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OPENSEQ.org
204
Genes: A B A+B
Length: 72 337 396
Sequences: 1737 5559 116
Seq/Len: 24.12 16.5 0.29
MirrorTree (Pazo et al. 2001) 0.21
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 0.05 0.04 0.01
2 0.05 0.04 0.02
5 0.06 0.06 0.06
10 0.06 0.08 0.14
20 0.07 0.09 0.28
100 0.09 0.13 0.89
∞ 0.16 0.21 1.93
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
65_T 151_L 1.27 0.27 0.00
6_K 276_A 1.02 0.16 0.00
19_P 70_L 1.01 0.16 0.00
47_K 91_Q 0.96 0.14 0.00
19_P 278_L 0.94 0.13 0.00
46_G 197_P 0.92 0.13 0.00
19_P 50_L 0.91 0.12 0.00
54_T 81_A 0.89 0.12 0.00
28_A 336_P 0.87 0.11 0.00
56_S 307_D 0.86 0.11 0.00
55_L 307_D 0.84 0.11 0.00
51_D 329_A 0.82 0.10 0.00
60_I 231_M 0.79 0.09 0.00
19_P 46_I 0.79 0.09 0.00
6_K 99_I 0.78 0.09 0.00
42_L 123_F 0.77 0.09 0.00
26_V 15_Y 0.77 0.09 0.00
63_E 20_V 0.77 0.09 0.00
23_I 204_M 0.77 0.09 0.00
59_N 295_K 0.76 0.09 0.00
28_A 77_F 0.76 0.09 0.00
19_P 192_K 0.76 0.09 0.00
6_K 28_E 0.76 0.09 0.00
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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