DVU_0413 is a TrkH-family potassium uptake protein that functions as the membrane pore-forming subunit of the Trk/Ktr K+ uptake system. It contains the TrkH domain (PF02386) and Cat_transpt domain (IPR003445), which are canonical for inner-membrane K+ conductance channels. The protein forms a dimeric channel that couples to a TrkA RCK ring for allosteric regulation. The system functions as an ATP-gated, low-affinity K+ uptake channel that exploits membrane potential for inward K+ flux when extracellular K+ is relatively high (mM range). ATP binding to the RCK octamer stabilizes an active conformation, while ADP-bound states are inactive. The system plays a key role in K+ homeostasis and osmoadaptation, particularly important under salt stress conditions. TrkH-family transporters are strongly associated with salinity adaptation in environmental metagenomics studies (Chiang et al. 2024, Foster et al. 2024, Wu et al. 2024).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0098655
monoatomic cation transmembrane transport
|
IEA
GO_REF:0000108 |
MODIFY |
Summary: This annotation is correct but overly general. TrkH-family proteins are specifically potassium ion channels, not general cation transporters. The term was inferred from the MF annotation GO:0008324 (monoatomic cation transmembrane transporter activity).
Reason: DVU_0413 is a TrkH-family K+ uptake pore subunit with well-characterized specificity for potassium ions. Structural studies of homologous KtrAB complexes demonstrate K+ selectivity through a selectivity filter (Chiang et al. 2024). The term should be made more specific to potassium ion transmembrane transport.
Proposed replacements:
potassium ion transmembrane transport
Supporting Evidence:
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
KtrAB-type complexes are gated by RCK octameric rings (KtrA/TrkA); ATP binding (vs ADP) adopts an activating conformation
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
Trk/Ktr systems: Bacterial low-affinity K+ uptake assemblies composed of a membrane pore subunit (TrkH/KtrB/KtrD) and a cytosolic regulatory ring
|
|
GO:0005886
plasma membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Correct cellular component annotation. TrkH/KtrB homologs are integral inner-membrane proteins forming the K+ conductance pathway. In bacteria, the plasma membrane is equivalent to the inner/cytoplasmic membrane where this protein localizes.
Reason: The TrkH domain architecture and transmembrane nature support inner-membrane (plasma membrane) localization. This is consistent with the established function of TrkH-family proteins as membrane-embedded K+ channels (Foster et al. 2024).
Supporting Evidence:
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
TrkH/KtrB homologs are integral inner-membrane proteins forming the K+ conductance pathway
|
|
GO:0006811
monoatomic ion transport
|
IEA
GO_REF:0000043 |
MODIFY |
Summary: This is a very general parent term that is technically correct but uninformative. The annotation comes from UniProtKB keyword mapping. Given that DVU_0413 specifically transports potassium ions, more specific terms are warranted.
Reason: This general term does not capture the specific substrate (K+) of the TrkH-family transporter. While not incorrect, it should be replaced with the more specific potassium ion transport term for informative annotation.
Proposed replacements:
potassium ion transport
Supporting Evidence:
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
TrkH/KtrB-family pores are selective for K+ and operate as low-affinity, membrane-potential-driven channels
|
|
GO:0006812
monoatomic cation transport
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: Derived from InterPro:IPR003445 (Cat_transpt domain). This is a correct but overly broad annotation that encompasses all cation transport. TrkH proteins are specifically K+ selective.
Reason: The Cat_transpt domain (IPR003445) is found in cation transporters, but TrkH-family proteins have evolved specificity for K+. Structural and biochemical evidence from homologous systems confirms K+ selectivity, warranting a more specific term.
Proposed replacements:
potassium ion transport
Supporting Evidence:
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB
|
|
GO:0008324
monoatomic cation transmembrane transporter activity
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: This molecular function annotation from InterPro is correct but should be made more specific. DVU_0413 has potassium ion transmembrane transporter activity, not general cation transporter activity.
Reason: TrkH-family proteins function specifically as K+ channels. The protein enables transfer of K+ ions across the membrane through a selectivity filter, with activity regulated by the RCK domain of the cognate TrkA partner. A more specific MF term better captures the actual molecular function.
