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OPENSEQ.org
trial1
Genes: A B A+B
Length: 550 457 954
Sequences: 3489 1465 53
Seq/Len: 6.34 3.21 0.06
MirrorTree (Pazo et al. 2001) 0.11
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 0.03 0.06 0.00
2 0.03 0.07 0.01
5 0.05 0.07 0.02
10 0.05 0.07 0.04
20 0.08 0.08 0.05
100 0.10 0.09 0.17
∞ 0.19 0.13 0.36
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
481_V 129_S 1.57 0.17 0.00
201_I 125_E 1.50 0.15 0.00
330_V 188_S 1.48 0.14 0.00
42_P 114_D 1.46 0.14 0.00
415_A 85_F 1.37 0.12 0.00
377_L 64_I 1.36 0.12 0.00
156_E 330_M 1.23 0.10 0.00
496_V 377_L 1.20 0.09 0.00
77_H 118_D 1.18 0.09 0.00
78_P 258_V 1.16 0.09 0.00
36_V 368_I 1.15 0.09 0.00
259_V 101_W 1.15 0.09 0.00
240_K 278_S 1.14 0.08 0.00
443_A 196_S 1.14 0.08 0.00
401_K 9_T 1.13 0.08 0.00
214_F 368_I 1.13 0.08 0.00
63_S 400_S 1.13 0.08 0.00
350_A 159_F 1.11 0.08 0.00
259_V 81_I 1.11 0.08 0.00
178_F 202_I 1.10 0.08 0.00
159_E 64_I 1.10 0.08 0.00
332_G 148_G 1.09 0.08 0.00
445_A 298_N 1.09 0.08 0.00
401_K 299_M 1.08 0.08 0.00
247_E 149_T 1.08 0.08 0.00
330_V 195_H 1.07 0.08 0.00
496_V 105_H 1.07 0.08 0.00
36_V 330_M 1.07 0.08 0.00
159_E 72_T 1.07 0.07 0.00
99_T 17_G 1.06 0.07 0.00
144_A 148_G 1.06 0.07 0.00
52_L 85_F 1.05 0.07 0.00
331_G 7_I 1.04 0.07 0.00
103_I 145_S 1.04 0.07 0.00
445_A 378_F 1.03 0.07 0.00
41_K 79_S 1.03 0.07 0.00
326_V 30_L 1.02 0.07 0.00
393_L 64_I 1.02 0.07 0.00
445_A 233_M 1.02 0.07 0.00
396_A 130_L 1.01 0.07 0.00
237_N 135_I 1.01 0.07 0.00
401_K 316_F 1.01 0.07 0.00
499_P 214_T 1.01 0.07 0.00
389_V 139_L 1.01 0.07 0.00
201_I 353_V 1.00 0.07 0.00
374_C 64_I 1.00 0.07 0.00
454_C 146_G 1.00 0.07 0.00
140_I 278_S 0.99 0.07 0.00
464_I 125_E 0.99 0.07 0.00
162_A 11_Q 0.99 0.07 0.00
326_V 265_F 0.99 0.07 0.00
35_A 265_F 0.98 0.07 0.00
502_V 64_I 0.98 0.07 0.00
496_V 127_C 0.98 0.07 0.00
282_L 330_M 0.98 0.07 0.00
459_F 118_D 0.98 0.07 0.00
42_P 116_V 0.98 0.07 0.00
165_A 230_S 0.98 0.07 0.00
214_F 299_M 0.98 0.07 0.00
112_A 63_S 0.97 0.06 0.00
234_K 312_T 0.97 0.06 0.00
446_L 368_I 0.97 0.06 0.00
496_V 92_F 0.96 0.06 0.00
129_Y 382_G 0.95 0.06 0.00
341_I 176_S 0.95 0.06 0.00
481_V 1_M 0.95 0.06 0.00
428_S 118_D 0.95 0.06 0.00
278_I 301_A 0.95 0.06 0.00
236_F 383_D 0.95 0.06 0.00
505_N 85_F 0.95 0.06 0.00
332_G 233_M 0.95 0.06 0.00
185_A 415_M 0.94 0.06 0.00
436_Q 118_D 0.94 0.06 0.00
220_F 114_D 0.94 0.06 0.00
217_G 104_G 0.94 0.06 0.00
217_G 184_N 0.94 0.06 0.00
412_G 104_G 0.94 0.06 0.00
412_G 184_N 0.94 0.06 0.00
399_I 230_S 0.94 0.06 0.00
404_L 299_M 0.94 0.06 0.00
58_Q 82_G 0.94 0.06 0.00
62_I 188_S 0.94 0.06 0.00
45_G 146_G 0.93 0.06 0.00
46_P 146_G 0.93 0.06 0.00
95_G 146_G 0.93 0.06 0.00
96_D 146_G 0.93 0.06 0.00
97_G 146_G 0.93 0.06 0.00
289_G 159_F 0.93 0.06 0.00
332_G 378_F 0.93 0.06 0.00
470_L 415_M 0.93 0.06 0.00
