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OPENSEQ.org
ZE
Genes: A B A+B
Length: 222 383 534
Sequences: 88685 2098 2048
Seq/Len: 399.48 5.48 3.84
MirrorTree (Pazo et al. 2001) 0.02
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 0.09 0.02 0.01
2 0.10 0.02 0.04
5 0.14 0.02 0.15
10 0.19 0.02 0.35
20 0.25 0.02 0.89
100 0.36 0.03 3.39
∞ 0.37 0.05 4.52
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
66_I 206_M 0.75 0.41 0.00
11_Y 216_V 0.66 0.30 0.00
81_I 42_V 0.66 0.29 0.00
148_I 289_N 0.61 0.25 0.00
210_L 214_R 0.60 0.24 0.00
203_R 241_E 0.60 0.23 0.00
25_M 162_T 0.60 0.23 0.00
159_L 80_A 0.59 0.23 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
13125 3.84 ZE Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
12176 5.12 Ec EZ inf Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
12174 1.01 Ec EZ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
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