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AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
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Any other Nor genes responsible for NO -> N2O? #109

Open B-1991-ing opened 2 years ago

B-1991-ing commented 2 years ago

Hi Zhichao,

In my current MAG, there is no NorB and C genes (they are responsible for the step "NO ---> N2O", dash lines represent no Nor genes in the MAG, as shown in the pdf file). Is there any other Nor genes can cat on this step? Then, I can check the extra Nor genes, eg., NorQ and NorD, to be sure no any Nor gene there? But, I am not sure about the cutoff.

The presence absence pattern (PAP) of Nor genes in the two MAGs, as shown in the pdf file MAG_N.pdf

If I want to check the PAP of extra Nor gene responsible for the step "NO ---> N2O", what kind of cutoff should I use when blasting the extra Nor genes with my MAG?

Best,

Bing

ChaoLab commented 2 years ago

I just followed the Kofam cutoff settings when dealing with HMMs that are not in our custom HMM database. Maybe you can try first to see if there are any HMMs related to other Nor genes in Kofam's database