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OPENSEQ.org
ACP_FAAL
Genes: A B A+B
Length: 90 584 636
Sequences: 23126 24683 2513
Seq/Len: 256.96 42.27 3.95
MirrorTree (Pazo et al. 2001) 0.30
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 0.17 0.09 1.19
2 0.19 0.10 1.77
5 0.20 0.13 2.29
10 0.22 0.14 2.50
20 0.23 0.15 2.69
100 0.25 0.20 3.73
∞ 0.30 0.27 5.80
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_V 180_K 0.77 0.43 0.00
58_I 390_R 0.65 0.29 0.00
29_R 68_I 0.65 0.29 0.00
50_Y 41_T 0.65 0.29 0.00
71_L 402_L 0.63 0.27 0.00
28_L 381_A 0.63 0.27 0.00
82_T 175_S 0.62 0.26 0.00
35_I 183_V 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
13353 6.25 Lydia Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13352 3.95 ACP_FAAL Δgene:(1, 100) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13350 2.84 ACP_FAAL Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.01 Done - Shared
13346 0 ACP_FAAL Δgene:(1, 20) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed - Shared
13345 0.25 ACP_FAAL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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