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OPENSEQ.org
uaf30 hhf1 (A, 110-200)
Genes: A B A+B
Length: 91 103 191
Sequences: 1141 758 149
Seq/Len: 12.54 7.36 0.78
MirrorTree (Pazo et al. 2001) 0.11
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 0.05 0.01
2 0.03 0.05 0.01
5 0.03 0.06 0.01
10 0.03 0.06 0.03
20 0.04 0.07 0.05
100 0.04 0.12 0.20
∞ 0.07 0.16 0.77
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 78_K 1.12 0.38 0.00
26_G 49_G 1.05 0.33 0.00
26_G 50_L 0.96 0.26 0.00
18_S 24_R 0.93 0.24 0.00
17_L 84_S 0.87 0.21 0.00
20_S 30_I 0.87 0.20 0.00
54_K 81_T 0.86 0.20 0.00
50_N 47_I 0.84 0.19 0.00
67_L 70_S 0.82 0.18 0.00
61_E 98_L 0.76 0.15 0.00
45_A 87_V 0.75 0.15 0.00
14_K 55_V 0.75 0.15 0.00
28_H 70_S 0.74 0.14 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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