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Hsp104-Pab1 (B, 120-500)
Genes: A B A+B
Length: 221 381 589
Sequences: 10438 728 122
Seq/Len: 47.23 1.91 0.21
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 0.00 0.03 0.00
2 0.00 0.03 0.00
5 0.00 0.03 0.00
10 0.00 0.03 0.01
20 0.00 0.03 0.01
100 0.01 0.03 0.05
∞ 0.07 0.05 0.20
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
19_P 126_I 1.06 0.14 0.00
125_G 162_D 0.97 0.12 0.00
158_Q 68_N 0.97 0.12 0.00
125_G 98_H 0.97 0.12 0.00
87_K 102_L 0.94 0.11 0.00
86_S 207_V 0.93 0.11 0.00
91_V 207_V 0.92 0.11 0.00
19_P 367_P 0.89 0.10 0.00
87_K 216_D 0.89 0.10 0.00
121_L 152_D 0.87 0.10 0.00
146_F 125_P 0.86 0.09 0.00
63_T 140_K 0.86 0.09 0.00
162_I 256_A 0.85 0.09 0.00
193_Y 143_G 0.85 0.09 0.00
37_A 120_F 0.84 0.09 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
6320 0.1 Hsp104-Pab1 (B, 120-500) Δgene:(1, ∞) A:(1E-20, 4) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
6319 0.21 Hsp104-Pab1 (B, 120-500) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
6318 0.01 Hsp104-Pab1 (B, 120-500) Δgene:(1, 20) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) Killed - Shared
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