Proposed replacements:
potassium ion transmembrane transporter activity
Supporting Evidence:
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
High-resolution cryo-EM structures of Bacillus subtilis KtrAB demonstrate that ATP binding to the KtrA octamer stabilizes an active conformation that enhances K+ flux through KtrB
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
The membrane subunit (e.g., TrkH/KtrB) provides the ion-conducting pathway
|
|
GO:0030001
metal ion transport
|
IEA
GO_REF:0000117 |
REMOVE |
Summary: This ARBA-derived annotation is problematic. While potassium is technically a metal (alkali metal), in GO ontology conventions, "metal ion transport" (GO:0030001) is typically used for transition metals and heavy metals (Fe, Zn, Cu, etc.), not for alkali metal cations like K+ and Na+. Potassium ion transport has its own dedicated branch (GO:0006813).
Reason: This annotation represents a mapping error or overly broad inference. In GO usage and biological convention, K+ is classified under "monoatomic cation" and "potassium ion" terms rather than "metal ion" terms. The term GO:0030001 is a sibling of GO:0006812 (monoatomic cation transport), not a parent, and is typically reserved for transition/heavy metals. Retaining this annotation would be misleading about the substrate specificity of DVU_0413.
Supporting Evidence:
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
Trk/Ktr systems: Bacterial low-affinity K+ uptake assemblies composed of a membrane pore subunit (TrkH/KtrB/KtrD)
|
|
GO:0055085
transmembrane transport
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: This is the most general transmembrane transport term. While technically correct (DVU_0413 does perform transmembrane transport), it provides minimal information about the actual function.
Reason: This very general term is implied by more specific annotations. It is not incorrect, but adds no functional insight beyond what is captured by potassium-specific terms. Keeping as non-core maintains the hierarchical relationship without cluttering the core annotation set.
Supporting Evidence:
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
The membrane subunit (e.g., TrkH/KtrB) provides the ion-conducting pathway
|
|
GO:1990573
potassium ion import across plasma membrane
|
ISS
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md |
NEW |
Summary: TrkH/Ktr systems function specifically in K+ uptake (import) rather than export. This term captures the directionality of transport that is missing from the existing annotations.
Reason: DVU_0413 is part of the Trk K+ uptake system, which specifically imports K+ into the cell. The deep research clearly indicates this is an uptake/import system operating when external K+ is in the mM range. This term more precisely describes the biological process than the bidirectional "transport" terms.
Supporting Evidence:
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
Trk/Ktr systems are generally ATP-gated channels that exploit the membrane potential for inward K+ flux when extracellular K+ is relatively high (mM range)
file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
Trk-type K+ transporter ranked as the top genomic feature linked to high salinity, highlighting the ecological importance of TrkH-mediated salt-in strategies
|
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-01-15T10:40:09.818301'
end_time: '2026-01-15T10:45:14.806707'
duration_seconds: 304.99
template_file: templates/gene_research_go_focused.md
template_variables:
organism: DESVH
gene_id: Q72F05
gene_symbol: Q72F05
uniprot_accession: Q72F05
protein_description: 'SubName: Full=Potassium uptake protein, TrkH family {ECO:0000313|EMBL:AAS94896.1};'
gene_info: OrderedLocusNames=DVU_0413 {ECO:0000313|EMBL:AAS94896.1};
organism_full: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG
34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
protein_family: Not specified in UniProt
protein_domains: Cat_transpt. (IPR003445); TrkH (PF02386)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 19
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'Q72F05' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene Q72F05 (gene ID: Q72F05, UniProt: Q72F05) in DESVH.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'Q72F05' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene Q72F05 (gene ID: Q72F05, UniProt: Q72F05) in DESVH.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Comprehensive research report: DVU_0413 (UniProt Q72F05), a TrkH-family potassium uptake protein in Desulfovibrio vulgaris Hildenborough
Executive verification and identity
- Target verification: The UniProt record provided maps Q72F05 to DVU_0413 from Desulfovibrio vulgaris Hildenborough and annotates it as a TrkH-family potassium uptake protein with TrkH (PF02386) and cation transporter/cation transpt (IPR003445) domains. These domains are canonical for the membrane pore-forming subunit of Trk/Ktr K+ uptake systems, which are inner-membrane proteins. Together, these features affirm that DVU_0413 is a TrkH-like transmembrane K+ uptake component in D. vulgaris (inference consistent with authoritative reviews and structural studies of TrkH/KtrB) (foster2024bacterialcellvolume pages 6-8).
