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OPENSEQ.org
DH
Genes: A B A+B
Length: 492 290 766
Sequences: 1661 610 364
Seq/Len: 3.38 2.1 0.48
MirrorTree (Pazo et al. 2001) 0.69
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 0.84 0.02 0.24
2 0.86 0.02 0.28
5 0.87 0.03 0.44
10 0.87 0.04 0.46
20 0.87 0.07 0.47
100 0.87 0.11 0.47
∞ 0.87 0.18 0.49
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
165_S 250_D 1.47 0.52 0.00
148_I 75_D 1.27 0.38 0.00
339_V 172_Y 1.24 0.36 0.00
337_A 200_L 1.21 0.33 0.00
224_A 59_M 1.20 0.33 0.00
431_F 51_H 1.16 0.30 0.00
395_G 202_N 1.16 0.30 0.00
225_I 169_I 1.15 0.30 0.00
257_G 34_V 1.12 0.28 0.00
333_P 64_E 1.11 0.27 0.00
122_D 172_Y 1.11 0.27 0.00
319_S 195_E 1.11 0.27 0.00
132_A 231_Y 1.11 0.27 0.00
81_I 115_A 1.11 0.27 0.00
417_K 239_D 1.11 0.27 0.00
125_F 111_E 1.09 0.26 0.00
122_D 117_E 1.08 0.26 0.00
473_K 234_K 1.08 0.25 0.00
152_S 85_K 1.06 0.24 0.00
89_G 28_A 1.04 0.23 0.00
217_A 26_A 1.04 0.23 0.00
334_E 189_N 1.03 0.23 0.00
79_I 256_I 1.02 0.22 0.00
75_I 28_A 1.01 0.22 0.00
130_K 209_I 1.01 0.21 0.00
292_I 152_C 1.01 0.21 0.00
150_V 177_S 1.01 0.21 0.00
326_E 57_T 1.00 0.21 0.00
397_S 246_R 1.00 0.21 0.00
487_K 76_V 1.00 0.21 0.00
180_P 76_V 0.99 0.21 0.00
202_V 57_T 0.99 0.21 0.00
407_Y 247_K 0.99 0.21 0.00
212_E 189_N 0.99 0.21 0.00
344_P 235_A 0.99 0.21 0.00
367_Y 225_R 0.99 0.20 0.00
249_C 263_D 0.99 0.20 0.00
160_G 145_A 0.99 0.20 0.00
89_G 109_F 0.98 0.20 0.00
340_A 248_V 0.98 0.20 0.00
220_P 256_I 0.98 0.20 0.00
116_S 113_E 0.98 0.20 0.00
163_I 76_V 0.98 0.20 0.00
178_I 75_D 0.97 0.20 0.00
244_E 195_E 0.97 0.20 0.00
202_V 198_I 0.97 0.20 0.00
75_I 260_I 0.97 0.20 0.00
311_A 84_V 0.96 0.19 0.00
245_M 183_L 0.96 0.19 0.00
14_Q 6_C 0.96 0.19 0.00
292_I 232_D 0.95 0.19 0.00
249_C 48_L 0.95 0.19 0.00
423_S 270_M 0.95 0.19 0.00
38_A 231_Y 0.95 0.19 0.00
322_K 57_T 0.95 0.19 0.00
84_G 140_I 0.95 0.19 0.00
397_S 118_D 0.95 0.19 0.00
268_V 177_S 0.95 0.18 0.00
325_E 143_N 0.95 0.18 0.00
172_A 252_K 0.95 0.18 0.00
38_A 252_K 0.94 0.18 0.00
27_D 5_Q 0.94 0.18 0.00
136_D 235_A 0.94 0.18 0.00
223_V 148_I 0.94 0.18 0.00
178_I 6_C 0.94 0.18 0.00
480_E 34_V 0.94 0.18 0.00
224_A 103_V 0.93 0.18 0.00
130_K 74_E 0.92 0.17 0.00
314_A 260_I 0.91 0.17 0.00
257_G 235_A 0.91 0.17 0.00
413_V 254_L 0.91 0.17 0.00
334_E 28_A 0.91 0.17 0.00
350_R 143_N 0.90 0.17 0.00
179_V 212_V 0.90 0.17 0.00
323_K 194_D 0.90 0.17 0.00
35_N 25_A 0.90 0.16 0.00
324_C 26_A 0.90 0.16 0.00
353_L 159_M 0.90 0.16 0.00
81_I 146_Q 0.89 0.16 0.00
477_A 235_A 0.89 0.16 0.00
121_K 202_N 0.89 0.16 0.00
143_P 103_V 0.89 0.16 0.00
312_I 29_E 0.89 0.16 0.00
305_T 252_K 0.88 0.16 0.00
14_Q 83_G 0.88 0.16 0.00
118_F 116_Y 0.88 0.15 0.00
368_E 195_E 0.88 0.15 0.00
178_I 118_D 0.88 0.15 0.00
471_C 117_E 0.87 0.15 0.00
237_S 59_M 0.87 0.15 0.00
260_S 248_V 0.87 0.15 0.00
110_V 76_V 0.87 0.15 0.00
13_I 262_M 0.87 0.15 0.00
290_Y 226_M 0.87 0.15 0.00
206_V 142_E 0.86 0.15 0.00
247_L 206_T 0.86 0.15 0.00
36_D 250_D 0.86 0.15 0.00
181_V 172_Y 0.86 0.15 0.00
390_T 74_E 0.86 0.15 0.00
254_S 119_D 0.86 0.15 0.00
481_A 262_M 0.86 0.15 0.00
437_P 23_L 0.85 0.15 0.00
475_L 6_C 0.85 0.15 0.00
174_L 89_S 0.85 0.15 0.00
