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OPENSEQ.org
x250-s
Genes: A B A+B
Length: 250 239 464
Sequences: 7113 82970 804
Seq/Len: 28.45 347.15 1.73
MirrorTree (Pazo et al. 2001) 0.11
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 0.07
2 0.06 0.07 0.16
5 0.07 0.10 0.39
10 0.07 0.14 0.82
20 0.08 0.18 1.64
100 0.10 0.28 4.63
∞ 0.20 0.32 6.85
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
216_E 71_L 0.83 0.30 0.00
169_T 176_S 0.82 0.30 0.00
146_V 49_D 0.81 0.29 0.00
63_N 155_I 0.76 0.25 0.00
28_L 185_E 0.72 0.22 0.00
223_T 153_I 0.72 0.22 0.00
54_H 183_I 0.71 0.21 0.00
173_V 70_M 0.70 0.20 0.00
56_E 130_I 0.70 0.20 0.00
216_E 212_D 0.66 0.17 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
11250 0.04 x250-s2 Δgene:(1, 100) A:(1E-80, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
11249 0.2 x250-s1 Δgene:(1, 100) A:(1E-04, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11222 4.88 x250-s Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11221 1.73 x250-s Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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