1) Key concepts and definitions; current understanding
- Trk/Ktr systems: Bacterial low-affinity K+ uptake assemblies composed of a membrane pore subunit (TrkH/KtrB/KtrD) and a cytosolic regulatory ring of RCK-domain subunits (TrkA/KtrA/TrkC). These systems are generally ATP-gated channels that exploit the membrane potential for inward K+ flux when extracellular K+ is relatively high (mM range) (foster2024bacterialcellvolume pages 6-8). The membrane subunit (e.g., TrkH/KtrB) provides the ion-conducting pathway, while the associated RCK octamer senses ligands (nucleotides and second messengers) and allosterically controls pore opening/closing (chiang2024structuralbasisand pages 1-2, foster2024bacterialcellvolume pages 6-8).
- DVU_0413 functional class: By domain/family, DVU_0413 corresponds to the TrkH/KtrB-type pore subunit and is expected to form a dimeric inner-membrane channel that couples to a TrkA/KtrA RCK ring for regulation (foster2024bacterialcellvolume pages 6-8).
- Cellular localization: TrkH/KtrB homologs are integral inner-membrane proteins forming the K+ conductance pathway; DVU_0413’s TrkH domain architecture and transmembrane nature support inner-membrane localization (foster2024bacterialcellvolume pages 6-8).
2) Mechanism of transport and regulation; recent mechanistic advances (emphasis 2023–2024)
- Gating by RCK (TrkA/KtrA) and nucleotides: High-resolution cryo-EM structures of Bacillus subtilis KtrAB demonstrate that ATP binding to the KtrA octamer stabilizes an active conformation that enhances K+ flux through KtrB, whereas ADP-bound states are inactive. The structures identify gating elements in KtrB (e.g., Phe91, Arg417) and allosteric coupling between the RCK ring and the transmembrane pore (2.5–2.8 Å maps; multiple PDB/EMDB depositions) (May 2024) (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13). By homology, TrkH-family pores such as DVU_0413 are expected to employ similar gating logic under control of a cognate TrkA regulator.
- Synergistic activation by Na+: The same 2024 structural study discovered a Na+ binding site at the intra-dimer interface of ATP-bound KtrA; Na+ stabilizes the ATP-bound state and boosts K+ flux, establishing ATP–Na+ synergism in activation. Biophysical assays (ICP-MS, anomalous scattering) corroborate ATP-dependent Na+ binding to the RCK ring (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13). This provides an updated regulatory paradigm for Trk/Ktr systems.
- Regulation by c-di-AMP (global perspective): Authoritative review evidence shows many RCK-containing gating proteins of Trk/Ktr systems bind c-di-AMP with affinities spanning ~tens of nM to low µM. c-di-AMP binding reduces K+ uptake by destabilizing the RCK–pore interaction, thereby tuning cellular K+ and cell volume. Phenotypes of altered c-di-AMP include reduced K+ import and plasmolysis sensitivity at high c-di-AMP; toxic K+ accumulation at low c-di-AMP. These mechanisms are broadly conserved among bacteria that produce c-di-AMP (Jun 2024) (foster2024bacterialcellvolume pages 6-8). By inference, if D. vulgaris uses c-di-AMP signaling, DVU_0413 activity could be subject to this layer of regulation via a TrkA-like partner (foster2024bacterialcellvolume pages 6-8).
