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OPENSEQ.org
BxI
Genes: A B A+B
Length: 362 461 784
Sequences: 1858 5981 1237
Seq/Len: 5.13 12.97 1.58
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 0.22 0.00
2 0.00 0.48 0.01
5 0.01 0.50 0.05
10 0.01 0.52 0.57
20 0.02 0.53 1.29
100 0.03 0.56 1.50
∞ 0.07 0.58 1.76
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
126_I 320_I 1.32 0.77 0.03
309_V 144_V 1.15 0.61 0.02
346_Y 384_V 1.13 0.59 0.02
141_I 303_I 1.13 0.59 0.02
137_S 92_Q 1.11 0.57 0.01
342_L 360_I 1.10 0.56 0.01
210_V 243_K 1.06 0.52 0.01
12_P 10_L 1.06 0.52 0.01
176_T 213_D 1.06 0.52 0.01
158_A 277_K 1.06 0.52 0.01
109_Q 220_T 1.04 0.50 0.01
205_L 294_T 1.03 0.49 0.01
200_L 161_L 1.03 0.49 0.01
16_K 116_A 1.02 0.47 0.01
271_Y 155_C 0.99 0.45 0.01
180_Q 22_I 0.98 0.43 0.01
308_V 421_F 0.97 0.43 0.01
344_F 312_D 0.96 0.41 0.01
231_Q 78_F 0.94 0.40 0.01
31_D 152_L 0.93 0.39 0.01
325_D 78_F 0.92 0.38 0.01
266_T 283_V 0.92 0.38 0.01
13_T 364_E 0.92 0.37 0.01
265_I 217_I 0.91 0.37 0.01
145_I 103_V 0.91 0.37 0.01
122_N 294_T 0.91 0.37 0.01
109_Q 221_S 0.91 0.36 0.01
36_V 41_D 0.90 0.36 0.01
103_V 424_N 0.90 0.36 0.01
12_P 203_I 0.90 0.35 0.01
309_V 123_M 0.90 0.35 0.01
25_N 105_D 0.88 0.34 0.01
152_G 424_N 0.88 0.33 0.01
121_P 57_A 0.88 0.33 0.01
313_N 220_T 0.88 0.33 0.01
270_H 165_A 0.87 0.33 0.01
100_I 404_S 0.87 0.33 0.01
201_I 349_I 0.87 0.32 0.01
202_I 78_F 0.86 0.32 0.01
141_I 111_K 0.86 0.32 0.01
137_S 43_V 0.86 0.32 0.01
276_R 133_M 0.86 0.31 0.01
239_K 347_I 0.85 0.31 0.01
229_Y 125_I 0.85 0.30 0.01
199_F 326_S 0.84 0.30 0.01
42_V 269_A 0.84 0.30 0.01
26_V 360_I 0.84 0.30 0.01
210_V 326_S 0.84 0.30 0.01
35_I 252_I 0.83 0.29 0.01
187_R 175_M 0.83 0.29 0.01
254_M 211_L 0.83 0.29 0.01
204_V 320_I 0.82 0.29 0.01
38_L 377_S 0.82 0.28 0.01
262_D 182_S 0.82 0.28 0.01
237_Q 22_I 0.82 0.28 0.01
9_T 360_I 0.82 0.28 0.01
10_E 132_A 0.82 0.28 0.01
110_F 182_S 0.82 0.28 0.01
188_A 32_I 0.82 0.28 0.01
105_G 266_I 0.82 0.28 0.01
41_G 96_S 0.82 0.28 0.01
144_S 105_D 0.82 0.28 0.01
340_E 30_I 0.81 0.28 0.01
323_A 372_F 0.81 0.28 0.01
227_D 279_Y 0.81 0.27 0.01
289_A 34_G 0.81 0.27 0.01
344_F 227_M 0.81 0.27 0.01
87_V 432_Q 0.80 0.27 0.01
227_D 356_V 0.80 0.27 0.01
15_K 201_E 0.80 0.27 0.01
152_G 237_S 0.80 0.27 0.01
93_P 277_K 0.80 0.26 0.01
172_V 347_I 0.80 0.26 0.01
96_L 403_I 0.80 0.26 0.01
112_F 356_V 0.79 0.26 0.01
224_E 332_I 0.79 0.26 0.01
338_V 242_F 0.79 0.26 0.01
14_S 153_L 0.79 0.26 0.01
143_E 397_K 0.79 0.26 0.01
22_K 370_R 0.79 0.25 0.01
15_K 404_S 0.78 0.25 0.01
201_I 337_E 0.78 0.25 0.01
284_A 167_S 0.78 0.25 0.01
279_T 127_R 0.78 0.25 0.01
313_N 221_S 0.78 0.25 0.01
131_G 288_P 0.78 0.25 0.01
265_I 146_V 0.78 0.24 0.01
273_V 374_R 0.77 0.24 0.01
126_I 416_N 0.77 0.24 0.01
146_K 177_M 0.77 0.24 0.01
121_P 231_G 0.77 0.24 0.01
152_G 118_E 0.77 0.24 0.01
262_D 199_I 0.77 0.24 0.01
176_T 104_V 0.76 0.24 0.01
263_V 315_D 0.76 0.24 0.01
43_T 204_Q 0.76 0.24 0.01
208_F 220_T 0.76 0.23 0.01
46_L 305_A 0.76 0.23 0.01
308_V 366_K 0.76 0.23 0.01
