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OPENSEQ.org
mexx-opmh
Genes: A B A+B
Length: 396 482 772
Sequences: 13622 13105 5327
Seq/Len: 34.4 27.19 6.9
MirrorTree (Pazo et al. 2001) 0.68
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 2.54
2 0.03 0.00 5.15
5 0.04 0.02 5.73
10 0.06 0.04 5.90
20 0.07 0.06 6.07
100 0.13 0.14 6.86
∞ 0.21 0.21 7.96
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 392_I 2.23 1.00 0.99
131_D 396_V 1.80 1.00 0.97
136_R 182_K 1.57 0.99 0.94
135_D 173_E 1.46 0.99 0.92
136_R 175_F 1.22 0.96 0.80
139_S 181_D 1.16 0.94 0.75
131_D 177_V 1.15 0.94 0.74
137_A 392_I 1.14 0.94 0.73
129_Y 398_T 1.10 0.92 0.70
135_D 388_E 1.08 0.91 0.68
129_Y 179_L 1.05 0.89 0.64
137_A 389_A 0.90 0.77 0.46
137_A 173_E 0.75 0.57 0.28
140_E 178_G 0.70 0.49 0.23
136_R 395_Q 0.67 0.45 0.20
141_R 179_L 0.66 0.43 0.19
135_D 169_D 0.65 0.41 0.18
136_R 166_R 0.60 0.34 0.14
137_A 170_Q 0.59 0.33 0.13
132_L 398_T 0.54 0.26 0.10
89_A 103_S 0.53 0.26 0.09
132_L 179_L 0.52 0.24 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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