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OPENSEQ.org
mexc-opmh
Genes: A B A+B
Length: 387 482 767
Sequences: 14488 13105 5923
Seq/Len: 37.44 27.19 7.72
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 3.00
2 0.03 0.00 5.86
5 0.04 0.02 6.47
10 0.06 0.04 6.63
20 0.07 0.06 6.82
100 0.14 0.14 7.58
∞ 0.21 0.21 8.64
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
133_I 392_I 2.25 1.00 0.99
129_P 396_V 1.69 1.00 0.96
134_Q 182_K 1.60 1.00 0.95
133_I 173_E 1.56 1.00 0.94
134_Q 175_F 1.37 0.99 0.89
135_A 392_I 1.18 0.96 0.77
133_I 388_E 1.15 0.95 0.74
129_P 177_V 1.09 0.93 0.69
137_S 181_D 1.08 0.93 0.68
127_Y 398_T 1.05 0.92 0.65
127_Y 179_L 0.95 0.85 0.54
135_A 389_A 0.86 0.76 0.42
135_A 173_E 0.84 0.73 0.39
133_I 169_D 0.79 0.67 0.33
134_Q 395_Q 0.71 0.55 0.24
134_Q 166_R 0.64 0.42 0.17
138_Q 178_G 0.61 0.38 0.15
130_L 179_L 0.58 0.34 0.13
139_Q 179_L 0.58 0.34 0.12
140_D 179_L 0.55 0.30 0.11
135_A 170_Q 0.55 0.29 0.10
140_D 393_G 0.53 0.27 0.09
130_L 398_T 0.51 0.25 0.08
320_M 287_Q 0.51 0.25 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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