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OPENSEQ.org
Grasx6
Genes: A B A+B
Length: 307 346 553
Sequences: 1803 18912 655
Seq/Len: 5.87 54.66 1.18
MirrorTree (Pazo et al. 2001) 0.21
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.00 0.00
2 0.03 0.01 0.03
5 0.03 0.02 0.05
10 0.03 0.04 0.08
20 0.03 0.07 0.12
100 0.03 0.15 0.42
∞ 0.08 0.22 1.00
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
11_T 267_R 1.08 0.45 0.00
45_M 102_Q 0.93 0.31 0.00
185_K 249_I 0.92 0.31 0.00
160_M 59_I 0.91 0.30 0.00
12_G 129_H 0.84 0.24 0.00
196_D 194_D 0.82 0.23 0.00
11_T 273_D 0.81 0.23 0.00
12_G 237_N 0.77 0.20 0.00
254_Y 277_I 0.77 0.20 0.00
9_G 237_N 0.77 0.20 0.00
68_A 136_T 0.76 0.19 0.00
110_I 97_D 0.74 0.18 0.00
208_P 135_V 0.74 0.18 0.00
105_Q 250_S 0.72 0.17 0.00
203_K 272_K 0.72 0.17 0.00
63_N 326_L 0.71 0.17 0.00
146_V 151_K 0.71 0.17 0.00
235_Y 272_K 0.71 0.16 0.00
36_D 304_V 0.71 0.16 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
10137 0.09 grasx10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10135 0.09 Grasx9 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-06, 4) msa: HHblits (2015_06) 0.01 Done - Shared
10134 0 Grasx8 Δgene:(1, 1) A:(1E-60, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
10133 0 Grasx7 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) Killed - Shared
10131 1.18 Grasx6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 2) msa: HHblits (2015_06) 0.00 Done - Shared
10130 1.2 Grasx5 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) 0.00 Done - Shared
10129 0.68 Grasx4 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10128 0.16 Grasx3 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10127 0.09 grasx2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10126 0.72 grasx1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10124 1.16 Grasx Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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