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OPENSEQ.org
beta flap (A, 1-660)
Genes: A B A+B
Length: 660 50 679
Sequences: 5808 622 58
Seq/Len: 8.8 12.44 0.09
MirrorTree (Pazo et al. 2001) 0.75
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 0.07 0.07 0.00
2 0.07 0.07 0.01
5 0.07 0.07 0.02
10 0.08 0.07 0.06
20 0.08 0.07 0.08
100 0.16 0.07 0.33
∞ 0.24 0.07 1.78
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
249_V 40_V 1.55 0.21 0.00
614_Q 40_V 1.25 0.12 0.00
245_N 39_D 1.23 0.12 0.00
634_P 39_D 1.13 0.10 0.00
609_I 6_A 1.09 0.10 0.00
602_R 39_D 1.08 0.09 0.00
293_L 39_D 1.07 0.09 0.00
136_P 39_D 1.02 0.08 0.00
459_N 40_V 1.01 0.08 0.00
308_P 40_V 1.00 0.08 0.00
383_G 40_V 0.99 0.08 0.00
576_V 35_G 0.97 0.08 0.00
328_N 19_A 0.96 0.07 0.00
535_L 39_D 0.95 0.07 0.00
449_D 39_D 0.94 0.07 0.00
454_S 39_D 0.92 0.07 0.00
532_V 39_D 0.92 0.07 0.00
424_A 39_D 0.92 0.07 0.00
152_K 39_D 0.89 0.07 0.00
477_Y 39_D 0.89 0.07 0.00
451_I 39_D 0.89 0.07 0.00
309_K 43_F 0.89 0.07 0.00
573_F 6_A 0.87 0.07 0.00
511_N 39_D 0.87 0.06 0.00
219_Y 28_R 0.87 0.06 0.00
309_K 39_D 0.85 0.06 0.00
193_D 37_I 0.85 0.06 0.00
371_L 5_T 0.85 0.06 0.00
142_R 39_D 0.84 0.06 0.00
533_A 39_D 0.84 0.06 0.00
285_N 43_F 0.84 0.06 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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