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OPENSEQ.org
oprmA
Genes: A B A+B
Length: 485 383 796
Sequences: 13022 14469 5996
Seq/Len: 26.85 37.78 7.53
MirrorTree (Pazo et al. 2001) 0.66
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 0.00 0.02 3.09
2 0.00 0.02 5.99
5 0.02 0.04 6.59
10 0.04 0.05 6.77
20 0.06 0.07 6.91
100 0.14 0.14 7.65
∞ 0.21 0.21 8.72
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
419_K 126_D 2.27 1.00 0.99
423_T 122_L 1.80 1.00 0.98
220_A 127_Q 1.61 1.00 0.95
211_R 126_D 1.58 1.00 0.95
213_Y 127_Q 1.42 0.99 0.90
215_V 122_L 1.19 0.96 0.78
415_Q 126_D 1.14 0.95 0.74
419_K 128_A 1.14 0.94 0.73
425_V 120_Y 1.08 0.93 0.68
219_S 130_S 1.05 0.91 0.65
217_V 120_Y 1.05 0.91 0.65
211_R 128_A 0.84 0.73 0.40
416_L 128_A 0.82 0.70 0.37
207_D 126_D 0.76 0.61 0.29
422_R 127_Q 0.73 0.56 0.26
217_V 132_Q 0.65 0.45 0.18
208_L 128_A 0.63 0.41 0.16
216_G 131_K 0.62 0.39 0.15
420_R 133_Q 0.60 0.37 0.14
204_K 127_Q 0.56 0.30 0.11
217_V 123_L 0.55 0.29 0.10
323_A 250_V 0.53 0.27 0.10
128_I 66_V 0.53 0.27 0.09
214_D 126_D 0.53 0.26 0.09
217_V 133_Q 0.52 0.26 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)
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