PA3760

Summary: PA3760 is a soluble cytoplasmic PTS protein.

Reason: PA3760 has no transmembrane segments or signal peptide. Its EIIA, HPr and EI domains are cytoplasmic PTS components that phosphorylate the membrane-bound EIIBC from the cytoplasmic side. The UniProt SubCell line rests on an ARBA rule, so it is not quoted as support.

Summary: PA3760 contains a complete Enzyme I module, which transfers the phosphoryl group from PEP to the HPr histidine.

Reason: The IBA is seeded by E. coli PtsI and PtsP at an Enzyme I node. PA3760 has all EI domains (EIN, PEP-utilizer mobile and C-terminal domains; TIGR01417) and so falls inside the clade that inherited the activity. This is the core catalytic activity.

Summary: EC 2.7.3.9 mapping, consistent with the Enzyme I domain architecture.

Reason: This row agrees with the IBA row and with the domain content. The EI module is complete.

Summary: PA3760 contains the EI, HPr and EIIA modules of a PEP-dependent sugar phosphotransferase system.

Reason: This is the general process term for the PTS. It is supported by the domain architecture, and specifically by GlcNAc-dependent growth.

Summary: True for PA3760, but the IBD that produces it is placed at an Enzyme I node too broad for a substrate-specific term.

Reason: PA3760 is the sole seed (its own PseudoCAP IMP, which is expected and not circular), and GlcNAc transport is well supported for PA3760 itself, so this row is retained. At node level the term does not fit, on evidence rather than nomenclature: leaf UniProtKB:P08839 (E. coli PtsI) is experimentally the general, non-sugar-specific EI (GO:0008965 EXP, curated FUNCTION with ECO:0000269); leaf UniProtKB:P37177 has a GAF domain PtsI lacks and IDA GO:0008965 and GO:0006468 as the nitrogen-PTS EI-Ntr; and the sister leaf UniProtKB:Q9HY55 (PA3562), in the same subfamily and the same organism, is experimentally a fructose PTS protein in the very paper that seeds this IBD. The fused leaves differ from PA3760 in EIIA subtype (type-2 fructose-class PF00359 versus PA3760's type-1 PF00358). The resulting 43 GlcNAc-transport IBAs are mostly unsupported (see source_defects).

Summary: The PA3760 Tn5 mutant cannot grow on N-acetylglucosamine. The gene is induced by GlcNAc and lies in a GlcNAc/glucosamine utilisation operon with the EIIBC gene PA3761.

Reason: Taken alone, a growth defect is an indirect read-out of transport. Here it agrees with the domain content (EIIA-HPr-EI that phosphorylates an EIIBC), the operon context and substrate induction. PA3760 does part of the work of PTS-mediated GlcNAc uptake by delivering the phosphoryl group to the PA3761 EIIBC, and FruI cannot substitute. A possible polar effect on PA3761 does not affect the claim, because both are components of the same PTS.

Summary: "Kinase" keyword mapping. In GO, the EI activity is not classified under kinase activity.

Reason: The essence (phosphoryl transfer) is right, but GO:0008965 PEP-protein phosphotransferase activity (EC 2.7.3.9) sits under phosphotransferase activity with a nitrogenous group as acceptor, not under kinase activity. The correct, specific term is GO:0008965, which the gene already carries.

Proposed replacements: phosphoenolpyruvate-protein phosphotransferase activity

Summary: The term is correct but uninformative.

Reason: The specific transferase activity is PEP-protein phosphotransferase activity (GO:0008965, a descendant), which is already annotated.

Proposed replacements: phosphoenolpyruvate-protein phosphotransferase activity

Summary: The term is correct but general.

Reason: The specific activity is PEP-protein phosphotransferase activity (GO:0008965, an is_a descendant via GO:0016775), which is already annotated.

Proposed replacements: phosphoenolpyruvate-protein phosphotransferase activity