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OPENSEQ.org
1GPW
Genes: A B A+B
Length: 253 200 435
Sequences: 3715 2203 1680
Seq/Len: 14.68 11.02 3.86
MirrorTree (Pazo et al. 2001) 0.54
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.62 0.00 3.31
2 0.68 0.00 3.59
5 0.69 0.00 3.68
10 0.71 0.00 3.71
20 0.71 0.00 3.71
100 0.72 0.00 3.81
∞ 0.76 0.01 4.17
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
104_T 10_P 0.87 0.57 0.00
167_E 183_S 0.72 0.37 0.00
100_V 9_G 0.71 0.36 0.00
168_I 158_Y 0.71 0.36 0.00
221_A 166_A 0.71 0.35 0.00
7_I 163_F 0.70 0.34 0.00
225_S 189_L 0.69 0.34 0.00
121_G 183_S 0.67 0.30 0.00
67_E 46_L 0.67 0.30 0.00
27_R 118_L 0.66 0.29 0.00
217_G 110_V 0.66 0.29 0.00
188_R 188_K 0.65 0.29 0.00
153_L 56_E 0.65 0.29 0.00
65_L 46_L 0.65 0.29 0.00
62_M 121_M 0.64 0.28 0.00
220_A 57_G 0.64 0.27 0.00
209_H 135_G 0.64 0.27 0.00
46_E 174_G 0.64 0.27 0.00
142_T 87_M 0.62 0.26 0.00
104_T 16_L 0.62 0.26 0.00
102_I 57_G 0.62 0.26 0.00
68_K 188_K 0.61 0.24 0.00
70_A 190_L 0.60 0.23 0.00
223_A 190_L 0.59 0.22 0.00
113_I 70_V 0.58 0.22 0.00
168_I 133_P 0.57 0.21 0.00
210_F 34_L 0.57 0.21 0.00
27_R 117_R 0.57 0.21 0.00
66_V 161_E 0.57 0.21 0.00
68_K 143_Y 0.57 0.21 0.00
184_T 121_M 0.57 0.20 0.00
21_S 183_S 0.56 0.20 0.00
225_S 137_Y 0.56 0.20 0.00
116_I 54_F 0.56 0.20 0.00
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 (0.71 > 0.4) of paralogs.
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