Anto007
commented
2 years ago Just noticed that a similar issue may be there with "N-S-02:Ammonia oxidation" module too (the "nitrate reduction to ammonia" steps appear to be incorrectly included within this module). It would be useful to know firsthand what submodules are actually covered under "N-S-02:Ammonia oxidation"?
ChaoLab
I was wondering if there is any way to properly know what submodules are covered under for example "C-S-08:Methanotrophy" and "C-S-07:Methanogenesis" on MW-score_result.txt? What I noticed in my MW-score result file is that methanogenic archaeal phyla (e.g. Halobacteriota) are contributing to "C-S-08:Methanotrophy" as well as "C-S-07:Methanogenesis". This is incorrect as these archaea lack the capacity for methanotrophy (using methane as sole carbon & energy source) but instead are capable of only performing methanogenesis (methane formation). What I suspect is going on here is that the submodules "Methane oxidation" and "Methane production" have been clubbed together under "C-S-8: Methanotrophy". I suggest restricting "C-S-08:Methanotrophy" to including only pmoA, pmoB, pmoC and mmoD and excluding the rest within it such as mcrABC (methanogenesis genes), and mmoB (a regulatory protein that is in no way confirmatory for the capacity to perform methanotrophy).