ampDh2 (PA5485, Q9HT86) review notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE Q9HT86 --alias ampDh2; accession matches the worklist.
Unreviewed entry. No deep-research provider was used; literature from the cached seed paper,
PubMed MCP and web searches ("AmpDh2", "AmpDh3 Pseudomonas"). Reviewed together with ampD and
ampDh3 (shared PAINT nodes).

Literature

Seed paper PMID:23510438 (Zhang et al. 2013), full text cached and read. Kinetics with six
synthetic substrates and sacculus digestion PMID:23510438. No localization experiment: PMID:23510438. No beta-lactamase assay; the AmpC link is interpretive PMID:23510438.
PMID:23931161 (Lee et al. 2013, full text): PMID:23931161
UniProt Q9HT86: SignalP signal peptide 1-16 and PROSITE PS51257 lipoprotein site; PG_binding_1
domain; crystal structures 4BJ4, 4BOL.

Annotation decisions

GO:0008745 (IBA, IDA, IEA): ACCEPT, core MF.
GO:0009253 (IEA), GO:0009254 (IBA): ACCEPT.
GO:0009276 cell wall (IBA, IDA): ACCEPT; true for this lipoprotein acting on the sacculus.
The IDA code overstates the evidence (PSEUDOCAP WRONG_EVIDENCE_CODE, CONFIRMED).
GO:0033252 regulation of beta-lactamase activity (IDA): REMOVE; PSEUDOCAP WRONG_TERM,
CONFIRMED (full text read).
NEW GO:0009279 cell outer membrane (IC): signal peptide plus lipobox, and the laboratory's
structural work.
Action counts: ACCEPT 7, REMOVE 1, NEW 1.

PseudoCAP IBA-seed assessment

Node assessments are recorded once in genes/PSEAE/ampD/ampD-notes.md; summary below.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN001252273	GO:0008745 N-acetylmuramoyl-L-alanine amidase activity	5	37 (19 taxa)	GO:0008745, IDA, PMID:23510438	SOUND	Kinetics with purified enzyme and sacculus digestion (full text).	E. coli AmpD P13016, AmiD P75820, ampD, ampDh3	Yes
PTN002019137	GO:0009276 Gram-negative-bacterium-type cell wall	3	18 (11 taxa)	GO:0009276, IDA, PMID:23510438	SOUND	Location correct (outer-membrane lipoprotein acting on the sacculus), but not assayed in the paper; evidence code is IDA where TAS/IC fits.	ampD (WRONG), ampDh3 (location unsettled)	No: the node term does not suit the clade, which includes the cytoplasmic AmpD lineage. GO_CENTRAL defect recorded once, on the ampD review