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OPENSEQ.org
cI_1_4_cI_3_4_tt
Genes: A B A+B
Length: 438 783 1169
Sequences: 2611 1268 985
Seq/Len: 5.96 1.62 0.84
MirrorTree (Pazo et al. 2001) 0.61
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 0.72
2 0.01 0.00 0.74
5 0.01 0.01 0.75
10 0.02 0.01 0.75
20 0.03 0.01 0.75
100 0.05 0.03 0.75
∞ 0.14 0.09 0.81
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 1.59 0.78 0.02
389_A 102_E 1.34 0.59 0.01
52_E 479_A 1.18 0.45 0.01
390_L 110_F 1.12 0.40 0.01
266_L 19_V 1.10 0.38 0.01
386_N 156_R 1.07 0.36 0.01
90_I 204_E 1.05 0.34 0.01
396_G 99_V 1.04 0.34 0.01
227_V 584_V 1.04 0.33 0.01
198_N 185_K 1.02 0.32 0.01
57_V 105_A 1.01 0.31 0.01
69_G 767_A 0.98 0.29 0.00
389_A 156_R 0.94 0.26 0.00
309_T 576_A 0.93 0.25 0.00
106_I 488_E 0.92 0.25 0.00
69_G 79_L 0.92 0.25 0.00
361_E 114_N 0.92 0.24 0.00
189_M 204_E 0.91 0.24 0.00
410_V 37_K 0.90 0.23 0.00
89_L 397_L 0.90 0.23 0.00
115_I 7_N 0.90 0.23 0.00
55_E 7_N 0.89 0.23 0.00
171_L 527_R 0.89 0.23 0.00
121_A 461_W 0.89 0.22 0.00
51_D 492_K 0.88 0.22 0.00
335_V 613_H 0.88 0.22 0.00
141_A 433_A 0.86 0.21 0.00
223_T 415_E 0.85 0.20 0.00
69_G 735_A 0.85 0.20 0.00
266_L 52_I 0.84 0.20 0.00
123_Y 89_D 0.84 0.20 0.00
69_G 622_L 0.84 0.20 0.00
226_S 92_V 0.84 0.20 0.00
224_L 87_V 0.83 0.19 0.00
214_K 451_F 0.83 0.19 0.00
386_N 607_F 0.83 0.19 0.00
51_D 736_V 0.83 0.19 0.00
150_K 327_L 0.83 0.19 0.00
192_L 18_S 0.83 0.19 0.00
313_Y 676_L 0.83 0.19 0.00
143_D 446_D 0.82 0.19 0.00
312_S 453_P 0.82 0.19 0.00
168_S 591_H 0.81 0.18 0.00
274_E 89_D 0.81 0.18 0.00
38_Y 236_L 0.81 0.18 0.00
239_A 602_L 0.81 0.18 0.00
369_N 207_V 0.80 0.18 0.00
49_T 578_K 0.80 0.18 0.00
163_F 157_F 0.80 0.18 0.00
166_D 3_R 0.80 0.18 0.00
28_T 626_P 0.80 0.17 0.00
327_G 93_V 0.80 0.17 0.00
202_K 44_A 0.79 0.17 0.00
72_T 397_L 0.79 0.17 0.00
122_G 213_T 0.79 0.17 0.00
382_K 3_R 0.79 0.17 0.00
187_A 753_V 0.79 0.17 0.00
192_L 271_S 0.79 0.17 0.00
202_K 769_L 0.79 0.17 0.00
96_S 121_T 0.79 0.17 0.00
53_V 671_E 0.79 0.17 0.00
153_R 1_M 0.78 0.17 0.00
268_M 23_V 0.78 0.17 0.00
328_V 93_V 0.78 0.17 0.00
29_L 332_G 0.78 0.17 0.00
240_Q 396_A 0.78 0.17 0.00
173_V 751_E 0.78 0.17 0.00
192_L 19_V 0.78 0.17 0.00
106_I 749_H 0.78 0.17 0.00
278_E 579_G 0.78 0.17 0.00
231_M 424_H 0.78 0.16 0.00
271_T 321_T 0.77 0.16 0.00
417_F 584_V 0.77 0.16 0.00
238_F 747_V 0.77 0.16 0.00
415_R 597_Y 0.77 0.16 0.00
425_A 502_N 0.77 0.16 0.00
42_K 480_L 0.77 0.16 0.00
90_I 605_P 0.77 0.16 0.00
278_E 323_E 0.77 0.16 0.00
69_G 386_S 0.77 0.16 0.00
173_V 573_P 0.77 0.16 0.00
278_E 614_L 0.76 0.16 0.00
162_L 644_L 0.76 0.16 0.00
314_E 342_G 0.76 0.15 0.00
60_S 369_L 0.76 0.15 0.00
223_T 329_L 0.75 0.15 0.00
357_T 225_N 0.75 0.15 0.00
268_M 505_L 0.75 0.15 0.00
60_S 302_D 0.75 0.15 0.00
143_D 479_A 0.75 0.15 0.00
