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OPENSEQ.org
PglC-A
Genes: A B A+B
Length: 200 376 553
Sequences: 6462 9582 2167
Seq/Len: 32.31 25.48 3.92
MirrorTree (Pazo et al. 2001) 0.26
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 0.04 1.01
2 0.01 0.06 1.64
5 0.01 0.10 2.59
10 0.02 0.12 3.24
20 0.04 0.13 3.76
100 0.07 0.15 4.41
∞ 0.16 0.24 5.92
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.
No inter signal detected.
ID Seq/Len Name Options I_Prob Status
14241 3.92 PglC-A Δgene:(1, 20) A:(1E-20, 1) B:(1E-20, 1) msa: HHblits (2015_06) 0.00 Done - Shared
10923 10.41 KOT005 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
10922 10.4 KOT005 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
10921 11.93 KOT004 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done
9250 8.28 PglC PglA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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