alr (PA4930, Q9HUN4) review notes

No deep-research API was available. Manual research on 2026-11-05: cached
abstracts (PMID:20971724, PMID:10977898, PMID:29964014, PMID:14674749), a Europe
PMC title search for "alanine racemase" AND "Pseudomonas aeruginosa" (PubMed MCP
and NCBI E-utilities returned server errors), UniProt (reviewed), and QuickGO for
other seeds.

Biology

P. aeruginosa has two alanine racemases, biosynthetic Alr (PA4930) and
catabolic DadX (PA5302). Both were cloned, shown to complement E. coli
D-alanine auxotrophs, purified and characterised PMID:10977898.
UniProt records Km 1.1 mM for both enantiomers and Vmax 40-44 umol/min/mg from
this paper.
Crystal structure of Alr (PDB 6A2F): conserved homodimer, guest D-lysine in the
active site PMID:29964014. (PMID:14674749 is the DadX structure, not Alr.)
Monomer-dimer equilibrium and Vmax were compared for seven bacterial alanine
racemases including P. aeruginosa enzymes PMID:20971724.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000775508	GO:0008784 alanine racemase activity	8	51 (33 taxa)	GO:0008784, IDA, PMID:20971724 (PseudoCAP)	SOUND	Abstract reports Vmax for the P. aeruginosa racemases studied; independently, purified Alr was characterised (PMID:10977898) and UniProt has ECO:0000269 kinetics.	P. aeruginosa DadX Q9HTQ2, E. coli Alr P0A6B4 and DadX P29012, M. tuberculosis Alr P9WQA9, V. cholerae Q9KUY6 and BsrV Q9KSE5, S. pombe SPCC965.08c	Yes

Shared node with dadX (PA5302, reviewed in parallel): no node-level defect is
needed. The alanine racemase term suits the clade (BsrV is a broad-specificity
racemase that still racemises alanine). The PseudoCAP seed is sound, so no
PSEUDOCAP or GO_CENTRAL defect is recorded here, and there is none for dadX to
cross-reference. The dadX review (genes/PSEAE/dadX) reached the same verdict:
its seed (IDA, PMID:10977898) is SOUND with no node defect.

Action summary

ACCEPT: GO:0008784 (IBA, IDA, IEA), GO:0030632 (IBA, IEA).
KEEP_AS_NON_CORE: GO:0005829 (IBA), GO:0030170 (IBA, IEA), GO:0009252 (IEA).
TOO_GENERAL: GO:0003824 (IEA).