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OPENSEQ.org
DNJB1HSPA4
Genes: A B A+B
Length: 340 520 784
Sequences: 4321 5369 1033
Seq/Len: 12.71 10.32 1.32
MirrorTree (Pazo et al. 2001) 0.54
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 0.06 0.06 0.98
2 0.06 0.07 1.13
5 0.06 0.07 1.16
10 0.06 0.07 1.17
20 0.06 0.08 1.20
100 0.07 0.09 1.40
∞ 0.12 0.14 2.05
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
172_L 261_R 1.18 0.59 0.00
27_Q 198_V 1.15 0.56 0.00
202_K 62_N 1.13 0.54 0.00
320_V 246_E 1.13 0.54 0.00
192_P 433_T 1.09 0.50 0.00
283_V 429_S 1.06 0.46 0.00
29_L 321_L 1.05 0.46 0.00
253_D 338_V 1.05 0.45 0.00
49_A 430_K 1.03 0.44 0.00
22_R 195_P 1.03 0.44 0.00
291_P 64_V 1.02 0.42 0.00
277_D 224_A 1.00 0.40 0.00
324_E 40_S 0.96 0.37 0.00
16_S 286_L 0.96 0.37 0.00
28_A 486_V 0.95 0.36 0.00
303_P 219_K 0.95 0.36 0.00
237_F 245_C 0.95 0.36 0.00
289_I 48_I 0.95 0.36 0.00
66_R 446_Y 0.94 0.35 0.00
29_L 357_F 0.94 0.35 0.00
256_Y 25_T 0.93 0.34 0.00
335_E 461_Q 0.93 0.34 0.00
226_Q 50_A 0.93 0.34 0.00
44_K 314_L 0.93 0.34 0.00
168_L 429_S 0.92 0.34 0.00
172_L 457_P 0.92 0.33 0.00
219_T 197_N 0.91 0.33 0.00
54_V 419_V 0.91 0.33 0.00
230_N 267_S 0.90 0.31 0.00
230_N 299_G 0.89 0.31 0.00
316_I 363_S 0.89 0.31 0.00
300_E 315_A 0.89 0.30 0.00
210_K 457_P 0.88 0.30 0.00
337_V 331_K 0.87 0.29 0.00
129_D 306_F 0.87 0.29 0.00
62_E 236_F 0.87 0.29 0.00
298_P 23_I 0.87 0.29 0.00
58_P 184_Y 0.87 0.29 0.00
206_I 184_Y 0.86 0.28 0.00
143_N 178_A 0.86 0.28 0.00
35_K 463_S 0.86 0.28 0.00
1_M 224_A 0.86 0.28 0.00
5_Y 458_A 0.86 0.28 0.00
299_G 312_D 0.85 0.28 0.00
254_V 322_R 0.85 0.27 0.00
71_G 115_E 0.84 0.27 0.00
17_D 491_S 0.84 0.27 0.00
263_R 224_A 0.84 0.27 0.00
72_L 115_E 0.84 0.27 0.00
59_R 246_E 0.84 0.26 0.00
295_R 32_D 0.84 0.26 0.00
260_I 444_A 0.84 0.26 0.00
278_G 178_A 0.83 0.26 0.00
262_L 418_E 0.82 0.25 0.00
204_L 226_A 0.82 0.25 0.00
254_V 120_M 0.82 0.25 0.00
231_I 336_Y 0.82 0.25 0.00
317_E 419_V 0.82 0.25 0.00
212_W 267_S 0.82 0.25 0.00
298_P 421_S 0.82 0.25 0.00
49_A 219_K 0.81 0.25 0.00
332_T 433_T 0.81 0.24 0.00
256_Y 14_Y 0.81 0.24 0.00
218_I 283_D 0.81 0.24 0.00
288_V 286_L 0.81 0.24 0.00
239_L 84_K 0.80 0.24 0.00
184_K 42_G 0.80 0.24 0.00
287_D 380_C 0.80 0.23 0.00
30_R 418_E 0.80 0.23 0.00
71_G 421_S 0.80 0.23 0.00
25_R 487_H 0.80 0.23 0.00
150_R 245_C 0.80 0.23 0.00
218_I 455_P 0.79 0.23 0.00
236_V 185_K 0.79 0.23 0.00
295_R 267_S 0.78 0.22 0.00
276_L 301_M 0.78 0.22 0.00
237_F 352_E 0.78 0.22 0.00
333_V 25_T 0.78 0.22 0.00
296_K 316_R 0.78 0.22 0.00
184_K 275_K 0.78 0.22 0.00
171_S 65_Q 0.77 0.22 0.00
170_V 166_N 0.77 0.22 0.00
26_R 452_L 0.77 0.22 0.00
303_P 290_C 0.77 0.21 0.00
11_L 444_A 0.77 0.21 0.00
187_H 461_Q 0.77 0.21 0.00
56_S 38_C 0.77 0.21 0.00
303_P 46_R 0.77 0.21 0.00
299_G 198_V 0.77 0.21 0.00
263_R 201_V 0.76 0.21 0.00
48_I 67_F 0.76 0.21 0.00
199_N 151_A 0.76 0.21 0.00
29_L 24_E 0.76 0.21 0.00
304_L 23_I 0.76 0.21 0.00
297_V 245_C 0.76 0.21 0.00
208_V 418_E 0.76 0.20 0.00