476_Q 32_K 0.85 0.14 0.00
169_V 51_H 0.85 0.14 0.00
212_E 84_V 0.85 0.14 0.00
252_Q 5_Q 0.85 0.14 0.00
72_W 103_V 0.85 0.14 0.00
374_V 51_H 0.85 0.14 0.00
254_S 197_I 0.84 0.14 0.00
242_L 172_Y 0.84 0.14 0.00
212_E 6_C 0.84 0.14 0.00
124_V 203_K 0.84 0.14 0.00
339_V 117_E 0.84 0.14 0.00
152_S 76_V 0.84 0.14 0.00
303_T 30_M 0.84 0.14 0.00
315_K 212_V 0.84 0.14 0.00
125_F 103_V 0.84 0.14 0.00
326_E 252_K 0.84 0.14 0.00
373_E 195_E 0.84 0.14 0.00
344_P 74_E 0.83 0.14 0.00
435_G 20_T 0.83 0.14 0.00
258_S 34_V 0.83 0.14 0.00
145_N 103_V 0.83 0.14 0.00
160_G 104_I 0.83 0.14 0.00
169_V 177_S 0.83 0.14 0.00
292_I 74_E 0.83 0.14 0.00
107_N 210_H 0.82 0.13 0.00
340_A 30_M 0.82 0.13 0.00
124_V 172_Y 0.82 0.13 0.00
202_V 271_E 0.82 0.13 0.00
35_N 225_R 0.82 0.13 0.00
335_W 109_F 0.82 0.13 0.00
317_D 84_V 0.82 0.13 0.00
12_L 81_Y 0.82 0.13 0.00
132_A 166_S 0.82 0.13 0.00
165_S 172_Y 0.82 0.13 0.00
307_E 118_D 0.82 0.13 0.00
254_S 77_L 0.82 0.13 0.00
289_K 76_V 0.82 0.13 0.00
178_I 34_V 0.81 0.13 0.00
249_C 261_T 0.81 0.13 0.00
249_C 166_S 0.81 0.13 0.00
366_A 226_M 0.81 0.13 0.00
224_A 181_G 0.81 0.13 0.00
287_E 108_N 0.81 0.13 0.00
154_C 145_A 0.81 0.13 0.00
396_D 152_C 0.81 0.13 0.00
314_A 200_L 0.81 0.13 0.00
372_M 84_V 0.81 0.13 0.00
223_V 217_V 0.81 0.13 0.00
13_I 85_K 0.81 0.13 0.00
165_S 212_V 0.81 0.13 0.00
242_L 256_I 0.81 0.13 0.00
11_S 208_M 0.81 0.13 0.00
264_L 256_I 0.81 0.13 0.00
202_V 274_I 0.81 0.13 0.00
329_A 208_M 0.80 0.13 0.00
204_D 83_G 0.80 0.13 0.00
421_I 254_L 0.80 0.13 0.00
25_R 59_M 0.80 0.13 0.00
312_I 206_T 0.80 0.13 0.00
480_E 198_I 0.80 0.13 0.00
352_M 49_I 0.80 0.13 0.00
223_V 74_E 0.80 0.13 0.00
243_E 202_N 0.80 0.13 0.00
146_K 33_K 0.80 0.13 0.00
411_E 196_L 0.80 0.13 0.00
380_E 159_M 0.80 0.13 0.00
310_R 114_G 0.80 0.13 0.00
307_E 175_S 0.80 0.12 0.00
243_E 203_K 0.80 0.12 0.00
412_F 197_I 0.80 0.12 0.00
367_Y 143_N 0.80 0.12 0.00
474_K 172_Y 0.80 0.12 0.00
295_M 117_E 0.79 0.12 0.00
305_T 57_T 0.79 0.12 0.00
474_K 236_K 0.79 0.12 0.00
86_V 69_E 0.79 0.12 0.00
150_V 85_K 0.79 0.12 0.00
353_L 76_V 0.79 0.12 0.00
342_Y 234_K 0.79 0.12 0.00
267_K 232_D 0.79 0.12 0.00
106_V 49_I 0.79 0.12 0.00
477_A 220_R 0.79 0.12 0.00
72_W 226_M 0.79 0.12 0.00
469_N 172_Y 0.79 0.12 0.00
462_D 116_Y 0.78 0.12 0.00
177_T 28_A 0.78 0.12 0.00
125_F 144_K 0.78 0.12 0.00
123_I 76_V 0.78 0.12 0.00
287_E 75_D 0.78 0.12 0.00
118_F 33_K 0.78 0.12 0.00
39_V 263_D 0.78 0.12 0.00
10_E 6_C 0.78 0.12 0.00
241_L 57_T 0.78 0.12 0.00
344_P 200_L 0.78 0.12 0.00
338_V 76_V 0.78 0.12 0.00
254_S 198_I 0.78 0.12 0.00
471_C 34_V 0.78 0.12 0.00
261_E 260_I 0.78 0.12 0.00
369_D 6_C 0.78 0.12 0.00
225_I 267_E 0.78 0.12 0.00
261_E 6_C 0.78 0.12 0.00
480_E 23_L 0.77 0.12 0.00
24_A 270_M 0.77 0.12 0.00
121_K 256_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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.87 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
3938 0.48 DH Δgene:(1, 20) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done
3675 0.94 DH Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.29 Done
3671 1 DH Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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