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OPENSEQ.org
3dge_A_C
Genes: A B A+B
Length: 258 122 357
Sequences: 83232 89235 33769
Seq/Len: 322.6 731.43 94.59
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 0.11 72.42
2 0.07 0.13 77.03
5 0.11 0.16 80.71
10 0.14 0.19 84.58
20 0.18 0.23 88.87
100 0.28 0.31 98.84
∞ 0.32 0.34 101.31
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
40_A 17_I 1.97 1.00 0.99
67_Q 13_V 1.69 1.00 0.96
36_T 14_L 1.60 1.00 0.95
63_V 16_K 1.47 1.00 0.92
60_F 20_F 1.46 1.00 0.91
59_E 16_K 1.45 1.00 0.91
66_D 13_V 1.41 0.99 0.89
63_V 13_V 1.30 0.99 0.84
48_S 24_K 1.14 0.97 0.73
43_E 109_P 1.10 0.96 0.69
37_A 13_V 1.06 0.95 0.64
43_E 108_S 1.05 0.94 0.64
44_T 21_N 1.03 0.94 0.62
47_N 24_K 1.00 0.93 0.58
41_Y 17_I 0.95 0.90 0.52
47_N 110_S 0.91 0.86 0.46
69_N 108_S 0.83 0.80 0.37
37_A 11_S 0.83 0.79 0.37
56_T 20_F 0.81 0.77 0.35
56_T 23_K 0.78 0.73 0.31
70_H 11_S 0.76 0.70 0.28
37_A 14_L 0.71 0.62 0.23
44_T 20_F 0.69 0.59 0.21
41_Y 16_K 0.66 0.54 0.18
43_E 110_S 0.64 0.51 0.17
39_K 108_S 0.60 0.44 0.14
47_N 109_P 0.60 0.44 0.14
47_N 25_E 0.54 0.34 0.10
37_A 17_I 0.54 0.34 0.09
47_N 21_N 0.53 0.32 0.09
32_R 84_A 0.53 0.32 0.09
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
7896 0 tmful Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
7684 94.59 3dge_A_C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.99 Done - Shared
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