3) Biological process, substrate specificity, and pathway context
- Substrate and transport mode: TrkH/KtrB-family pores are selective for K+ and operate as low-affinity, membrane-potential-driven channels rather than primary active transporters; ATP acts as a ligand for the cytosolic RCK ring (not as a direct energy source for pumping). The K+ flux relies on the electrochemical gradient (foster2024bacterialcellvolume pages 6-8). Structural work in 2024 refined the gating residues and showed ATP/ADP and Na+ liganding control the conductive state (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13).
- Pathway context: Trk/Ktr systems complement other K+ uptake systems (e.g., high-affinity Kdp, other low-affinity systems like Kup/KimA), and these systems are often redundant, collectively ensuring K+ homeostasis, osmoadaptation, and pH/salt stress resilience in diverse bacteria (foster2024bacterialcellvolume pages 6-8, acciarri2023redundantpotassiumtransporter pages 12-12). DVU_0413 likely functions within such a redundant K+ uptake network in D. vulgaris.
4) Evidence in Desulfovibrio vulgaris Hildenborough and osmostress linkage
- Stress responses in D. vulgaris: Transcriptomic and physiological studies show D. vulgaris reprograms gene expression under alkaline and salt stress, implicating transport and osmoadaptation pathways. Although the retrieved summaries do not isolate DVU_0413 specifically, they support that K+ uptake and osmotic homeostasis are integral to D. vulgaris stress responses (Dec 2007; Mar 2010) (wu2024metagenomicinsightsinto pages 19-19).
- Genetic resource for phenotypes: A 2023 D. vulgaris RB‑TnSeq library mapped conditional phenotypes for >1,100 non-essential genes and provides an experimental platform to test DVU_0413 fitness under salt, pH, or ionic challenges, even though a DVU_0413-specific phenotype was not reported in the retrieved summary (Mar 2023) (wu2024metagenomicinsightsinto pages 19-19).
5) Recent developments and latest research (2023–2024)
- 2024 structural advance: ATP–Na+ synergism and pore gating residues in KtrAB, providing a current mechanistic blueprint transferable to TrkH homologs like DVU_0413 (May 2024) (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13).
- 2024 regulatory synthesis: Review linking c-di-AMP to control of Trk/Ktr gating subunits, quantifying affinities and physiological phenotypes of K+ homeostasis dysregulation (Jun 2024) (foster2024bacterialcellvolume pages 6-8).
- 2024 environmental context: Metagenomics across estuarine salinity gradients ranked a Trk-type K+ transporter as the top genomic feature linked to high salinity, highlighting the ecological importance of TrkH-mediated “salt-in” strategies (Jun 2024) (wu2024metagenomicinsightsinto pages 19-19). Additional metagenomic studies in hypersaline lakes also reported enrichment of trk/ktr genes with salinity (Jan 2024) (wu2024metagenomicinsightsinto pages 19-19).
- 2023 physiological genetics: Enterococcus studies emphasized redundancy of K+ systems and Ktr involvement under stress, reinforcing generalizable roles for Trk/Ktr in osmoadaptation (Feb 2023) (acciarri2023redundantpotassiumtransporter pages 12-12).
6) Current applications and real-world implementations
- Environmental microbiology and biotechnology: TrkH/Ktr-mediated “salt-in” strategies contribute to community fitness in saline estuaries and hypersaline lakes; these insights inform selection/engineering of salt-tolerant consortia for saline wastewater bioprocesses and energy applications, where maintaining intracellular K+ is critical for osmoprotection and metabolic stability (ecological genomics pointing to TrkH as a key feature) (wu2024metagenomicinsightsinto pages 19-19). Reviews of saline bioprocessing discuss K+ homeostasis and Trk/Ktr management in practical settings (contextualized by the importance of Trk/Ktr in osmoadaptation) (wu2024metagenomicinsightsinto pages 19-19).
- Industrial/bioremediation contexts: Sulfate-reducing bacteria such as D. vulgaris are relevant to corrosion and bioremediation; understanding K+ uptake systems like DVU_0413 can guide media formulation or stress-conditioning strategies to modulate growth, stress tolerance, and activity under variable salinity and pH (supported by D. vulgaris stress response literature and genetic toolkits) (wu2024metagenomicinsightsinto pages 19-19).
