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Wrong HMM in essential.hmm #15

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iimog opened this issue Nov 6, 2015 · 0 comments
Open

Wrong HMM in essential.hmm #15

iimog opened this issue Nov 6, 2015 · 0 comments

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@iimog
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iimog commented Nov 6, 2015

The essential.hmm file contains a model for TIGR00775 (NhaD: Na+/H+ antiporter, NhaD family). On the other hand a model for TIGR00755 (ksgA: ribosomal RNA small subunit methyltransferase A) is missing. This is an error as the Table S1 one of the cited reference doi:10.1038/ismej.2011.189 contains the latter but not the first.
A search in over 2700 complete bacterial genomes on NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.faa.tar.gz) found TIGR00775 in ~4% of all genomes while TIGR00755 was found in ~97% of all genomes. So TIGR00775 should not be considered essential.
iimog added a commit to iimog/multi-metagenome that referenced this issue Nov 6, 2015
@iimog
Add missing HMM TIGR00755 to essential.hmm
d628609 
The missing HMM was taken from TIGRFAMs_10.0 to stay consistent with the versions of the other HMMs.
Fixes: MadsAlbertsen#15
@iimog iimog mentioned this issue Nov 6, 2015
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