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OPENSEQ.org
cI_1_40_cI_3_40_tt
Genes: A B A+B
Length: 438 783 1179
Sequences: 2218 1200 902
Seq/Len: 5.06 1.53 0.77
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 0.01 0.00 0.67
2 0.01 0.00 0.69
5 0.01 0.01 0.70
10 0.02 0.01 0.70
20 0.02 0.02 0.70
100 0.04 0.03 0.71
∞ 0.12 0.10 0.74
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
386_N 156_R 1.40 0.61 0.00
392_P 102_E 1.37 0.59 0.00
389_A 102_E 1.19 0.43 0.00
389_A 156_R 1.19 0.43 0.00
57_V 105_A 1.15 0.40 0.00
390_L 110_F 1.10 0.36 0.00
266_L 19_V 1.08 0.35 0.00
69_G 767_A 1.06 0.33 0.00
171_L 527_R 1.04 0.32 0.00
69_G 79_L 1.04 0.31 0.00
122_G 213_T 1.00 0.29 0.00
223_T 415_E 1.00 0.29 0.00
59_R 194_V 1.00 0.28 0.00
232_E 413_L 1.00 0.28 0.00
150_K 327_L 0.99 0.28 0.00
227_V 584_V 0.97 0.27 0.00
198_N 185_K 0.95 0.26 0.00
396_G 99_V 0.95 0.25 0.00
231_M 89_D 0.95 0.25 0.00
274_E 89_D 0.95 0.25 0.00
165_T 654_F 0.94 0.25 0.00
361_E 114_N 0.94 0.25 0.00
69_G 735_A 0.94 0.25 0.00
235_A 107_M 0.94 0.24 0.00
69_G 386_S 0.93 0.24 0.00
273_R 567_Y 0.93 0.24 0.00
226_S 92_V 0.93 0.24 0.00
90_I 204_E 0.92 0.23 0.00
114_L 188_V 0.92 0.23 0.00
386_N 607_F 0.92 0.23 0.00
85_K 89_D 0.91 0.23 0.00
202_K 769_L 0.90 0.22 0.00
106_I 393_A 0.90 0.22 0.00
369_N 207_V 0.90 0.22 0.00
410_V 37_K 0.90 0.22 0.00
69_G 622_L 0.89 0.21 0.00
329_I 105_A 0.88 0.21 0.00
236_D 745_A 0.88 0.21 0.00
166_D 1_M 0.88 0.21 0.00
187_A 753_V 0.88 0.21 0.00
390_L 312_R 0.88 0.21 0.00
312_S 453_P 0.87 0.20 0.00
419_D 667_R 0.86 0.20 0.00
189_M 204_E 0.86 0.20 0.00
198_N 157_F 0.85 0.20 0.00
308_D 532_V 0.85 0.19 0.00
231_M 627_A 0.85 0.19 0.00
271_T 321_T 0.84 0.19 0.00
69_G 776_L 0.84 0.19 0.00
162_L 644_L 0.84 0.19 0.00
285_E 389_D 0.84 0.19 0.00
121_A 453_P 0.84 0.19 0.00
238_F 2_V 0.84 0.19 0.00
171_L 360_L 0.84 0.19 0.00
214_K 270_R 0.84 0.19 0.00
237_W 212_G 0.84 0.18 0.00
153_R 1_M 0.83 0.18 0.00
53_V 361_A 0.83 0.18 0.00
100_S 201_D 0.83 0.18 0.00
173_V 573_P 0.83 0.18 0.00
329_I 3_R 0.82 0.18 0.00
318_A 753_V 0.82 0.18 0.00
231_M 424_H 0.82 0.18 0.00
186_T 596_R 0.81 0.17 0.00
36_G 729_P 0.81 0.17 0.00
29_L 332_G 0.81 0.17 0.00
55_E 396_A 0.81 0.17 0.00
69_G 270_R 0.81 0.17 0.00
181_I 132_D 0.81 0.17 0.00
166_D 369_L 0.81 0.17 0.00
28_T 626_P 0.81 0.17 0.00
115_I 7_N 0.81 0.17 0.00
118_M 98_D 0.81 0.17 0.00
49_T 578_K 0.81 0.17 0.00
72_T 369_L 0.80 0.17 0.00
402_L 768_G 0.80 0.17 0.00
166_D 3_R 0.80 0.17 0.00
74_L 454_Y 0.80 0.17 0.00
121_A 526_E 0.80 0.17 0.00
314_E 342_G 0.80 0.17 0.00
69_G 754_P 0.80 0.17 0.00
173_V 751_E 0.80 0.17 0.00
150_K 735_A 0.80 0.17 0.00
218_I 333_L 0.80 0.17 0.00
187_A 584_V 0.80 0.17 0.00
357_T 189_R 0.80 0.17 0.00
61_G 505_L 0.80 0.17 0.00
357_T 225_N 0.79 0.16 0.00
119_I 692_F 0.79 0.16 0.00
308_D 552_G 0.79 0.16 0.00
377_G 673_M 0.79 0.16 0.00
410_V 7_N 0.79 0.16 0.00
122_G 25_H 0.79 0.16 0.00
72_T 397_L 0.79 0.16 0.00
192_L 18_S 0.79 0.16 0.00
417_F 584_V 0.79 0.16 0.00
61_G 413_L 0.79 0.16 0.00
363_V 636_G 0.79 0.16 0.00
330_L 472_E 0.79 0.16 0.00
38_Y 236_L 0.79 0.16 0.00
313_Y 676_L 0.78 0.16 0.00
46_K 728_L 0.78 0.16 0.00
415_R 597_Y 0.78 0.16 0.00
326_G 736_V 0.78 0.16 0.00
224_L 87_V 0.78 0.16 0.00
