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OPENSEQ.org
Gx-Vf
Genes: A B A+B
Length: 307 253 502
Sequences: 1803 81320 933
Seq/Len: 5.87 321.42 1.86
MirrorTree (Pazo et al. 2001) 0.08
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 0.01
5 0.03 0.15 0.14
10 0.03 0.20 0.25
20 0.03 0.25 0.44
100 0.03 0.35 1.14
∞ 0.08 0.37 1.67
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 1.15 0.66 0.01
131_P 30_I 0.81 0.31 0.00
259_D 102_V 0.81 0.30 0.00
14_I 113_Q 0.75 0.25 0.00
151_S 26_I 0.74 0.24 0.00
260_Y 64_I 0.74 0.24 0.00
55_Y 197_I 0.67 0.19 0.00
162_V 9_L 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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