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OPENSEQ.org
mexc-tolc
Genes: A B A+B
Length: 387 493 766
Sequences: 14488 12959 5840
Seq/Len: 37.44 26.29 7.62
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 2.91
2 0.03 0.00 5.69
5 0.04 0.02 6.30
10 0.06 0.04 6.46
20 0.07 0.06 6.64
100 0.14 0.14 7.41
∞ 0.21 0.20 8.47
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 382_A 2.23 1.00 0.99
129_P 386_V 1.68 1.00 0.96
133_I 164_Q 1.57 1.00 0.94
134_Q 173_I 1.55 1.00 0.94
134_Q 166_F 1.36 0.99 0.88
135_A 382_A 1.16 0.95 0.76
129_P 168_V 1.14 0.95 0.73
133_I 378_D 1.11 0.94 0.71
137_S 172_A 1.09 0.93 0.69
127_Y 388_T 1.02 0.90 0.62
127_Y 170_L 0.91 0.81 0.49
135_A 379_A 0.83 0.71 0.38
135_A 164_Q 0.82 0.71 0.37
133_I 160_D 0.81 0.69 0.35
134_Q 385_S 0.73 0.58 0.27
134_Q 157_R 0.62 0.40 0.16
138_Q 169_G 0.58 0.34 0.12
135_A 161_Q 0.57 0.33 0.12
130_L 170_L 0.57 0.33 0.12
139_Q 170_L 0.56 0.31 0.11
140_D 383_G 0.55 0.29 0.10
140_D 170_L 0.53 0.28 0.10
320_M 277_G 0.52 0.26 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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