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OPENSEQ.org
CmeA-CmeC
Genes: A B A+B
Length: 473 347 750
Sequences: 13235 16698 6993
Seq/Len: 27.98 48.12 9.32
MirrorTree (Pazo et al. 2001) 0.62
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 0.00 0.03 3.94
2 0.00 0.03 7.48
5 0.02 0.05 8.20
10 0.04 0.06 8.37
20 0.06 0.08 8.53
100 0.14 0.15 9.29
∞ 0.21 0.22 10.34
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
402_E 111_K 2.20 1.00 0.99
406_I 107_A 1.69 1.00 0.96
201_E 112_N 1.59 1.00 0.95
192_E 111_K 1.50 1.00 0.93
194_F 112_N 1.43 0.99 0.91
402_E 113_A 1.23 0.98 0.80
196_V 107_A 1.10 0.95 0.70
398_E 111_K 1.07 0.94 0.67
200_G 115_S 1.03 0.93 0.63
408_E 105_S 1.01 0.92 0.60
198_A 105_S 0.97 0.90 0.56
192_E 113_A 0.92 0.86 0.49
399_I 113_A 0.82 0.77 0.37
405_D 112_N 0.77 0.69 0.30
185_E 112_N 0.74 0.66 0.28
188_R 111_K 0.73 0.63 0.26
198_A 117_K 0.61 0.44 0.15
403_R 118_E 0.61 0.43 0.15
198_A 118_E 0.59 0.41 0.14
189_I 113_A 0.57 0.37 0.12
198_A 108_L 0.56 0.36 0.11
306_L 235_S 0.55 0.34 0.11
197_G 116_Q 0.52 0.29 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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