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OPENSEQ.org
FAAL__ACP
Genes: A B A+B
Length: 584 90 640
Sequences: 24683 23126 1815
Seq/Len: 42.27 256.96 2.84
MirrorTree (Pazo et al. 2001) 0.47
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 0.09 0.17 1.19
2 0.10 0.19 1.77
5 0.13 0.20 2.29
10 0.14 0.22 2.50
20 0.15 0.23 2.69
100 0.20 0.25 3.73
∞ 0.27 0.30 5.79
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
41_T 50_Y 1.00 0.63 0.01
169_L 58_I 0.82 0.41 0.00
183_V 35_I 0.78 0.37 0.00
169_L 46_L 0.77 0.35 0.00
68_I 29_R 0.76 0.34 0.00
73_G 77_L 0.75 0.34 0.00
175_S 16_V 0.75 0.33 0.00
554_M 80_V 0.74 0.32 0.00
315_L 16_V 0.74 0.32 0.00
558_E 82_T 0.73 0.31 0.00
114_A 38_D 0.73 0.31 0.00
449_F 57_D 0.72 0.30 0.00
145_V 38_D 0.72 0.30 0.00
295_S 36_D 0.69 0.28 0.00
27_A 41_L 0.69 0.27 0.00
416_E 26_D 0.68 0.26 0.00
534_N 35_I 0.67 0.25 0.00
430_G 76_S 0.66 0.25 0.00
253_L 69_T 0.66 0.24 0.00
82_A 34_E 0.66 0.24 0.00
461_H 55_C 0.65 0.24 0.00
260_V 41_L 0.65 0.23 0.00
114_A 80_V 0.65 0.23 0.00
287_A 24_V 0.65 0.23 0.00
446_G 81_A 0.64 0.23 0.00
543_V 84_L 0.64 0.22 0.00
67_V 32_A 0.64 0.22 0.00
172_S 39_A 0.64 0.22 0.00
154_P 84_L 0.63 0.22 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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