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OPENSEQ.org
N4NMtoNO1
Genes: A B A+B
Length: 505 314 743
Sequences: 362 5641 64
Seq/Len: 0.72 17.96 0.09
MirrorTree (Pazo et al. 2001) 0.10
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 0.06 0.07 0.00
2 0.07 0.08 0.00
5 0.08 0.08 0.00
10 0.08 0.09 0.01
20 0.08 0.10 0.02
100 0.08 0.11 0.04
∞ 0.08 0.15 0.08
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
253_I 156_K 1.21 0.12 0.00
417_N 82_Y 1.19 0.11 0.00
402_S 240_P 1.16 0.11 0.00
348_W 249_G 1.12 0.10 0.00
36_P 237_W 1.10 0.10 0.00
53_C 237_W 1.10 0.10 0.00
317_E 252_I 1.09 0.10 0.00
338_A 153_V 1.06 0.09 0.00
106_W 282_L 1.03 0.09 0.00
438_Y 231_K 1.02 0.09 0.00
332_C 18_W 0.99 0.08 0.00
334_C 18_W 0.99 0.08 0.00
319_A 55_T 0.98 0.08 0.00
80_C 237_W 0.98 0.08 0.00
459_T 239_P 0.96 0.08 0.00
108_S 237_W 0.95 0.07 0.00
315_P 292_I 0.94 0.07 0.00
54_G 237_W 0.94 0.07 0.00
92_S 209_T 0.93 0.07 0.00
61_Y 175_Y 0.93 0.07 0.00
407_A 250_Y 0.92 0.07 0.00
331_T 120_V 0.92 0.07 0.00
298_N 292_I 0.92 0.07 0.00
379_Y 247_I 0.92 0.07 0.00
378_F 166_K 0.91 0.07 0.00
327_N 190_V 0.91 0.07 0.00
90_L 190_V 0.91 0.07 0.00
272_I 292_I 0.90 0.07 0.00
298_N 288_Y 0.90 0.07 0.00
180_I 215_T 0.89 0.07 0.00
340_T 223_V 0.89 0.07 0.00
403_A 190_V 0.89 0.07 0.00
394_P 240_P 0.89 0.07 0.00
456_D 217_P 0.88 0.07 0.00
213_A 133_T 0.88 0.07 0.00
149_D 301_G 0.88 0.07 0.00
459_T 234_I 0.88 0.07 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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