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OPENSEQ.org
cI_3_4_cI_4_4_tt
Genes: A B A+B
Length: 783 409 1138
Sequences: 1268 3475 723
Seq/Len: 1.62 8.5 0.64
MirrorTree (Pazo et al. 2001) 0.40
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 0.01 0.01
2 0.00 0.01 0.02
5 0.01 0.03 0.39
10 0.01 0.04 0.39
20 0.01 0.05 0.40
100 0.03 0.06 0.43
∞ 0.09 0.13 0.61
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
747_V 184_E 1.12 0.34 0.00
18_S 131_V 1.10 0.32 0.00
399_L 107_A 1.08 0.31 0.00
627_A 52_V 1.07 0.30 0.00
200_L 393_M 1.04 0.28 0.00
290_I 395_A 1.03 0.28 0.00
522_R 357_I 1.03 0.27 0.00
616_N 295_E 1.01 0.26 0.00
255_T 368_V 1.01 0.26 0.00
93_V 221_V 1.00 0.26 0.00
398_V 221_V 1.00 0.25 0.00
421_K 52_V 0.97 0.23 0.00
302_D 192_K 0.96 0.23 0.00
22_A 140_L 0.96 0.23 0.00
524_L 133_L 0.96 0.23 0.00
645_A 283_M 0.95 0.23 0.00
87_V 390_V 0.95 0.22 0.00
716_L 109_V 0.94 0.22 0.00
722_T 52_V 0.94 0.22 0.00
89_D 157_L 0.91 0.20 0.00
644_L 397_I 0.91 0.20 0.00
304_N 108_V 0.90 0.20 0.00
15_P 106_G 0.90 0.20 0.00
751_E 52_V 0.90 0.19 0.00
629_I 52_V 0.89 0.19 0.00
461_W 28_L 0.89 0.19 0.00
611_R 159_L 0.89 0.19 0.00
667_R 108_V 0.89 0.19 0.00
254_T 126_L 0.88 0.19 0.00
13_V 291_K 0.88 0.19 0.00
732_A 285_E 0.88 0.18 0.00
750_R 221_V 0.87 0.18 0.00
587_L 65_G 0.87 0.18 0.00
444_R 290_I 0.87 0.18 0.00
82_S 299_P 0.87 0.18 0.00
618_E 131_V 0.86 0.18 0.00
278_R 55_V 0.85 0.17 0.00
270_R 80_T 0.85 0.17 0.00
23_V 303_R 0.84 0.17 0.00
350_T 357_I 0.84 0.17 0.00
583_V 285_E 0.83 0.16 0.00
418_R 391_P 0.83 0.16 0.00
134_T 368_V 0.83 0.16 0.00
211_I 163_V 0.83 0.16 0.00
734_V 48_S 0.83 0.16 0.00
309_P 329_K 0.83 0.16 0.00
82_S 210_E 0.82 0.16 0.00
423_P 44_M 0.82 0.16 0.00
585_M 123_L 0.81 0.16 0.00
334_K 126_L 0.81 0.15 0.00
274_L 219_R 0.81 0.15 0.00
630_E 288_K 0.81 0.15 0.00
730_E 227_E 0.81 0.15 0.00
215_D 140_L 0.80 0.15 0.00
294_G 101_V 0.80 0.15 0.00
719_H 128_S 0.80 0.15 0.00
291_C 173_I 0.80 0.15 0.00
660_A 381_L 0.80 0.15 0.00
481_L 52_V 0.80 0.15 0.00
366_T 396_I 0.80 0.15 0.00
618_E 74_T 0.79 0.15 0.00
522_R 52_V 0.79 0.14 0.00
213_T 65_G 0.79 0.14 0.00
332_G 264_V 0.79 0.14 0.00
299_E 407_V 0.79 0.14 0.00
453_P 390_V 0.79 0.14 0.00
747_V 65_G 0.78 0.14 0.00
290_I 131_V 0.78 0.14 0.00
386_S 355_Y 0.78 0.14 0.00
491_A 28_L 0.78 0.14 0.00
635_E 250_K 0.78 0.14 0.00
350_T 232_L 0.78 0.14 0.00
106_G 393_M 0.77 0.14 0.00
584_V 53_L 0.77 0.14 0.00
663_A 295_E 0.77 0.14 0.00
320_A 52_V 0.77 0.14 0.00
524_L 396_I 0.77 0.14 0.00
447_K 131_V 0.77 0.14 0.00
398_V 394_V 0.77 0.14 0.00
512_L 200_R 0.76 0.13 0.00
635_E 278_V 0.76 0.13 0.00
285_V 342_V 0.76 0.13 0.00
488_E 390_V 0.76 0.13 0.00
613_H 107_A 0.76 0.13 0.00
644_L 201_I 0.76 0.13 0.00
563_A 295_E 0.75 0.13 0.00
92_V 52_V 0.75 0.13 0.00
673_M 250_K 0.75 0.13 0.00
573_P 263_D 0.75 0.13 0.00
568_Y 100_A 0.75 0.13 0.00
704_A 263_D 0.75 0.13 0.00
694_L 221_V 0.75 0.13 0.00
728_L 373_P 0.75 0.13 0.00
393_A 149_A 0.75 0.13 0.00
627_A 227_E 0.75 0.13 0.00
167_H 128_S 0.74 0.13 0.00
583_V 364_M 0.74 0.13 0.00
274_L 149_A 0.74 0.13 0.00
44_A 399_S 0.74 0.13 0.00
102_E 223_V 0.74 0.13 0.00
2_V 100_A 0.74 0.13 0.00
605_P 190_L 0.74 0.13 0.00
268_D 74_T 0.74 0.12 0.00
108_V 43_L 0.74 0.12 0.00
738_T 132_F 0.74 0.12 0.00
389_D 28_L 0.74 0.12 0.00
327_L 52_V 0.74 0.12 0.00
627_A 119_I 0.74 0.12 0.00
723_A 79_I 0.74 0.12 0.00
94_D 393_M 0.73 0.12 0.00
532_V 398_A 0.73 0.12 0.00
30_V 379_Q 0.73 0.12 0.00
285_V 221_V 0.73 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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