ppx (PA5241, Q9ZN70) review notes
No deep-research API was available. Manual research on 2026-11-05: cached
publications (PMID:10382967 and PMID:24275100 abstract only; PMID:26576296 full
text), UniProt (reviewed), and QuickGO for the other PAINT seeds. PubMed MCP and
NCBI E-utilities returned server errors.
Biology
- ppx encodes a 506-residue GppA/Ppx-family exopolyphosphatase, 41% identical to
E. coli Ppx, located next to (and divergent from) ppk PMID:10382967. Overproduced paPPX releases Pi from polyP of chain length 79 and 750
PMID:10382967.
- Purified recombinant paPpx: hydrolysis of polyP to polyPn-1 + Pi, activated by
K+, NH4+ and Zn2+; Km 1.3-11 uM by chain length, kcat 40-57 s-1
PMID:26576296. The same active site also transfers phosphate from
polyP to ADP to make ATP PMID:26576296, with kcat about 4 s-1, roughly
a tenth of the hydrolase rate. This is a genuine secondary activity
(KEEP_AS_NON_CORE for GO:0008976).
- Regulation and phenotypes [PMID:24275100, abstract only]: ppx is expressed from
a sigma54/NtrC promoter under nitrogen limitation and a sigma70/PhoB promoter
under Pi limitation; a ppx null mutant is altered in motility, pyocyanin,
C6-C12 AHLs, rhamnolipids and biofilm PMID:24275100.
These are downstream consequences of altered polyP/Pi homeostasis. Ppx does not
catalyse rhamnolipid synthesis or make or sense AHLs, so the glycolipid
biosynthetic process and quorum sensing rows are indirect-phenotype
annotations (REMOVE, PSEUDOCAP WRONG_TERM, PROBABLE: the abstract states the
data are mutant phenotypes, but I could not read the full text). Biofilm,
swimming and swarming are organism-level process terms that GO routinely
annotates from mutant phenotypes; kept as non-core.
- The "cellular response to nitrogen/phosphate starvation" IDA rows rest on
promoter regulation (expression), which GO guidance does not treat as
sufficient for "response to" terms; the abstract also notes that Ppx levels
are held constant across conditions PMID:24275100.
Marked as over-annotated.
- Location: peripheral membrane by similarity to E. coli Ppx (UniProt
ECO:0000250); no direct data for P. aeruginosa.
PseudoCAP IBA-seed assessment
Other seeds read from .cache/paint/IBD.gaf; their experimental MF rows checked in
QuickGO on 2026-11-05.
| PTN node |
node term |
n_seeds |
leaf IBAs |
seed annotation (term, evidence, PMID) |
verdict |
rationale |
other seeds |
IBD stands without this seed? |
| PTN000768198 |
GO:0016462 pyrophosphatase activity |
4 |
48 (39 taxa) |
GO:0004309, IDA, PMID:10382967 (PseudoCAP); also EXP PMID:26576296 (UniProt) |
SOUND |
Overproduced enzyme releases Pi from polyP; confirmed with purified enzyme and kinetics in PMID:26576296. Exopolyphosphatase is_a pyrophosphatase. |
E. coli Ppx P0AFL6, M. tuberculosis Ppx1 P9WHV5 (EXP GO:0004309, PMID:22880033), E. coli GppA P25552 (EXP/IDA GO:0008894) |
Yes |
| PTN000768205 |
GO:0004309 exopolyphosphatase activity |
2 |
8 (8 taxa) |
as above |
SOUND |
as above |
E. coli Ppx P0AFL6 |
Yes |
The generic pyrophosphatase term at PTN000768198 correctly spans Ppx and GppA
(pppGpp 5'-phosphohydrolase); the exopolyphosphatase term sits on the Ppx
subclade. Both suit their clades. No PSEUDOCAP or GO_CENTRAL defect on the seed
rows. ppx itself receives the GO:0004309 and GO:0006798 IBAs from PTN000768205,
not the generic GO:0016462.
Action summary
ACCEPT: GO:0004309 (EXP, IBA, IDA, IEA), GO:0006798 (IBA).
KEEP_AS_NON_CORE: GO:0008976 (EXP, IEA), GO:0005886 (ISS, IEA), GO:0044010,
GO:0071977, GO:0071978. MARK_AS_OVER_ANNOTATED: GO:0006995, GO:0016036.
TOO_GENERAL: GO:0006793. REMOVE: GO:0009247, GO:0009372 (PSEUDOCAP defects,
PROBABLE).