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OPENSEQ.org
uaf30 hhf1 (A, 1-65)
Genes: A B A+B
Length: 65 103 166
Sequences: 960 758 137
Seq/Len: 14.77 7.36 0.83
MirrorTree (Pazo et al. 2001) -0.01
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 0.05 0.05 0.01
2 0.06 0.05 0.01
5 0.06 0.06 0.02
10 0.06 0.06 0.02
20 0.06 0.07 0.08
100 0.06 0.12 0.22
∞ 0.08 0.16 0.82
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
15_L 70_S 1.75 0.86 0.14
40_V 61_S 1.12 0.40 0.02
24_T 87_V 1.12 0.40 0.02
29_R 78_K 0.97 0.28 0.01
48_N 84_S 0.92 0.24 0.01
14_L 2_S 0.88 0.22 0.01
40_V 86_D 0.88 0.22 0.01
23_V 78_K 0.85 0.20 0.01
40_V 47_I 0.81 0.18 0.01
44_G 84_S 0.81 0.18 0.01
42_S 21_K 0.80 0.18 0.01
51_I 67_I 0.79 0.17 0.01
44_G 65_S 0.78 0.17 0.01
44_G 74_T 0.78 0.16 0.01
48_N 55_V 0.78 0.16 0.01
46_A 70_S 0.78 0.16 0.01
26_K 61_S 0.77 0.16 0.01
27_K 32_K 0.77 0.16 0.01
17_D 82_V 0.76 0.16 0.01
11_I 84_S 0.75 0.15 0.01
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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