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OPENSEQ.org
N-B2
Genes: A B A+B
Length: 462 807 1250
Sequences: 2572 1607 434
Seq/Len: 5.57 1.99 0.35
MirrorTree (Pazo et al. 2001) 0.24
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.06 0.00 0.00
2 0.07 0.00 0.00
5 0.08 0.01 0.00
10 0.09 0.01 0.01
20 0.10 0.01 0.01
100 0.14 0.01 0.07
∞ 0.19 0.04 0.34
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
356_G 260_L 1.66 0.57 0.00
74_I 599_L 1.21 0.27 0.00
422_L 229_Y 1.16 0.25 0.00
424_W 55_S 1.12 0.23 0.00
124_L 260_L 1.12 0.23 0.00
439_S 260_L 1.08 0.21 0.00
394_S 108_E 1.05 0.19 0.00
91_A 329_D 1.03 0.19 0.00
407_G 432_Y 1.03 0.18 0.00
53_D 260_L 1.00 0.17 0.00
434_F 458_F 0.99 0.17 0.00
418_I 599_L 0.98 0.16 0.00
12_N 436_S 0.97 0.16 0.00
312_L 260_L 0.96 0.16 0.00
329_W 294_S 0.96 0.16 0.00
59_N 329_D 0.96 0.16 0.00
422_L 329_D 0.96 0.16 0.00
367_Q 165_L 0.92 0.14 0.00
393_S 622_Y 0.92 0.14 0.00
286_L 647_G 0.91 0.14 0.00
88_L 273_V 0.90 0.13 0.00
318_F 767_A 0.90 0.13 0.00
65_S 625_L 0.89 0.13 0.00
418_I 559_V 0.88 0.13 0.00
76_G 759_D 0.88 0.13 0.00
90_V 761_G 0.88 0.13 0.00
335_D 394_F 0.87 0.12 0.00
328_A 647_G 0.86 0.12 0.00
109_P 769_V 0.86 0.12 0.00
384_L 394_F 0.85 0.12 0.00
107_N 292_K 0.85 0.12 0.00
250_A 256_I 0.84 0.12 0.00
118_L 270_S 0.84 0.12 0.00
178_N 256_I 0.84 0.12 0.00
106_L 771_L 0.84 0.12 0.00
459_L 489_I 0.83 0.12 0.00
310_T 155_V 0.83 0.11 0.00
112_V 351_R 0.82 0.11 0.00
457_G 335_V 0.82 0.11 0.00
439_S 708_L 0.82 0.11 0.00
322_G 260_L 0.81 0.11 0.00
310_T 650_V 0.81 0.11 0.00
95_Q 444_V 0.81 0.11 0.00
60_A 788_V 0.81 0.11 0.00
418_I 159_P 0.80 0.11 0.00
139_L 329_D 0.80 0.11 0.00
133_V 341_V 0.80 0.11 0.00
326_G 110_L 0.80 0.10 0.00
311_A 609_D 0.80 0.10 0.00
419_E 307_A 0.80 0.10 0.00
336_A 130_L 0.80 0.10 0.00
61_L 352_I 0.80 0.10 0.00
73_R 426_F 0.79 0.10 0.00
163_V 612_Y 0.79 0.10 0.00
166_D 471_L 0.79 0.10 0.00
337_T 180_I 0.78 0.10 0.00
357_R 586_N 0.78 0.10 0.00
296_D 337_L 0.78 0.10 0.00
333_Q 733_V 0.78 0.10 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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