pvdJ

Summary: PseudoCAP IMP seed of the PTN002378821 secondary metabolite biosynthetic process IBD. The cited paper deleted pvdJ in Pseudomonas syringae pv. tabaci 6605, not in P. aeruginosa.

Reason: The claim is true for PAO1 PvdJ: it is one of the pyoverdine NRPSs identified from the PAO1 iron-regulated cytoplasmic proteins and genome, and it does part of the work by assembling part of the peptide. But the cited evidence is a mutant of a same-named gene in another organism, so IMP on the PAO1 gene is wrong; at most it is ISS, and pyoverdine NRPS genes are named by position in strain-specific loci that make different peptides, so even the orthology is loose. Seed verdict WRONG (wrong organism); recorded as a source defect.

Summary: True but uninformative, and based on the P. syringae pvdJ mutant (see the GO:0002049 row for the defect).

Reason: PvdJ is a two-module NRPS with adenylation, condensation and carrier domains; the specific activity is non-ribosomal peptide synthetase activity (GO:1904091), a descendant of catalytic activity.

Proposed replacements: non-ribosomal peptide synthetase activity

Summary: Automatic catalytic activity; true but uninformative.

Reason: Replace by non-ribosomal peptide synthetase activity (GO:1904091).

Proposed replacements: non-ribosomal peptide synthetase activity

Summary: True but general; the cytosol row is accepted.

Reason: GO:0005829 cytosol, accepted in this review, is part_of cytoplasm.

Summary: Cytosol IBD from E. coli EntF. The pyoverdine NRPSs were identified as soluble iron-regulated cytoplasmic proteins.

Reason: PvdJ has no transmembrane segment or signal peptide, and the pyoverdine NRPSs were found among cytoplasmic proteins. They may also associate with the inner membrane, but the soluble location is supported.

Summary: Propagated from E. coli EntF at PTN002378853. P. aeruginosa does not make enterobactin; PvdJ makes part of pyoverdine.

Reason: Enterobactin is an E. coli catecholate siderophore made from 2,3-dihydroxybenzoate and serine by EntF with EntE/EntB. PvdJ is a pyoverdine NRPS, the PAO1 genome has no enterobactin pathway, and PvdJ is not the PAO1 enterobactin synthetase. Product specificity of NRPS modules is lineage specific, so the EntF product does not transfer.

Summary: Propagated from E. coli EntF; PvdJ is not part of an enterobactin synthetase.

Reason: Same over-propagation as the enterobactin process row. The EntBDEF complex is E. coli-specific; PvdJ works with the other pyoverdine NRPSs.

Summary: EntF's specific activity, propagated to PvdJ.

Reason: 2,3-Dihydroxybenzoate is not part of pyoverdine, and PvdJ has no role in enterobactin synthesis. The substrate specificity of NRPS adenylation domains differs between members of the clade.

Summary: PvdJ has two peptidyl carrier domains with phosphopantetheine attachment sites.

Reason: Two PP-binding carrier domains carry the 4'-phosphopantetheine arm.

Summary: Same claim as the IBA row.

Reason: Carrier domains are present.

Summary: Obsolete term. Amino acid activation by the two adenylation domains is true of PvdJ.

Reason: With the activation term obsolete, the supported process is GO:0002049 pyoverdine biosynthetic process; the activation step is captured by non-ribosomal peptide synthetase activity in core_functions.

Proposed replacements: pyoverdine biosynthetic process

Summary: Obsolete term; same claim as the IBA row.

Reason: Replace by GO:0002049 pyoverdine biosynthetic process, as for the IBA row.

Proposed replacements: pyoverdine biosynthetic process

Summary: True but general.

Reason: GO:0002049 pyoverdine biosynthetic process, accepted in this review, is_a secondary metabolite biosynthetic process.