Duplicate Branched-Chain Ketoacid Dehydrogenase Reactions

[Devlin-Moyer]

Current behavior:

There are currently two parallel/redundant reactions/pathways for oxidative decarboxylation of 2-oxo-3-methylvalerate (MAM00669m) and 3-methyl-2-oxobutyrate (MAM00824m):

ID	Reaction	Notes
MAR03748	3-methyl-2-oxobutyrate [m] + CoA [m] + NAD+ [m] ⇒ CO2 [m] + NADH [m] + isobutyryl-CoA [m]	One-step version
MAR06416	3-methyl-2-oxobutyrate [m] + H+ [m] + lipoamide [m] ⇒ CO2 [m] + S-(2-methylpropanoyl)-dihydrolipoamide [m]	First step of three-step version
MAR06417	CoA [m] + S-(2-methylpropanoyl)-dihydrolipoamide [m] ⇔ dihydrolipoamide [m] + isobutyryl-CoA [m]	Second step of three-step version
MAR06409	H+ [m] + NADH [m] + lipoamide [m] ⇔ NAD+ [m] + dihydrolipoamide [m]	Third step of three-step version
MAR03780	2-oxo-3-methylvalerate [m] + CoA [m] + NAD+ [m] ⇒ 2-methylbutyryl-CoA [m] + CO2 [m] + NADH [m]	One-step version
MAR06419	2-oxo-3-methylvalerate [m] + H+ [m] + lipoamide [m] ⇒ CO2 [m] + S-(2-methylbutanoyl)-dihydrolipoamide [m]	First step of three-step version
MAR06420	CoA [m] + S-(2-methylbutanoyl)-dihydrolipoamide [m] ⇒ 2-methylbutyryl-CoA [m] + dihydrolipoamide [m]	Second step of three-step version
MAR06409	H+ [m] + NADH [m] + lipoamide [m] ⇔ NAD+ [m] + dihydrolipoamide [m]	Third step of three-step version

Expected feature/value/output:

This situation is analogous to the situations in #524 and #633; these are reactions catalyzed by the branched-chain alpha-ketoacid dehydrogenase (BCKDH) complex, which uses lipoic acid (bound to a lysine residue on one of the subunits, hence the lipo amide) as a cofactor (source). In line with the changes we made when resolving the duplicate representations of the other alpha-ketoacid dehydrogenase complexes, I think the one-step versions, i.e. MAR03748 and MAR03780, should be removed.

Proposed changes:

• Remove MAR03748 for being a duplicate of MAR06416 + MAR06417 + MAR06409
• Remove MAR03780 for being a duplciate of MAR06419 + MAR06420 + MAR06409

[haowang-bioinfo]

Very clear, makes sense, go ahead please

[haowang-bioinfo]

fixed by #743