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Hsp104-Pab1 (B, 120-500)
Genes: A B A+B
Length: 221 381 589
Sequences: 5021 728 57
Seq/Len: 22.72 1.91 0.1
MirrorTree (Pazo et al. 2001) 0.08
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 0.00
20 0.00 0.03 0.01
100 0.01 0.03 0.03
∞ 0.07 0.05 0.09
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
169_K 264_N 1.46 0.19 0.00
53_K 160_L 1.10 0.10 0.00
10_V 115_Q 1.07 0.10 0.00
158_Q 68_N 1.07 0.10 0.00
149_I 170_L 1.06 0.10 0.00
169_K 279_Q 0.97 0.08 0.00
94_I 311_A 0.97 0.08 0.00
94_I 210_L 0.97 0.08 0.00
10_V 136_D 0.95 0.08 0.00
109_A 270_G 0.94 0.08 0.00
192_R 106_N 0.94 0.08 0.00
169_K 266_Q 0.92 0.07 0.00
64_A 120_F 0.92 0.07 0.00
149_I 145_V 0.91 0.07 0.00
155_S 338_N 0.91 0.07 0.00
212_A 306_A 0.89 0.07 0.00
211_C 113_D 0.89 0.07 0.00
169_K 27_F 0.88 0.07 0.00
155_S 123_F 0.88 0.07 0.00
212_A 303_A 0.88 0.07 0.00
194_L 150_H 0.87 0.07 0.00
61_A 224_A 0.86 0.07 0.00
25_P 306_A 0.86 0.07 0.00
62_L 292_I 0.85 0.06 0.00
166_L 275_V 0.84 0.06 0.00
41_I 127_V 0.84 0.06 0.00
41_I 90_S 0.84 0.06 0.00
56_S 165_L 0.84 0.06 0.00
84_E 270_G 0.84 0.06 0.00
194_L 53_H 0.83 0.06 0.00
111_I 63_A 0.83 0.06 0.00
49_L 229_I 0.83 0.06 0.00
53_K 297_Q 0.82 0.06 0.00
79_V 226_Y 0.82 0.06 0.00
89_L 114_E 0.82 0.06 0.00
214_V 250_F 0.81 0.06 0.00
185_T 46_S 0.81 0.06 0.00
8_I 115_Q 0.81 0.06 0.00
160_V 159_A 0.81 0.06 0.00
160_V 147_Y 0.81 0.06 0.00
90_I 53_H 0.81 0.06 0.00
140_G 229_I 0.81 0.06 0.00
100_L 167_G 0.80 0.06 0.00
30_T 124_G 0.80 0.06 0.00
119_G 124_G 0.80 0.06 0.00
142_F 69_G 0.80 0.06 0.00
169_K 93_E 0.80 0.06 0.00
204_L 69_G 0.79 0.06 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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