dgcP (PA5487, Q9HT84) review notes

Reviewed UniProt entry (DGCP_PSEAE), 671 aa, GGEEF domain with DGCcoil
(PF20975). No TRANSMEM feature; a Kyte-Doolittle scan (19-residue window, mean
above 1.6, run in this session) finds no hydrophobic window. UniProt places DgcP
at the inner membrane only by similarity to PA14 DgcP (A0A0H2ZJS2), via
FimV-dependent polar recruitment, which would make it a peripheral membrane
protein.

Literature (no deep-research provider available; own reading)

Kulasakara et al. 2006 (PMID:16477007; cached copy abstract only, full text
PMC1413825 read on the PMC web page, excerpts verbatim below). Cells
overexpressing PA5487 accumulated 109 pmol c-di-GMP per mg wet cell weight;
PA5487 insertion abolished biofilm formation in PA14.
Aragon et al. 2015 (PMID:25809128; abstract only). DgcP activity in P.
savastanoi depends on an intact GGDEF domain; deletion of dgcP in P.
savastanoi and P. aeruginosa PAK increases motility and reduces biofilm
PMID:25809128. Source of the UniProt EXP row. From the abstract it
is unclear whether the P. aeruginosa protein itself was assayed; the term is
correct regardless (PMID:16477007).
UniProt FUNCTION (curated, ECO:0000269 PubMed:25809128): "Catalyzes the
synthesis of cyclic-di-GMP (c-di-GMP) via the condensation of 2 GTP
molecules".

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?
PTN002895344	GO:0052621 diguanylate cyclase activity	19	205 (28 taxa)	GO:0052621, IDA, PMID:16477007 (PseudoCAP)	SOUND	Cells overexpressing PA5487 accumulated 109 pmol/mg c-di-GMP (Table 1, full text read).	E. coli DosC, DgcC, DgcJ, DgcM, DgcN, DgcQ, DgcZ and others; B. subtilis DgcK, DgcP; Shewanella Q8EGF8; P. aeruginosa wspR, PA1107, PA2870, PA3177, PA3343, PA4332, PA4843	Yes. Many seeds with direct activity evidence; DgcP also has a UniProt EXP row. No GO_CENTRAL defect.

Batch consistency: see wspR-notes.md. All seed rows for PTN002895344 in this
batch are SOUND except the wspR IMP (PMID:12426335).

Non-seed IBA node PTN002895351

The node-level GO_CENTRAL defects for PTN002895351 (plasma membrane; GO:0043709)
are recorded once, on wspR. For DgcP:

PM (IBA, IEA, ISS): KEEP_AS_NON_CORE. The IBA's reasoning (TM seeds) does not
apply, but polar, FimV-dependent membrane association by similarity to PA14
DgcP makes a peripheral PM location plausible.
GO:0043709 IBA: MARK_AS_OVER_ANNOTATED (regulates biofilm through c-di-GMP).
GO:1902201 IBA: ACCEPT (deletion is hypermotile, PMID:25809128).

Verbatim excerpts from PMID:16477007 full text (PMC1413825, PMC web page)

PA5487 GGEEF +(109)
DGC activity is measured as pmol of c-diGMP produced per mg wet cell weight.
Insertions in PA0169 , PA1120 , PA4959 , and PA5487 abolished biofilm formation