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OPENSEQ.org
cI_3_40_cI_4_40_tt
Genes: A B A+B
Length: 783 409 1143
Sequences: 1200 1636 595
Seq/Len: 1.53 4 0.52
MirrorTree (Pazo et al. 2001) 0.64
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 0.00 0.00 0.01
2 0.00 0.00 0.01
5 0.01 0.00 0.34
10 0.01 0.01 0.35
20 0.02 0.01 0.35
100 0.03 0.01 0.36
∞ 0.10 0.05 0.50
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
421_K 52_V 1.59 0.64 0.00
93_V 221_V 1.34 0.45 0.00
728_L 250_K 1.33 0.45 0.00
18_S 131_V 1.26 0.39 0.00
290_I 395_A 1.18 0.33 0.00
645_A 283_M 1.15 0.31 0.00
108_V 43_L 1.14 0.30 0.00
673_M 264_V 1.11 0.29 0.00
10_I 59_I 1.11 0.28 0.00
616_N 295_E 1.10 0.28 0.00
398_V 221_V 1.09 0.27 0.00
640_V 109_V 1.06 0.26 0.00
99_V 144_T 1.05 0.25 0.00
177_D 157_L 1.05 0.25 0.00
552_G 244_V 1.05 0.25 0.00
522_R 357_I 1.04 0.24 0.00
284_E 385_C 1.03 0.24 0.00
7_N 235_T 1.03 0.24 0.00
30_V 133_L 1.03 0.24 0.00
673_M 250_K 1.02 0.23 0.00
629_I 52_V 1.02 0.23 0.00
14_P 52_V 1.00 0.22 0.00
579_G 391_P 1.00 0.22 0.00
157_F 194_L 1.00 0.22 0.00
538_A 291_K 1.00 0.22 0.00
2_V 357_I 0.99 0.22 0.00
4_V 250_K 0.98 0.21 0.00
740_F 36_S 0.98 0.21 0.00
754_P 280_I 0.97 0.20 0.00
106_G 393_M 0.96 0.20 0.00
437_I 285_E 0.96 0.20 0.00
730_E 244_V 0.96 0.20 0.00
240_A 222_G 0.96 0.20 0.00
270_R 80_T 0.95 0.20 0.00
583_V 285_E 0.95 0.20 0.00
304_N 108_V 0.95 0.20 0.00
26_A 218_A 0.94 0.19 0.00
82_S 210_E 0.94 0.19 0.00
107_M 398_A 0.94 0.19 0.00
747_V 184_E 0.94 0.19 0.00
255_T 368_V 0.93 0.18 0.00
728_L 52_V 0.93 0.18 0.00
309_P 329_K 0.92 0.18 0.00
413_L 221_V 0.92 0.18 0.00
229_I 320_S 0.91 0.18 0.00
280_R 79_I 0.91 0.18 0.00
453_P 339_K 0.91 0.17 0.00
575_E 44_M 0.90 0.17 0.00
450_L 221_V 0.89 0.17 0.00
753_V 168_F 0.89 0.17 0.00
658_L 285_E 0.89 0.17 0.00
243_R 104_L 0.89 0.17 0.00
524_L 140_L 0.89 0.17 0.00
749_H 269_R 0.89 0.17 0.00
428_H 98_A 0.89 0.17 0.00
524_L 316_L 0.88 0.17 0.00
734_V 109_V 0.88 0.17 0.00
417_V 70_M 0.88 0.16 0.00
424_H 48_S 0.88 0.16 0.00
587_L 65_G 0.88 0.16 0.00
134_T 368_V 0.88 0.16 0.00
732_A 285_E 0.88 0.16 0.00
212_G 218_A 0.88 0.16 0.00
13_V 291_K 0.87 0.16 0.00
274_L 272_V 0.87 0.16 0.00
539_A 242_S 0.87 0.16 0.00
102_E 99_L 0.87 0.16 0.00
635_E 386_K 0.87 0.16 0.00
758_L 48_S 0.87 0.16 0.00
404_E 36_S 0.86 0.16 0.00
342_G 385_C 0.86 0.16 0.00
277_I 397_I 0.86 0.16 0.00
30_V 227_E 0.85 0.15 0.00
511_V 395_A 0.85 0.15 0.00
127_A 222_G 0.85 0.15 0.00
19_V 45_V 0.85 0.15 0.00
737_E 259_T 0.85 0.15 0.00
169_P 390_V 0.85 0.15 0.00
260_P 295_E 0.85 0.15 0.00
716_L 109_V 0.85 0.15 0.00
350_T 232_L 0.85 0.15 0.00
132_D 81_Y 0.85 0.15 0.00
87_V 166_Q 0.85 0.15 0.00
357_A 232_L 0.85 0.15 0.00
556_A 385_C 0.84 0.15 0.00
618_E 131_V 0.84 0.15 0.00
416_F 250_K 0.84 0.15 0.00
82_S 213_I 0.84 0.15 0.00
723_A 79_I 0.84 0.15 0.00
30_V 104_L 0.84 0.15 0.00
311_V 279_R 0.83 0.14 0.00
557_S 235_T 0.83 0.14 0.00
327_L 52_V 0.83 0.14 0.00
444_R 36_S 0.83 0.14 0.00
744_E 107_A 0.82 0.14 0.00
350_T 357_I 0.82 0.14 0.00
394_D 194_L 0.82 0.14 0.00
