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OPENSEQ.org
murmurs
Genes: A B A+B
Length: 451 443 800
Sequences: 3405 8692 475
Seq/Len: 7.55 19.62 0.59
MirrorTree (Pazo et al. 2001) 0.48
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 0.07 0.01
2 0.08 0.14 0.07
5 0.09 0.28 0.53
10 0.09 0.40 0.53
20 0.09 0.40 0.54
100 0.09 0.42 0.55
∞ 0.09 0.46 0.60
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
227_G 257_F 1.37 0.51 0.00
434_F 219_P 1.31 0.46 0.00
231_E 340_A 1.29 0.45 0.00
76_M 51_I 1.26 0.43 0.00
210_I 106_L 1.24 0.40 0.00
307_F 126_K 1.22 0.39 0.00
131_A 187_V 1.21 0.39 0.00
434_F 336_K 1.19 0.37 0.00
136_A 108_V 1.19 0.36 0.00
20_S 29_V 1.18 0.36 0.00
107_Y 402_V 1.18 0.36 0.00
304_L 356_E 1.18 0.36 0.00
231_E 419_M 1.14 0.33 0.00
163_T 312_I 1.13 0.32 0.00
252_A 430_S 1.13 0.32 0.00
181_P 188_F 1.12 0.32 0.00
405_A 291_L 1.10 0.31 0.00
295_I 51_I 1.10 0.30 0.00
377_V 174_D 1.09 0.30 0.00
197_H 332_K 1.09 0.30 0.00
189_L 220_I 1.09 0.30 0.00
189_L 348_T 1.08 0.29 0.00
434_F 327_D 1.08 0.29 0.00
352_I 169_I 1.07 0.29 0.00
344_F 424_I 1.07 0.28 0.00
84_Y 410_N 1.07 0.28 0.00
231_E 197_Q 1.06 0.28 0.00
274_V 211_L 1.05 0.27 0.00
185_V 167_Y 1.03 0.26 0.00
197_H 371_Q 1.03 0.26 0.00
93_L 168_S 1.02 0.25 0.00
122_G 329_A 1.01 0.24 0.00
14_V 402_V 1.01 0.24 0.00
327_N 302_T 1.00 0.24 0.00
98_P 16_S 1.00 0.24 0.00
231_E 392_K 1.00 0.24 0.00
290_A 108_V 1.00 0.24 0.00
37_V 213_E 0.99 0.24 0.00
377_V 125_L 0.98 0.23 0.00
122_G 342_F 0.98 0.23 0.00
361_E 425_Q 0.98 0.23 0.00
274_V 108_V 0.98 0.23 0.00
97_I 185_E 0.98 0.23 0.00
147_I 25_M 0.97 0.23 0.00
431_Y 433_E 0.97 0.23 0.00
76_M 413_N 0.97 0.22 0.00
327_N 331_Q 0.96 0.22 0.00
25_A 174_D 0.96 0.22 0.00
99_V 335_S 0.96 0.22 0.00
271_D 60_S 0.96 0.22 0.00
272_I 106_L 0.96 0.21 0.00
124_T 168_S 0.95 0.21 0.00
352_I 134_L 0.95 0.21 0.00
98_P 67_A 0.95 0.21 0.00
197_H 123_H 0.95 0.21 0.00
231_E 249_Y 0.95 0.21 0.00
221_V 368_Y 0.94 0.21 0.00
331_S 175_F 0.94 0.21 0.00
115_I 190_A 0.94 0.21 0.00
402_V 417_V 0.94 0.21 0.00
144_A 230_D 0.93 0.20 0.00
25_A 292_K 0.93 0.20 0.00
406_V 323_I 0.93 0.20 0.00
418_V 286_L 0.93 0.20 0.00
98_P 143_S 0.93 0.20 0.00
231_E 354_L 0.92 0.20 0.00
98_P 306_I 0.92 0.20 0.00
402_V 295_S 0.92 0.20 0.00
94_E 108_V 0.92 0.20 0.00
117_I 30_Q 0.92 0.20 0.00
