DavD is the glutarate-semialdehyde dehydrogenase of the Dav pathway. It oxidizes 5-oxopentanoate to glutarate after the DavT reaction, completing conversion of L-lysine-derived 5-aminovalerate to glutarate. Orthology to Pseudomonas aeruginosa DavD supports NADP+ use, although Q88RC0 cofactor preference has not been measured directly.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004777 succinate-semialdehyde dehydrogenase (NAD+) activity | IEA GO_REF:0000118 | REMOVE | Summary: Incorrect succinate-semialdehyde substrate assignment transferred from a broad family node. Reason: DavD is assigned to oxidation of 5-oxopentanoate in the lysine-derived Dav pathway, whereas GO:0004777 specifies succinate semialdehyde. This substrate mismatch is independent of the unresolved NAD versus NADP preference of Q88RC0. Supporting Evidence: file:PSEPK/davD/davD-uniprot.txt Reaction=5-oxopentanoate + NADP(+) + H2O = glutarate + NADPH + 2 H(+) |
| GO:0005829 cytosol | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Plausible electronic localization that is not part of the core functional claim. Reason: Cytosol is consistent with a soluble bacterial metabolic enzyme, but the annotation is electronic and no direct localization evidence was found. It therefore should not define the curated core function. Supporting Evidence: file:PSEPK/davD/davD-uniprot.txt GO; GO:0005829; C:cytosol |
| GO:0009013 succinate-semialdehyde dehydrogenase [NAD(P)+] activity | IEA GO_REF:0000002 | REMOVE | Summary: Incorrect substrate-generalized succinate-semialdehyde activity. Reason: Family membership does not override the exact 5-oxopentanoate reaction assigned to DavD. Supporting Evidence: file:PSEPK/davD/davD-uniprot.txt Reaction=5-oxopentanoate + NADP(+) + H2O = glutarate + NADPH + 2 H(+) |
| GO:0009450 GABA catabolic process | IEA GO_REF:0000120 | UNDECIDED | Summary: Family-transferred GABA-catabolism role is unresolved for Q88RC0. Reason: DavD is established in the 5-aminovalerate pathway, but the available evidence does not test whether Q88RC0 also accepts succinate semialdehyde or contributes to GABA catabolism. Supporting Evidence: PMID:31064836 Only 3 genes shared fitness defects between 5AVA and l-lysine (davT, davD, and lghO), and all three have been previously implicated in 5AVA metabolism file:PSEPK/davD/davD-uniprot.txt Catalyzes the conversion of 5-oxopentanoate (glutarate |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Correct but uninformative oxidoreductase parent. Reason: The substrate- and cofactor-specific activity GO:0102810 is available. |
| GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: Mechanistically correct but less informative than the enzyme-specific activity. Reason: GO:0102810 captures the physiological substrate and NADP dependence. |
| GO:0102810 glutarate-semialdehyde dehydrogenase (NADP+) activity | IEA GO_REF:0000116 | ACCEPT | Summary: Correct enzyme-specific molecular function. Reason: The reviewed exact record assigns the 5-oxopentanoate-to-glutarate reaction with NADP+, and KT2440 profiling places davD in 5AVA metabolism. Supporting Evidence: file:PSEPK/davD/davD-uniprot.txt Reaction=5-oxopentanoate + NADP(+) + H2O = glutarate + NADPH + 2 H(+) PMID:31064836 Only 3 genes shared fitness defects between 5AVA and l-lysine (davT, davD, and lghO), and all three have been previously implicated in 5AVA metabolism |
| GO:0102810 glutarate-semialdehyde dehydrogenase (NADP+) activity | ISS GO_REF:0000024 | ACCEPT | Summary: Correct enzyme-specific molecular function. Reason: The reviewed exact record assigns the 5-oxopentanoate-to-glutarate reaction with NADP+, and KT2440 profiling places davD in 5AVA metabolism. Supporting Evidence: file:PSEPK/davD/davD-uniprot.txt Reaction=5-oxopentanoate + NADP(+) + H2O = glutarate + NADPH + 2 H(+) PMID:31064836 Only 3 genes shared fitness defects between 5AVA and l-lysine (davT, davD, and lghO), and all three have been previously implicated in 5AVA metabolism |
| GO:0019477 L-lysine catabolic process | ISS GO_REF:0000024 | ACCEPT | Summary: Correct biological-process assignment. Reason: KT2440 fitness and expression data connect davD to the 5AVA segment of L-lysine catabolism. Supporting Evidence: PMID:31064836 Only 3 genes shared fitness defects between 5AVA and l-lysine (davT, davD, and lghO), and all three have been previously implicated in 5AVA metabolism |
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Experiment: Measure DavD steady-state kinetics across glutarate semialdehyde and succinate semialdehyde with both nicotinamide cofactors, and test davD complementation during growth on 5AVA.
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