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OPENSEQ.org
UHK3
Genes: A B A+B
Length: 66 111 176
Sequences: 5598 50266 5258
Seq/Len: 84.82 452.85 29.88
MirrorTree (Pazo et al. 2001) 0.13
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 0.04 0.11 31.33
2 0.05 0.13 31.53
5 0.07 0.15 31.72
10 0.08 0.17 32.05
20 0.10 0.19 32.42
100 0.13 0.24 33.73
∞ 0.19 0.28 34.62
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
37_D 12_L 1.82 1.00 0.97
22_F 13_L 1.33 0.99 0.84
28_K 20_D 1.32 0.99 0.84
47_D 107_S 1.30 0.99 0.82
34_R 16_T 1.25 0.98 0.79
28_K 108_E 1.22 0.98 0.78
38_Y 16_T 0.93 0.89 0.48
24_H 108_E 0.91 0.87 0.45
25_L 16_T 0.81 0.77 0.33
18_G 9_A 0.79 0.74 0.30
41_T 12_L 0.73 0.66 0.24
24_H 107_S 0.69 0.59 0.20
17_N 10_N 0.61 0.46 0.14
45_S 9_A 0.61 0.45 0.13
59_F 86_M 0.54 0.34 0.09
44_K 9_A 0.53 0.33 0.09
24_H 17_L 0.52 0.32 0.08
41_T 9_A 0.52 0.31 0.08
7_N 51_Q 0.50 0.29 0.07
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
3639 46.02 UHK4 Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.99 Done - Shared
3625 29.88 UHK3 Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
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