L-lysine catabolism through 5-aminovalerate

A reusable four-reaction Dav pathway that converts L-lysine to glutarate through 5-aminopentanamide, 5-aminopentanoate (5-aminovalerate), and 5-oxopentanoate (glutarate semialdehyde). The module represents the DavB, DavA, DavT, and DavD reaction roles independently of genomic organization. Downstream CoA-dependent and CoA-independent routes from glutarate to central metabolism are outside the boundary.

MODULE:lysine_dav_catabolismDRAFTMetabolic Pathwaymodules/lysine_dav_catabolism.yaml
L-lysine catabolic processGO:0019477
GO:0019477
L-lysine catabolic process
GO:0019477 provides the biological-process context.
PMID:16237033
Multiple and interconnected pathways for L-lysine catabolism in Pseudomonas putida KT2440
Target-strain genetics identifies davB and davA in the aminovalerate route and distinguishes it from the parallel aminoadipate route.
PMID:31064836
Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism
KT2440 fitness and proteomics data support the Dav pathway, distinguish its L-lysine and 5-aminovalerate segments, and connect DavT and DavD to growth on 5-aminovalerate.
PMID:11679348
Expression of a Pseudomonas putida aminotransferase involved in lysine catabolism is induced in the rhizosphere
Genetic and biochemical evidence establishes the DavT 5-aminovalerate-aminotransferase role.
PMID:25012259
Enzymatic production of 5-aminovalerate from L-lysine using L-lysine monooxygenase and 5-aminovaleramide amidohydrolase
Purified P. putida KT2440 DavB and DavA establish the first two substrate-specific reactions directly.
file:projects/P_PUTIDA/deep-research/PSEPK__lysine_dav_catabolism__ppu00310-deep-research-openscientist.md
OpenScientist PSEPK ppu00310 satisfiability review
The species-aware review evaluates the Dav route in Pseudomonas putida KT2440 against the broader lysine-degradation map.
file:PSEPK/davB/davB-ai-review.yaml
PSEPK davB gene review
Q88QV1 supplies the L-lysine 2-monooxygenase step.
file:PSEPK/davA/davA-ai-review.yaml
PSEPK davA gene review
Q88QV2 supplies the 5-aminopentanamidase step.
file:PSEPK/davT/davT-ai-review.yaml
PSEPK davT gene review
Q88RB9 supplies the 5-aminovalerate aminotransferase step.
file:PSEPK/davD/davD-ai-review.yaml
PSEPK davD gene review
Q88RC0 supplies the glutarate-semialdehyde dehydrogenase step.
5Nodes
4Parts
0Variant Sets
0Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:lysine_dav_catabolism deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

4 gene-function check(s) reflected in core functions · 0 conflict(s) · 6 evidence or coverage gap(s) (10 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
davB_activity PSEPK DavB
UniProtKB:Q88QV1
Family Representative 		lysine 2-monooxygenase activity
GO:0050067 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
davA_activity PSEPK DavA
UniProtKB:Q88QV2
Family Representative 		5-aminopentanamidase activity
GO:0047588 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
davT_activity PSEPK DavT
UniProtKB:Q88RB9
Family Representative 		5-aminovalerate:2-oxoglutarate transaminase activity
GO:0047589 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
davT_activity Pseudomonas aeruginosa DavT
UniProtKB:Q9I6M4
Family Representative 		5-aminovalerate:2-oxoglutarate transaminase activity
GO:0047589 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
davD_activity PSEPK DavD
UniProtKB:Q88RC0
Family Representative 		glutarate-semialdehyde dehydrogenase (NADP+) activity
GO:0102810 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
davD_activity Pseudomonas aeruginosa DavD
UniProtKB:Q9I6M5
Family Representative 		glutarate-semialdehyde dehydrogenase (NADP+) activity
GO:0102810 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
davB_activity flavin monoamine oxidase family
PANTHER:PTHR10742
Family 		lysine 2-monooxygenase activity
GO:0050067 		Family Scope Restricted
GO:0050067 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. P. putida DavB in SF410, which lysine_dav_catabolism selects through the base family.
davA_activity carbon-nitrogen hydrolase superfamily
PANTHER:PTHR43674
Family 		5-aminopentanamidase activity
GO:0047588 		Family Function Unreviewed
The family review has no applicable adjudication supporting or excluding GO:0047588.
davT_activity class III aminotransferases
PANTHER:PTHR11986
Family 		5-aminovalerate:2-oxoglutarate transaminase activity
GO:0047589 		Family Scope Restricted
GO:0047589 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. DavT activity of the Pseudomonas SF58 members. SF58 also holds 4-aminobutyrate aminotransferases (PuuE, Bacillus GabT), so even SF58 is only a candidate set. The lysine DAV catabolism module selects the whole family PTHR11986 for this activity, which is too broad for any functional transfer.
davD_activity aldehyde dehydrogenase family
PANTHER:PTHR43353
Family 		glutarate-semialdehyde dehydrogenase (NADP+) activity
GO:0102810 		Family Scope Restricted
GO:0102810 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. Glutarate-semialdehyde dehydrogenase for the DavD clade of SF5, as lysine_dav_catabolism selects.

