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OPENSEQ.org
beta flap (A, 1-700)
Genes: A B A+B
Length: 700 50 679
Sequences: 4885 622 54
Seq/Len: 6.98 12.44 0.08
MirrorTree (Pazo et al. 2001) 0.74
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 0.08 0.07 0.00
2 0.08 0.07 0.01
5 0.09 0.07 0.02
10 0.09 0.07 0.05
20 0.09 0.07 0.07
100 0.11 0.07 0.24
∞ 0.19 0.07 1.68
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 1.24 0.12 0.00
634_P 39_D 1.16 0.10 0.00
602_R 39_D 1.15 0.10 0.00
245_N 39_D 1.14 0.10 0.00
136_P 39_D 1.03 0.08 0.00
609_I 6_A 1.02 0.08 0.00
383_G 40_V 1.02 0.08 0.00
533_A 39_D 1.00 0.08 0.00
532_V 39_D 1.00 0.08 0.00
424_A 39_D 0.98 0.07 0.00
152_K 39_D 0.96 0.07 0.00
614_Q 40_V 0.96 0.07 0.00
287_R 39_D 0.96 0.07 0.00
449_D 39_D 0.94 0.07 0.00
434_A 39_D 0.92 0.07 0.00
535_L 39_D 0.92 0.07 0.00
477_Y 39_D 0.90 0.07 0.00
462_D 40_V 0.90 0.06 0.00
328_N 19_A 0.89 0.06 0.00
248_V 36_I 0.88 0.06 0.00
451_I 39_D 0.88 0.06 0.00
576_V 35_G 0.87 0.06 0.00
594_E 39_D 0.87 0.06 0.00
322_S 39_D 0.86 0.06 0.00
270_F 39_D 0.86 0.06 0.00
44_R 39_D 0.84 0.06 0.00
279_V 37_I 0.84 0.06 0.00
454_S 39_D 0.83 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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