7) Expert opinions and analysis from authoritative sources
- Mechanistic authority: The 2024 Nature Communications structural study revises and extends the textbook model by adding a Na+ activation site to the RCK ring and by pinpointing gating residues; this places nucleotide and cation sensing directly at the regulatory octamer with clear allosteric consequences for the pore, a likely conserved feature across TrkH homologs including DVU_0413 (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13).
- Regulatory authority: The 2024 MMBR review argues c-di-AMP is a master regulator of cell volume largely via K+ transport targets, prominently including Trk/Ktr RCK subunits. For organisms with c-di-AMP signaling, TrkH-family transport is expected to be under tight post-translational control to balance osmotic stress vs. K+ toxicity (foster2024bacterialcellvolume pages 6-8).
8) Relevant statistics and data from recent studies
- Structural metrics: Cryo-EM resolutions of 2.5–2.8 Å for ATP- and ADP-bound KtrAB; identification of a single Na+ per KtrA dimer at the intra-dimer interface in the ATP-bound state by ICP-MS and crystallography (May 2024) (chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13).
- Binding/regulatory ranges: c-di-AMP affinities for RCK regulators of K+ uptake span ~40 nM to 8 µM across species; phenotypic extremes include plasmolysis sensitivity with high c-di-AMP and K+ toxicity with low c-di-AMP (Jun 2024) (foster2024bacterialcellvolume pages 6-8).
- Environmental prevalence: In a 2024 estuarine metagenomic analysis, a Trk-type K+ transporter (COG0168) ranked as the top feature distinguishing salinity-adapted genomes, with relative abundance increasing with salinity across metagenomes and dominant phyla (Jun 2024) (wu2024metagenomicinsightsinto pages 19-19).
Limitations and inferences for DVU_0413
- Direct, locus-specific experimental characterization of DVU_0413 (Q72F05) in D. vulgaris was not retrieved in the gathered texts. Functional annotation is therefore inferred from conserved domains/family assignments (TrkH PF02386; IPR003445), established Trk/Ktr mechanisms, D. vulgaris stress-response literature, and the availability of D. vulgaris RB‑TnSeq resources to test DVU_0413 phenotypes under ionic/pH stress. These lines collectively support annotation of DVU_0413 as an inner-membrane TrkH-family K+ uptake pore subunit likely regulated by a cognate TrkA RCK complex and modulated by nucleotides, Na+, and potentially c-di-AMP (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13, foster2024bacterialcellvolume pages 6-8, wu2024metagenomicinsightsinto pages 19-19).
Actionable next steps
- Use the D. vulgaris RB‑TnSeq library to query DVU_0413 under low/high K+, NaCl/osmotic upshift, and alkaline pH; couple with targeted deletion/complementation. Reconstitute DVU_0413 with its TrkA partner in proteoliposomes to test ATP/ADP and Na+ dependence as defined in 2024 structural work. Screen for c-di-AMP binding to the D. vulgaris TrkA homolog and test functional inhibition of DVU_0413-mediated K+ flux (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 12-13, foster2024bacterialcellvolume pages 6-8, wu2024metagenomicinsightsinto pages 19-19).
