How to get more carbon sources or fermentation products in fill step?

[Erique29]

Hi again, I tried the new function of prediction of carbon sources and fermentation products, and it is useful for me. I can get two lists of the same kind of 186 carbon sources or fermentation products. Can I add more carbon sources or fermentation products in this step? I don't know which is the key file. Thanks! Best, Erique

[Waschina]

Hi Erique,

could you provide some more detail on what you would like to achieve? Are you referring to the gapseq medium module to predict a gap-fill medium? At what stage of the gapseq workflow do you want to add additional carbon sources?

[jotech]

just to add to add shortly: candidate carbon sources and fermentation products are listed in: https://github.com/jotech/gapseq/blob/master/dat/subex.tbl

[Erique29]

Hi @Waschina, In the last step (gapseq fill), I use the new function (-w) to get the information of carbon sources and fermentation products. But many carbon sources that I want to explore are not on the list. So, I want to add more targets to the results. I will add some carbon sources in dat/subex.tbl as @jotech suggested. Thanks a lot. Best, Erique

[Erique29]

Hi @jotech, I will try it, Thanks! Best, Erique

[jotech]

Hi @Erique29 do you mind to share which carbon sources are missing? Maybe we can add them so that they could be found by default

[Erique29]

Hi @jotech , Sure, I check subex.tbl, some carbon sources from BIOLOG test were not included. Like,

• β-Methyl-D-Glucoside EX_cpd11603_e0
• N-Acetyl-β-D-Mannosamine EX_cpd27563_e0
• D-Fucose EX_cpd00750_e0
• D-Fructose-6-PO4 EX_cpd00072_e0
• Gelatin EX_cpd11879_e0
• D-Malic Acid EX_cpd00386_e0
• D-Aspartic Acid EX_cpd00320_e0
• Glycyl-L-Proline EX_cpd22832_e0
• Acetoacetic Acid EX_cpd00142_e2
• Methyl Pyruvate EX_cpd24420_e2
• D-Lactic Acid Methyl Ester EX_cpd24428_e2
• 3-Methyl Glucose EX_cpd26351_e2
• L-Galactonic Acid Lactone EX_cpd00820_e3
• p-Hydroxy-Phenylacetic Acid EX_cpd00489_e3
• Bromo-Succinic Acid EX_cpd23859_e4
• γ-Amino-Butryric Acid EX_cpd00281_e5
• β-Hydroxy-D,L Butyric Acid EX_cpd02042_e6

Can I ask another question? There are 369 candidate carbon sources and fermentation products in the list. But there was only part of them shown in the cs.tbl and ferm.tbl. How can I get the full list? Thank!

cs.xls

Best

[jchmiel4]

@jotech Apologies for hijacking this closed comment, but it might be useful for other bacteria. Would it be possible to add the following compound to the list?

Oxalic Acid;oxalate EX_oxa(e) EX_cpd00180_e0 Carboxylic acids

[jotech]

Many thanks for reviving this thread! Yes, adding oxalate makes sense, and I just committed it!

The problem with the compounds @Erique29 provided some time ago was that many of them are, as far as I see, not well connected with downstream reactions and would potentially lead to artifacts slowing down the gap-filling.

But maybe it makes sense to rethink some of them. Anyway sorry for the late reply @Erique29!