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OPENSEQ.org
UHK4
Genes: A B A+B
Length: 66 111 177
Sequences: 13470 84665 8146
Seq/Len: 204.09 762.75 46.02
MirrorTree (Pazo et al. 2001) 0.63
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 0.02 0.10 62.82
2 0.03 0.13 64.19
5 0.05 0.15 65.66
10 0.06 0.18 67.94
20 0.07 0.22 70.60
100 0.14 0.30 78.15
∞ 0.21 0.34 80.59
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 2.10 1.00 0.99
28_K 20_D 1.96 1.00 0.99
22_F 13_L 1.71 1.00 0.97
34_R 16_T 1.71 1.00 0.97
24_H 108_E 1.66 1.00 0.96
28_K 108_E 1.32 0.99 0.86
47_D 107_S 1.32 0.99 0.86
18_G 9_A 1.14 0.97 0.73
24_H 107_S 1.05 0.95 0.65
41_T 12_L 1.05 0.94 0.64
38_Y 16_T 0.95 0.90 0.54
41_T 9_A 0.94 0.89 0.51
21_G 13_L 0.81 0.76 0.35
25_L 16_T 0.76 0.70 0.29
17_N 10_N 0.76 0.69 0.29
44_K 9_A 0.67 0.56 0.20
45_S 9_A 0.66 0.53 0.19
34_R 20_D 0.64 0.51 0.17
37_D 16_T 0.64 0.51 0.17
24_H 17_L 0.62 0.47 0.15
34_R 19_E 0.58 0.40 0.12
59_F 86_M 0.57 0.40 0.12
7_N 51_Q 0.57 0.39 0.12
24_H 109_R 0.55 0.35 0.10
8_M 85_A 0.52 0.31 0.09
22_F 12_L 0.52 0.30 0.09
18_G 7_N 0.46 0.23 0.06
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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