Gene-review completeness (4/6 grounded genes reviewed)

2 complete review(s) · 2 with deep research · 2 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
davA Q88QV2 ✓ ✓ ✗
davB Q88QV1 ✓ ✓ ✗
davD Q88RC0 ✓ 8/9 ✓
davT Q88RB9 ✓ 6/7 ✓
Pseudomonas aeruginosa DavT Q9I6M4 ✗ — —
Pseudomonas aeruginosa DavD Q9I6M5 ✗ — —

Details

L-lysine catabolism through 5-aminovalerateMetabolic Pathwaylysine_dav_catabolism
L-lysine catabolic processGO:0019477

Exact UniProt exemplars delimit the four reaction roles without restricting the module taxonomically. PANTHER terms are retained only where they provide honest fold-level containers. PTHR10742 and PTHR11986 describe the DavB and DavT folds, respectively, while exact exemplars and leaf molecular functions establish reaction specificity. The out-of-family Q9I6M4 DavT exemplar is intentional. No ancestral PTN node is asserted without verified PAINT IBD evidence. Glutarate degradation after DavD is modeled separately.

Connections

davB_step -> davA_step Provides Input For
DavB supplies 5-aminopentanamide to DavA.
davA_step -> davT_step Provides Input For
DavA supplies 5-aminovalerate to DavT.
davT_step -> davD_step Provides Input For
DavT supplies glutarate semialdehyde to DavD.
Part 1: 5-aminopentanamide formation
L-lysine 2-monooxygenaseReactiondavB_step

Annotons

L-lysine 2-monooxygenase
davB_activity
Participant: Family: flavin monoamine oxidase family
Family:
flavin monoamine oxidase familyPANTHER:PTHR10742
Representative Members: PSEPK DavBUniProtKB:Q88QV1

Function

lysine 2-monooxygenase activityGO:0050067
Substrates: L-lysine oxygen
Products: 5-aminopentanamide carbon dioxide water

Oxidatively decarboxylates L-lysine to the DavA substrate.

Part 2: 5-aminovalerate formation
5-aminopentanamidaseReactiondavA_step

Annotons

5-aminopentanamidase
davA_activity
Participant: Family: carbon-nitrogen hydrolase superfamily
Family:
carbon-nitrogen hydrolase superfamilyPANTHER:PTHR43674
Representative Members: PSEPK DavAUniProtKB:Q88QV2

Function

5-aminopentanamidase activityGO:0047588
Substrates: 5-aminopentanamide water
Products: 5-aminopentanoate ammonium

Hydrolyzes 5-aminopentanamide to 5-aminovalerate.

Part 3: glutarate-semialdehyde formation
5-aminovalerate aminotransferaseReactiondavT_step

Annotons

5-aminovalerate aminotransferase
davT_activity
Participant: Family: class III aminotransferases
Family:
class III aminotransferasesPANTHER:PTHR11986
Representative Members: PSEPK DavTUniProtKB:Q88RB9 Pseudomonas aeruginosa DavTUniProtKB:Q9I6M4

Function

5-aminovalerate:2-oxoglutarate transaminase activityGO:0047589
Substrates: 5-aminopentanoate 2-oxoglutarate
Products: 5-oxopentanoate L-glutamate

Transfers the amino group of 5-aminovalerate to 2-oxoglutarate.

Part 4: glutarate formation
Glutarate-semialdehyde dehydrogenaseReactiondavD_step

Annotons

Glutarate-semialdehyde dehydrogenase
davD_activity
Participant: Family: aldehyde dehydrogenase family
Family:
aldehyde dehydrogenase familyPANTHER:PTHR43353
Representative Members: PSEPK DavDUniProtKB:Q88RC0 Pseudomonas aeruginosa DavDUniProtKB:Q9I6M5

Function

glutarate-semialdehyde dehydrogenase (NADP+) activityGO:0102810
Substrates: 5-oxopentanoate NADP+ water
Products: glutarate NADPH proton

Oxidizes glutarate semialdehyde to glutarate.