kdpB

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0071805 potassium ion transmembrane transport	IEA GO_REF:0000108	ACCEPT	Summary: KdpB is the catalytic subunit of the KdpFABC high-affinity K+ pump that drives potassium ion transmembrane transport. This annotation is correctly inferred from the GO:0008556 molecular function annotation via logical inference. Reason: KdpB is definitively involved in potassium ion transmembrane transport as the ATP-hydrolyzing catalytic subunit of KdpFABC. The UniProt function annotation explicitly states this is a high-affinity ATP-driven potassium transport system. This is the primary biological process for this protein. Supporting Evidence: file:DESVH/Q725T7/Q725T7-deep-research-falcon.md KdpB hydrolyzes ATP and cycles through E1/E2 conformations with a catalytic aspartyl phosphate, driving K+ translocation across the inner membrane
GO:0000166 nucleotide binding	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: KdpB binds nucleotides (specifically ATP) as part of its P-type ATPase catalytic mechanism. This is correct but overly general - GO:0005524 (ATP binding) is also annotated and is more specific and informative. Reason: While technically correct (KdpB does bind nucleotides), this annotation is redundant with the more specific GO:0005524 (ATP binding) annotation. The protein specifically binds ATP at defined residues. For annotation parsimony, the more specific ATP binding term is preferred. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Nucleotide-binding {ECO:0000256\|ARBA:ARBA00022741, ECO:0000256\|HAMAP-Rule:MF_00285}
GO:0000287 magnesium ion binding	IEA GO_REF:0000104	ACCEPT	Summary: KdpB requires Mg2+ as a cofactor for ATP hydrolysis, as is typical for P-type ATPases. UniProt annotation identifies Mg2+ binding sites at positions 514 and 518. This is a core function required for catalysis. Reason: Magnesium ion binding is essential for P-type ATPase catalytic function. The Mg2+ cofactor is required for ATP hydrolysis. UniProt HAMAP annotation identifies specific Mg2+ binding residues (positions 514 and 518) in KdpB. This represents a genuine molecular function of the protein. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Magnesium {ECO:0000256\|ARBA:ARBA00022842, ECO:0000256\|HAMAP-Rule:MF_00285}
GO:0005524 ATP binding	IEA GO_REF:0000120	ACCEPT	Summary: KdpB is the ATP-binding catalytic subunit of KdpFABC. ATP binding is essential for its P-type ATPase function. Multiple ATP binding residues are annotated in UniProt (339, 343, 371-378, 389). This is a core molecular function. Reason: ATP binding is fundamental to KdpB's function as a P-type ATPase. The protein hydrolyzes ATP to drive K+ transport. The catalytic reaction is: ATP + H2O + K+(out) = ADP + phosphate + K+(in) (EC 7.2.2.6). ATP binding is clearly a core molecular function that should be retained. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt ATP-binding {ECO:0000256\|ARBA:ARBA00022840, ECO:0000256\|HAMAP-Rule:MF_00285}
GO:0005886 plasma membrane	IEA GO_REF:0000120	ACCEPT	Summary: KdpB localizes to the inner membrane (equivalent to plasma membrane in bacteria). UniProt annotation confirms cell inner membrane localization as a multi-pass membrane protein with 7 transmembrane helices. Reason: KdpFABC is an inner membrane complex in bacteria. UniProt explicitly annotates KdpB as localized to the cell inner membrane. The protein has 7 transmembrane helices. For bacteria, plasma membrane and inner membrane are equivalent terms. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Cell inner membrane {ECO:0000256\|HAMAP-Rule:MF_00285}
GO:0006811 monoatomic ion transport	IEA GO_REF:0000043	MARK AS OVER ANNOTATED	Summary: KdpB is involved in monoatomic ion transport (specifically K+). However, this term is overly general when more specific terms (GO:0006813 potassium ion transport, GO:0071805 potassium ion transmembrane transport) are also annotated. Reason: While technically correct, this annotation is redundant with the more specific GO:0006813 (potassium ion transport) and GO:0071805 (potassium ion transmembrane transport) annotations. KdpB specifically transports K+, not generic ions. The more specific BP terms should be preferred for annotation parsimony. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Ion transport {ECO:0000256\|ARBA:ARBA00023065, ECO:0000256\|HAMAP-Rule:MF_00285}