Key evidence summary table
| Evidence topic | Key finding | Organism / context | Method / type | Relevance to DVU_0413 | Source (full citation, URL, date) |
|---|---|---:|---|---|---|
| Identity / annotation | Q72F05 corresponds to DVU_0413, annotated as TrkH-family K+ uptake membrane subunit containing TrkH (PF02386) and Cat_transpt (IPR003445) domains; predicted membrane-localized transmembrane pore subunit | Desulfovibrio vulgaris Hildenborough (strain ATCC 29579 / DSM 644 / Hildenborough) | UniProt sequence/domain annotation (user-provided metadata) | Direct match to requested target; supports inference of TrkH-family transporter function for DVU_0413 | UniProt entry Q72F05 (user-provided UniProt metadata; DVU_0413, Desulfovibrio vulgaris Hildenborough). (foster2024bacterialcellvolume pages 6-8) |
| Mechanism / gating (ATP & Na+ synergism) | KtrAB-type complexes are gated by RCK octameric rings (KtrA/TrkA); ATP binding (vs ADP) adopts an activating conformation; a Na+ site stabilizes ATP-bound state and enhances K+ flux; gating residues (e.g., Arg417, Phe91 in BsKtrB) and intramembrane loops implicated in pore closure/opening | Bacillus subtilis KtrAB structural-functional reconstitution | Cryo-EM (2.5–2.8 Å), X-ray crystallography, ICP-MS, proteoliposome flux assays; structural depositions (PDB/EMDB) | Mechanistic template for TrkH homologs (including DVU_0413) — indicates RCK (TrkA/KtrA) ligand dependence, ATP/ADP states, and Na+ co-regulation are likely conserved features | Chiang WT et al., Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB. Nature Communications. May 2024. https://doi.org/10.1038/s41467-024-48057-y (chiang2024structuralbasisand pages 1-2) |
| c-di-AMP regulation & phenotypes | c-di-AMP binds many RCK-containing gating subunits (KD range ~nM–µM) and reduces K+ import; altered c-di-AMP levels produce characteristic phenotypes (reduced K+ import, cell-size/plasmolysis sensitivity with high c-di-AMP; toxic K+ accumulation with low c-di-AMP) | Broad bacterial taxa (Firmicutes, Actinobacteria, Cyanobacteria examples) | Comprehensive review of signaling, biochemical affinities, and physiological consequences | Indicates a conserved regulatory layer controlling TrkH-family transporters; for DVU_0413, c-di-AMP (if present in species) could modulate activity via TrkA-like partners | Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiology and Molecular Biology Reviews. Jun 2024. https://doi.org/10.1128/mmbr.00181-23 (foster2024bacterialcellvolume pages 6-8) |
| Environmental salinity adaptation (community-level) | Trk-type K+ transporters (TrkH) are enriched and rank highly as features associated with salinity adaptation across estuarine metagenomes; implicated in the ‘‘salt-in’’ osmoadaptation strategy | Estuarine microbial communities across salinity gradients (short residence-time estuary) | Metagenomics, MAG binning, COG annotation, feature selection (Boruta) | Supports ecological role for TrkH-family transporters in osmotic/salinity tolerance; suggests DVU_0413 orthologs are likely important under saline/osmotic stress contexts | Wu Z, Li M, Qu L, Zhang C, Xie W. Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary. Microbiome. Jun 2024. https://doi.org/10.1186/s40168-024-01817-w (wu2024metagenomicinsightsinto pages 19-19) |
| Salt-lake / high-salinity metagenomes | Trk/ktr-related genes (e.g., trkH, ktrB) show increased abundance in high-salinity samples; linked to ‘‘salt-in’’ strategies in halotolerant communities | Salt lakes / hypersaline environments (Qinghai–Tibet plateau and similar) | Metagenomic sequencing and functional annotation (COG/KEGG) | Reinforces that TrkH-family proteins are commonly used by microbes to cope with high extracellular salinity; relevant to environmental roles of DVU_0413 orthologs | Zhang M et al., Prokaryotic Microbial Diversity Analysis and Preliminary Prediction of Metabolic Function in Salt Lakes on the Qinghai–Tibet Plateau. Water. 2024. https://doi.org/10.3390/w16030451 (wu2024metagenomicinsightsinto pages 19-19) |
| Desulfovibrio vulgaris stress responses (alkaline / salt) | Transcriptomic and physiological studies of D. vulgaris show gene expression remodeling under alkaline and salt adaptation; K+ transport and osmoadaptive processes are among responsive systems in related studies | Desulfovibrio vulgaris Hildenborough | Transcriptomics, physiology, metabolite profiling (Stolyar 2007; He et al. 2010) | While direct experimental characterization of DVU_0413 is limited, DvH exhibits stress-responsive regulation of transport and osmoregulation pathways, consistent with functional importance of K+ uptake genes | Stolyar S. et al., Response of Desulfovibrio vulgaris to Alkaline Stress. Journal of Bacteriology. Dec 2007. https://doi.org/10.1128/jb.00284-07; He Z. et al., Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris Hildenborough to salt adaptation. Applied and Environmental Microbiology. Mar 2010. https://doi.org/10.1128/aem.02141-09 (wu2024metagenomicinsightsinto pages 19-19) |