332_T 246_E 0.76 0.20 0.00
216_T 490_F 0.75 0.20 0.00
193_D 358_F 0.75 0.20 0.00
314_L 351_K 0.75 0.20 0.00
330_S 267_S 0.75 0.20 0.00
273_V 310_C 0.75 0.20 0.00
255_I 419_V 0.75 0.20 0.00
213_K 416_D 0.74 0.20 0.00
58_P 452_L 0.74 0.20 0.00
223_E 461_Q 0.74 0.20 0.00
216_T 344_A 0.74 0.20 0.00
253_D 421_S 0.74 0.20 0.00
216_T 466_K 0.74 0.20 0.00
254_V 38_C 0.74 0.19 0.00
29_L 229_T 0.74 0.19 0.00
197_I 178_A 0.74 0.19 0.00
48_I 315_A 0.74 0.19 0.00
28_A 383_L 0.74 0.19 0.00
82_G 201_V 0.74 0.19 0.00
335_E 215_F 0.73 0.19 0.00
180_T 467_V 0.73 0.19 0.00
29_L 226_A 0.73 0.19 0.00
333_V 40_S 0.73 0.19 0.00
185_I 25_T 0.73 0.19 0.00
253_D 184_Y 0.73 0.19 0.00
48_I 457_P 0.73 0.19 0.00
172_L 443_E 0.73 0.19 0.00
296_K 433_T 0.73 0.19 0.00
330_S 83_E 0.73 0.19 0.00
39_P 371_A 0.73 0.19 0.00
29_L 199_V 0.72 0.18 0.00
71_G 3_V 0.72 0.18 0.00
8_T 386_A 0.72 0.18 0.00
132_S 354_I 0.72 0.18 0.00
24_Y 345_T 0.72 0.18 0.00
277_D 268_Q 0.72 0.18 0.00
13_R 76_S 0.72 0.18 0.00
324_E 283_D 0.71 0.18 0.00
39_P 491_S 0.71 0.18 0.00
68_G 432_L 0.71 0.18 0.00
246_I 201_V 0.71 0.18 0.00
260_I 378_L 0.71 0.18 0.00
25_R 216_N 0.71 0.18 0.00
335_E 254_L 0.71 0.18 0.00
322_F 64_V 0.71 0.18 0.00
269_C 441_T 0.71 0.18 0.00
298_P 136_P 0.71 0.18 0.00
61_R 361_E 0.71 0.18 0.00
53_D 380_C 0.71 0.18 0.00
27_Q 116_Q 0.71 0.18 0.00
316_I 18_A 0.71 0.18 0.00
25_R 198_V 0.71 0.17 0.00
203_I 121_L 0.70 0.17 0.00
261_S 314_L 0.70 0.17 0.00
284_V 331_K 0.70 0.17 0.00
48_I 198_V 0.70 0.17 0.00
63_I 432_L 0.70 0.17 0.00
317_E 116_Q 0.70 0.17 0.00
22_R 151_A 0.70 0.17 0.00
300_E 267_S 0.70 0.17 0.00
29_L 298_S 0.70 0.17 0.00
49_A 201_V 0.70 0.17 0.00
335_E 361_E 0.70 0.17 0.00
271_V 198_V 0.70 0.17 0.00
12_A 319_P 0.70 0.17 0.00
73_K 275_K 0.70 0.17 0.00
250_D 331_K 0.70 0.17 0.00
226_Q 71_H 0.70 0.17 0.00
30_R 378_L 0.69 0.17 0.00
66_R 418_E 0.69 0.17 0.00
69_E 243_H 0.69 0.17 0.00
217_K 201_V 0.69 0.17 0.00
165_T 51_A 0.69 0.17 0.00
28_A 392_F 0.69 0.17 0.00
163_P 201_V 0.69 0.17 0.00
212_W 284_L 0.69 0.17 0.00
316_I 215_F 0.69 0.17 0.00
311_R 382_I 0.69 0.17 0.00
174_E 263_L 0.69 0.17 0.00
302_L 374_R 0.69 0.17 0.00
220_F 180_A 0.69 0.17 0.00
39_P 243_H 0.69 0.17 0.00
287_D 458_A 0.69 0.17 0.00
264_E 283_D 0.69 0.17 0.00
176_Y 378_L 0.69 0.17 0.00
11_L 23_I 0.69 0.17 0.00
61_R 219_K 0.69 0.17 0.00
259_R 328_T 0.69 0.16 0.00
153_Q 136_P 0.69 0.16 0.00
227_T 142_V 0.69 0.16 0.00
304_L 67_F 0.68 0.16 0.00
283_V 223_L 0.68 0.16 0.00
170_V 383_L 0.68 0.16 0.00
266_L 416_D 0.68 0.16 0.00
261_S 498_V 0.68 0.16 0.00
321_I 223_L 0.68 0.16 0.00
239_L 466_K 0.68 0.16 0.00
331_R 322_R 0.68 0.16 0.00
185_I 64_V 0.68 0.16 0.00
166_H 268_Q 0.68 0.16 0.00
61_R 335_I 0.68 0.16 0.00
315_I 290_C 0.68 0.16 0.00
29_L 197_N 0.68 0.16 0.00
172_L 322_R 0.68 0.16 0.00
212_W 38_C 0.68 0.16 0.00
24_Y 384_S 0.68 0.16 0.00
218_I 466_K 0.68 0.16 0.00
238_V 131_S 0.67 0.16 0.00
171_S 361_E 0.67 0.16 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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