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OPENSEQ.org
uaf30 hht1 (A, 1-65)
Genes: A B A+B
Length: 65 136 198
Sequences: 960 712 104
Seq/Len: 14.77 5.24 0.53
MirrorTree (Pazo et al. 2001) 0.00
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 0.06 0.01
5 0.06 0.07 0.01
10 0.06 0.08 0.01
20 0.06 0.08 0.02
100 0.06 0.09 0.13
∞ 0.08 0.12 0.52
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
39_D 33_T 1.23 0.37 0.00
44_G 96_S 1.07 0.26 0.00
12_D 54_R 1.01 0.23 0.00
54_H 54_R 0.99 0.22 0.00
54_H 90_I 0.93 0.19 0.00
26_K 42_Y 0.90 0.17 0.00
26_K 88_S 0.88 0.17 0.00
29_R 131_L 0.85 0.15 0.00
47_I 42_Y 0.81 0.14 0.00
10_M 55_F 0.81 0.14 0.00
39_D 74_E 0.80 0.13 0.00
18_M 42_Y 0.77 0.12 0.00
11_I 42_Y 0.77 0.12 0.00
49_K 33_T 0.75 0.12 0.00
26_K 90_I 0.75 0.12 0.00
16_S 60_E 0.74 0.12 0.00
17_D 42_Y 0.74 0.11 0.00
26_K 54_R 0.74 0.11 0.00
25_T 111_A 0.72 0.11 0.00
40_V 134_E 0.72 0.11 0.00
39_D 32_S 0.72 0.11 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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