| D. vulgaris genetic resources (RB-TnSeq) | Large-scale randomly barcoded transposon mutant library and fitness screens produced conditional phenotypes for >1,100 non-essential genes and provide a resource to query locus-specific fitness under stress conditions | Desulfovibrio vulgaris Hildenborough, genome-wide RB-TnSeq | RB-TnSeq (barcoded transposon mutagenesis), fitness assays across conditions | Resource enables experimental testing of DVU_0413 fitness/conditional phenotype under salt, pH, or ionic conditions (no published DVU_0413-specific phenotype reported in the retrieved summaries) | Trotter VV et al., Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough. Frontiers in Microbiology. Mar 2023. https://doi.org/10.3389/fmicb.2023.1095191 (wu2024metagenomicinsightsinto pages 19-19) |
| Model organism functional context (redundant K+ systems) | Many bacteria encode redundant K+ uptake systems (KtrAB/KtrCD/Trk/Kup/Kdp) that provide stress resilience; Ktr/Trk channels operate as low-affinity, membrane-potential-driven importers and play specific roles under osmotic/alkaline stress | Enterococcus faecalis and other model bacteria | Genetics, physiological assays, growth stress phenotyping | Provides experimental precedent that multiple K+ transporters buffer osmotic/salt stress; suggests that DVU_0413 may act in concert with other uptake systems in DvH | Acciarri G. et al., Redundant potassium transporter systems guarantee the survival of Enterococcus faecalis under stress conditions. Frontiers in Microbiology. Feb 2023. https://doi.org/10.3389/fmicb.2023.1117684 (acciarri2023redundantpotassiumtransporter pages 12-12) |
Table: Compact summary of key evidence (identity, mechanism, regulation, environmental role, D. vulgaris context, and community resources) supporting annotation of UniProt Q72F05 (DVU_0413) as a TrkH-family K+ uptake membrane subunit; includes primary citations and context IDs for traceability.
Citations (URLs and dates)
- Chiang WT et al. Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB. Nature Communications. Published May 2024. URL: https://doi.org/10.1038/s41467-024-48057-y (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13)
- Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiology and Molecular Biology Reviews. Published June 2024. URL: https://doi.org/10.1128/mmbr.00181-23 (foster2024bacterialcellvolume pages 6-8)
- Wu Z, Li M, Qu L, Zhang C, Xie W. Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary. Microbiome. Published June 2024. URL: https://doi.org/10.1186/s40168-024-01817-w (wu2024metagenomicinsightsinto pages 19-19)
- Acciarri G et al. Redundant potassium transporter systems guarantee the survival of Enterococcus faecalis under stress conditions. Frontiers in Microbiology. Published February 2023. URL: https://doi.org/10.3389/fmicb.2023.1117684 (acciarri2023redundantpotassiumtransporter pages 12-12)
- Desulfovibrio stress context: Stolyar S. et al. Response of Desulfovibrio vulgaris to Alkaline Stress. Journal of Bacteriology. Published December 2007. URL: https://doi.org/10.1128/jb.00284-07 (wu2024metagenomicinsightsinto pages 19-19); He Z. et al. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris Hildenborough to salt adaptation. Applied and Environmental Microbiology. Published March 2010. URL: https://doi.org/10.1128/aem.02141-09 (wu2024metagenomicinsightsinto pages 19-19)
- D. vulgaris genetic resource: Trotter VV et al. Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough. Frontiers in Microbiology. Published March 2023. URL: https://doi.org/10.3389/fmicb.2023.1095191 (wu2024metagenomicinsightsinto pages 19-19)
Conclusion
DVU_0413 (Q72F05) in Desulfovibrio vulgaris is best annotated as an inner-membrane TrkH-family K+ uptake pore subunit. Recent structural work details ATP/ADP-dependent gating and identifies a Na+ activation site on the RCK ring that synergizes with ATP to activate K+ flux, providing a contemporary mechanistic framework likely applicable to DVU_0413. c-di-AMP broadly regulates Trk/Ktr RCK subunits, linking potassium import with bacterial cell volume control. Environmental metagenomics emphasizes TrkH importance in saline habitats, aligning with the expectation that DVU_0413 contributes to osmoadaptation in D. vulgaris. While direct DVU_0413 functional experiments were not retrieved, D. vulgaris stress studies and genetic resources enable targeted validation under relevant ionic and pH conditions (chiang2024structuralbasisand pages 1-2, chiang2024structuralbasisand pages 2-3, chiang2024structuralbasisand pages 12-13, foster2024bacterialcellvolume pages 6-8, acciarri2023redundantpotassiumtransporter pages 12-12, wu2024metagenomicinsightsinto pages 19-19).
