PA1257 (Q9I487) review notes

Sources and research (2026-11-05)

Manual research (no deep-research provider). Sources: UniProt Q9I487 (TrEMBL), the GOA
file, and the cached full text of PMID:18833300 (Johnson et al. 2008, PLoS Genet).

PA1257 is the membrane (permease) subunit of a polar-amino-acid ABC transporter: four
Phobius TM helices, the ABC_TM1 domain (PF00528, PS50928), NCBIfam TIGR01726
(HEQRo_perm_3TM), InterPro IPR043429 ArtM/GltK/GlnP/TcyL/YhdX-like. PANTHER places it in
PTHR30614:SF0, named after E. coli TcyL.
Its operon partners are PA1256 (ATP-binding protein) and PA1260 (periplasmic
substrate-binding protein) PMID:18833300.
Johnson et al. screened sequenced, PCR-confirmed Mini-Tn5 transporter mutants on Biolog
Phenotype MicroArrays and measured induction by qRT-PCR. PA1257 is one of the mutants in the
PAO1 background (Table 1, "PA1257PA01amino acid ABC transporter membrane protein").
PMID:18833300
PMID:18833300
PMID:18833300.
No uptake assay with labelled hydroxyproline is reported. The transport claim rests on the
growth defect of three subunit mutants, their substrate-specific induction, and the
permease identity; together these are a good genetic case for a hydroxyproline ABC
importer.

PseudoCAP IBA-seed assessment

Seeds of PTN000770157 for GO:0006865 amino acid transport (.cache/paint/IBD.gaf, column 8):
P0AFT2 (E. coli TcyL), P0AEQ6 (E. coli GlnP), Q9I404 and Q9I403 (PAO1 glutamate/glutamine
permease subunits, both PseudoCAP IMP from the same paper), and Q9I487 (this gene, through its
GO:0034589 row; GO:0034589 is_a GO:0006865). QuickGO (2026-11-05): TcyL has IDA and IGI for
L-cystine transport (EcoCyc, PMID:25139244, PMID:26350134); GlnP has EXP for glutamine
transport (EcoCyc, PMID:3027504).

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000770157	GO:0006865 amino acid transport	5	84 (28 taxa)	GO:0034589 hydroxyproline transport, IMP, PMID:18833300 (PseudoCAP)	SOUND	A sequenced, PCR-confirmed PAO1 transposon mutant of this permease cannot grow on hydroxy-L-proline as carbon source, and the operon is induced specifically by hydroxy-L-proline. No direct uptake assay, but for a permease subunit this is direct genetic evidence of the transport it performs. Node term (amino acid transport) suits a polar-amino-acid permease clade. Full text read.	E. coli TcyL (IDA/IGI), E. coli GlnP (EXP), PAO1 Q9I404, Q9I403	Yes, on the E. coli seeds. No GO_CENTRAL defect for this node.

Second node, not seeded by PA1257

PA1257 also receives GO:0015184 L-cystine transmembrane transporter activity and GO:0015811
L-cystine transport by IBA from PTN000770175, whose only seed for both terms is E. coli TcyL
(P0AFT2). The only experimental data on PA1257 point to hydroxy-L-proline, and in these
binding-protein-dependent systems substrate choice is set largely by the periplasmic binding
protein, which differs between operons; the cystine IBD therefore probably spans permeases of
different specificity. No assay has tested PA1257 with cystine, so this is not a refutation:
both rows are MARK_AS_OVER_ANNOTATED with a GO_CENTRAL CHECK defect, now CONFIRMED after the tree
check below, recorded on the GO:0015184 row.

PANTHER tree check (2026-11-05)

Topology of PTN000770175 in PTHR30614 fetched with projects/PSEUDOCAP/panther_tree.py node PTN000770175 --depth 5 and --contains. The node is a SPECIATION node (Proteobacteria),
18 leaves, all PTHR30614:SF0.

Child node	Event	Leaves	Subfamilies	Contents	Verdict
PTN002826365 / PTN002826366 / PTN001577545	LEAF	1 each	SF0	H. pylori HP_0939, N. meningitidis NMB0788, G. sulfurreducens GSU0799 ("amino acid ABC transporter permease")	specificity unknown
PTN002826367	DUPLICATION	2	SF0	Bradyrhizobium blr2225, blr3310	specificity unknown
PTN000770168	SPECIATION (Gammaproteobacteria)	13	SF0	the four clades below	mixed
PTN008625440	HORIZ_TRANSFER	4	SF0	B. subtilis TcyB, B. cereus BC_0873 (cystine), S. aureus SAOUHSC_02698, H. influenzae HI_1079	cystine for the two named
PTN008625441	HORIZ_TRANSFER	2	SF0	B. subtilis YxeN, V. cholerae VC_0009	specificity unknown
PTN002413080	DUPLICATION	3	SF0	PA1257, PA1258, PA0313 (PA0313 = YecS-like L-cysteine system permease)	hydroxyproline operon for PA1257/PA1258
PTN002024099	SPECIATION (Enterobacteriaceae)	4	SF0	E. coli TcyL (the seed), Salmonella YecS and STM1636, Yersinia YecS	cystine/YecS throughout

Verdict: the earlier concern holds and is now CONFIRMED on primary data. The node is not a clade of
cystine permeases: it mixes permeases of several specificities across two horizontal transfers and
three lineage-specific duplications. --contains P0AFT2,Q7CQB5,A0A380PDF6,Q8ZPA0 returns
PTN002024099, i.e. every cystine/YecS-named enterobacterial member sits in that one 4-leaf clade, so
the cystine-specific support stops there. --contains P0AFT2,P42200 and --contains P0AFT2,Q9I6H8
both return the whole 13-leaf PTN000770168, confirming that the other cystine-named leaves (B.
subtilis TcyB, PAO1 PA0313) are not monophyletic with TcyL and so cannot be gathered into a single
narrower cystine node. --contains Q9I486,Q9I487 returns PTN002413080, the Pseudomonas duplication
that produced the hydroxyproline permeases.

Recommendation recorded in the defect: move the GO:0015184 / GO:0015811 IBDs down to
PTN002024099, and if a term is wanted at PTN000770175 use GO:0015424 ABC-type amino acid
transporter activity (plus GO:0006865 for the process), which the node's composition supports.

Annotation decisions

GO:0034589 hydroxyproline transport (IMP): ACCEPT, core process.
GO:0005886 plasma membrane (IBA, IEA): ACCEPT. GO:0016020 membrane: TOO_GENERAL.
GO:0022857 transmembrane transporter activity: MODIFY to GO:0015424 ABC-type amino acid
transporter activity (hydroxyproline is an amino acid in GO: GO:0034590 is_a GO:0015179).
GO:0043190 ABC transporter complex: MODIFY to GO:0055052 (substrate-binding
subunit-containing), since the operon encodes the periplasmic binding protein PA1260.
GO:0055085 transmembrane transport: MODIFY to GO:0003333 amino acid transmembrane transport.
GO:0015184 and GO:0015811 (IBA from PTN000770175): MARK_AS_OVER_ANNOTATED.