.06 0.01 10.52
100 0.14 0.07 11.35
∞ 0.22 0.12 12.75
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
49_T 12_N 0.86 0.82 0.00
51_R 19_K 0.79 0.73 0.00
55_E 9_V 0.78 0.72 0.00
46_V 28_T 0.77 0.71 0.00
30_L 25_G 0.76 0.70 0.00
76_Y 5_K 0.74 0.67 0.00
56_K 15_N 0.74 0.67 0.00
70_R 17_A 0.74 0.67 0.00
18_A 29_I 0.73 0.65 0.00
49_T 82_A 0.72 0.64 0.00
24_V 84_E 0.71 0.62 0.00
44_R 8_Q 0.70 0.61 0.00
34_V 65_D 0.69 0.59 0.00
11_F 70_R 0.69 0.59 0.00
51_R 85_I 0.69 0.59 0.00
55_E 59_D 0.68 0.57 0.00
22_G 93_I 0.68 0.57 0.00
77_M 107_I 0.67 0.56 0.00
47_D 8_Q 0.67 0.55 0.00
51_R 82_A 0.67 0.55 0.00
71_R 56_L 0.66 0.54 0.00
36_G 19_K 0.66 0.54 0.00
46_V 75_T 0.65 0.53 0.00
42_D 2_D 0.63 0.49 0.00
28_E 9_V 0.62 0.48 0.00
30_L 4_D 0.61 0.45 0.00
34_V 57_I 0.60 0.43 0.00
44_R 12_N 0.59 0.42 0.00
50_V 98_E 0.59 0.42 0.00
21_T 50_P 0.58 0.41 0.00
71_R 5_K 0.58 0.40 0.00
48_V 56_L 0.58 0.40 0.00
57_I 13_I 0.58 0.40 0.00
52_R 8_Q 0.58 0.40 0.00
33_T 75_T 0.57 0.39 0.00
44_R 24_G 0.57 0.39 0.00
11_F 40_L 0.57 0.39 0.00
58_E 12_N 0.57 0.38 0.00
71_R 15_N 0.57 0.38 0.00
49_T 45_Q 0.57 0.38 0.00
43_V 15_N 0.56 0.37 0.00
18_A 4_D 0.56 0.37 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
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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