GO:0006813 potassium ion transport	IEA GO_REF:0000120	ACCEPT	Summary: KdpB is the catalytic subunit of the high-affinity K+ uptake system KdpFABC. Potassium ion transport is the core biological process. GO:0071805 (potassium ion transmembrane transport) is also annotated and is slightly more specific. Reason: Potassium ion transport is definitively the core biological process of KdpB. While GO:0071805 (potassium ion transmembrane transport) is more specific, retaining both annotations is acceptable as GO:0006813 is a broader parent term that captures the general function. The high-affinity Kdp system is expressed under severe K+ limitation to import K+ into the cytoplasm. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm
GO:0008556 P-type potassium transmembrane transporter activity	IEA GO_REF:0000120	ACCEPT	Summary: GO:0008556 is the most specific and appropriate molecular function term for KdpB. It precisely describes the P-type ATPase mechanism that couples ATP hydrolysis to K+ transport via aspartyl-phosphate intermediate formation. This is the core molecular function annotation. Reason: This is the correct and most informative molecular function term for KdpB. The GO definition matches exactly: "Enables the transfer of K+ from one side of a membrane to the other according to the reaction: ATP + H2O + K+(out) = ADP + phosphate + K+(in)." KdpB forms a 4-aspartylphosphate intermediate at Asp302 during the E1/E2 catalytic cycle, characteristic of P-type ATPases. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Reaction=K(+)(out) + ATP + H2O = K(+)(in) + ADP + phosphate + H(+)
GO:0016020 membrane	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: KdpB is a membrane protein with 7 transmembrane helices. However, GO:0005886 (plasma membrane) is more specific and is already annotated. Reason: While correct, this term is redundant with the more specific GO:0005886 (plasma membrane) annotation. The protein is specifically localized to the inner/plasma membrane, not just generically associated with membranes. For annotation parsimony, the more specific CC term is preferred. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Membrane {ECO:0000256\|ARBA:ARBA00023136, ECO:0000256\|HAMAP-Rule:MF_00285}
GO:0016787 hydrolase activity	IEA GO_REF:0000043	MARK AS OVER ANNOTATED	Summary: KdpB has hydrolase activity (hydrolyzes ATP). However, this is an overly generic term when GO:0016887 (ATP hydrolysis activity) is also annotated and provides much more specific information. Reason: This annotation is technically correct but uninformative. KdpB specifically hydrolyzes ATP, not generic substrates. GO:0016887 (ATP hydrolysis activity) is already annotated and is far more informative. The generic "hydrolase activity" term should be avoided in favor of more specific enzyme activity terms. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Hydrolase {ECO:0000313\|EMBL:AAS97806.1}
GO:0016887 ATP hydrolysis activity	IEA GO_REF:0000002	ACCEPT	Summary: KdpB hydrolyzes ATP to drive K+ transport. This molecular function is core to the protein's role as a P-type ATPase. The annotation is correct and informative. Reason: ATP hydrolysis is the energy-providing reaction that drives K+ transport in KdpFABC. KdpB is the catalytic subunit responsible for this hydrolysis. The reaction (ATP + H2O = ADP + phosphate) is coupled to conformational changes that translocate K+. This is a core molecular function that should be retained alongside GO:0008556. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm
GO:0046872 metal ion binding	IEA GO_REF:0000043	MARK AS OVER ANNOTATED	Summary: KdpB binds metal ions (specifically Mg2+ as a cofactor). However, GO:0000287 (magnesium ion binding) is more specific and is already annotated. Reason: This annotation is redundant with the more specific GO:0000287 (magnesium ion binding) annotation. KdpB specifically binds Mg2+ as a catalytic cofactor, not generic metal ions. The specific term provides more informative annotation. Supporting Evidence: file:DESVH/Q725T7/Q725T7-uniprot.txt Metal-binding {ECO:0000256\|ARBA:ARBA00022723, ECO:0000256\|HAMAP-Rule:MF_00285}