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OPENSEQ.org
cI_3_20_cI_4_20_tt
Genes: A B A+B
Length: 783 409 1143
Sequences: 1254 2519 676
Seq/Len: 1.6 6.16 0.59
MirrorTree (Pazo et al. 2001) 0.49
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 0.01 0.38
10 0.01 0.02 0.38
20 0.01 0.02 0.39
100 0.03 0.04 0.41
∞ 0.10 0.10 0.57
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
732_A 285_E 1.46 0.58 0.00
747_V 184_E 1.21 0.38 0.00
583_V 285_E 1.17 0.36 0.00
577_L 394_V 1.13 0.33 0.00
93_V 221_V 1.13 0.33 0.00
421_K 52_V 1.12 0.32 0.00
18_S 131_V 1.08 0.29 0.00
673_M 250_K 1.08 0.29 0.00
656_L 235_T 1.08 0.29 0.00
644_L 397_I 1.08 0.29 0.00
290_I 395_A 1.06 0.28 0.00
522_R 357_I 1.06 0.28 0.00
316_R 52_V 1.02 0.25 0.00
592_P 346_T 0.99 0.23 0.00
398_V 221_V 0.99 0.23 0.00
14_P 52_V 0.98 0.23 0.00
108_V 43_L 0.97 0.23 0.00
309_P 329_K 0.96 0.21 0.00
260_P 295_E 0.96 0.21 0.00
587_L 65_G 0.95 0.21 0.00
723_A 79_I 0.94 0.21 0.00
254_T 126_L 0.93 0.20 0.00
524_L 133_L 0.93 0.20 0.00
635_E 21_L 0.93 0.20 0.00
338_G 65_G 0.92 0.20 0.00
106_G 393_M 0.92 0.20 0.00
740_F 36_S 0.92 0.20 0.00
394_D 107_A 0.92 0.20 0.00
578_K 235_T 0.92 0.20 0.00
453_P 339_K 0.91 0.19 0.00
350_T 357_I 0.90 0.18 0.00
82_S 52_V 0.90 0.18 0.00
758_L 48_S 0.90 0.18 0.00
720_P 295_E 0.90 0.18 0.00
501_K 52_V 0.89 0.18 0.00
487_S 52_V 0.89 0.18 0.00
240_A 222_G 0.88 0.18 0.00
327_L 52_V 0.88 0.18 0.00
22_A 140_L 0.88 0.18 0.00
568_Y 306_N 0.88 0.17 0.00
635_E 386_K 0.88 0.17 0.00
758_L 342_V 0.87 0.17 0.00
23_V 303_R 0.87 0.17 0.00
22_A 74_T 0.87 0.17 0.00
504_V 52_V 0.87 0.17 0.00
560_E 230_I 0.87 0.17 0.00
366_T 396_I 0.87 0.17 0.00
270_R 80_T 0.86 0.17 0.00
94_D 393_M 0.86 0.17 0.00
320_A 402_P 0.86 0.17 0.00
413_L 393_M 0.86 0.17 0.00
304_N 108_V 0.86 0.17 0.00
82_S 299_P 0.86 0.17 0.00
493_A 258_E 0.85 0.16 0.00
584_V 53_L 0.84 0.16 0.00
19_V 45_V 0.84 0.16 0.00
166_K 80_T 0.84 0.16 0.00
28_Y 109_V 0.84 0.16 0.00
102_E 99_L 0.84 0.16 0.00
730_E 227_E 0.84 0.16 0.00
443_R 235_T 0.84 0.16 0.00
26_A 218_A 0.83 0.16 0.00
255_T 368_V 0.83 0.15 0.00
561_P 100_A 0.83 0.15 0.00
93_V 184_E 0.83 0.15 0.00
719_H 295_E 0.83 0.15 0.00
278_R 55_V 0.82 0.15 0.00
419_D 398_A 0.82 0.15 0.00
332_G 264_V 0.82 0.15 0.00
394_D 194_L 0.82 0.15 0.00
101_R 346_T 0.82 0.15 0.00
274_L 149_A 0.82 0.15 0.00
303_Q 221_V 0.82 0.15 0.00
645_A 340_G 0.82 0.15 0.00
243_R 104_L 0.82 0.15 0.00
208_H 96_A 0.82 0.15 0.00
606_T 79_I 0.82 0.15 0.00
213_T 283_M 0.82 0.15 0.00
413_L 140_L 0.82 0.15 0.00
566_A 225_P 0.82 0.15 0.00
667_R 108_V 0.81 0.15 0.00
157_F 194_L 0.81 0.15 0.00
134_T 368_V 0.81 0.15 0.00
10_I 390_V 0.81 0.14 0.00
706_G 133_L 0.81 0.14 0.00
584_V 140_L 0.81 0.14 0.00
168_H 348_S 0.80 0.14 0.00
102_E 223_V 0.80 0.14 0.00
648_L 100_A 0.80 0.14 0.00
477_L 400_L 0.80 0.14 0.00
169_P 398_A 0.80 0.14 0.00
89_D 157_L 0.80 0.14 0.00
92_V 52_V 0.80 0.14 0.00
512_L 126_L 0.80 0.14 0.00
82_S 210_E 0.79 0.14 0.00
428_H 98_A 0.79 0.14 0.00
616_N 295_E 0.79 0.14 0.00
270_R 303_R 0.79 0.14 0.00
573_P 263_D 0.79 0.14 0.00
444_R 290_I 0.79 0.14 0.00
30_V 133_L 0.79 0.14 0.00
99_V 144_T 0.79 0.14 0.00
741_G 346_T 0.79 0.14 0.00
679_R 290_I 0.79 0.14 0.00
722_T 52_V 0.78 0.14 0.00
754_P 280_I 0.78 0.14 0.00
303_Q 216_E 0.78 0.14 0.00
719_H 128_S 0.78 0.14 0.00
674_G 370_V 0.78 0.14 0.00
11_V 114_E 0.78 0.14 0.00
107_M 357_I 0.78 0.13 0.00
718_A 260_Y 0.78 0.13 0.00
129_E 76_L 0.78 0.13 0.00
129_E 335_F 0.78 0.13 0.00
342_G 385_C 0.78 0.13 0.00
87_V 376_V 0.78 0.13 0.00
418_R 391_P 0.77 0.13 0.00
536_T 323_A 0.77 0.13 0.00
618_E 131_V 0.77 0.13 0.00
558_W 44_M 0.77 0.13 0.00
312_R 123_L 0.77 0.13 0.00
621_V 320_S 0.77 0.13 0.00
611_R 159_L 0.77 0.13 0.00
298_H 47_L 0.77 0.13 0.00
338_G 261_T 0.77 0.13 0.00
1_M 379_Q 0.77 0.13 0.00
735_A 194_L 0.77 0.13 0.00
98_D 266_L 0.77 0.13 0.00
285_V 342_V 0.76 0.13 0.00
645_A 283_M 0.76 0.13 0.00
606_T 263_D 0.76 0.13 0.00
585_M 311_P 0.76 0.13 0.00
389_D 259_T 0.76 0.13 0.00
261_V 140_L 0.76 0.13 0.00
303_Q 266_L 0.76 0.13 0.00
87_V 21_L 0.76 0.13 0.00
562_G 294_L 0.76 0.13 0.00
290_I 28_L 0.76 0.13 0.00
7_N 393_M 0.75 0.12 0.00
692_F 280_I 0.75 0.12 0.00
291_C 173_I 0.75 0.12 0.00
211_I 163_V 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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