Bacterial NADPH-dependent GS-GOGAT ammonia assimilation

A reusable bacterial module for high-affinity assimilation of ammonium through the NADPH-dependent glutamine synthetase-glutamate synthase (GS-GOGAT) cycle. Glutamine synthetase first ligates ammonium to L-glutamate, forming L-glutamine. The NADPH-dependent GltB/GltD glutamate synthase complex then transfers the glutamine amide nitrogen to 2-oxoglutarate, producing two molecules of L-glutamate and regenerating the substrate for glutamine synthetase. Direct reductive amination by NAD(P)-dependent glutamate dehydrogenase is a distinct, generally lower-affinity alternative and is not a required part of this module.

The module is species-neutral and is grounded by Pseudomonas putida KT2440 and Escherichia coli K-12 exemplars. GdhA-family glutamate dehydrogenases can connect ammonium directly to glutamate, but reaction direction and physiological contribution depend on organism and nitrogen regime; that route is therefore an explicit boundary alternative rather than a third required step. Nitrogen sensing, PII signaling, GlnA adenylylation, ammonium transport, nitrate reduction, and downstream amino-acid biosynthesis are outside the core. Ferredoxin- and NADH-linked glutamate synthases are distinct implementations of the broader GS-GOGAT logic; this module is deliberately scoped to the bacterial NADPH-dependent GltB/GltD route. The broader `ammonia_assimilation` node in `modules/nitrogen_cycle.yaml` is a coarse nitrogen-cycle view of the same chemistry; this module is the focused reusable reaction-level treatment.