TreeGrafter-generated GO annotations

TreeGrafter supplied a membrane annotation that is not supported by the curated NicD entry.

file:PSEPK/nicD/nicD-uniprot.txt

UniProtKB reviewed entry for nicD

UniProt identifies NicD as N-formylmaleamate deformylase in nicotinate degradation and gives the hydrolysis reaction.

Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440

The KT2440 nic cluster paper identifies NicD as the enzyme converting N-formylmaleamic acid to formic and maleamic acid.

file:PSEPK/nicD/nicD-deep-research-falcon.md

Falcon (Edison Scientific) deep research report: N-formylmaleamate deformylase (nicD, Q88FY3) in Pseudomonas putida KT2440

"NicD catalyzes **N-formylmaleamic acid (NFM) → maleamic acid + formic acid**; this corresponds to **EC 3.5.1.106** (N-formylmaleamate deformylase) and removes the N-formyl group generated after pyridine-ring cleavage."
"Site-directed mutagenesis supports **S101–D125–H245** as the catalytic triad; **S101A, D125A, H245A** abolished activity, whereas **E221A** retained ~**70%** of wild-type activity, arguing E221 is not the catalytic acid."
"Best current annotation is **cytosolic**: NicD was assayed in **soluble crude extracts** after heterologous expression; no membrane segment, signal peptide, or export evidence is reported in the cited sources."
"Disruption of **nicD** prevented growth on **nicotinic acid** as sole carbon source, supporting an essential pathway role in KT2440; the nic cluster as a cassette restored NA utilization in nondegrading backgrounds."