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OPENSEQ.org
Vi-Vc
Genes: A B A+B
Length: 77 128 193
Sequences: 12566 36051 5120
Seq/Len: 163.19 281.65 26.53
MirrorTree (Pazo et al. 2001) 0.53
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 0.01 24.98
2 0.00 0.01 25.75
5 0.01 0.02 27.05
10 0.03 0.02 29.02
20 0.05 0.04 31.24
100 0.09 0.07 40.17
∞ 0.16 0.14 49.40
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
55_E 9_V 0.79 0.74 0.00
71_R 58_F 0.65 0.52 0.00
49_T 81_I 0.61 0.46 0.00
36_G 67_A 0.61 0.45 0.00
49_T 12_N 0.60 0.44 0.00
52_R 67_A 0.56 0.38 0.00
45_T 8_Q 0.55 0.36 0.00
9_R 66_K 0.51 0.30 0.00
28_E 19_K 0.51 0.30 0.00
65_E 107_I 0.51 0.29 0.00
3_E 36_T 0.50 0.28 0.00
44_R 12_N 0.49 0.27 0.00
71_R 60_R 0.48 0.26 0.00
7_T 21_S 0.48 0.25 0.00
6_L 87_K 0.47 0.25 0.00
11_F 73_G 0.47 0.24 0.00
52_R 12_N 0.46 0.22 0.00
47_D 8_Q 0.45 0.22 0.00
76_Y 13_I 0.45 0.21 0.00
2_T 26_K 0.45 0.21 0.00
55_E 74_G 0.44 0.21 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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