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OPENSEQ.org
cI_3_4_cI_5_4_tt
Genes: A B A+B
Length: 783 207 925
Sequences: 1268 1052 495
Seq/Len: 1.62 5.08 0.54
MirrorTree (Pazo et al. 2001) 0.84
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 0.00
2 0.00 0.00 0.00
5 0.01 0.01 0.39
10 0.01 0.01 0.39
20 0.01 0.01 0.40
100 0.03 0.01 0.41
∞ 0.09 0.03 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
6_V 49_L 1.55 0.63 0.00
12_E 29_L 1.36 0.48 0.00
330_K 23_G 1.30 0.43 0.00
579_G 90_V 1.26 0.40 0.00
627_A 29_L 1.25 0.39 0.00
177_D 32_E 1.17 0.33 0.00
407_P 89_F 1.17 0.33 0.00
718_A 91_R 1.15 0.32 0.00
304_N 32_E 1.15 0.32 0.00
19_V 98_D 1.11 0.29 0.00
413_L 62_D 1.08 0.28 0.00
627_A 98_D 1.08 0.27 0.00
361_A 91_R 1.07 0.27 0.00
311_V 10_A 1.06 0.27 0.00
712_A 46_F 1.06 0.26 0.00
447_K 54_G 1.05 0.25 0.00
455_R 98_D 1.04 0.25 0.00
3_R 110_S 1.03 0.24 0.00
22_A 125_V 1.02 0.24 0.00
204_E 77_L 1.01 0.23 0.00
725_A 122_F 1.01 0.23 0.00
723_A 55_L 0.99 0.22 0.00
318_V 3_L 0.99 0.22 0.00
636_G 118_V 0.99 0.22 0.00
238_L 118_V 0.98 0.22 0.00
437_I 110_S 0.98 0.22 0.00
660_A 104_V 0.97 0.21 0.00
605_P 162_G 0.97 0.21 0.00
543_G 128_G 0.96 0.20 0.00
194_V 48_F 0.95 0.20 0.00
311_V 88_F 0.95 0.20 0.00
399_L 34_F 0.95 0.20 0.00
49_L 53_V 0.94 0.20 0.00
382_F 30_P 0.94 0.19 0.00
360_L 107_L 0.94 0.19 0.00
157_F 112_N 0.93 0.19 0.00
562_G 70_V 0.93 0.19 0.00
26_A 187_G 0.93 0.19 0.00
627_A 125_V 0.92 0.19 0.00
32_L 178_D 0.92 0.18 0.00
596_R 104_V 0.92 0.18 0.00
397_L 112_N 0.92 0.18 0.00
615_V 32_E 0.91 0.18 0.00
554_K 104_V 0.91 0.18 0.00
341_V 32_E 0.91 0.18 0.00
340_E 114_L 0.91 0.18 0.00
254_T 55_L 0.91 0.18 0.00
626_P 135_I 0.90 0.18 0.00
9_R 27_V 0.90 0.18 0.00
26_A 135_I 0.90 0.18 0.00
765_P 32_E 0.90 0.18 0.00
736_V 73_E 0.90 0.18 0.00
409_L 130_P 0.90 0.18 0.00
716_L 54_G 0.90 0.17 0.00
546_A 38_M 0.90 0.17 0.00
649_G 88_F 0.90 0.17 0.00
355_L 127_E 0.89 0.17 0.00
340_E 25_L 0.89 0.17 0.00
444_R 27_V 0.89 0.17 0.00
575_E 37_E 0.89 0.17 0.00
89_D 31_R 0.89 0.17 0.00
548_G 55_L 0.89 0.17 0.00
49_L 54_G 0.88 0.17 0.00
444_R 54_G 0.88 0.17 0.00
309_P 133_R 0.88 0.17 0.00
521_A 38_M 0.88 0.17 0.00
167_H 109_G 0.88 0.17 0.00
633_E 150_Y 0.88 0.17 0.00
598_A 23_G 0.88 0.17 0.00
100_V 128_G 0.88 0.17 0.00
736_V 119_Y 0.88 0.17 0.00
565_Y 69_A 0.88 0.17 0.00
356_L 166_I 0.87 0.17 0.00
100_V 170_F 0.87 0.17 0.00
333_L 135_I 0.87 0.16 0.00
109_E 147_R 0.87 0.16 0.00
123_D 99_P 0.87 0.16 0.00
576_A 55_L 0.87 0.16 0.00
356_L 160_R 0.87 0.16 0.00
752_D 52_I 0.86 0.16 0.00
129_E 178_D 0.86 0.16 0.00
413_L 86_S 0.86 0.16 0.00
243_R 142_E 0.86 0.16 0.00
309_P 149_D 0.86 0.16 0.00
539_A 103_T 0.86 0.16 0.00
544_L 73_E 0.86 0.16 0.00
616_N 135_I 0.85 0.16 0.00
82_S 150_Y 0.85 0.16 0.00
390_L 112_N 0.85 0.16 0.00
454_Y 33_R 0.85 0.16 0.00
274_L 112_N 0.85 0.15 0.00
621_V 179_P 0.85 0.15 0.00
334_K 122_F 0.84 0.15 0.00
750_R 137_T 0.84 0.15 0.00
