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OPENSEQ.org
Oxa23-OmpW
Genes: A B A+B
Length: 273 193 456
Sequences: 11667 9504 2592
Seq/Len: 42.74 49.24 5.68
MirrorTree (Pazo et al. 2001) 0.07
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 0.03 0.04 0.02
2 0.03 0.05 0.06
5 0.04 0.06 0.14
10 0.05 0.06 0.38
20 0.06 0.07 0.76
100 0.15 0.18 2.82
∞ 0.23 0.25 5.56
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
213_I 7_V 0.78 0.55 0.00
214_F 66_S 0.72 0.47 0.00
244_F 80_L 0.65 0.37 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
0703 0.78 Oxa23-OmpW Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0701 5.68 Oxa23-OmpW Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0699 0.13 Oxa23-OmpW Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
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