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OPENSEQ.org
xtric8AxtGa13
Genes: A B A+B
Length: 539 374 871
Sequences: 397 2186 60
Seq/Len: 0.74 5.84 0.07
MirrorTree (Pazo et al. 2001) 0.33
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 0.05 0.10 0.00
2 0.05 0.10 0.00
5 0.05 0.11 0.00
10 0.05 0.11 0.01
20 0.05 0.12 0.01
100 0.05 0.14 0.01
∞ 0.05 0.17 0.07
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
343_L 99_L 1.29 0.12 0.00
370_D 237_F 1.28 0.12 0.00
167_R 205_G 1.26 0.11 0.00
501_E 38_L 1.26 0.11 0.00
68_E 35_D 1.21 0.10 0.00
464_V 64_F 1.21 0.10 0.00
167_R 50_K 1.19 0.10 0.00
126_I 30_K 1.15 0.09 0.00
319_E 26_E 1.14 0.09 0.00
487_E 330_F 1.13 0.09 0.00
368_L 297_E 1.12 0.09 0.00
239_T 298_E 1.12 0.09 0.00
321_L 167_E 1.11 0.09 0.00
238_I 192_S 1.11 0.09 0.00
288_V 77_D 1.11 0.09 0.00
284_V 24_E 1.10 0.09 0.00
123_C 187_K 1.08 0.08 0.00
491_L 191_P 1.07 0.08 0.00
361_R 154_A 1.06 0.08 0.00
46_L 222_D 1.06 0.08 0.00
238_I 139_T 1.05 0.08 0.00
464_V 317_H 1.05 0.08 0.00
461_I 109_P 1.05 0.08 0.00
292_L 184_L 1.04 0.08 0.00
232_L 288_L 1.04 0.08 0.00
284_V 36_R 1.03 0.08 0.00
441_G 71_I 1.03 0.08 0.00
232_L 233_W 1.03 0.08 0.00
471_K 43_T 1.03 0.08 0.00
370_D 152_L 1.02 0.07 0.00
381_L 85_R 1.02 0.07 0.00
464_V 76_F 1.02 0.07 0.00
168_L 149_I 1.01 0.07 0.00
70_I 122_M 1.00 0.07 0.00
388_L 86_A 1.00 0.07 0.00
342_V 192_S 1.00 0.07 0.00
345_L 265_L 0.99 0.07 0.00
430_A 188_D 0.99 0.07 0.00
259_A 122_M 0.99 0.07 0.00
111_D 104_E 0.99 0.07 0.00
73_L 298_E 0.98 0.07 0.00
96_A 24_E 0.98 0.07 0.00
495_F 50_K 0.98 0.07 0.00
70_I 183_K 0.98 0.07 0.00
428_L 38_L 0.97 0.07 0.00
369_R 190_L 0.97 0.07 0.00
206_S 47_R 0.97 0.07 0.00
477_D 326_L 0.96 0.07 0.00
461_I 99_L 0.96 0.07 0.00
47_G 21_T 0.96 0.07 0.00
412_V 182_D 0.96 0.07 0.00
434_L 149_I 0.96 0.07 0.00
502_Q 191_P 0.95 0.07 0.00
232_L 205_G 0.95 0.07 0.00
81_S 99_L 0.95 0.07 0.00
59_Q 151_S 0.95 0.07 0.00
404_L 346_F 0.95 0.07 0.00
426_G 191_P 0.95 0.07 0.00
86_R 181_L 0.95 0.07 0.00
504_I 186_D 0.94 0.07 0.00
345_L 103_R 0.94 0.07 0.00
28_E 50_K 0.94 0.07 0.00
515_L 36_R 0.94 0.07 0.00
238_I 113_P 0.94 0.07 0.00
266_L 31_S 0.94 0.07 0.00
118_A 153_W 0.94 0.07 0.00
223_E 141_V 0.94 0.07 0.00
415_F 326_L 0.94 0.07 0.00
199_S 30_K 0.94 0.07 0.00
48_E 89_Y 0.93 0.07 0.00
187_L 108_I 0.93 0.07 0.00
232_L 237_F 0.93 0.06 0.00
75_R 189_Y 0.93 0.06 0.00
265_C 152_L 0.93 0.06 0.00
164_F 181_L 0.93 0.06 0.00
453_E 192_S 0.93 0.06 0.00
290_L 239_S 0.92 0.06 0.00
406_V 86_A 0.92 0.06 0.00
381_L 34_I 0.92 0.06 0.00
325_L 197_L 0.92 0.06 0.00
504_I 188_D 0.92 0.06 0.00
236_F 188_D 0.92 0.06 0.00
137_K 238_D 0.92 0.06 0.00
130_V 47_R 0.92 0.06 0.00
464_V 372_Q 0.91 0.06 0.00
501_E 355_R 0.91 0.06 0.00
487_E 230_R 0.91 0.06 0.00
74_S 81_K 0.91 0.06 0.00
479_M 250_S 0.91 0.06 0.00
416_V 188_D 0.91 0.06 0.00
484_K 189_Y 0.91 0.06 0.00
95_Y 261_Q 0.90 0.06 0.00
378_G 152_L 0.90 0.06 0.00
357_R 284_V 0.90 0.06 0.00
126_I 185_G 0.90 0.06 0.00
513_G 252_Y 0.90 0.06 0.00
487_E 191_P 0.90 0.06 0.00
245_R 279_R 0.89 0.06 0.00
81_S 141_V 0.89 0.06 0.00
236_F 38_L 0.89 0.06 0.00
399_C 109_P 0.89 0.06 0.00
401_A 88_I 0.88 0.06 0.00
330_D 93_I 0.88 0.06 0.00
357_R 294_D 0.88 0.06 0.00
364_V 85_R 0.88 0.06 0.00
512_D 283_N 0.88 0.06 0.00
322_I 87_T 0.88 0.06 0.00
508_G 158_I 0.88 0.06 0.00
392_V 166_R 0.88 0.06 0.00
334_K 85_R 0.88 0.06 0.00
167_R 352_T 0.87 0.06 0.00
195_D 36_R 0.87 0.06 0.00
262_L 46_K 0.87 0.06 0.00
422_G 208_E 0.87 0.06 0.00
265_C 296_L 0.87 0.06 0.00
167_R 370_L 0.86 0.06 0.00
391_H 88_I 0.86 0.06 0.00
339_L 320_E 0.86 0.06 0.00
461_I 329_C 0.86 0.06 0.00
325_L 309_F 0.86 0.06 0.00
481_E 179_D 0.86 0.06 0.00
491_L 330_F 0.86 0.06 0.00
79_A 188_D 0.86 0.06 0.00
503_I 285_S 0.86 0.06 0.00
480_T 243_I 0.86 0.06 0.00
332_G 317_H 0.85 0.06 0.00
149_L 274_T 0.85 0.06 0.00
121_G 30_K 0.85 0.06 0.00
464_V 360_D 0.85 0.06 0.00
123_C 188_D 0.85 0.06 0.00
322_I 335_R 0.84 0.06 0.00
151_L 186_D 0.84 0.06 0.00
478_G 152_L 0.84 0.06 0.00
346_L 296_L 0.84 0.06 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
9708 0.07 xtric8AxtGa13 Δgene:(0, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9621 0.01 xtric8AxtGa13 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) Killed - Shared
9342 0.06 xtRic8AxtGa13 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9299 0 xtRic8AxtGa13 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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