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rodA-pbp2a-diamer

Genes: A B A+B
Length: 393 240 588
Sequences: 3814 393 158
Seq/Len: 9.7 1.64 0.27
MirrorTree (Pazo et al. 2001) 0.85
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 0.02 0.00 0.07
2 0.02 0.00 0.08
5 0.02 0.00 0.19
10 0.02 0.00 0.19
20 0.02 0.00 0.20
100 0.07 0.01 0.25
0.24 0.05 0.46
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
  • ERROR: Not enough sequences to run GREMLIN analysis on (0.27 < 0.6).

ID Seq/Len Name Options I_Prob Status
0485 0.49 rodA-pbp2a-diamer Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0484 0.27 rodA-pbp2a-diamer Δgene:(1, 100) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) Killed - Shared
0482 0.22 rodA-pbp2a-diamer Δgene:(1, 100) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
0479 0.21 rodA-pbp2a-diamer Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared

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