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OPENSEQ.org
twin2
Genes: A B A+B
Length: 22 258 261
Sequences: 1503 1568 898
Seq/Len: 68.32 6.08 3.44
MirrorTree (Pazo et al. 2001) 0.53
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 0.42 0.01 3.01
2 0.42 0.01 3.15
5 0.42 0.01 3.18
10 0.42 0.01 3.20
20 0.42 0.01 3.21
100 0.45 0.01 3.26
∞ 0.51 0.02 3.87
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
18_V 21_L 1.75 0.99 0.94
12_V 202_V 1.56 0.97 0.89
18_V 24_I 1.23 0.88 0.68
20_L 104_R 0.99 0.67 0.42
16_G 198_V 0.94 0.62 0.37
15_I 163_M 0.94 0.61 0.37
11_L 206_L 0.92 0.59 0.34
17_L 130_F 0.90 0.57 0.33
4_I 101_K 0.90 0.57 0.33
15_I 201_F 0.89 0.55 0.31
20_L 238_G 0.89 0.55 0.31
5_G 194_P 0.88 0.55 0.31
16_G 184_T 0.86 0.51 0.28
1_M 134_F 0.84 0.49 0.27
11_L 8_P 0.84 0.49 0.27
14_I 47_A 0.84 0.49 0.26
18_V 86_V 0.81 0.46 0.24
12_V 98_A 0.78 0.41 0.21
20_L 222_M 0.78 0.41 0.20
18_V 20_L 0.77 0.41 0.20
18_V 146_Q 0.77 0.41 0.20
15_I 219_A 0.77 0.40 0.20
17_L 116_L 0.76 0.39 0.19
15_I 198_V 0.76 0.38 0.19
17_L 87_I 0.72 0.35 0.16
11_L 191_K 0.72 0.34 0.16
16_G 45_V 0.72 0.34 0.16
20_L 167_V 0.71 0.33 0.15
15_I 129_V 0.70 0.32 0.14
14_I 28_I 0.69 0.31 0.14
15_I 20_L 0.69 0.31 0.14
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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.42 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
0279 3.44 twin2 Δgene:(1, 20) A:(1E-04, 4) B:(1E-20, 8) msa: HHblits (2013_03) 0.94 Done
0277 0 twin2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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