why some missed hmm from the METABOLIC_result.xlsx in the MW-score_reaction_table.txt?

[B-1991-ing]

Hi Zhichao,

Sometimes /METABOLIC/METABOLIC_template_and_database/MW-score_reaction_table.txt does not include all hmm models that present in the METABOLIC_result.xlsx.

For example, in MW-score_reaction_table.txt, O-S-01:Iron reduction doesn't contain FmnA.hmm from METABOLIC_result.xlsx. Is it because the FmnA.hmm doesn't participate in the process of O-S-01:Iron reduction, although it can do Iron reduction?

For example, in MW-score_reaction_table.txt, C-S-05:Hydrogen generation doesn't contain fefe-group-c2.hmm from METABOLIC_result.xlsx. Is it because the fefe-group-c2.hmm doesn't participate in the process of C-S-05:Hydrogen generation, although it can do Hydrogen generation?

Best,

Bing

[ChaoLab]

Hi Bing, For Iron reduction, the gene clusters for dissimilatory iron reduction is: (Table 1 https://www.frontiersin.org/articles/10.3389/fmicb.2020.00037/full) I used "MtrA.hmm,MtrB_TIGR03509.hmm,MtrC_TIGR03507.hmm,CymA.hmm,OmcF.hmm,OmcS.hmm,OmcZ.hmm,Ndh2.hmm,DFE_0450.hmm,DFE_0464.hmm" as the marker genes for these gene clusters.

For Hydrogen generation, I used "fe.hmm,nife-group-3abd.hmm,fefe-group-b.hmm,fefe-group-a13.hmm,nife-group-4a-g.hmm" because that they are either for H2-evolution or bidirection. fefe-group-c2 is for H2-sensing, but not for either H2-evolution (generation) or uptake (oxidation).

[B-1991-ing]

Okay, thank you very much for your reply, Zhichao.