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OPENSEQ.org
DT
Genes: A B A+B
Length: 141 239 356
Sequences: 8772 7786 3383
Seq/Len: 62.21 32.58 9.5
MirrorTree (Pazo et al. 2001) 0.59
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 0.06 0.00 5.14
2 0.06 0.00 8.65
5 0.06 0.00 8.77
10 0.06 0.00 8.84
20 0.06 0.01 8.90
100 0.08 0.01 9.48
∞ 0.14 0.06 11.12
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
129_K 46_S 1.14 0.97 0.18
130_I 32_V 0.73 0.64 0.04
43_V 180_F 0.71 0.60 0.04
66_L 52_P 0.70 0.60 0.04
66_L 185_D 0.70 0.59 0.04
44_D 202_F 0.67 0.54 0.03
102_I 203_E 0.66 0.52 0.03
119_M 41_P 0.66 0.52 0.03
35_M 180_F 0.66 0.52 0.03
36_V 51_T 0.66 0.52 0.03
66_L 53_A 0.65 0.50 0.03
10_D 24_V 0.64 0.49 0.03
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
10530 18.75 ExbD-TonB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.10 Done
10528 11.86 ExbD-TonB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done
10526 0.22 ExbD-TonB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
8585 21.61 Dale 6-20 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.60 Done - Shared
8568 19.56 DT gene 8, -6 jack Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.40 Done - Shared
8566 0.22 DT gene 8 -6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8565 0.02 DT -6 Δgene:(1, 20) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
8564 0.02 DT gene 100 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
8563 16.31 DT -10 Jack Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.45 Done - Shared
8562 0.02 DT -10 Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
8561 17.39 Dale Δgene:(1, 20) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.61 Done - Shared
7825 9.5 DT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.18 Done - Shared
7822 0.02 DT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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