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OPENSEQ.org
mexa-opmh
Genes: A B A+B
Length: 383 482 755
Sequences: 14469 13105 6051
Seq/Len: 37.78 27.19 8.01
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 0.02 0.00 3.18
2 0.02 0.00 6.06
5 0.04 0.02 6.66
10 0.05 0.04 6.83
20 0.07 0.06 7.00
100 0.14 0.14 7.72
∞ 0.21 0.21 8.77
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
126_D 392_I 2.25 1.00 0.99
122_L 396_V 1.74 1.00 0.97
127_Q 182_K 1.60 1.00 0.95
126_D 173_E 1.53 1.00 0.94
127_Q 175_F 1.38 0.99 0.89
122_L 177_V 1.16 0.96 0.75
126_D 388_E 1.12 0.95 0.72
128_A 392_I 1.08 0.93 0.68
120_Y 398_T 1.05 0.92 0.65
130_S 181_D 1.02 0.90 0.62
120_Y 179_L 1.00 0.89 0.59
128_A 173_E 0.81 0.71 0.36
128_A 389_A 0.81 0.71 0.36
126_D 169_D 0.75 0.62 0.29
127_Q 395_Q 0.70 0.54 0.23
131_K 178_G 0.64 0.44 0.17
132_Q 179_L 0.62 0.41 0.15
128_A 170_Q 0.60 0.38 0.14
133_Q 393_G 0.59 0.36 0.13
127_Q 166_R 0.56 0.33 0.12
66_V 92_K 0.53 0.28 0.10
126_D 176_D 0.52 0.26 0.09
250_V 286_Y 0.51 0.26 0.09
123_L 179_L 0.51 0.26 0.08
133_Q 179_L 0.51 0.26 0.08
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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