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OPENSEQ.org
CPR
Genes: A B A+B
Length: 500 688 1076
Sequences: 18808 1812 535
Seq/Len: 37.62 2.63 0.5
MirrorTree (Pazo et al. 2001) 0.13
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 0.11 0.03 0.01
2 0.13 0.03 0.01
5 0.14 0.03 0.02
10 0.16 0.04 0.04
20 0.17 0.04 0.07
100 0.23 0.05 0.19
∞ 0.28 0.09 0.45
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
348_L 640_V 1.29 0.40 0.00
453_V 175_Y 1.24 0.37 0.00
390_I 193_I 1.22 0.35 0.00
373_S 543_V 1.14 0.30 0.00
321_R 658_I 1.12 0.29 0.00
75_V 330_V 1.06 0.25 0.00
60_K 103_L 1.01 0.22 0.00
69_L 589_D 1.00 0.21 0.00
243_E 188_F 0.96 0.20 0.00
398_G 330_V 0.96 0.20 0.00
364_P 297_K 0.92 0.18 0.00
182_C 175_Y 0.92 0.18 0.00
305_S 589_D 0.92 0.18 0.00
168_N 640_V 0.92 0.18 0.00
305_S 191_I 0.91 0.17 0.00
404_W 635_E 0.91 0.17 0.00
126_R 620_K 0.91 0.17 0.00
139_I 502_C 0.91 0.17 0.00
283_S 543_V 0.90 0.17 0.00
361_L 313_F 0.90 0.17 0.00
247_D 200_C 0.90 0.17 0.00
322_V 330_V 0.89 0.17 0.00
324_K 104_S 0.89 0.16 0.00
359_M 347_G 0.89 0.16 0.00
430_L 395_R 0.88 0.16 0.00
351_L 204_A 0.88 0.16 0.00
299_G 403_A 0.88 0.16 0.00
397_I 330_V 0.88 0.16 0.00
177_I 96_A 0.88 0.16 0.00
297_M 230_L 0.88 0.16 0.00
179_N 575_F 0.88 0.16 0.00
375_E 431_I 0.88 0.16 0.00
411_F 461_P 0.87 0.15 0.00
81_E 668_S 0.87 0.15 0.00
77_I 543_V 0.86 0.15 0.00
251_Q 543_V 0.86 0.15 0.00
388_S 674_V 0.86 0.15 0.00
434_G 687_V 0.86 0.15 0.00
306_T 636_G 0.85 0.15 0.00
313_I 391_L 0.85 0.15 0.00
386_K 87_I 0.85 0.15 0.00
60_K 502_C 0.84 0.15 0.00
86_V 320_I 0.84 0.15 0.00
417_M 175_Y 0.84 0.14 0.00
313_I 621_M 0.84 0.14 0.00
416_F 463_L 0.84 0.14 0.00
177_I 575_F 0.83 0.14 0.00
254_K 525_I 0.83 0.14 0.00
168_N 291_V 0.83 0.14 0.00
169_L 209_E 0.83 0.14 0.00
316_L 137_A 0.83 0.14 0.00
297_M 330_V 0.83 0.14 0.00
139_I 573_L 0.83 0.14 0.00
165_K 543_V 0.83 0.14 0.00
414_E 540_I 0.83 0.14 0.00
328_D 417_H 0.82 0.14 0.00
270_A 175_Y 0.82 0.14 0.00
62_G 230_L 0.82 0.14 0.00
159_E 337_E 0.82 0.14 0.00
358_T 585_F 0.81 0.13 0.00
121_Y 543_V 0.81 0.13 0.00
414_E 510_V 0.81 0.13 0.00
343_A 585_F 0.81 0.13 0.00
269_L 312_E 0.81 0.13 0.00
186_I 391_L 0.81 0.13 0.00
315_E 172_Q 0.80 0.13 0.00
141_S 523_I 0.80 0.13 0.00
322_V 137_A 0.80 0.13 0.00
290_I 556_L 0.80 0.13 0.00
462_D 239_K 0.80 0.13 0.00
61_Y 620_K 0.80 0.13 0.00
325_K 133_K 0.80 0.13 0.00
449_T 347_G 0.80 0.13 0.00
59_K 104_S 0.80 0.13 0.00
457_L 411_E 0.80 0.13 0.00
316_L 311_L 0.79 0.13 0.00
416_F 304_S 0.79 0.13 0.00
119_G 487_L 0.79 0.13 0.00
175_N 638_L 0.79 0.12 0.00
129_C 188_F 0.79 0.12 0.00
290_I 343_G 0.78 0.12 0.00
458_I 506_M 0.78 0.12 0.00
359_M 502_C 0.78 0.12 0.00
288_T 636_G 0.78 0.12 0.00
86_V 347_G 0.78 0.12 0.00
353_M 543_V 0.78 0.12 0.00
333_V 330_V 0.78 0.12 0.00
312_A 391_L 0.78 0.12 0.00
328_D 403_A 0.78 0.12 0.00
399_R 585_F 0.78 0.12 0.00
355_V 588_E 0.78 0.12 0.00
325_K 657_T 0.78 0.12 0.00
263_D 175_Y 0.77 0.12 0.00
328_D 204_A 0.77 0.12 0.00
350_Y 592_N 0.77 0.12 0.00
483_A 87_I 0.77 0.12 0.00
212_I 540_I 0.77 0.12 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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