Bacterial Kdp potassium-homeostasis system

A reusable bacterial module coupling KdpD/KdpE phosphorelay control to the high-affinity KdpFABC potassium pump. KdpD senses conditions associated with potassium limitation and phosphorylates KdpE, activated KdpE promotes kdpFABC transcription, and the membrane KdpFABC complex couples ATP hydrolysis to potassium uptake. Constitutive potassium channels and lower-affinity uptake systems are outside this module.

The Kdp system is conserved across phylogenetically distant bacteria (Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria) and also occurs in some haloarchaea, so the module is species-neutral. Escherichia coli K-12 KdpFABC/KdpDE is the canonical, structurally and biochemically characterized system and seeds every PAINT node used here; Pseudomonas putida KT2440 provides a second, sequence-inferred proteobacterial implementation, and a Desulfovibrio KdpB adds a deltaproteobacterial pump exemplar. The module context is kept at Bacteria because the archaeal members are known here only from PANTHER membership, not from characterization. The KdpD/KdpE sensor and response-regulator steps are grouped as an inner phosphorelay bundle that `conforms_to` MODULE:two_component_relay WITH_DEVIATIONS: it is a simple two-tier system with direct His-to-Asp transfer and no histidine-phosphotransfer (Hpt, GO:0009927) protein, so the validator's tier-count, tier-function and topology advisories for the missing Hpt tier are expected. The pump output remains a free extension outside the conforming bundle. KdpE carries two annotons, matching the two core functions its gene reviews keep separate: the receiver-domain phosphotransfer (GO:0000156) inside the bundle, and cis-regulatory DNA binding (GO:0000987) driving transcription as a sibling part outside it. Fusing the phosphorelay function with the transcription process would assert that GO:0000156 is the activity performing GO:0045893, which neither the gene reviews nor the ontology support. The environmental input to KdpD integrates potassium limitation, ionic strength and membrane-state signals differently among bacteria, so the first role is described conservatively; truncated cyanobacterial KdpD-like proteins lack the transmitter region and fall outside the sensor kinase role. KdpC and KdpF are retained as pump components but are not assigned independent catalytic molecular functions. KdpF stabilization is grounded by E. coli biochemical evidence; conservation of that quantitative contribution in other bacteria remains inferential. KdpF is grounded on NCBIfam:TIGR02115 (integrated in InterPro IPR011726) because this 29-residue membrane peptide has no PANTHER family assignment; both KdpF exemplars carry the TIGR02115 match. The KdpE family (PTHR48111) is a broad OmpR/PhoB-type response-regulator family; it is grounded at the KdpE subfamily SF50 because target genes and regulatory sign differ between subfamilies. PAINT and GOA assign the Kdp subunits to GO:1903103 potassium:proton antiporter complex; the family and gene reviews treat that as a mis-mapping of GO:0031004, since KdpFABC is an ATP-driven importer.