274_E 559_D 0.78 0.16 0.00
309_T 576_A 0.78 0.16 0.00
89_L 732_A 0.78 0.16 0.00
218_I 344_Y 0.78 0.16 0.00
288_Q 104_Q 0.78 0.16 0.00
202_K 44_A 0.78 0.15 0.00
223_T 329_L 0.78 0.15 0.00
414_L 472_E 0.78 0.15 0.00
227_V 227_T 0.77 0.15 0.00
51_D 492_K 0.77 0.15 0.00
419_D 215_D 0.77 0.15 0.00
161_N 273_E 0.77 0.15 0.00
213_G 365_K 0.77 0.15 0.00
51_D 417_V 0.77 0.15 0.00
292_P 194_V 0.77 0.15 0.00
253_Q 111_T 0.77 0.15 0.00
90_I 750_R 0.77 0.15 0.00
114_L 229_I 0.77 0.15 0.00
134_V 237_D 0.76 0.15 0.00
165_T 417_V 0.76 0.15 0.00
240_Q 396_A 0.76 0.15 0.00
152_A 126_G 0.76 0.15 0.00
388_E 630_E 0.76 0.15 0.00
53_V 626_P 0.76 0.15 0.00
168_S 592_P 0.76 0.15 0.00
96_S 628_P 0.76 0.15 0.00
420_Q 278_R 0.76 0.15 0.00
83_D 19_V 0.76 0.15 0.00
96_S 269_T 0.76 0.15 0.00
226_S 179_E 0.76 0.15 0.00
266_L 52_I 0.76 0.15 0.00
266_L 136_E 0.76 0.15 0.00
55_E 724_R 0.76 0.15 0.00
154_A 729_P 0.76 0.15 0.00
109_D 30_V 0.75 0.15 0.00
34_R 662_K 0.75 0.15 0.00
292_P 280_R 0.75 0.15 0.00
119_I 467_V 0.75 0.15 0.00
285_E 51_R 0.75 0.14 0.00
212_W 329_L 0.75 0.14 0.00
160_K 478_L 0.75 0.14 0.00
172_H 21_D 0.74 0.14 0.00
123_Y 89_D 0.74 0.14 0.00
382_K 3_R 0.74 0.14 0.00
30_D 94_D 0.74 0.14 0.00
237_W 350_T 0.74 0.14 0.00
39_E 728_L 0.74 0.14 0.00
326_G 638_L 0.74 0.14 0.00
316_L 341_V 0.74 0.14 0.00
48_K 648_L 0.74 0.14 0.00
250_K 622_L 0.74 0.14 0.00
226_S 20_M 0.74 0.14 0.00
72_T 746_R 0.74 0.14 0.00
238_F 740_F 0.74 0.14 0.00
236_D 10_I 0.74 0.14 0.00
402_L 451_F 0.74 0.14 0.00
161_N 440_R 0.74 0.14 0.00
53_V 364_L 0.74 0.14 0.00
118_M 101_R 0.73 0.14 0.00
132_I 307_K 0.73 0.14 0.00
106_I 186_R 0.73 0.14 0.00
275_L 360_L 0.73 0.14 0.00
179_A 205_R 0.73 0.14 0.00
259_K 630_E 0.73 0.14 0.00
171_L 188_V 0.73 0.14 0.00
260_R 716_L 0.73 0.14 0.00
181_I 77_P 0.73 0.14 0.00
308_D 736_V 0.73 0.14 0.00
308_D 674_G 0.73 0.13 0.00
326_G 652_P 0.73 0.13 0.00
379_G 245_R 0.72 0.13 0.00
86_Q 524_L 0.72 0.13 0.00
391_L 21_D 0.72 0.13 0.00
192_L 19_V 0.72 0.13 0.00
314_E 554_K 0.72 0.13 0.00
51_D 736_V 0.72 0.13 0.00
119_I 579_G 0.72 0.13 0.00
192_L 257_A 0.71 0.13 0.00
59_R 7_N 0.71 0.13 0.00
59_R 724_R 0.71 0.13 0.00
90_I 138_G 0.71 0.13 0.00
327_G 220_S 0.71 0.13 0.00
407_V 228_D 0.71 0.13 0.00
169_F 618_E 0.71 0.13 0.00
342_W 258_L 0.71 0.13 0.00
223_T 29_D 0.71 0.13 0.00
141_A 432_F 0.71 0.13 0.00
192_L 271_S 0.71 0.13 0.00
55_E 9_R 0.71 0.13 0.00
425_A 502_N 0.71 0.13 0.00
199_P 233_G 0.71 0.13 0.00
192_L 246_N 0.71 0.13 0.00
53_V 478_L 0.71 0.13 0.00
206_P 85_T 0.71 0.13 0.00
69_G 744_E 0.71 0.13 0.00
160_K 562_G 0.70 0.13 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
4770 0.74 cI_1_4_cI_3_4_d1_tt Δgene:(1, 1) A:(1E-04, 1) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4747 0.8 cI_1_60_1_cI_3_4_tt Δgene:(1, ∞) A:(1E-60, 1) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4746 0.16 cI_1_20_1_cI_3_20_1_tt Δgene:(1, ∞) A:(1E-20, 1) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4745 0.86 cI_1_4_cI_3_2_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4744 0.84 cI_1_4_cI_3_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4742 0.77 cI_1_40_cI_3_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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