PA3177 (Q9HZ57) review notes

Unreviewed UniProt entry, no gene name; folder and gene_symbol use the locus tag.
307 aa, C-terminal GGDEF domain (UniProt DOMAIN 177..307, Pfam PF00990), GGEEF
active-site motif. No TRANSMEM feature; a Kyte-Doolittle scan (19-residue window,
mean above 1.6, run in this session) finds no hydrophobic window, so the protein
is predicted soluble. The UniProt "Cell inner membrane" location rests on an ARBA
rule only.

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

Poudyal & Sauer 2018 (PMID:30082282; full text cached and read).
A PA3177 deletion has 5-fold less c-di-GMP in biofilm cells; multicopy
PA3177 restores it, but the GGAAF active-site mutant does not
PMID:30082282 PMID:30082282.
No effect on planktonic c-di-GMP, and none on attachment or biofilm
formation PMID:30082282.
Motility: the deletion swims and swarms like wild type; only overexpression
reduces motility, GGEEF-dependently PMID:30082282.
PA3177-made c-di-GMP is needed for BrlR levels and DNA binding, and so for
biofilm tolerance to tobramycin and H2O2.
Kulasakara et al. 2006 (PMID:16477007; full text read on PMC, see
wspR-notes.md): PA3177 gave no detectable c-di-GMP when overexpressed in PA14
("PA3177 GGEEF —"), but the authors note the HPLC detection limit (12 pmol/mg)
and do not conclude inactivity. Not cited by any PA3177 GOA row.

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, IMP, PMID:30082282 (PseudoCAP)	SOUND	Deletion lowers biofilm c-di-GMP 5-fold; complementation restores it, the GGAAF active-site mutant does not (full text read).	E. coli DosC, DgcC, DgcJ, DgcM, DgcN, DgcQ, DgcZ and others; B. subtilis DgcK, DgcP; Shewanella Q8EGF8; P. aeruginosa dgcP, wspR, PA1107, PA2870, PA3343, PA4332, PA4843	Yes. Many seeds have direct activity evidence (e.g. WspR purified enzyme, PMID:16186483). No GO_CENTRAL defect.

Batch consistency: all five genes in this batch seed PTN002895344; every seed row
is SOUND except the wspR IMP (PMID:12426335, INDIRECT-PHENOTYPE), which does not
affect the node.

Non-seed IBA node PTN002895351

PA3177 receives the plasma membrane, GO:0043709 and GO:1902201 IBAs from
PTN002895351 (seeded by E. coli proteins only). The node-level GO_CENTRAL defects
(PM; GO:0043709) are recorded once, on wspR (see wspR-notes.md). For PA3177:

PM IBA and IEA: MARK_AS_OVER_ANNOTATED (no TM segment).
GO:0043709 IBA: REMOVE. The deletion has no effect on attachment or biofilm
formation, so the inferred adhesion role is contradicted for this gene.
GO:1902201 IBA: KEEP_AS_NON_CORE. Supported only by overexpression; the
deletion is not hypermotile.