36_V 186_T 0.93 0.06 0.00
449_I 66_V 0.93 0.06 0.00
311_N 61_P 0.93 0.06 0.00
162_A 12_C 0.93 0.06 0.00
282_L 148_G 0.92 0.06 0.00
418_M 135_I 0.92 0.06 0.00
314_C 381_V 0.92 0.06 0.00
42_P 119_V 0.92 0.06 0.00
446_L 138_S 0.92 0.06 0.00
490_D 125_E 0.92 0.06 0.00
156_E 202_I 0.91 0.06 0.00
395_D 422_Y 0.91 0.06 0.00
405_Q 230_S 0.91 0.06 0.00
375_T 31_D 0.91 0.06 0.00
44_L 231_S 0.91 0.06 0.00
220_F 135_I 0.90 0.06 0.00
332_G 229_V 0.90 0.06 0.00
132_A 70_P 0.90 0.06 0.00
282_L 371_S 0.90 0.06 0.00
443_A 319_G 0.90 0.06 0.00
390_E 225_L 0.90 0.06 0.00
179_V 151_L 0.90 0.06 0.00
454_C 144_G 0.89 0.06 0.00
252_A 230_S 0.89 0.06 0.00
409_I 316_F 0.89 0.06 0.00
42_P 152_I 0.89 0.06 0.00
496_V 299_M 0.89 0.06 0.00
28_S 72_T 0.89 0.06 0.00
445_A 166_T 0.89 0.06 0.00
53_I 64_I 0.89 0.06 0.00
137_V 250_L 0.89 0.06 0.00
311_N 151_L 0.88 0.06 0.00
125_I 125_E 0.88 0.06 0.00
259_V 72_T 0.88 0.06 0.00
482_V 63_S 0.88 0.06 0.00
112_A 116_V 0.88 0.06 0.00
445_A 293_M 0.88 0.06 0.00
424_L 59_W 0.88 0.06 0.00
34_V 288_E 0.87 0.06 0.00
276_Q 197_D 0.87 0.06 0.00
270_I 166_T 0.87 0.06 0.00
495_F 87_P 0.87 0.06 0.00
446_L 186_T 0.87 0.06 0.00
414_G 187_L 0.87 0.06 0.00
457_A 169_V 0.87 0.05 0.00
101_V 250_L 0.87 0.05 0.00
447_E 1_M 0.86 0.05 0.00
418_M 400_S 0.86 0.05 0.00
355_M 7_I 0.86 0.05 0.00
500_A 368_I 0.86 0.05 0.00
49_S 188_S 0.86 0.05 0.00
291_N 188_S 0.86 0.05 0.00
450_P 241_R 0.86 0.05 0.00
451_R 76_V 0.86 0.05 0.00
454_C 79_S 0.86 0.05 0.00
331_G 10_G 0.86 0.05 0.00
401_K 293_M 0.85 0.05 0.00
498_E 367_F 0.85 0.05 0.00
49_S 64_I 0.85 0.05 0.00
45_G 104_G 0.85 0.05 0.00
45_G 184_N 0.85 0.05 0.00
46_P 104_G 0.85 0.05 0.00
46_P 184_N 0.85 0.05 0.00
421_S 229_V 0.85 0.05 0.00
474_K 179_V 0.85 0.05 0.00
165_A 16_I 0.85 0.05 0.00
462_I 73_I 0.85 0.05 0.00
181_M 229_V 0.85 0.05 0.00
326_V 167_F 0.85 0.05 0.00
47_L 126_G 0.85 0.05 0.00
496_V 194_E 0.85 0.05 0.00
240_K 4_I 0.84 0.05 0.00
398_M 344_W 0.84 0.05 0.00
413_G 273_L 0.84 0.05 0.00
390_E 61_P 0.84 0.05 0.00
415_A 209_D 0.84 0.05 0.00
445_A 64_I 0.84 0.05 0.00
158_L 422_Y 0.84 0.05 0.00
395_D 398_Y 0.84 0.05 0.00
330_V 5_I 0.84 0.05 0.00
496_V 159_F 0.84 0.05 0.00
376_L 409_S 0.84 0.05 0.00
457_A 149_T 0.83 0.05 0.00
504_I 117_M 0.83 0.05 0.00
496_V 368_I 0.83 0.05 0.00
259_V 115_S 0.83 0.05 0.00
393_L 285_T 0.83 0.05 0.00
95_G 104_G 0.83 0.05 0.00
95_G 184_N 0.83 0.05 0.00
96_D 104_G 0.83 0.05 0.00
96_D 184_N 0.83 0.05 0.00
97_G 104_G 0.83 0.05 0.00
97_G 184_N 0.83 0.05 0.00
520_V 273_L 0.83 0.05 0.00
388_E 125_E 0.83 0.05 0.00
133_V 342_V 0.83 0.05 0.00
179_V 326_V 0.83 0.05 0.00
389_V 102_A 0.83 0.05 0.00
390_E 312_T 0.83 0.05 0.00
201_I 338_S 0.83 0.05 0.00
460_D 125_E 0.83 0.05 0.00
95_G 17_G 0.83 0.05 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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