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OPENSEQ.org
cI_3_4_cI_9_4_tt
Genes: A B A+B
Length: 783 182 899
Sequences: 1268 870 453
Seq/Len: 1.62 4.78 0.5
MirrorTree (Pazo et al. 2001) 0.63
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 0.31
5 0.01 0.01 0.31
10 0.01 0.01 0.31
20 0.01 0.01 0.31
100 0.03 0.01 0.34
∞ 0.09 0.02 0.47
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
563_A 17_L 1.24 0.36 0.00
88_A 112_A 1.11 0.28 0.00
273_E 73_A 1.08 0.26 0.00
718_A 131_Y 1.08 0.26 0.00
514_D 15_K 1.07 0.26 0.00
350_T 8_Q 1.07 0.25 0.00
581_R 134_E 1.05 0.24 0.00
368_H 107_A 1.05 0.24 0.00
493_A 134_E 1.04 0.23 0.00
167_H 131_Y 1.03 0.23 0.00
750_R 24_V 1.03 0.23 0.00
320_A 85_E 1.03 0.23 0.00
562_G 15_K 1.02 0.22 0.00
310_L 128_D 1.01 0.22 0.00
618_E 19_S 0.99 0.21 0.00
437_I 156_P 0.99 0.21 0.00
327_L 12_I 0.99 0.21 0.00
505_L 134_E 0.98 0.21 0.00
324_E 12_I 0.98 0.21 0.00
525_A 26_Y 0.97 0.20 0.00
413_L 55_G 0.97 0.20 0.00
251_E 135_D 0.97 0.20 0.00
649_G 82_S 0.97 0.20 0.00
644_L 29_A 0.97 0.20 0.00
766_A 7_A 0.96 0.20 0.00
426_Y 67_A 0.95 0.19 0.00
269_T 107_A 0.94 0.18 0.00
765_P 119_F 0.93 0.18 0.00
534_A 112_A 0.93 0.18 0.00
358_S 24_V 0.93 0.18 0.00
558_W 4_K 0.92 0.18 0.00
458_L 15_K 0.92 0.18 0.00
728_L 12_I 0.92 0.18 0.00
570_F 146_Q 0.92 0.18 0.00
229_I 14_L 0.92 0.17 0.00
502_N 85_E 0.91 0.17 0.00
536_T 15_K 0.91 0.17 0.00
390_L 134_E 0.91 0.17 0.00
742_R 15_K 0.90 0.17 0.00
24_F 96_L 0.90 0.17 0.00
390_L 17_L 0.90 0.17 0.00
445_T 2_T 0.90 0.17 0.00
502_N 15_K 0.90 0.17 0.00
607_F 71_E 0.89 0.17 0.00
12_E 152_R 0.89 0.16 0.00
498_E 151_K 0.89 0.16 0.00
80_A 117_Y 0.88 0.16 0.00
270_R 130_V 0.88 0.16 0.00
736_V 139_D 0.88 0.16 0.00
513_Q 152_R 0.87 0.16 0.00
670_P 107_A 0.87 0.16 0.00
618_E 129_L 0.87 0.16 0.00
649_G 47_P 0.87 0.16 0.00
11_V 139_D 0.87 0.16 0.00
201_D 52_K 0.86 0.15 0.00
581_R 82_S 0.85 0.15 0.00
743_V 2_T 0.85 0.15 0.00
569_G 143_T 0.85 0.15 0.00
761_S 131_Y 0.85 0.15 0.00
392_Q 134_E 0.84 0.14 0.00
308_T 17_L 0.84 0.14 0.00
369_L 73_A 0.84 0.14 0.00
418_R 125_E 0.84 0.14 0.00
496_A 82_S 0.84 0.14 0.00
129_E 96_L 0.84 0.14 0.00
323_E 17_L 0.84 0.14 0.00
15_P 134_E 0.84 0.14 0.00
134_T 72_P 0.83 0.14 0.00
596_R 119_F 0.83 0.14 0.00
763_L 4_K 0.83 0.14 0.00
92_V 15_K 0.83 0.14 0.00
563_A 47_P 0.83 0.14 0.00
659_E 17_L 0.82 0.14 0.00
727_A 120_E 0.82 0.14 0.00
645_A 15_K 0.82 0.14 0.00
80_A 33_L 0.82 0.14 0.00
585_M 33_L 0.82 0.14 0.00
260_P 120_E 0.82 0.14 0.00
4_V 17_L 0.81 0.14 0.00
659_E 2_T 0.81 0.13 0.00
576_A 10_L 0.81 0.13 0.00
586_H 119_F 0.81 0.13 0.00
229_I 117_Y 0.81 0.13 0.00
204_E 112_A 0.81 0.13 0.00
481_L 17_L 0.80 0.13 0.00
578_K 118_D 0.80 0.13 0.00
390_L 19_S 0.80 0.13 0.00
566_A 85_E 0.80 0.13 0.00
273_E 66_Y 0.80 0.13 0.00
513_Q 119_F 0.80 0.13 0.00
305_R 64_P 0.80 0.13 0.00
176_L 150_A 0.80 0.13 0.00
597_Y 10_L 0.80 0.13 0.00
764_G 24_V 0.79 0.13 0.00
748_V 17_L 0.79 0.13 0.00
291_C 16_Y 0.79 0.13 0.00
503_P 2_T 0.79 0.13 0.00
402_P 125_E 0.79 0.12 0.00
741_G 17_L 0.79 0.12 0.00
123_D 13_T 0.79 0.12 0.00
15_P 112_A 0.79 0.12 0.00
733_Q 17_L 0.79 0.12 0.00
444_R 47_P 0.79 0.12 0.00
484_K 107_A 0.79 0.12 0.00
373_G 113_I 0.79 0.12 0.00
331_E 26_Y 0.78 0.12 0.00
334_K 2_T 0.78 0.12 0.00
337_R 26_Y 0.78 0.12 0.00
213_T 10_L 0.78 0.12 0.00
369_L 6_L 0.78 0.12 0.00
260_P 2_T 0.78 0.12 0.00
584_V 22_V 0.78 0.12 0.00
158_E 85_E 0.77 0.12 0.00
605_P 61_A 0.77 0.12 0.00
20_M 103_L 0.77 0.12 0.00
330_K 28_D 0.77 0.12 0.00
419_D 107_A 0.77 0.12 0.00
274_L 89_K 0.77 0.12 0.00
290_I 143_T 0.77 0.12 0.00
417_V 131_Y 0.77 0.12 0.00
541_A 19_S 0.77 0.12 0.00
229_I 151_K 0.76 0.12 0.00
396_A 150_A 0.76 0.12 0.00
640_V 150_A 0.76 0.12 0.00
429_G 82_S 0.76 0.12 0.00
722_T 26_Y 0.76 0.12 0.00
88_A 107_A 0.76 0.12 0.00
718_A 10_L 0.75 0.11 0.00
394_D 74_E 0.75 0.11 0.00
441_M 16_Y 0.75 0.11 0.00
397_L 107_A 0.75 0.11 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
4967 0.57 cI_3_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4959 0.54 cI_3_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4958 0.5 cI_3_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4957 0.63 cI_3_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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