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OPENSEQ.org
PilBC
Genes: A B A+B
Length: 568 405 952
Sequences: 2848 3552 2117
Seq/Len: 5.01 8.77 2.22
MirrorTree (Pazo et al. 2001) 0.83
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 0.00 0.00 1.66
2 0.01 0.00 2.03
5 0.01 0.00 2.10
10 0.01 0.00 2.16
20 0.01 0.01 2.18
100 0.04 0.05 2.20
∞ 0.15 0.15 2.28
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
392_M 213_V 1.19 0.75 0.03
392_M 392_M 1.19 0.75 0.03
356_V 178_A 1.07 0.63 0.02
409_A 382_G 1.07 0.63 0.02
202_I 294_V 1.02 0.58 0.02
439_F 28_V 1.01 0.57 0.02
198_K 323_P 0.98 0.53 0.02
348_N 195_F 0.96 0.51 0.01
562_R 271_A 0.96 0.51 0.01
416_L 213_V 0.95 0.50 0.01
314_I 162_L 0.95 0.50 0.01
297_M 135_L 0.94 0.49 0.01
317_P 40_I 0.91 0.45 0.01
337_S 355_A 0.90 0.44 0.01
390_I 156_I 0.90 0.44 0.01
241_I 289_D 0.90 0.43 0.01
282_K 183_V 0.90 0.43 0.01
436_V 142_G 0.89 0.43 0.01
310_F 337_M 0.89 0.43 0.01
373_G 355_A 0.88 0.42 0.01
348_N 183_V 0.86 0.40 0.01
235_I 337_M 0.86 0.40 0.01
243_A 214_I 0.85 0.39 0.01
321_V 212_F 0.85 0.38 0.01
509_Q 280_L 0.84 0.37 0.01
524_G 255_A 0.84 0.37 0.01
248_A 347_M 0.83 0.36 0.01
392_M 329_V 0.83 0.36 0.01
9_L 191_V 0.82 0.35 0.01
550_L 344_T 0.81 0.34 0.01
348_N 210_T 0.81 0.34 0.01
85_A 287_I 0.81 0.34 0.01
289_D 135_L 0.80 0.34 0.01
246_D 218_N 0.80 0.33 0.01
441_V 196_A 0.80 0.33 0.01
244_D 289_D 0.80 0.33 0.01
282_K 397_F 0.79 0.32 0.01
363_I 133_V 0.79 0.32 0.01
182_P 386_G 0.79 0.32 0.01
242_M 307_V 0.78 0.32 0.01
202_I 363_D 0.78 0.31 0.01
198_K 281_I 0.78 0.31 0.01
41_L 80_S 0.78 0.31 0.01
204_I 157_E 0.77 0.30 0.01
363_I 387_G 0.77 0.30 0.01
433_N 393_Y 0.77 0.30 0.01
323_V 354_I 0.77 0.30 0.01
407_K 71_T 0.77 0.30 0.01
408_A 188_L 0.77 0.30 0.01
19_E 274_T 0.76 0.29 0.01
289_D 192_I 0.76 0.29 0.01
511_M 134_N 0.75 0.29 0.01
307_L 329_V 0.75 0.28 0.01
202_I 166_V 0.75 0.28 0.01
407_K 156_I 0.75 0.28 0.01
423_D 280_L 0.74 0.28 0.01
246_D 148_I 0.74 0.28 0.01
204_I 119_D 0.74 0.27 0.01
362_G 389_V 0.74 0.27 0.01
414_L 403_V 0.74 0.27 0.01
534_S 209_P 0.74 0.27 0.01
282_K 195_F 0.73 0.27 0.01
556_S 165_Q 0.73 0.27 0.01
313_A 310_V 0.73 0.26 0.01
449_T 132_Y 0.73 0.26 0.01
349_I 66_D 0.72 0.26 0.01
356_V 214_I 0.72 0.26 0.01
416_L 87_C 0.72 0.26 0.01
550_L 148_I 0.72 0.25 0.01
444_A 111_V 0.72 0.25 0.01
379_A 393_Y 0.71 0.25 0.01
390_I 329_V 0.71 0.25 0.01
392_M 298_A 0.71 0.25 0.01
337_S 144_I 0.71 0.25 0.01
348_N 391_A 0.71 0.25 0.01
362_G 76_T 0.71 0.24 0.01
188_N 179_I 0.71 0.24 0.01
467_I 113_G 0.70 0.24 0.01
239_I 7_E 0.70 0.24 0.01
324_T 382_G 0.70 0.24 0.01
393_I 119_D 0.70 0.24 0.01
348_N 94_Q 0.70 0.24 0.01
552_E 93_S 0.69 0.23 0.01
417_S 176_I 0.69 0.23 0.01
239_I 134_N 0.69 0.23 0.01
557_F 109_E 0.69 0.23 0.01
289_D 272_R 0.69 0.23 0.01
342_L 17_K 0.69 0.23 0.01
391_I 134_N 0.69 0.23 0.01
375_T 165_Q 0.69 0.23 0.01
389_D 347_M 0.69 0.23 0.01
550_L 361_E 0.69 0.23 0.01
431_L 135_L 0.68 0.23 0.01
366_V 195_F 0.68 0.23 0.01