182_I 81_Y 0.82 0.14 0.00
7_N 169_H 0.82 0.14 0.00
746_R 65_G 0.82 0.14 0.00
89_D 98_A 0.82 0.14 0.00
94_D 393_M 0.82 0.14 0.00
365_K 226_P 0.82 0.14 0.00
92_V 52_V 0.82 0.14 0.00
413_L 52_V 0.82 0.14 0.00
219_P 370_V 0.82 0.14 0.00
595_E 280_I 0.82 0.14 0.00
316_R 52_V 0.81 0.14 0.00
644_L 397_I 0.81 0.14 0.00
213_T 65_G 0.81 0.14 0.00
296_F 291_K 0.81 0.14 0.00
278_R 55_V 0.81 0.14 0.00
267_A 332_T 0.81 0.14 0.00
407_P 222_G 0.81 0.14 0.00
129_E 80_T 0.81 0.14 0.00
651_R 59_I 0.81 0.14 0.00
315_G 99_L 0.81 0.14 0.00
758_L 106_G 0.81 0.13 0.00
355_L 52_V 0.81 0.13 0.00
213_T 126_L 0.80 0.13 0.00
213_T 107_A 0.80 0.13 0.00
680_L 376_V 0.80 0.13 0.00
719_H 395_A 0.80 0.13 0.00
255_T 281_R 0.80 0.13 0.00
96_L 280_I 0.80 0.13 0.00
19_V 336_H 0.80 0.13 0.00
39_L 156_I 0.80 0.13 0.00
597_Y 231_D 0.80 0.13 0.00
200_L 216_E 0.79 0.13 0.00
493_A 315_H 0.79 0.13 0.00
24_F 76_L 0.79 0.13 0.00
159_F 241_A 0.79 0.13 0.00
544_L 218_A 0.79 0.13 0.00
625_S 133_L 0.79 0.13 0.00
87_V 207_L 0.79 0.13 0.00
722_T 52_V 0.79 0.13 0.00
501_K 168_F 0.79 0.13 0.00
298_H 47_L 0.79 0.13 0.00
581_R 101_V 0.79 0.13 0.00
395_F 304_D 0.79 0.13 0.00
394_D 107_A 0.79 0.13 0.00
472_E 111_P 0.79 0.13 0.00
291_C 173_I 0.79 0.13 0.00
21_D 200_R 0.79 0.13 0.00
482_G 385_C 0.79 0.13 0.00
505_L 280_I 0.78 0.13 0.00
232_V 182_L 0.78 0.13 0.00
191_F 370_V 0.78 0.12 0.00
307_K 248_V 0.78 0.12 0.00
260_P 225_P 0.78 0.12 0.00
96_L 108_V 0.78 0.12 0.00
52_I 353_L 0.78 0.12 0.00
82_S 52_V 0.78 0.12 0.00
501_K 390_V 0.78 0.12 0.00
82_S 214_F 0.78 0.12 0.00
736_V 86_D 0.77 0.12 0.00
274_L 210_E 0.77 0.12 0.00
545_E 131_V 0.77 0.12 0.00
758_L 305_P 0.77 0.12 0.00
202_F 74_T 0.77 0.12 0.00
549_V 109_V 0.77 0.12 0.00
274_L 215_Y 0.77 0.12 0.00
484_K 221_V 0.77 0.12 0.00
611_R 398_A 0.77 0.12 0.00
30_V 379_Q 0.77 0.12 0.00
12_E 70_M 0.77 0.12 0.00
532_V 250_K 0.77 0.12 0.00
312_R 123_L 0.77 0.12 0.00
351_L 366_Y 0.77 0.12 0.00
105_A 273_F 0.77 0.12 0.00
621_V 336_H 0.77 0.12 0.00
11_V 201_I 0.77 0.12 0.00
435_L 400_L 0.77 0.12 0.00
389_D 199_H 0.77 0.12 0.00
432_F 315_H 0.77 0.12 0.00
688_R 114_E 0.77 0.12 0.00
18_S 28_L 0.77 0.12 0.00
751_E 114_E 0.76 0.12 0.00
637_A 111_P 0.76 0.12 0.00
140_Y 344_V 0.76 0.12 0.00
410_H 94_D 0.76 0.12 0.00
16_G 154_E 0.76 0.12 0.00
691_A 290_I 0.76 0.12 0.00
92_V 379_Q 0.76 0.12 0.00
28_Y 132_F 0.76 0.12 0.00
600_V 140_L 0.76 0.12 0.00
621_V 74_T 0.76 0.12 0.00
732_A 225_P 0.76 0.12 0.00
566_A 235_T 0.76 0.12 0.00
104_Q 224_I 0.76 0.12 0.00
319_E 248_V 0.76 0.12 0.00
410_H 192_K 0.76 0.12 0.00
124_K 293_A 0.76 0.12 0.00
391_L 109_V 0.76 0.12 0.00
419_D 398_A 0.76 0.12 0.00
562_G 199_H 0.75 0.12 0.00
129_E 79_I 0.75 0.12 0.00
735_A 362_G 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
4968 0.59 cI_3_20_cI_4_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4809 0.52 cI_3_40_cI_4_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4808 0.64 cI_3_4_cI_4_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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