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OPENSEQ.org
TPR-kinase
Genes: A B A+B
Length: 141 286 401
Sequences: 2799 2859 503
Seq/Len: 19.85 10 1.25
MirrorTree (Pazo et al. 2001) 0.07
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 0.05 0.06 0.01
2 0.05 0.06 0.01
5 0.08 0.08 0.04
10 0.08 0.08 0.07
20 0.08 0.09 0.14
100 0.10 0.12 0.50
∞ 0.13 0.17 1.18
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
70_Y 270_E 1.07 0.46 0.00
33_A 144_G 0.92 0.32 0.00
96_G 32_K 0.91 0.31 0.00
37_L 254_L 0.87 0.28 0.00
51_I 73_R 0.87 0.28 0.00
83_F 261_D 0.81 0.24 0.00
89_A 143_D 0.79 0.22 0.00
101_S 111_K 0.79 0.22 0.00
82_A 270_E 0.78 0.21 0.00
85_H 87_V 0.78 0.21 0.00
62_Q 239_E 0.78 0.21 0.00
24_N 217_K 0.76 0.20 0.00
103_Q 267_S 0.75 0.20 0.00
5_L 240_I 0.75 0.19 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
3293 1.25 TPR-kinase Δgene:(1, ∞) A:(1E-04, 4) B:(1E-40, 2) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3201 0.14 TPR-kinase Δgene:(1, 20) A:(1E-04, 4) B:(1E-40, 2) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3200 0 TPR-kinase Δgene:(1, 20) A:(1E-20, 8) B:(1E-40, 2) msa: Jackhmmer (2015_06) Killed - Shared
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