187_A 584_V 0.75 0.15 0.00
286_P 323_E 0.75 0.15 0.00
149_I 450_L 0.75 0.15 0.00
106_I 393_A 0.75 0.15 0.00
236_D 601_V 0.75 0.15 0.00
326_G 652_P 0.75 0.15 0.00
165_T 654_F 0.75 0.15 0.00
173_V 312_R 0.75 0.15 0.00
153_R 413_L 0.75 0.15 0.00
223_T 29_D 0.74 0.15 0.00
89_L 692_F 0.74 0.15 0.00
34_R 662_K 0.74 0.15 0.00
327_G 220_S 0.74 0.15 0.00
53_V 626_P 0.74 0.15 0.00
419_D 667_R 0.74 0.15 0.00
166_D 1_M 0.74 0.15 0.00
275_L 360_L 0.74 0.15 0.00
410_V 7_N 0.74 0.15 0.00
292_P 280_R 0.73 0.14 0.00
90_I 750_R 0.73 0.14 0.00
114_L 229_I 0.73 0.14 0.00
59_R 194_V 0.73 0.14 0.00
186_T 596_R 0.73 0.14 0.00
326_G 638_L 0.73 0.14 0.00
167_F 734_V 0.73 0.14 0.00
208_Q 11_V 0.73 0.14 0.00
288_Q 104_Q 0.72 0.14 0.00
260_R 579_G 0.72 0.14 0.00
42_K 26_A 0.72 0.14 0.00
241_M 606_T 0.72 0.14 0.00
218_I 88_A 0.72 0.14 0.00
51_D 417_V 0.72 0.14 0.00
72_T 746_R 0.72 0.14 0.00
39_E 89_D 0.72 0.14 0.00
237_W 212_G 0.71 0.14 0.00
374_I 483_D 0.71 0.14 0.00
157_Y 290_I 0.71 0.14 0.00
390_L 312_R 0.71 0.14 0.00
213_G 641_L 0.71 0.14 0.00
149_I 462_A 0.71 0.14 0.00
236_D 413_L 0.71 0.14 0.00
91_C 712_A 0.71 0.14 0.00
235_A 517_A 0.71 0.14 0.00
318_A 753_V 0.71 0.13 0.00
308_D 314_E 0.71 0.13 0.00
417_F 718_A 0.71 0.13 0.00
56_E 100_V 0.71 0.13 0.00
236_D 745_A 0.71 0.13 0.00
132_I 307_K 0.71 0.13 0.00
179_A 205_R 0.70 0.13 0.00
72_T 85_T 0.70 0.13 0.00
186_T 550_L 0.70 0.13 0.00
42_K 462_A 0.70 0.13 0.00
253_Q 111_T 0.70 0.13 0.00
238_F 302_D 0.70 0.13 0.00
30_D 15_P 0.70 0.13 0.00
414_L 157_F 0.70 0.13 0.00
236_D 733_Q 0.70 0.13 0.00
382_K 12_E 0.70 0.13 0.00
115_I 8_D 0.70 0.13 0.00
57_V 355_L 0.70 0.13 0.00
402_L 768_G 0.70 0.13 0.00
34_R 479_A 0.70 0.13 0.00
100_S 201_D 0.69 0.13 0.00
371_F 569_G 0.69 0.13 0.00
213_G 365_K 0.69 0.13 0.00
301_P 26_A 0.69 0.13 0.00
57_V 621_V 0.69 0.13 0.00
368_V 462_A 0.69 0.13 0.00
119_I 323_E 0.69 0.13 0.00
114_L 204_E 0.69 0.13 0.00
28_T 687_E 0.69 0.13 0.00
420_Q 278_R 0.69 0.13 0.00
144_R 30_V 0.69 0.13 0.00
187_A 503_P 0.69 0.13 0.00
250_K 622_L 0.69 0.13 0.00
258_V 212_G 0.69 0.13 0.00
30_D 678_F 0.69 0.13 0.00
55_E 9_R 0.69 0.13 0.00
52_E 335_E 0.69 0.13 0.00
119_I 101_R 0.69 0.12 0.00
181_I 77_P 0.69 0.12 0.00
150_K 735_A 0.69 0.12 0.00
106_I 693_Y 0.69 0.12 0.00
30_D 94_D 0.69 0.12 0.00
171_L 157_F 0.68 0.12 0.00
370_L 96_L 0.68 0.12 0.00
388_E 496_A 0.68 0.12 0.00
48_K 648_L 0.68 0.12 0.00
205_F 641_L 0.68 0.12 0.00
258_V 76_Q 0.68 0.12 0.00
326_G 642_A 0.68 0.12 0.00
387_L 28_Y 0.68 0.12 0.00
7_S 105_A 0.68 0.12 0.00
82_D 579_G 0.68 0.12 0.00
249_M 338_G 0.68 0.12 0.00
227_V 227_T 0.68 0.12 0.00
218_I 142_K 0.68 0.12 0.00
50_P 772_E 0.68 0.12 0.00
171_L 505_L 0.68 0.12 0.00
170_D 89_D 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
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