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OPENSEQ.org
Gx-Vf1
Genes: A B A+B
Length: 307 253 502
Sequences: 1803 81320 971
Seq/Len: 5.87 321.42 1.93
MirrorTree (Pazo et al. 2001) 0.12
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 0.03 0.11 0.01
2 0.03 0.12 0.02
5 0.03 0.15 0.16
10 0.03 0.20 0.29
20 0.03 0.25 0.50
100 0.03 0.35 1.24
∞ 0.08 0.37 1.73
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
63_N 198_I 1.08 0.60 0.00
110_I 102_V 0.86 0.36 0.00
249_E 216_L 0.79 0.30 0.00
162_V 9_L 0.77 0.27 0.00
55_Y 197_I 0.72 0.24 0.00
5_V 53_L 0.71 0.23 0.00
190_K 188_R 0.69 0.21 0.00
239_Q 30_I 0.68 0.20 0.00
98_G 107_M 0.66 0.19 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
10756 0.17 XF Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10193 1.83 Gx-Vf2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 4) msa: HHblits (2015_06) 0.00 Done - Shared
10190 1.93 Gx-Vf1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 4) msa: HHblits (2015_06) 0.00 Done - Shared
10147 1.86 Gx-Vf Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) 0.01 Done - Shared
10139 1.95 X-F1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.04 Done - Shared
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