May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_1_4_cI_3_2_tt
Genes: A B A+B
Length: 438 783 1169
Sequences: 2611 1296 1006
Seq/Len: 5.96 1.66 0.86
MirrorTree (Pazo et al. 2001) 0.58
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 0.73
2 0.01 0.00 0.75
5 0.01 0.01 0.76
10 0.02 0.01 0.76
20 0.03 0.01 0.76
100 0.05 0.03 0.77
∞ 0.14 0.10 0.82
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
392_P 102_E 1.33 0.59 0.00
390_L 110_F 1.29 0.55 0.00
389_A 102_E 1.19 0.47 0.00
389_A 156_R 1.18 0.46 0.00
396_G 99_V 1.14 0.43 0.00
198_N 185_K 1.04 0.34 0.00
57_V 105_A 1.03 0.33 0.00
171_L 527_R 1.02 0.33 0.00
115_I 8_D 1.02 0.33 0.00
266_L 19_V 1.02 0.32 0.00
386_N 156_R 1.01 0.32 0.00
52_E 479_A 1.00 0.31 0.00
361_E 114_N 0.98 0.29 0.00
69_G 767_A 0.96 0.28 0.00
90_I 204_E 0.96 0.28 0.00
227_V 584_V 0.95 0.27 0.00
237_W 212_G 0.94 0.26 0.00
328_V 93_V 0.94 0.26 0.00
278_E 614_L 0.93 0.26 0.00
369_N 207_V 0.92 0.25 0.00
231_M 424_H 0.91 0.25 0.00
150_K 327_L 0.90 0.24 0.00
208_Q 22_A 0.89 0.23 0.00
410_V 37_K 0.89 0.23 0.00
268_M 23_V 0.88 0.23 0.00
189_M 204_E 0.88 0.22 0.00
69_G 79_L 0.87 0.22 0.00
59_R 194_V 0.87 0.22 0.00
226_S 92_V 0.86 0.21 0.00
268_M 505_L 0.86 0.21 0.00
69_G 735_A 0.85 0.21 0.00
309_T 576_A 0.85 0.21 0.00
238_F 747_V 0.85 0.21 0.00
335_V 613_H 0.85 0.20 0.00
154_A 689_K 0.85 0.20 0.00
122_G 213_T 0.84 0.20 0.00
163_F 157_F 0.84 0.20 0.00
240_Q 487_S 0.84 0.20 0.00
60_S 369_L 0.84 0.20 0.00
205_F 641_L 0.84 0.20 0.00
386_N 607_F 0.83 0.20 0.00
51_D 492_K 0.83 0.20 0.00
69_G 622_L 0.83 0.19 0.00
123_Y 89_D 0.83 0.19 0.00
224_L 87_V 0.83 0.19 0.00
84_G 82_S 0.82 0.19 0.00
192_L 577_L 0.82 0.19 0.00
385_E 488_E 0.82 0.19 0.00
266_L 627_A 0.81 0.19 0.00
161_N 440_R 0.81 0.19 0.00
202_K 44_A 0.81 0.19 0.00
264_Y 130_L 0.81 0.18 0.00
53_V 626_P 0.81 0.18 0.00
115_I 16_G 0.81 0.18 0.00
55_E 7_N 0.81 0.18 0.00
165_T 654_F 0.80 0.18 0.00
134_V 474_R 0.80 0.18 0.00
163_F 591_H 0.80 0.18 0.00
30_D 15_P 0.79 0.17 0.00
223_T 29_D 0.79 0.17 0.00
266_L 52_I 0.79 0.17 0.00
202_K 769_L 0.79 0.17 0.00
238_F 302_D 0.79 0.17 0.00
425_A 502_N 0.79 0.17 0.00
218_I 88_A 0.79 0.17 0.00
410_V 7_N 0.79 0.17 0.00
114_L 188_V 0.79 0.17 0.00
214_K 451_F 0.78 0.17 0.00
206_P 85_T 0.78 0.17 0.00
51_D 484_K 0.78 0.17 0.00
143_D 446_D 0.78 0.17 0.00
57_V 552_G 0.78 0.17 0.00
162_L 644_L 0.78 0.17 0.00
235_A 450_L 0.77 0.17 0.00
69_G 386_S 0.77 0.17 0.00
260_R 88_A 0.77 0.16 0.00
69_G 776_L 0.77 0.16 0.00
89_L 324_E 0.77 0.16 0.00
53_V 215_D 0.77 0.16 0.00
45_L 567_Y 0.76 0.16 0.00
361_E 245_R 0.76 0.16 0.00
415_R 597_Y 0.76 0.16 0.00
91_C 712_A 0.76 0.16 0.00
281_G 486_G 0.76 0.16 0.00
96_S 121_T 0.75 0.16 0.00
154_A 476_I 0.75 0.15 0.00
187_A 753_V 0.75 0.15 0.00
