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OPENSEQ.org
cI_3_20_cI_9_20_tt
Genes: A B A+B
Length: 783 182 904
Sequences: 1254 979 572
Seq/Len: 1.6 5.38 0.63
MirrorTree (Pazo et al. 2001) 0.74
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 0.45
5 0.01 0.01 0.45
10 0.01 0.02 0.46
20 0.01 0.02 0.46
100 0.03 0.03 0.48
∞ 0.10 0.07 0.59
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
390_L 134_E 1.48 0.62 0.00
123_D 86_R 1.23 0.41 0.00
360_L 113_I 1.21 0.40 0.00
270_R 130_V 1.17 0.37 0.00
423_P 122_A 1.16 0.36 0.00
556_A 10_L 1.12 0.33 0.00
24_F 96_L 1.11 0.33 0.00
82_S 24_V 1.06 0.29 0.00
430_T 134_E 1.06 0.29 0.00
269_T 107_A 1.05 0.29 0.00
476_I 10_L 1.03 0.27 0.00
441_M 16_Y 1.02 0.26 0.00
604_A 112_A 1.01 0.26 0.00
269_T 8_Q 1.01 0.26 0.00
514_D 15_K 1.01 0.26 0.00
82_S 13_T 1.01 0.26 0.00
21_D 20_K 0.99 0.24 0.00
493_A 134_E 0.98 0.24 0.00
341_V 28_D 0.98 0.24 0.00
396_A 120_E 0.98 0.24 0.00
157_F 132_G 0.97 0.23 0.00
394_D 119_F 0.96 0.23 0.00
241_R 86_R 0.96 0.23 0.00
135_V 129_L 0.95 0.22 0.00
586_H 119_F 0.95 0.22 0.00
165_D 161_Y 0.95 0.22 0.00
396_A 150_A 0.95 0.22 0.00
488_E 8_Q 0.94 0.21 0.00
260_P 120_E 0.94 0.21 0.00
205_R 9_S 0.93 0.21 0.00
766_A 7_A 0.93 0.21 0.00
30_V 15_K 0.93 0.21 0.00
541_A 15_K 0.92 0.21 0.00
732_A 2_T 0.92 0.20 0.00
736_V 153_T 0.91 0.20 0.00
211_I 67_A 0.91 0.20 0.00
706_G 151_K 0.91 0.20 0.00
513_Q 152_R 0.91 0.20 0.00
238_L 106_E 0.90 0.19 0.00
441_M 134_E 0.90 0.19 0.00
442_P 10_L 0.90 0.19 0.00
163_H 95_M 0.90 0.19 0.00
390_L 26_Y 0.90 0.19 0.00
741_G 17_L 0.89 0.19 0.00
215_D 2_T 0.89 0.19 0.00
576_A 10_L 0.89 0.19 0.00
320_A 26_Y 0.89 0.19 0.00
394_D 74_E 0.89 0.19 0.00
381_L 10_L 0.88 0.19 0.00
409_L 71_E 0.88 0.18 0.00
751_E 7_A 0.88 0.18 0.00
351_L 47_P 0.87 0.18 0.00
324_E 26_Y 0.87 0.18 0.00
369_L 73_A 0.87 0.18 0.00
18_S 149_E 0.86 0.18 0.00
704_A 18_F 0.86 0.17 0.00
734_V 15_K 0.86 0.17 0.00
134_T 55_G 0.86 0.17 0.00
320_A 85_E 0.86 0.17 0.00
408_I 55_G 0.86 0.17 0.00
389_D 22_V 0.85 0.17 0.00
569_G 143_T 0.85 0.17 0.00
391_L 72_P 0.85 0.17 0.00
129_E 130_V 0.85 0.17 0.00
164_V 37_F 0.84 0.17 0.00
753_V 120_E 0.84 0.16 0.00
129_E 96_L 0.84 0.16 0.00
215_D 119_F 0.84 0.16 0.00
15_P 134_E 0.84 0.16 0.00
618_E 129_L 0.83 0.16 0.00
269_T 112_A 0.83 0.16 0.00
764_G 24_V 0.83 0.16 0.00
633_E 18_F 0.83 0.16 0.00
23_V 60_A 0.83 0.16 0.00
503_P 2_T 0.83 0.16 0.00
416_F 125_E 0.82 0.16 0.00
448_M 10_L 0.82 0.16 0.00
12_E 125_E 0.82 0.16 0.00
123_D 72_P 0.82 0.16 0.00
620_R 74_E 0.82 0.16 0.00
270_R 72_P 0.82 0.16 0.00
656_L 14_L 0.82 0.16 0.00
525_A 26_Y 0.82 0.16 0.00
408_I 86_R 0.81 0.15 0.00
664_L 103_L 0.81 0.15 0.00
395_F 47_P 0.81 0.15 0.00
211_I 54_I 0.81 0.15 0.00
618_E 119_F 0.81 0.15 0.00
88_A 112_A 0.80 0.15 0.00
321_T 26_Y 0.80 0.15 0.00
750_R 24_V 0.80 0.15 0.00
310_L 62_A 0.80 0.15 0.00
691_A 17_L 0.80 0.15 0.00
166_K 131_Y 0.79 0.15 0.00
241_R 57_S 0.79 0.15 0.00
273_E 73_A 0.79 0.14 0.00
678_F 62_A 0.79 0.14 0.00
229_I 14_L 0.79 0.14 0.00
396_A 30_P 0.79 0.14 0.00
534_A 112_A 0.79 0.14 0.00
274_L 89_K 0.79 0.14 0.00
426_Y 76_D 0.78 0.14 0.00
620_R 131_Y 0.78 0.14 0.00
707_K 121_M 0.78 0.14 0.00
445_T 2_T 0.78 0.14 0.00
157_F 52_K 0.78 0.14 0.00
502_N 24_V 0.78 0.14 0.00
399_L 73_A 0.78 0.14 0.00
724_R 145_P 0.78 0.14 0.00
413_L 55_G 0.77 0.14 0.00
324_E 12_I 0.77 0.14 0.00
313_K 17_L 0.77 0.14 0.00
481_L 19_S 0.77 0.14 0.00
87_V 34_K 0.77 0.14 0.00
387_L 20_K 0.77 0.14 0.00
15_P 112_A 0.77 0.13 0.00
313_K 100_F 0.76 0.13 0.00
303_Q 10_L 0.76 0.13 0.00
179_E 69_Y 0.76 0.13 0.00
747_V 19_S 0.76 0.13 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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