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OPENSEQ.org
YjhBC
Genes: A B A+B
Length: 405 372 750
Sequences: 86606 12205 2643
Seq/Len: 213.84 32.81 3.52
MirrorTree (Pazo et al. 2001) 0.12
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 0.06 0.04 0.34
2 0.08 0.05 0.58
5 0.13 0.08 1.19
10 0.17 0.10 2.09
20 0.22 0.11 3.40
100 0.33 0.15 7.61
∞ 0.36 0.23 9.87
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
119_G 6_V 0.84 0.50 0.00
77_Y 338_E 0.68 0.30 0.00
275_G 87_V 0.65 0.26 0.00
247_G 138_I 0.64 0.26 0.00
212_K 111_G 0.64 0.26 0.00
115_L 251_I 0.61 0.23 0.00
89_I 66_V 0.61 0.23 0.00
112_I 101_V 0.60 0.22 0.00
196_I 339_A 0.59 0.22 0.00
73_M 138_I 0.59 0.21 0.00
361_L 79_K 0.59 0.21 0.00
256_L 116_A 0.58 0.20 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
8243 10.31 YjhBC Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8234 3.52 YjhBC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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