How to include new instances to a compound class

asked 2020-06-29 10:15:22 -0500

bcamara
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Hello!

I am working in the biomass reaction of my PGDB and I would like to include lipids specific of my organism, most of them are not included in the MetaCyc database. I have checked that certain reactions of the biosynthesis pathway, there are not all the instances included. When I try to include these instances compounds by myself, the model does not recognize them.

For example: pe161 <- ps161 -> cdpdhdec9eg 1. PHOSPHASERDECARB-RXN: pe161 <- ps161 2. PHOSPHASERSYN-RXN: ps161 <- cdpdhdec9eg

pe161: Phosphatidylethanolamine (dihexadec-9enoyl, n-C16:1) -> CPD-17086 ps161: Phosphatidylserine (dihexadec-9-enoyl, n-C16:1) -> ?? cdpdhdec9eg: CDP-1,2-dihexadec-9-enoylglycerol -> ??

Could you help me in this matter??

Thank you so much

Beatriz

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answered 2020-06-30 23:58:38 -0500

bcamara
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Hi Waikit, I have tried to create an instance compound as you have indicated, but I can not figure out how to include the compound structure of these compounds. I have selected the option "Compound New" in the "Compound" Menu. Then, I have selected "lipid -> phospholipid -> phosphoglyceride -> a 3-sn-phosphatidyl-L-serine" as Class. However, I can not find the way to include the chemical formula of the instance compounds that I want to create in my PGDB. Can you indicate me how I have to proceed? I have also tried to install the Marvin Compound Editor, but Pathway Tools does not recognize it, although the correct path is indicated in the MARVINJSPATH environment variable. I have been tried to include these instance compounds in the biomass reaction for several weeks. It is not being easy for me.

Thank you so much

Beatriz

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Hi Beatriz, Sorry for the delay. Our developers are looking into this and will get back to you as soon as possible. Thank you for your patience. Wai Kit

waikit ( 2020-07-01 13:29:02 -0500 )edit

Dear Waikit, Have you found a solution to include the chemical formula of the compounds instances to include in a model? I need to include specific compounds of my model and I can not find the way to do it. Thank you so much for your time Beatriz

bcamara ( 2020-07-17 04:50:33 -0500 )edit

Hi Beatriz, I'm so sorry I didn't see this message sooner. Markus has sent you an email with follow up questions but we haven't heard back from you, so I thought you figured it out. Please check your email, I'll resend that email, too, just in case.

waikit ( 2020-08-13 23:32:39 -0500 )edit

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answered 2020-06-29 13:32:59 -0500

waikit
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Hi Beatriz,

Indeed, MetaCyc does not seem to have the equivalent compound instances for ps161 and cdpdhdec9eg. It's not clear to me what you have tried to include these compound instances yourself. You would need to create the metabolites for ps161 and cdpdhdec9eg using the Pathway Tools Editor. Then, assign ps161 to be under the class L-1-PHOSPHATIDYL-SERINE which you got from the reaction PHOSPHASERDECARB-RXN and assign cdpdhdec9eg under the class CDPDIACYLGLYCEROL from the reaction PHOSPHASERSYN-RXN. If the metabolites are created correctly, with the compound structure included, and the reaction equation is balanced, then you should see this reaction instance when you run the model. If you are using the Pathway Tools Navigator, you can also right-click on PHOSPHASERDECARB-RXN -> Show -> Show reaction's validity check for usage in a model in a terminal to see if the reaction gets instantiated into the reaction you expected.

Hope that helps. Please let me know if you have further questions.

Thanks, Wai Kit

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Hi Waikit, I have tried to create an instance compound as you have indicated, but I can not figure out how to include the compound structure of these compounds. I have selected the option "Compound New" in the "Compound" Menu. Then, I have selected "lipid -> phospholipid -> phosphoglyceride -> a 3-sn-phosphatidyl-L-serine" as Class. However, I can not find the way to include the chemical formula of the instance compounds that I want to create in my PGDB. Can you indicate me how I have to proceed? I have also tried to install the Marvin Compound Editor, but Pathway Tools does not recognize it, although the correct path is indicated in the MARVIN_JS_PATH environment variable. I have been tried to include these instance compounds in the biomass reaction for several weeks. It is not being easy for me. Thank you so much Beatriz

bcamara ( 2020-06-30 05:18:45 -0500 )edit

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