517_A 161_E 0.84 0.15 0.00
410_H 4_E 0.84 0.15 0.00
129_E 152_L 0.84 0.15 0.00
453_P 10_A 0.84 0.15 0.00
90_G 151_P 0.84 0.15 0.00
108_V 55_L 0.84 0.15 0.00
167_H 178_D 0.84 0.15 0.00
237_D 178_D 0.83 0.15 0.00
32_L 179_P 0.83 0.15 0.00
157_F 169_E 0.83 0.15 0.00
319_E 3_L 0.83 0.15 0.00
407_P 157_T 0.83 0.15 0.00
396_A 70_V 0.83 0.15 0.00
645_A 6_V 0.83 0.14 0.00
331_E 108_W 0.83 0.14 0.00
389_D 36_E 0.83 0.14 0.00
8_D 149_D 0.83 0.14 0.00
615_V 73_E 0.82 0.14 0.00
396_A 72_Y 0.82 0.14 0.00
53_G 99_P 0.82 0.14 0.00
92_V 54_G 0.82 0.14 0.00
496_A 23_G 0.82 0.14 0.00
272_G 38_M 0.82 0.14 0.00
732_A 37_E 0.81 0.14 0.00
507_L 42_K 0.81 0.14 0.00
351_L 135_I 0.81 0.14 0.00
479_A 101_L 0.81 0.14 0.00
19_V 170_F 0.81 0.14 0.00
253_P 154_E 0.81 0.14 0.00
742_R 63_P 0.81 0.14 0.00
268_D 179_P 0.81 0.14 0.00
285_V 29_L 0.81 0.14 0.00
432_F 122_F 0.80 0.14 0.00
4_V 31_R 0.80 0.14 0.00
21_D 169_E 0.80 0.14 0.00
535_M 184_Y 0.80 0.14 0.00
174_V 135_I 0.80 0.14 0.00
174_V 90_V 0.80 0.14 0.00
747_V 97_E 0.80 0.14 0.00
505_L 97_E 0.80 0.14 0.00
713_R 12_A 0.80 0.13 0.00
526_E 27_V 0.80 0.13 0.00
271_S 154_E 0.80 0.13 0.00
129_E 179_P 0.80 0.13 0.00
108_V 185_K 0.80 0.13 0.00
341_V 36_E 0.79 0.13 0.00
414_S 52_I 0.79 0.13 0.00
22_A 42_K 0.79 0.13 0.00
270_R 178_D 0.79 0.13 0.00
643_L 42_K 0.79 0.13 0.00
94_D 49_L 0.79 0.13 0.00
89_D 62_D 0.79 0.13 0.00
29_D 29_L 0.78 0.13 0.00
338_G 27_V 0.78 0.13 0.00
660_A 102_P 0.78 0.13 0.00
634_A 164_Y 0.78 0.13 0.00
329_L 11_R 0.78 0.13 0.00
541_A 114_L 0.78 0.13 0.00
380_S 15_Y 0.78 0.13 0.00
351_L 90_V 0.78 0.13 0.00
100_V 29_L 0.78 0.13 0.00
659_E 189_R 0.78 0.13 0.00
216_F 118_V 0.77 0.13 0.00
616_N 160_R 0.77 0.13 0.00
324_E 65_P 0.77 0.12 0.00
454_Y 15_Y 0.77 0.12 0.00
517_A 130_P 0.77 0.12 0.00
298_H 85_G 0.77 0.12 0.00
290_I 12_A 0.77 0.12 0.00
226_I 179_P 0.77 0.12 0.00
238_L 113_F 0.77 0.12 0.00
90_G 175_T 0.77 0.12 0.00
88_A 75_V 0.77 0.12 0.00
211_I 92_V 0.77 0.12 0.00
621_V 20_N 0.77 0.12 0.00
386_S 103_T 0.77 0.12 0.00
747_V 9_E 0.77 0.12 0.00
511_V 35_K 0.76 0.12 0.00
1_M 49_L 0.76 0.12 0.00
747_V 88_F 0.76 0.12 0.00
102_E 94_V 0.76 0.12 0.00
749_H 95_P 0.76 0.12 0.00
454_Y 78_P 0.76 0.12 0.00
320_A 43_A 0.76 0.12 0.00
364_L 88_F 0.76 0.12 0.00
650_V 122_F 0.76 0.12 0.00
419_D 16_P 0.76 0.12 0.00
506_I 53_V 0.76 0.12 0.00
273_E 74_L 0.76 0.12 0.00
502_N 12_A 0.76 0.12 0.00
175_I 75_V 0.76 0.12 0.00
634_A 121_L 0.76 0.12 0.00
503_P 34_F 0.76 0.12 0.00
489_M 88_F 0.76 0.12 0.00
20_M 10_A 0.75 0.12 0.00
678_F 101_L 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
4861 0.51 cI_3_2_cI_5_10_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4860 0.54 cI_3_2_cI_5_6_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4859 0.54 cI_3_2_cI_5_4_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4858 0.54 cI_3_4_cI_5_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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