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OPENSEQ.org
Juyong
Genes: A B A+B
Length: 349 335 629
Sequences: 3739 13383 628
Seq/Len: 10.71 39.95 1
MirrorTree (Pazo et al. 2001) 0.08
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 0.02 0.04 0.07
2 0.03 0.06 0.15
5 0.04 0.09 0.31
10 0.05 0.13 0.55
20 0.07 0.18 0.92
100 0.14 0.30 2.32
∞ 0.24 0.35 2.90
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
299_V 85_L 1.07 0.40 0.00
225_G 42_V 0.95 0.30 0.00
249_D 128_L 0.94 0.29 0.00
212_V 146_Y 0.88 0.25 0.00
59_E 85_L 0.83 0.21 0.00
305_S 199_G 0.83 0.21 0.00
294_C 111_L 0.81 0.20 0.00
207_I 319_M 0.80 0.20 0.00
312_T 215_M 0.78 0.18 0.00
226_K 323_Y 0.77 0.18 0.00
167_G 225_M 0.76 0.17 0.00
192_V 94_I 0.76 0.17 0.00
61_V 138_Y 0.75 0.17 0.00
275_V 151_G 0.75 0.17 0.00
133_S 39_Y 0.75 0.17 0.00
241_T 104_P 0.75 0.17 0.00
210_I 150_M 0.75 0.17 0.00
107_I 283_R 0.74 0.16 0.00
285_I 253_D 0.73 0.16 0.00
119_I 315_A 0.72 0.16 0.00
150_K 199_G 0.72 0.15 0.00
302_C 67_V 0.72 0.15 0.00
117_N 144_L 0.71 0.15 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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