pvdH (Q9I168, PA2413) — Pseudomonas aeruginosa PAO1

Curation notes for the review added alongside the
modules/pseudomonas_pyoverdine_precursor_supply.yaml module work. PAO1 PvdH is
the exemplar whose enzymology and mutant phenotype ground the module's
L-2,4-diaminobutyrate step; the KT2440 ortholog (Q88F75, genes/PSEPK/pvdH) was
already reviewed from orthology plus this same paper.

What is established

Reaction. Interconversion of L-aspartate beta-semialdehyde and
L-2,4-diaminobutyrate by a PLP-dependent transamination, on protein
hyperexpressed and purified from PAO1
PMID:15317763.
Highest specificity for alpha-ketoglutarate, 41-fold lower for pyruvate,
negligible for other keto acids, with a ping-pong mechanism
PMID:15317763
— i.e. EC 2.6.1.76, GO:0045303.
Pathway role. The pyoverdine chromophore is a condensation product of
D-tyrosine and L-2,4-diaminobutyrate, and both pvdH and asd mutants are
pyoverdine-negative unless the diamino acid is supplied
PMID:15317763.
Independent mutant-phenotype support comes from the PAO1 pyoverdine gene
screen PMID:12686626.
Conservation. PvdH homologues sit inside the pyoverdine loci of other
pseudomonads PMID:15317763,
which is what makes the module's genus-level scope defensible while keeping the
exemplars to PAO1 and KT2440.
Classification. Class-III PLP-dependent aminotransferase: Pfam
Aminotran_3, PROSITE AA_TRANSFER_CLASS_3, InterPro IPR004637 (Dat), NCBIfam
TIGR00709 (dat), PIRSF Transaminase_4ab_Lys_Orn. The entry is unreviewed
(TrEMBL) and PE 3: Inferred from homology, so its free-text cofactor note
carries only ARBA evidence and is not cited as support; the curated domain
signatures are.

Review decisions worth recording

All three GO:0008483 transaminase activity rows (IBA, IDA, IEA) →
MODIFY to GO:0045303. Same term, same claim, consistent actions: the
broad parent is true but the assayed reaction is the specific child. Added
GO:0045303 as a NEW row since GOA carries only the parent here, although
the KT2440 ortholog already has the specific term.
The IBA's WITH/FROM contains UniProtKB:Q9I168 itself, i.e. the gene appears
among the seeds of the PAINT node it later receives. Per the repo's IBA policy
this is expected and is a marker that experimental grounding exists on the
target — explicitly not CIRCULAR_OR_REDUNDANT. Recorded in
propagation_review with root_cause: TERM_SCOPING_PROBLEM and
source_status: SUPPORTS_TRANSFER.
GO:0030170 pyridoxal phosphate binding kept as KEEP_AS_NON_CORE:
genuinely supported by the class-III signatures and consistent with the
ping-pong mechanism, but a cofactor property rather than the catalytic role.
This matches the KT2440 review's treatment of the same term.

Family grounding

PANTHER:PTHR43552 is a clean family-level grounding, unlike the PvdA case: both
of its subfamilies (SF1 Dat/PvdH/RhbA, SF2 EctB) perform the same EC 2.6.1.76
transamination and differ only in which pathway consumes the product, so
interpro/panther/PTHR43552/PTHR43552-review.yaml scopes GO:0045303 as
FAMILY_WIDE and the module uses the family id on this annoton. What family
membership does not say is that a member serves pyoverdine — that comes from
the pyoverdine locus context.

Provider deep research

just deep-research-perplexity PSEAE pvdH is unavailable in this environment
(Provider 'perplexity' not available. Available: falcon, openscientist), the
falcon provider fails authentication here, and an openscientist run started
for the sibling gene pvdA produced no output before hitting a 15-minute limit,
so no provider route was usable. No -deep-research-*.md file was fabricated. The review rests on the cached publications (both abstract-only, as
recorded in full_text_unavailable) and on the curated domain/family
cross-references in the UniProt record.

PseudoCAP IBA-seed assessment

Audit added 2026-10-28 (PseudoCAP IBA-seed project, worklist rank 78). The
review itself was not rewritten.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002461253 (PTHR43552)	GO:0008483 transaminase activity	1 (sole seed)	11 (9 taxa)	GO:0008483, IDA, PMID:15317763 (PseudoCAP)	SOUND	The seed is a direct enzyme assay on PvdH purified from PAO1 PMID:15317763, not a mutant phenotype. The node term is the broad parent, and it suits a clade whose 11 PAINT leaves are all class-III PLP aminotransferases (EctB proteins, Dat P44951, SCO5799, a GabT-annotated archaeal member, and Chlamydomonas and Nitrosopumilus homologues). The broad term cannot overreach on substrate. PvdH's own data support the specific child GO:0045303, so the PseudoCAP row is under-specific but not wrong. That is a granularity point, already handled by MODIFY. Neither a PSEUDOCAP nor a GO_CENTRAL defect is needed. This matches the PTHR43552 family review.

Row consistency: all three GO:0008483 rows (IBA, IDA, IEA) are MODIFY to
GO:0045303, which agrees with a SOUND verdict on the seed: the claim is true,
and only its precision is at issue.