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OPENSEQ.org
METN - YOEB
Genes: A B A+B
Length: 343 84 425
Sequences: 1661 6071 1516
Seq/Len: 4.84 72.27 3.57
MirrorTree (Pazo et al. 2001) 0.03
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 0.00 0.00 0.00
2 0.00 0.02 0.01
5 0.00 0.05 0.04
10 0.00 0.07 0.08
20 0.01 0.10 0.15
100 0.04 0.21 0.69
∞ 0.41 0.69 3.55
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
28_V 80_C 0.71 0.34 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.41 > 0.4) of paralogs.
  • For sequence B, there is a high ratio (0.69 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
0015 3.57 METN - YOEB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) (2013_03) 0.00 Done - Shared
0014 0.15 METN - YOEB Δgene:(1, 20) A:(1E-20, 8) B:(1E-04, 8) (2013_03) Killed - Shared
0013 0.03 METN - YOEB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) Killed - Shared
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