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gringer
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How to retrieve logical expressionexpressions (KO based) for reactions from KEGG?

WhetherThe completeness of a module is complete can easily be checked by evaluatinglooking at the Definition entry associated with the module; e.gmodule. For example, in module M00010, it is given byas:

Definition  K01647 (K01681,K01682) (K00031,K00030)

which can be translated to:

K01647 AND (K01681 OR K01682) AND (K00031 OR K00030)

If this expression evaluates to TRUE, the module is considered complete.

I am wondering whether analogueanalogous information exists for a single reaction. So e.greaction. forFor example, when looking at reaction R00352, one finds the following information about its Orthology:

enter image description here

But how do I now know in whichcan't easily find the logical relation that correspond to the KOs are?

So itfor this reaction. It could be:

K01648 AND K15230 AND K15231 

or:

K01648 OR K15230 OR K15231

or:

K01648 OR (K15230 AND K15231)

and so on.

In the above example, I know that the correct expression would beis:

K01648 OR (K15230 AND K15231)

Onei.e. one either needs either K01648 or both of the other two subunits together.

Can this information be retrieved from KEGG for each reaction and if so, how?

How to retrieve logical expression (KO based) for reactions from KEGG?

Whether a module is complete can easily be checked by evaluating the Definition entry associated with the module; e.g. in module M00010, it is given by

Definition  K01647 (K01681,K01682) (K00031,K00030)

which can be translated to

K01647 AND (K01681 OR K01682) AND (K00031 OR K00030)

If this expression evaluates to TRUE, the module is complete.

I am wondering whether analogue information exists for a single reaction. So e.g. for R00352, one finds the following information about Orthology:

enter image description here

But how do I now know in which logical relation the KOs are?

So it could be

K01648 AND K15230 AND K15231 

or

K01648 OR K15230 OR K15231

or

K01648 OR (K15230 AND K15231)

and so on.

In the above example, the correct expression would be:

K01648 OR (K15230 AND K15231)

One either needs K01648 or the other two subunits together.

Can this information be retrieved from KEGG for each reaction and if so, how?

How to retrieve logical expressions (KO based) for reactions from KEGG?

The completeness of a module can easily be checked by looking at the Definition entry associated with the module. For example, in module M00010, it is given as:

Definition  K01647 (K01681,K01682) (K00031,K00030)

which can be translated to:

K01647 AND (K01681 OR K01682) AND (K00031 OR K00030)

If this expression evaluates to TRUE, the module is considered complete.

I am wondering whether analogous information exists for a single reaction. For example, when looking at reaction R00352, one finds the following information about its Orthology:

enter image description here

But I can't easily find the logical relation that correspond to the KOs for this reaction. It could be:

K01648 AND K15230 AND K15231 

or:

K01648 OR K15230 OR K15231

or:

K01648 OR (K15230 AND K15231)

and so on.

In the above example, I know that the correct expression is:

K01648 OR (K15230 AND K15231)

i.e. one either needs either K01648 or both of the other two subunits.

Can this information be retrieved from KEGG for each reaction and if so, how?

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Cleb
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How to retrieve logical expression (KO based) for reactions from KEGG?

Whether a module is complete can easily be checked by evaluating the Definition entry associated with the module; e.g. in module M00010, it is given by

Definition  K01647 (K01681,K01682) (K00031,K00030)

which can be translated to

K01647 AND (K01681 OR K01682) AND (K00031 OR K00030)

If this expression evaluates to TRUE, the module is complete.

I am wondering whether analogue information exists for a single reaction. So e.g. for R00352, one finds the following information about Orthology:

enter image description here

But how do I now know in which logical relation the KOs are?

So it could be

K01648 AND K15230 AND K15231 

or

K01648 OR K15230 OR K15231

or

K01648 OR (K15230 AND K15231)

and so on.

In the above example, the correct expression would be:

K01648 OR (K15230 AND K15231)

One either needs K01648 or the other two subunits together.

Can this information be retrieved from KEGG for each reaction and if so, how?