arcD (PA5170, P18275) notes

Identity

UniProt P18275 (ARCD_PSEAE), 482 aa, Swiss-Prot reviewed. Arginine:ornithine
antiporter of the APC superfamily, basic amino acid/polyamine antiporter (APA)
family, TC 2.A.3.2.3 (InterPro IPR022461 Arg/Orn_antiprt_ArcD, NCBIfam TIGR03810,
PANTHER PTHR42770:SF4). Thirteen hydrophobic segments; inner membrane.
First gene of the anaerobically induced arcDABC operon (arcA PA5171 ADI, arcB
catabolic OTC, arcC carbamate kinase).

Biology (literature)

Discovery: arcD ORF upstream of arcABC encodes a hydrophobic membrane protein;
arcD mutants cannot use external arginine as an energy source; antiport was
proposed from the coupling of arginine uptake and ornithine release
PMID:2158926;
PMID:2158926.
Direct transport assays: E. coli membrane vesicles carrying arcD and
proteoliposomes with reconstituted ArcD
PMID:1311296;
exchange is much faster than PMF-driven uptake
PMID:1311296;
lysine can also exchange PMID:1311296.
Localization and topology: Caa-tagged ArcD in the P. aeruginosa inner membrane;
N terminus cytoplasmic, C terminus periplasmic
PMID:8449902.
Relevant comparator: Chlamydophila pneumoniae AaxC, a member of the same clade,
exchanges arginine for agmatine and is not inhibited by ornithine
PMID:18790867.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN008675589	GO:0022857 transmembrane transporter activity	7	70 (24 taxa)	GO:0043858 arginine:ornithine antiporter activity, IMP, PMID:1311296 (PseudoCAP); also UniProt EXP PMID:2158926, PMID:8449902	SOUND	The PseudoCAP paper directly measures arginine/ornithine exchange by ArcD (vesicles, proteoliposomes). The generic term is right for an APC-superfamily node that also holds E. coli AdiC, CadB, PotE, PuuP and YjeH seeds. The IMP code is probably IDA (the abstract describes direct assays, not a mutant; full text not read), which does not affect the IBD.
PTN000208945	GO:0043858 arginine:ornithine antiporter activity	1 (sole seed)	16 (11 taxa)	GO:0043858 arginine:ornithine antiporter activity, IMP, PMID:1311296 (PseudoCAP); also UniProt EXP PMID:8449902 and PMID:2158926	SOUND	The seed is well supported for ArcD itself by two direct studies (PMID:1311296 reconstitution; PMID:8449902 exchange activity in P. aeruginosa). Of the two UniProt EXP rows, PMID:2158926 only proposes the antiport from a mutant phenotype, so it is the weakest support, but the IBD does not depend on it. The node term mostly suits the clade (ArcD-type exchangers from ADI-pathway organisms: Clostridium, Bacillus, Staphylococcus, Vibrio, Bradyrhizobium). One leaf is doubtful: C. trachomatis AaxC (O84379), whose C. pneumoniae ortholog is an arginine:agmatine exchanger insensitive to ornithine (PMID:18790867). That IBA is probably an over-propagation, and a NOT (or GO:0043862 arginine:agmatine antiporter activity) should be considered for the chlamydial subclade.

Decisions summary

ACCEPT: arginine:ornithine antiporter activity (IBA, IEA, EXP x2, IMP), plasma
membrane (IBA, IEA, EXP x2), L-arginine transmembrane transport (IEA, EXP).
MODIFY: amino acid transport and transmembrane transport to L-arginine and
L-ornithine transmembrane transport; membrane to plasma membrane; generic MF
rows (transmembrane transporter, antiporter, amino acid and carboxylic acid
transmembrane transporter activity) to arginine:ornithine antiporter activity.
KEEP_AS_NON_CORE: L-arginine catabolic process (IEA, IMP) and generation of
precursor metabolites and energy (IMP): ArcD supplies substrate and removes
product of the ADI pathway but performs no catabolic step.
NEW: L-ornithine transmembrane transport (IDA, PMID:1311296).
Source defects: PSEUDOCAP WRONG_EVIDENCE_CODE CHECK (PROBABLE; IMP should probably be IDA);
UNIPROT WRONG_REFERENCE CHECK (SUSPECTED) on the EXP MF row citing PMID:2158926,
which proposes but does not measure antiport; GO_CENTRAL CHECK (SUSPECTED) for
C. trachomatis AaxC under PTN000208945.

PANTHER tree check (2026-11-05)

Topology of PTN000208945 fetched with projects/PSEUDOCAP/panther_tree.py node PTN000208945 --depth 5 (PANTHER treeinfo for PTHR42770).

PTN000208945: SPECIATION, Eubacteria, 16 leaves (PTHR42770:SF4 13, SF14 3).

child node	event / taxon	leaves	subfamilies	content	verdict for GO:0043858
PTN001718796	SPECIATION Firmicutes	7	SF4 4, SF14 3	C. botulinum ArcD, S. aureus, and the Bacillales duplication PTN005129255 (B. subtilis YvsH group SF14, B. cereus pair SF4)	Arg/Orn antiporters; term plausible
PTN000926691	LEAF Chlamydia trachomatis	1	SF4	AaxC, arginine/agmatine antiporter	the one doubtful leaf
PTN000208950	SPECIATION Proteobacteria	8	SF4	Bradyrhizobium pair PTN000208951; Gammaproteobacteria PTN000208954 (Vibrio; PAO1 duplication PTN002449612 = ArcD PTN002449614 + PA1194 PTN002449613; Enterobacteriaceae YdgI clade PTN001718809)	includes the seed; term correct

Conclusions:

There is no chlamydial subclade. C. trachomatis is the only chlamydial member of
the tree and its leaf, PTN000926691, attaches directly to the annotated node. The
earlier request for "a NOT for the chlamydial subclade" is retargeted to that single
leaf -- either NOT GO:0043858 there, or GO:0043862 arginine:agmatine antiporter
activity.
The IBD cannot be relocated. Bacterial arginine/ornithine antiporters sit in both
of the other children (Firmicutes and Proteobacteria), so the smallest clade covering
them is PTN000208945 itself. A leaf-level correction is the only option.
The PAO1 paralog PA1194 (Q9I4E4, leaf PTN002449613) is ArcD's immediate duplication
sister (node PTN002449612), which is why it inherits the same term; the suggested
proteoliposome assay on PA1194 remains the way to test that.

Defect raised SUSPECTED -> PROBABLE: the propagation path and the exact correction
target are now verified against the tree, but whether C. trachomatis AaxC itself
excludes ornithine still rests on the C. pneumoniae ortholog (PMID:18790867), which
topology cannot settle. No annotation actions changed (the GO:0043858 IBA stays ACCEPT,
correct for ArcD itself).