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OPENSEQ.org
mexx-tolc
Genes: A B A+B
Length: 396 493 771
Sequences: 13622 12959 5249
Seq/Len: 34.4 26.29 6.81
MirrorTree (Pazo et al. 2001) 0.67
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 2.47
2 0.03 0.00 4.98
5 0.04 0.02 5.56
10 0.06 0.04 5.73
20 0.07 0.06 5.90
100 0.13 0.14 6.68
∞ 0.21 0.20 7.80
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
135_D 382_A 2.17 1.00 0.99
131_D 386_V 1.76 1.00 0.97
136_R 173_I 1.49 0.99 0.92
135_D 164_Q 1.46 0.99 0.92
139_S 172_A 1.20 0.95 0.78
136_R 166_F 1.18 0.95 0.77
131_D 168_V 1.16 0.94 0.75
137_A 382_A 1.13 0.93 0.73
129_Y 388_T 1.08 0.91 0.67
129_Y 170_L 1.02 0.88 0.61
135_D 378_D 1.02 0.87 0.61
137_A 379_A 0.86 0.72 0.41
137_A 164_Q 0.78 0.60 0.31
140_E 169_G 0.68 0.46 0.21
136_R 385_S 0.67 0.44 0.20
141_R 170_L 0.66 0.43 0.19
137_A 161_Q 0.65 0.42 0.18
135_D 160_D 0.63 0.38 0.16
136_R 157_R 0.61 0.36 0.15
89_A 94_T 0.61 0.35 0.14
132_L 388_T 0.56 0.29 0.11
132_L 170_L 0.54 0.27 0.10
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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