82_I 143_S 0.92 0.20 0.00
430_M 134_L 0.92 0.20 0.00
137_G 40_T 0.92 0.20 0.00
244_S 302_T 0.92 0.19 0.00
290_A 329_A 0.92 0.19 0.00
99_V 217_E 0.91 0.19 0.00
130_I 222_Y 0.91 0.19 0.00
13_L 282_I 0.91 0.19 0.00
185_V 59_I 0.91 0.19 0.00
274_V 193_D 0.91 0.19 0.00
289_V 427_Y 0.91 0.19 0.00
314_L 354_L 0.91 0.19 0.00
197_H 304_K 0.91 0.19 0.00
99_V 91_R 0.90 0.19 0.00
331_S 402_V 0.90 0.19 0.00
366_I 232_I 0.90 0.19 0.00
128_T 85_K 0.90 0.18 0.00
130_I 77_E 0.89 0.18 0.00
307_F 206_G 0.89 0.18 0.00
14_V 195_A 0.89 0.18 0.00
24_A 16_S 0.89 0.18 0.00
213_Q 424_I 0.88 0.18 0.00
439_D 185_E 0.88 0.18 0.00
416_G 129_T 0.88 0.18 0.00
431_Y 283_D 0.88 0.18 0.00
245_T 219_P 0.87 0.17 0.00
76_M 232_I 0.87 0.17 0.00
13_L 342_F 0.87 0.17 0.00
139_Q 60_S 0.87 0.17 0.00
375_M 206_G 0.87 0.17 0.00
375_M 210_K 0.87 0.17 0.00
434_F 363_Q 0.87 0.17 0.00
104_E 221_Y 0.87 0.17 0.00
376_V 369_L 0.86 0.17 0.00
339_K 351_I 0.86 0.17 0.00
227_G 60_S 0.86 0.17 0.00
422_S 24_Q 0.86 0.17 0.00
23_A 374_G 0.86 0.17 0.00
448_L 37_Y 0.85 0.17 0.00
431_Y 195_A 0.85 0.16 0.00
27_L 387_E 0.85 0.16 0.00
79_N 294_F 0.85 0.16 0.00
267_M 325_T 0.85 0.16 0.00
430_M 138_G 0.85 0.16 0.00
200_F 179_D 0.85 0.16 0.00
228_I 37_Y 0.85 0.16 0.00
103_V 297_V 0.85 0.16 0.00
382_A 329_A 0.85 0.16 0.00
231_E 25_M 0.85 0.16 0.00
352_I 324_A 0.85 0.16 0.00
444_T 29_V 0.85 0.16 0.00
274_V 56_P 0.85 0.16 0.00
325_F 103_F 0.84 0.16 0.00
20_S 428_E 0.84 0.16 0.00
367_P 341_I 0.84 0.16 0.00
341_L 430_S 0.84 0.16 0.00
83_P 143_S 0.83 0.16 0.00
201_E 416_Y 0.83 0.15 0.00
8_E 423_D 0.83 0.15 0.00
422_S 249_Y 0.83 0.15 0.00
102_E 385_K 0.83 0.15 0.00
336_A 243_S 0.83 0.15 0.00
245_T 139_T 0.83 0.15 0.00
231_E 147_N 0.82 0.15 0.00
107_Y 425_Q 0.82 0.15 0.00
229_S 419_M 0.82 0.15 0.00
323_I 246_K 0.82 0.15 0.00
445_F 119_G 0.82 0.15 0.00
212_N 416_Y 0.82 0.15 0.00
433_N 309_T 0.81 0.15 0.00
386_K 106_L 0.81 0.15 0.00
90_K 290_H 0.81 0.15 0.00
267_M 211_L 0.81 0.15 0.00
197_H 302_T 0.81 0.15 0.00
96_Q 40_T 0.81 0.15 0.00
139_Q 73_P 0.81 0.15 0.00
308_G 59_I 0.81 0.14 0.00
431_Y 23_H 0.81 0.14 0.00
100_L 16_S 0.81 0.14 0.00
165_V 40_T 0.80 0.14 0.00
14_V 358_A 0.80 0.14 0.00
175_G 210_K 0.80 0.14 0.00
82_I 283_D 0.80 0.14 0.00
444_T 179_D 0.80 0.14 0.00
367_P 396_H 0.80 0.14 0.00
350_I 134_L 0.80 0.14 0.00
208_W 193_D 0.80 0.14 0.00
