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smutan

Genes: A B A+B
Length: 255 113 349
Sequences: 82026 85559 33348
Seq/Len: 321.67 757.16 95.55
MirrorTree (Pazo et al. 2001) 1.06
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 0.10 73.25
2 0.07 0.13 78.05
5 0.10 0.16 81.96
10 0.14 0.19 85.98
20 0.18 0.23 90.62
100 0.28 0.31 101.43
0.31 0.34 104.17
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 1.89 1.00 0.98
58_E 12_P 1.68 1.00 0.96
29_T 13_I 1.61 1.00 0.94
50_S 15_D 1.58 1.00 0.94
54_V 15_D 1.49 1.00 0.92
51_F 19_F 1.45 1.00 0.90
57_D 12_P 1.43 1.00 0.90
54_V 12_P 1.25 0.99 0.81
36_E 104_S 1.14 0.97 0.71
36_E 105_N 1.12 0.96 0.70
41_G 23_K 1.10 0.96 0.68
30_S 12_P 1.01 0.93 0.59
37_A 20_N 1.01 0.93 0.58
40_D 23_K 1.00 0.92 0.57
34_Y 16_I 0.94 0.89 0.49
40_D 106_R 0.91 0.87 0.46
47_V 22_A 0.85 0.81 0.38
60_N 104_S 0.82 0.78 0.34
47_V 19_F 0.82 0.78 0.34
30_S 10_E 0.81 0.77 0.34
61_R 10_E 0.78 0.73 0.30
30_S 13_I 0.72 0.63 0.23
37_A 19_F 0.69 0.59 0.21
36_E 106_R 0.66 0.54 0.18
34_Y 15_D 0.65 0.52 0.17
32_K 104_S 0.57 0.38 0.11
40_D 105_N 0.56 0.38 0.11
25_R 80_A 0.55 0.35 0.10
40_D 24_E 0.55 0.35 0.10
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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