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OPENSEQ.org
MexA Oprm interactions
Genes: A B A+B
Length: 369 474 773
Sequences: 15472 13181 6396
Seq/Len: 41.93 27.81 8.27
MirrorTree (Pazo et al. 2001) 0.65
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 0.02 0.00 3.45
2 0.03 0.00 6.73
5 0.04 0.02 7.42
10 0.05 0.04 7.59
20 0.07 0.06 7.76
100 0.14 0.14 8.50
∞ 0.21 0.21 9.52
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
106_D 402_K 2.21 1.00 0.99
102_L 406_T 1.81 1.00 0.98
107_Q 203_A 1.70 1.00 0.96
106_D 194_R 1.56 1.00 0.94
107_Q 196_Y 1.51 1.00 0.93
108_A 402_K 1.31 0.98 0.86
106_D 398_Q 1.19 0.97 0.78
100_Y 408_V 1.14 0.95 0.73
110_S 202_S 1.09 0.94 0.69
102_L 198_V 1.07 0.93 0.67
100_Y 200_V 1.07 0.93 0.67
108_A 194_R 0.99 0.89 0.58
108_A 399_L 0.89 0.81 0.45
107_Q 187_K 0.88 0.80 0.44
107_Q 405_R 0.82 0.73 0.37
106_D 190_D 0.79 0.68 0.33
113_Q 403_R 0.69 0.52 0.21
108_A 191_L 0.64 0.46 0.18
111_K 199_G 0.63 0.43 0.16
112_Q 200_V 0.62 0.42 0.16
103_L 200_V 0.57 0.35 0.12
230_V 306_A 0.55 0.31 0.10
142_S 386_Q 0.53 0.29 0.10
109_V 408_V 0.53 0.29 0.10
113_Q 200_V 0.53 0.28 0.09
103_L 408_V 0.52 0.27 0.09
106_D 197_D 0.52 0.27 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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