327_N 267_I 0.80 0.14 0.00
55_E 73_P 0.79 0.14 0.00
13_L 187_V 0.79 0.14 0.00
373_K 214_I 0.79 0.14 0.00
96_Q 309_T 0.79 0.14 0.00
283_A 406_S 0.79 0.14 0.00
25_A 390_A 0.79 0.14 0.00
9_N 168_S 0.79 0.14 0.00
9_N 106_L 0.79 0.14 0.00
149_F 406_S 0.79 0.14 0.00
221_V 410_N 0.79 0.14 0.00
438_G 94_E 0.79 0.14 0.00
323_I 179_D 0.79 0.14 0.00
149_F 64_E 0.79 0.14 0.00
30_K 289_E 0.79 0.14 0.00
120_S 366_S 0.79 0.14 0.00
316_S 23_H 0.79 0.14 0.00
74_C 39_F 0.78 0.14 0.00
303_T 108_V 0.78 0.14 0.00
232_L 402_V 0.78 0.14 0.00
271_D 424_I 0.78 0.14 0.00
115_I 293_T 0.78 0.14 0.00
430_M 304_K 0.78 0.14 0.00
91_K 168_S 0.78 0.14 0.00
229_S 354_L 0.78 0.13 0.00
229_S 392_K 0.78 0.13 0.00
389_A 204_I 0.78 0.13 0.00
430_M 43_G 0.78 0.13 0.00
115_I 85_K 0.78 0.13 0.00
369_I 289_E 0.78 0.13 0.00
382_A 125_L 0.78 0.13 0.00
185_V 192_N 0.78 0.13 0.00
336_A 342_F 0.78 0.13 0.00
385_V 123_H 0.78 0.13 0.00
23_A 342_F 0.78 0.13 0.00
254_V 363_Q 0.77 0.13 0.00
73_F 187_V 0.77 0.13 0.00
114_L 183_G 0.77 0.13 0.00
55_E 312_I 0.77 0.13 0.00
402_V 310_V 0.77 0.13 0.00
113_Q 341_I 0.77 0.13 0.00
315_Q 338_I 0.77 0.13 0.00
104_E 16_S 0.77 0.13 0.00
293_A 247_V 0.77 0.13 0.00
232_L 227_D 0.77 0.13 0.00
244_S 267_I 0.77 0.13 0.00
183_I 428_E 0.77 0.13 0.00
191_P 322_I 0.77 0.13 0.00
362_F 184_L 0.77 0.13 0.00
25_A 302_T 0.77 0.13 0.00
402_V 234_K 0.77 0.13 0.00
179_F 208_D 0.77 0.13 0.00
430_M 123_H 0.77 0.13 0.00
315_Q 244_D 0.77 0.13 0.00
225_N 81_Y 0.76 0.13 0.00
141_G 254_I 0.76 0.13 0.00
165_V 297_V 0.76 0.13 0.00
94_E 73_P 0.76 0.13 0.00
37_V 40_T 0.76 0.13 0.00
246_T 89_F 0.76 0.13 0.00
197_H 426_L 0.76 0.13 0.00
331_S 429_R 0.76 0.13 0.00
64_H 413_N 0.76 0.13 0.00
250_D 126_K 0.76 0.13 0.00
273_G 188_F 0.76 0.13 0.00
327_N 124_V 0.76 0.13 0.00
5_T 297_V 0.75 0.12 0.00
149_F 257_F 0.75 0.12 0.00
439_D 126_K 0.75 0.12 0.00
331_S 320_T 0.75 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)
ID Seq/Len Name Options I_Prob Status
11333 0.59 murmurs Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11322 0.66 murmurs Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11321 0.01 murmurs Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
11320 3.23 murmurs Δgene:(0, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
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