239_I 24_S 0.68 0.22 0.01
436_V 384_T 0.68 0.22 0.01
100_L 4_F 0.68 0.22 0.01
521_I 240_K 0.68 0.22 0.01
215_Y 129_D 0.68 0.22 0.01
516_E 42_I 0.68 0.22 0.01
213_V 234_L 0.68 0.22 0.01
118_F 213_V 0.68 0.22 0.01
307_L 278_G 0.67 0.22 0.01
200_S 275_R 0.67 0.22 0.01
390_I 232_F 0.67 0.22 0.01
408_A 367_S 0.67 0.22 0.01
488_F 383_T 0.67 0.22 0.01
250_R 319_T 0.67 0.21 0.01
390_I 66_D 0.67 0.21 0.01
268_M 178_A 0.67 0.21 0.01
433_N 199_F 0.67 0.21 0.01
213_V 132_Y 0.67 0.21 0.01
436_V 83_P 0.67 0.21 0.01
445_V 107_V 0.67 0.21 0.01
257_R 392_M 0.67 0.21 0.01
273_S 199_F 0.66 0.21 0.01
446_N 310_V 0.66 0.21 0.01
545_S 61_K 0.66 0.21 0.01
239_I 343_A 0.66 0.21 0.01
546_G 84_L 0.66 0.21 0.01
316_K 263_P 0.66 0.21 0.01
217_I 379_V 0.66 0.21 0.01
390_I 380_F 0.66 0.21 0.01
403_E 101_K 0.66 0.21 0.01
190_I 273_F 0.66 0.21 0.01
556_S 166_V 0.66 0.21 0.01
409_A 76_T 0.66 0.20 0.01
530_I 184_V 0.66 0.20 0.01
332_T 284_G 0.66 0.20 0.01
223_E 71_T 0.66 0.20 0.01
491_T 257_K 0.66 0.20 0.01
133_S 344_T 0.66 0.20 0.01
88_Y 371_A 0.65 0.20 0.01
243_A 208_G 0.65 0.20 0.01
299_K 119_D 0.65 0.20 0.01
537_L 39_S 0.65 0.20 0.01
531_K 372_L 0.65 0.20 0.01
206_P 262_G 0.65 0.20 0.01
192_T 369_M 0.65 0.20 0.01
241_I 288_M 0.65 0.20 0.01
469_I 257_K 0.65 0.20 0.01
545_S 393_Y 0.65 0.20 0.01
406_I 16_Q 0.65 0.20 0.01
501_Y 385_V 0.65 0.20 0.01
183_V 380_F 0.65 0.20 0.01
191_L 142_G 0.65 0.20 0.01
368_M 7_E 0.65 0.20 0.01
287_L 152_L 0.65 0.20 0.01
366_V 283_S 0.65 0.20 0.01
380_L 385_V 0.65 0.20 0.01
245_L 336_Q 0.65 0.20 0.01
378_A 168_G 0.65 0.20 0.01
489_R 88_L 0.64 0.19 0.01
315_H 121_L 0.64 0.19 0.01
233_N 35_Y 0.64 0.19 0.01
532_R 24_S 0.64 0.19 0.01
270_Y 80_S 0.64 0.19 0.01
304_P 255_A 0.64 0.19 0.01
170_D 265_I 0.64 0.19 0.01
241_I 314_I 0.64 0.19 0.01
95_R 380_F 0.64 0.19 0.01
300_L 323_P 0.64 0.19 0.01
386_Q 152_L 0.64 0.19 0.01
274_V 360_D 0.63 0.19 0.01
433_N 397_F 0.63 0.19 0.01
558_E 214_I 0.63 0.19 0.01
11_V 117_F 0.63 0.19 0.01
391_I 175_T 0.63 0.19 0.01
416_L 158_K 0.63 0.19 0.01
52_L 391_A 0.63 0.19 0.01
390_I 269_S 0.63 0.19 0.01
390_I 129_D 0.63 0.18 0.01
438_P 180_A 0.63 0.18 0.01
283_V 292_E 0.63 0.18 0.01
466_E 101_K 0.63 0.18 0.01
332_T 394_L 0.63 0.18 0.01
181_A 187_I 0.63 0.18 0.01
274_V 226_L 0.63 0.18 0.01
332_T 192_I 0.63 0.18 0.01
391_I 69_V 0.63 0.18 0.01
183_V 212_F 0.62 0.18 0.01
144_Q 290_G 0.62 0.18 0.01
386_Q 392_M 0.62 0.18 0.01
521_I 340_V 0.62 0.18 0.01
513_M 376_M 0.62 0.18 0.01
546_G 75_A 0.62 0.18 0.01
91_V 280_L 0.62 0.18 0.01
505_V 340_V 0.62 0.18 0.01
409_A 195_F 0.62 0.18 0.01
366_V 389_V 0.62 0.18 0.01
332_T 141_V 0.62 0.18 0.01
456_R 222_K 0.62 0.18 0.01
248_A 142_G 0.62 0.18 0.01
182_P 378_M 0.62 0.18 0.01
518_R 388_L 0.62 0.18 0.01
178_T 24_S 0.62 0.18 0.01
363_I 183_V 0.62 0.18 0.01
427_T 313_A 0.62 0.18 0.01
442_A 333_M 0.62 0.18 0.01
239_I 280_L 0.62 0.18 0.01
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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