KEGG-derived model without compartmentalization

[gaeaberry]

Hello everyone.
I am trying to model a fungus with RAVEN but the thing is it creates a model with only one compartment as below

comps: {'s'}
compNames: {'System'}

Is it normal?
How can I make (induce) compartmentalization?

Thank you.

[edkerk]

I assume that you're using getKEGGModelForOrganism? Indeed, KEGG does not contain any compartment information.

We don't have a full tutorial on how to assign reactions to compartments, but you should have a look at predictLocalization, which can assign reactions based on scores from a localization predictor. These scores can be prepared by parseScores, which can take the output from three (WoLF PSORT, CELLO and DeepLoc) predictors and prepares it for use by predictLocalization. If you are running Unix, you can directly run WoLF PSORT with getWoLFScores.

[gaeaberry]

Thank you for your answer. @edkerk
One more question is: Do we need to take scores from all of the three predictors? or just one is enough?

[edkerk]

Just one is enough!

[gaeaberry]

hello @edkerk
I am having problems using predictLocalization code.

My code is as below:

load 'First_try.mat'
defaultCompartment = 'cytos'

[outModel, geneLocalization, transportStruct, scores,removedRxns] = predictLocalization (model, MergedGSS, defaultCompartment, 0.5, 15, false)`

It bumped into an error as below.

WARNING: For 121 of 1233 model genes no data was found in GSS

Error using vertcat
Dimensions of arrays being concatenated are not consistent.

Error in predictLocalization (line 624)
outModel.compNames=[outModel.compNames;GSS.compartments(2:end)'];
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in predictLocalisation (line 4)
[outModel, geneLocalization, transportStruct, scores,removedRxns] = predictLocalization (model, MergedGSS, defaultCompartment, 0.5, 15, false)
                                                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

I dont know what is the problem. I believe I followed the exact procedure. But maybe missed something?

Thank you for your help.