213_G 365_K 0.75 0.15 0.00
192_L 271_S 0.75 0.15 0.00
29_L 332_G 0.75 0.15 0.00
30_D 94_D 0.75 0.15 0.00
358_P 46_R 0.75 0.15 0.00
173_V 573_P 0.75 0.15 0.00
60_S 302_D 0.75 0.15 0.00
227_V 695_R 0.75 0.15 0.00
118_M 12_E 0.74 0.15 0.00
414_L 157_F 0.74 0.15 0.00
134_V 237_D 0.74 0.15 0.00
232_E 413_L 0.74 0.15 0.00
208_Q 11_V 0.74 0.15 0.00
59_R 584_V 0.74 0.15 0.00
382_K 3_R 0.74 0.15 0.00
150_K 500_A 0.74 0.15 0.00
89_L 156_R 0.74 0.15 0.00
363_V 205_R 0.74 0.15 0.00
165_T 417_V 0.73 0.15 0.00
218_I 414_S 0.73 0.15 0.00
121_A 461_W 0.73 0.15 0.00
312_S 453_P 0.73 0.14 0.00
420_Q 278_R 0.73 0.14 0.00
106_I 749_H 0.73 0.14 0.00
173_V 751_E 0.73 0.14 0.00
417_F 718_A 0.73 0.14 0.00
59_R 82_S 0.73 0.14 0.00
326_G 638_L 0.72 0.14 0.00
115_I 424_H 0.72 0.14 0.00
90_I 405_E 0.72 0.14 0.00
402_L 768_G 0.72 0.14 0.00
253_Q 111_T 0.72 0.14 0.00
144_R 30_V 0.72 0.14 0.00
84_G 581_R 0.72 0.14 0.00
72_T 397_L 0.72 0.14 0.00
72_T 505_L 0.72 0.14 0.00
173_V 678_F 0.72 0.14 0.00
305_E 532_V 0.72 0.14 0.00
243_T 546_A 0.72 0.14 0.00
38_Y 236_L 0.72 0.14 0.00
218_I 478_L 0.72 0.14 0.00
213_G 641_L 0.72 0.14 0.00
168_S 591_H 0.72 0.14 0.00
72_T 746_R 0.72 0.14 0.00
96_S 269_T 0.71 0.14 0.00
34_R 597_Y 0.71 0.14 0.00
166_D 1_M 0.71 0.14 0.00
288_Q 104_Q 0.71 0.14 0.00
61_G 505_L 0.71 0.14 0.00
90_I 750_R 0.71 0.14 0.00
259_K 4_V 0.71 0.14 0.00
122_G 11_V 0.71 0.14 0.00
381_E 338_G 0.71 0.14 0.00
181_I 313_K 0.71 0.14 0.00
59_R 7_N 0.71 0.14 0.00
304_E 481_L 0.71 0.14 0.00
160_K 30_V 0.70 0.13 0.00
106_I 644_L 0.70 0.13 0.00
357_T 225_N 0.70 0.13 0.00
224_L 273_E 0.70 0.13 0.00
328_V 511_V 0.70 0.13 0.00
164_G 313_K 0.70 0.13 0.00
61_G 413_L 0.70 0.13 0.00
72_T 331_E 0.70 0.13 0.00
72_T 715_E 0.70 0.13 0.00
425_A 573_P 0.70 0.13 0.00
238_F 255_T 0.70 0.13 0.00
49_T 578_K 0.69 0.13 0.00
48_K 648_L 0.69 0.13 0.00
202_K 302_D 0.69 0.13 0.00
154_A 436_Q 0.69 0.13 0.00
169_F 618_E 0.69 0.13 0.00
106_I 393_A 0.69 0.13 0.00
51_D 596_R 0.69 0.13 0.00
33_L 417_V 0.69 0.13 0.00
268_M 637_A 0.69 0.13 0.00
236_D 745_A 0.69 0.13 0.00
327_G 220_S 0.69 0.13 0.00
39_E 313_K 0.69 0.13 0.00
70_F 295_R 0.69 0.13 0.00
6_L 644_L 0.69 0.13 0.00
82_D 417_V 0.69 0.13 0.00
245_Q 330_K 0.69 0.13 0.00
391_L 89_D 0.69 0.13 0.00
370_L 96_L 0.69 0.13 0.00
36_G 729_P 0.69 0.13 0.00
114_L 204_E 0.69 0.13 0.00
121_A 453_P 0.69 0.13 0.00
327_G 93_V 0.69 0.13 0.00
258_V 605_P 0.68 0.13 0.00
100_S 201_D 0.68 0.13 0.00
179_A 205_R 0.68 0.13 0.00
192_L 18_S 0.68 0.13 0.00
260_R 715_E 0.68 0.12 0.00
110_V 113_L 0.68 0.12 0.00
218_I 142_K 0.68 0.12 0.00
417_F 584_V 0.68 0.12 0.00
69_G 754_P 0.68 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
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
Page generated in 1.2468 seconds.