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OPENSEQ.org
WalK
Genes: A B A+B
Length: 255 235 462
Sequences: 82179 33334 21241
Seq/Len: 322.27 141.85 45.98
MirrorTree (Pazo et al. 2001) 0.83
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 0.04 0.01 35.62
2 0.07 0.02 37.49
5 0.10 0.04 39.38
10 0.14 0.06 41.20
20 0.18 0.09 43.35
100 0.28 0.20 50.18
∞ 0.31 0.25 52.40
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
33_S 16_I 1.83 1.00 0.97
29_T 13_I 1.68 1.00 0.95
50_S 15_D 1.67 1.00 0.95
58_E 12_P 1.54 1.00 0.93
36_E 104_S 1.52 1.00 0.92
54_V 15_D 1.43 1.00 0.89
57_D 12_P 1.40 0.99 0.88
51_F 19_F 1.13 0.97 0.70
37_A 20_N 1.08 0.96 0.65
54_V 12_P 1.07 0.95 0.64
30_S 10_E 0.91 0.86 0.45
40_D 106_R 0.90 0.86 0.44
30_S 12_P 0.84 0.81 0.37
34_Y 16_I 0.82 0.78 0.34
30_S 13_I 0.82 0.78 0.34
36_E 105_N 0.82 0.78 0.34
74_R 82_D 0.81 0.77 0.33
60_N 104_S 0.76 0.69 0.27
61_R 10_E 0.75 0.68 0.26
47_V 22_A 0.71 0.63 0.22
40_D 23_K 0.68 0.57 0.19
25_R 100_T 0.65 0.53 0.17
41_G 23_K 0.65 0.52 0.17
40_D 105_N 0.64 0.50 0.15
36_E 106_R 0.60 0.43 0.13
30_S 16_I 0.59 0.42 0.12
47_V 19_F 0.59 0.42 0.12
37_A 19_F 0.57 0.39 0.11
67_T 82_D 0.55 0.35 0.10
29_T 103_F 0.52 0.30 0.08
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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