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OPENSEQ.org
GadBC
Genes: A B A+B
Length: 511 466 920
Sequences: 6770 3864 222
Seq/Len: 13.25 8.29 0.24
MirrorTree (Pazo et al. 2001) 0.64
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 0.04 0.02 0.09
2 0.04 0.02 0.11
5 0.05 0.03 0.14
10 0.05 0.03 0.18
20 0.07 0.03 0.23
100 0.13 0.05 0.51
∞ 0.22 0.12 1.25
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
226_E 158_V 1.53 0.38 0.00
465_A 257_D 1.38 0.29 0.00
250_S 244_A 1.32 0.27 0.00
293_I 357_I 1.22 0.22 0.00
271_V 137_M 1.21 0.21 0.00
226_E 20_A 1.12 0.18 0.00
458_A 414_E 1.12 0.18 0.00
338_P 378_V 1.11 0.17 0.00
283_A 104_V 1.10 0.17 0.00
352_A 357_I 1.10 0.17 0.00
420_L 240_M 1.09 0.17 0.00
247_C 217_Y 1.09 0.17 0.00
336_G 402_R 1.07 0.16 0.00
307_S 430_E 1.04 0.15 0.00
314_R 29_S 1.03 0.15 0.00
428_I 443_A 1.02 0.14 0.00
14_T 271_S 1.02 0.14 0.00
418_V 416_T 1.02 0.14 0.00
118_L 438_L 1.02 0.14 0.00
232_R 280_A 1.01 0.14 0.00
459_L 420_V 1.01 0.14 0.00
231_G 357_I 1.01 0.14 0.00
52_L 158_V 1.01 0.14 0.00
455_V 438_L 1.00 0.14 0.00
338_P 138_K 0.99 0.14 0.00
289_T 70_E 0.99 0.14 0.00
473_A 233_D 0.99 0.14 0.00
347_V 257_D 0.99 0.13 0.00
247_C 146_E 0.99 0.13 0.00
353_L 277_F 0.99 0.13 0.00
44_F 134_G 0.99 0.13 0.00
57_V 321_A 0.98 0.13 0.00
376_V 19_G 0.98 0.13 0.00
166_L 414_E 0.98 0.13 0.00
153_A 259_V 0.98 0.13 0.00
241_L 143_K 0.97 0.13 0.00
318_V 225_D 0.97 0.13 0.00
465_A 147_A 0.97 0.13 0.00
415_V 115_N 0.97 0.13 0.00
329_F 215_G 0.97 0.13 0.00
226_E 113_P 0.96 0.13 0.00
227_M 244_A 0.96 0.12 0.00
335_N 158_V 0.95 0.12 0.00
346_L 77_D 0.95 0.12 0.00
288_W 421_M 0.94 0.12 0.00
421_L 205_V 0.94 0.12 0.00
387_I 309_Q 0.94 0.12 0.00
165_L 217_Y 0.94 0.12 0.00
454_L 348_Q 0.93 0.12 0.00
370_A 320_P 0.93 0.12 0.00
455_V 32_F 0.93 0.12 0.00
260_I 427_R 0.92 0.12 0.00
173_A 384_D 0.92 0.12 0.00
370_A 196_E 0.92 0.11 0.00
230_P 46_I 0.91 0.11 0.00
262_G 357_I 0.91 0.11 0.00
421_L 72_V 0.91 0.11 0.00
173_A 416_T 0.91 0.11 0.00
418_V 383_K 0.91 0.11 0.00
458_A 11_S 0.90 0.11 0.00
321_Q 423_I 0.90 0.11 0.00
228_S 74_K 0.90 0.11 0.00
169_F 225_D 0.90 0.11 0.00
232_R 420_V 0.90 0.11 0.00
459_L 27_A 0.90 0.11 0.00
334_K 430_E 0.90 0.11 0.00
403_F 331_F 0.90 0.11 0.00
473_A 21_K 0.90 0.11 0.00
48_L 357_I 0.90 0.11 0.00
282_V 114_K 0.90 0.11 0.00
473_A 11_S 0.89 0.11 0.00
473_A 232_A 0.89 0.11 0.00
472_K 232_A 0.89 0.11 0.00
473_A 29_S 0.89 0.11 0.00
322_K 46_I 0.89 0.11 0.00
424_I 416_T 0.89 0.11 0.00
117_I 196_E 0.89 0.11 0.00
227_M 51_Y 0.89 0.11 0.00
302_L 103_M 0.89 0.11 0.00
439_G 12_E 0.89 0.11 0.00
421_L 442_K 0.88 0.11 0.00
456_V 16_S 0.88 0.11 0.00
85_P 365_F 0.88 0.11 0.00
453_F 28_E 0.88 0.10 0.00
457_L 114_K 0.88 0.10 0.00
295_A 95_A 0.88 0.10 0.00
474_N 26_I 0.88 0.10 0.00
459_L 12_E 0.88 0.10 0.00
87_W 109_H 0.88 0.10 0.00
173_A 391_T 0.88 0.10 0.00
373_L 378_V 0.88 0.10 0.00
38_S 121_T 0.88 0.10 0.00
290_V 157_L 0.88 0.10 0.00
129_T 29_S 0.87 0.10 0.00
470_K 27_A 0.87 0.10 0.00
201_V 109_H 0.87 0.10 0.00
470_K 233_D 0.87 0.10 0.00
145_Q 462_S 0.87 0.10 0.00
176_A 220_P 0.87 0.10 0.00
80_S 137_M 0.86 0.10 0.00
161_F 189_M 0.86 0.10 0.00
448_L 457_I 0.86 0.10 0.00
457_L 21_K 0.86 0.10 0.00
213_S 104_V 0.86 0.10 0.00
459_L 445_L 0.86 0.10 0.00
347_V 40_D 0.86 0.10 0.00
351_I 104_V 0.86 0.10 0.00
275_F 69_D 0.86 0.10 0.00
469_R 233_D 0.86 0.10 0.00
165_L 396_S 0.86 0.10 0.00
472_K 33_P 0.86 0.10 0.00
453_F 325_I 0.86 0.10 0.00
456_V 464_K 0.86 0.10 0.00
470_K 19_G 0.85 0.10 0.00
351_I 365_F 0.85 0.10 0.00
467_H 14_L 0.85 0.10 0.00
429_V 244_A 0.85 0.10 0.00
344_S 423_I 0.85 0.10 0.00
226_E 460_Q 0.85 0.10 0.00
168_A 205_V 0.85 0.10 0.00
14_T 259_V 0.85 0.10 0.00
433_P 60_L 0.85 0.10 0.00
39_G 243_D 0.85 0.10 0.00
329_F 341_K 0.84 0.10 0.00
11_K 355_D 0.84 0.10 0.00
388_G 394_D 0.84 0.10 0.00
128_I 22_S 0.84 0.10 0.00
438_Q 147_A 0.84 0.10 0.00
470_K 358_A 0.84 0.10 0.00
466_V 147_A 0.84 0.10 0.00
455_V 439_E 0.84 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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