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OPENSEQ.org
2ONK_AC
Genes: A B A+B
Length: 240 252 480
Sequences: 83362 33929 13520
Seq/Len: 347.34 134.64 28.17
MirrorTree (Pazo et al. 2001) 0.76
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 0.10 0.56 15.01
2 0.11 0.56 18.03
5 0.15 0.57 20.51
10 0.20 0.57 23.53
20 0.25 0.57 27.48
100 0.35 0.59 36.16
∞ 0.38 0.60 37.85
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
42_E 160_H 1.97 1.00 0.98
93_Y 175_T 1.71 1.00 0.96
93_Y 162_A 1.19 0.98 0.77
78_D 157_R 1.09 0.96 0.67
68_E 163_R 1.04 0.94 0.62
93_Y 167_S 0.99 0.92 0.57
96_R 175_T 0.95 0.89 0.51
97_N 171_R 0.89 0.85 0.44
84_H 180_L 0.83 0.79 0.36
47_I 164_T 0.82 0.78 0.35
97_N 167_S 0.79 0.74 0.32
82_F 165_L 0.75 0.69 0.27
76_P 161_V 0.61 0.45 0.14
97_N 175_T 0.56 0.37 0.11
94_G 165_L 0.55 0.36 0.10
80_A 161_V 0.54 0.34 0.10
97_N 166_G 0.52 0.31 0.09
68_E 168_S 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.57 > 0.4) of paralogs.
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