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OPENSEQ.org
cI_3_4_cI_9_4_tt
Genes: A B A+B
Length: 783 182 908
Sequences: 1296 1192 486
Seq/Len: 1.66 6.55 0.54
MirrorTree (Pazo et al. 2001) 0.48
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 0.05 0.23
5 0.01 0.05 0.23
10 0.01 0.06 0.23
20 0.01 0.06 0.24
100 0.03 0.06 0.28
∞ 0.10 0.09 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
390_L 17_L 1.27 0.41 0.00
618_E 19_S 1.21 0.36 0.00
390_L 153_T 1.20 0.35 0.00
563_A 17_L 1.13 0.31 0.00
513_Q 119_F 1.04 0.25 0.00
571_V 6_L 0.97 0.21 0.00
24_F 96_L 0.96 0.20 0.00
129_E 96_L 0.95 0.20 0.00
291_C 16_Y 0.95 0.20 0.00
716_L 14_L 0.94 0.20 0.00
269_T 107_A 0.94 0.20 0.00
15_P 112_A 0.94 0.19 0.00
396_A 120_E 0.93 0.19 0.00
589_H 107_A 0.93 0.19 0.00
92_V 15_K 0.92 0.19 0.00
324_E 12_I 0.91 0.18 0.00
604_A 112_A 0.91 0.18 0.00
710_E 85_E 0.90 0.18 0.00
444_R 47_P 0.90 0.18 0.00
503_P 7_A 0.90 0.18 0.00
417_V 131_Y 0.90 0.17 0.00
569_G 143_T 0.89 0.17 0.00
599_H 28_D 0.89 0.17 0.00
514_D 15_K 0.89 0.17 0.00
340_E 11_G 0.89 0.17 0.00
741_G 17_L 0.88 0.17 0.00
547_M 20_K 0.88 0.17 0.00
320_A 12_I 0.88 0.17 0.00
324_E 119_F 0.87 0.16 0.00
513_Q 19_S 0.87 0.16 0.00
167_H 131_Y 0.87 0.16 0.00
260_P 120_E 0.87 0.16 0.00
585_M 33_L 0.86 0.16 0.00
534_A 112_A 0.86 0.16 0.00
714_A 145_P 0.86 0.16 0.00
177_D 117_Y 0.85 0.16 0.00
649_G 82_S 0.85 0.15 0.00
488_E 155_K 0.85 0.15 0.00
566_A 12_I 0.85 0.15 0.00
358_S 24_V 0.83 0.15 0.00
763_L 4_K 0.83 0.15 0.00
350_T 8_Q 0.83 0.14 0.00
229_I 14_L 0.82 0.14 0.00
718_A 152_R 0.82 0.14 0.00
458_L 15_K 0.82 0.14 0.00
80_A 117_Y 0.82 0.14 0.00
341_V 30_P 0.82 0.14 0.00
488_E 24_V 0.82 0.14 0.00
627_A 125_E 0.81 0.14 0.00
430_T 134_E 0.81 0.14 0.00
320_A 85_E 0.81 0.14 0.00
621_V 151_K 0.81 0.14 0.00
761_S 131_Y 0.81 0.14 0.00
229_I 117_Y 0.81 0.14 0.00
748_V 149_E 0.81 0.14 0.00
305_R 64_P 0.81 0.14 0.00
88_A 112_A 0.81 0.14 0.00
447_K 151_K 0.80 0.14 0.00
527_R 150_A 0.80 0.14 0.00
546_A 146_Q 0.80 0.14 0.00
6_V 103_L 0.79 0.13 0.00
381_L 7_A 0.79 0.13 0.00
158_E 152_R 0.79 0.13 0.00
727_A 7_A 0.79 0.13 0.00
576_A 107_A 0.79 0.13 0.00
468_H 159_V 0.78 0.13 0.00
331_E 26_Y 0.78 0.13 0.00
361_A 113_I 0.78 0.13 0.00
77_P 22_V 0.78 0.13 0.00
226_I 146_Q 0.78 0.13 0.00
204_E 112_A 0.78 0.13 0.00
606_T 100_F 0.78 0.13 0.00
595_E 16_Y 0.78 0.13 0.00
513_Q 152_R 0.77 0.12 0.00
80_A 33_L 0.77 0.12 0.00
674_G 82_S 0.77 0.12 0.00
396_A 30_P 0.77 0.12 0.00
11_V 134_E 0.77 0.12 0.00
662_K 145_P 0.76 0.12 0.00
99_V 33_L 0.76 0.12 0.00
349_A 153_T 0.76 0.12 0.00
541_A 19_S 0.76 0.12 0.00
342_G 134_E 0.76 0.12 0.00
694_L 74_E 0.76 0.12 0.00
423_P 19_S 0.76 0.12 0.00
620_R 131_Y 0.76 0.12 0.00
282_V 38_H 0.75 0.12 0.00
367_P 26_Y 0.75 0.12 0.00
313_K 38_H 0.75 0.12 0.00
358_S 112_A 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
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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