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OPENSEQ.org
folA-thyA
Genes: A B A+B
Length: 159 264 422
Sequences: 3954 2455 1772
Seq/Len: 24.87 9.3 4.2
MirrorTree (Pazo et al. 2001) 0.40
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 0.01 0.06 3.47
2 0.01 0.06 3.78
5 0.01 0.06 4.00
10 0.01 0.06 4.13
20 0.01 0.06 4.19
100 0.01 0.06 4.36
∞ 0.02 0.07 4.85
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
110_L 227_L 0.55 0.20 0.00
67_G 223_E 0.55 0.20 0.00
133_W 135_V 0.52 0.17 0.00
105_P 188_M 0.51 0.17 0.00
134_E 229_K 0.49 0.15 0.00
56_G 9_Q 0.49 0.15 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)
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