218_L 396_D 0.76 0.23 0.01
224_E 136_G 0.76 0.23 0.01
314_P 218_V 0.76 0.23 0.01
250_A 339_T 0.76 0.23 0.01
130_K 212_D 0.76 0.23 0.01
101_A 140_E 0.75 0.23 0.01
187_R 269_A 0.75 0.23 0.01
159_F 332_I 0.75 0.23 0.01
242_I 256_V 0.75 0.23 0.01
19_D 201_E 0.75 0.23 0.01
263_V 132_A 0.75 0.23 0.01
342_L 141_V 0.75 0.23 0.01
328_D 427_L 0.75 0.23 0.01
114_F 302_T 0.75 0.23 0.01
307_N 425_Q 0.75 0.23 0.01
293_D 259_F 0.75 0.23 0.01
307_N 362_S 0.75 0.23 0.01
125_K 247_K 0.75 0.22 0.01
265_I 392_Q 0.74 0.22 0.01
287_V 377_S 0.74 0.22 0.01
274_A 34_G 0.74 0.22 0.01
343_G 390_A 0.74 0.22 0.01
53_G 175_M 0.74 0.22 0.01
23_E 38_G 0.74 0.22 0.01
307_N 113_G 0.74 0.22 0.01
144_S 351_N 0.74 0.22 0.01
43_T 266_I 0.74 0.22 0.01
38_L 306_F 0.74 0.22 0.01
36_V 408_F 0.74 0.22 0.01
308_V 105_D 0.74 0.22 0.01
330_I 192_I 0.74 0.22 0.01
52_M 192_I 0.74 0.22 0.01
191_L 305_A 0.74 0.22 0.01
110_F 225_A 0.74 0.22 0.01
135_L 366_K 0.73 0.21 0.01
219_R 46_V 0.73 0.21 0.01
134_N 57_A 0.73 0.21 0.01
347_N 361_I 0.73 0.21 0.01
19_D 404_S 0.73 0.21 0.01
111_G 103_V 0.73 0.21 0.01
298_R 129_P 0.73 0.21 0.01
261_A 34_G 0.73 0.21 0.01
284_A 166_G 0.73 0.21 0.01
102_G 238_V 0.73 0.21 0.01
88_L 88_D 0.73 0.21 0.01
287_V 302_T 0.73 0.21 0.01
5_D 213_D 0.73 0.21 0.00
351_K 335_S 0.73 0.21 0.00
135_L 362_S 0.73 0.21 0.00
6_Q 326_S 0.73 0.21 0.00
311_Y 380_K 0.72 0.21 0.00
330_I 216_I 0.72 0.21 0.00
127_N 343_I 0.72 0.21 0.00
314_P 150_D 0.72 0.21 0.00
101_A 79_K 0.72 0.21 0.00
319_E 333_V 0.72 0.20 0.00
284_A 390_A 0.72 0.20 0.00
70_E 267_G 0.72 0.20 0.00
158_A 269_A 0.72 0.20 0.00
71_F 372_F 0.72 0.20 0.00
339_A 281_P 0.72 0.20 0.00
298_R 318_D 0.71 0.20 0.00
39_I 65_Q 0.71 0.20 0.00
167_Q 15_L 0.71 0.20 0.00
258_V 372_F 0.71 0.20 0.00
134_N 312_D 0.71 0.20 0.00
110_F 324_S 0.71 0.20 0.00
351_K 221_S 0.71 0.20 0.00
235_D 179_V 0.71 0.20 0.00
341_V 106_P 0.71 0.20 0.00
343_G 384_V 0.71 0.20 0.00
311_Y 234_C 0.71 0.20 0.00
189_I 403_I 0.71 0.20 0.00
266_T 226_L 0.71 0.20 0.00
307_N 367_L 0.71 0.20 0.00
13_T 396_D 0.71 0.20 0.00
101_A 422_E 0.71 0.20 0.00
346_Y 382_N 0.71 0.20 0.00
297_L 388_I 0.71 0.20 0.00
151_V 45_L 0.71 0.20 0.00
299_I 177_M 0.71 0.20 0.00
100_I 122_Y 0.71 0.20 0.00
201_I 161_L 0.70 0.20 0.00
31_D 373_K 0.70 0.20 0.00
157_I 103_V 0.70 0.19 0.00
353_R 332_I 0.70 0.19 0.00
20_A 277_K 0.70 0.19 0.00
313_N 173_T 0.70 0.19 0.00
279_T 224_S 0.70 0.19 0.00
100_I 209_G 0.70 0.19 0.00
321_Y 209_G 0.70 0.19 0.00
94_I 26_S 0.70 0.19 0.00
340_E 149_I 0.70 0.19 0.00
208_F 221_S 0.70 0.19 0.00
326_V 219_A 0.70 0.19 0.00
272_A 224_S 0.70 0.19 0.00
223_Q 199_I 0.69 0.19 0.00
14_S 39_V 0.69 0.19 0.00
227_D 306_F 0.69 0.19 0.00
216_K 277_K 0.69 0.19 0.00
203_A 267_G 0.69 0.19 0.00
225_I 248_D 0.69 0.19 0.00
45_T 109_R 0.69 0.19 0.00
245_L 318_D 0.69 0.19 0.00
104_L 63_K 0.69 0.19 0.00
197_V 294_T 0.69 0.19 0.00
322_K 245_Q 0.69 0.19 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 B, there is a high ratio (0.56 > 0.4) of paralogs.
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