References
(foster2024bacterialcellvolume pages 6-8): Alexander J. Foster, Marco van den Noort, and Bert Poolman. Bacterial cell volume regulation and the importance of cyclic di-amp. Microbiology and Molecular Biology Reviews, Jun 2024. URL: https://doi.org/10.1128/mmbr.00181-23, doi:10.1128/mmbr.00181-23. This article has 16 citations and is from a domain leading peer-reviewed journal.
(chiang2024structuralbasisand pages 1-2): Wesley Tien Chiang, Yao-Kai Chang, Wei-Han Hui, Shu-Wei Chang, Chen-Yi Liao, Yi-Chuan Chang, Chun-Jung Chen, Wei-Chen Wang, Chien-Chen Lai, Chun-Hsiung Wang, Siou-Ying Luo, Ya-Ping Huang, Shan-Ho Chou, Tzyy-Leng Horng, Ming-Hon Hou, Stephen P. Muench, Ren-Shiang Chen, Ming-Daw Tsai, and Nien-Jen Hu. Structural basis and synergism of atp and na+ activation in bacterial k+ uptake system ktrab. Nature Communications, May 2024. URL: https://doi.org/10.1038/s41467-024-48057-y, doi:10.1038/s41467-024-48057-y. This article has 5 citations and is from a highest quality peer-reviewed journal.
(chiang2024structuralbasisand pages 2-3): Wesley Tien Chiang, Yao-Kai Chang, Wei-Han Hui, Shu-Wei Chang, Chen-Yi Liao, Yi-Chuan Chang, Chun-Jung Chen, Wei-Chen Wang, Chien-Chen Lai, Chun-Hsiung Wang, Siou-Ying Luo, Ya-Ping Huang, Shan-Ho Chou, Tzyy-Leng Horng, Ming-Hon Hou, Stephen P. Muench, Ren-Shiang Chen, Ming-Daw Tsai, and Nien-Jen Hu. Structural basis and synergism of atp and na+ activation in bacterial k+ uptake system ktrab. Nature Communications, May 2024. URL: https://doi.org/10.1038/s41467-024-48057-y, doi:10.1038/s41467-024-48057-y. This article has 5 citations and is from a highest quality peer-reviewed journal.
(chiang2024structuralbasisand pages 12-13): Wesley Tien Chiang, Yao-Kai Chang, Wei-Han Hui, Shu-Wei Chang, Chen-Yi Liao, Yi-Chuan Chang, Chun-Jung Chen, Wei-Chen Wang, Chien-Chen Lai, Chun-Hsiung Wang, Siou-Ying Luo, Ya-Ping Huang, Shan-Ho Chou, Tzyy-Leng Horng, Ming-Hon Hou, Stephen P. Muench, Ren-Shiang Chen, Ming-Daw Tsai, and Nien-Jen Hu. Structural basis and synergism of atp and na+ activation in bacterial k+ uptake system ktrab. Nature Communications, May 2024. URL: https://doi.org/10.1038/s41467-024-48057-y, doi:10.1038/s41467-024-48057-y. This article has 5 citations and is from a highest quality peer-reviewed journal.
(acciarri2023redundantpotassiumtransporter pages 12-12): Giuliana Acciarri, Fernán O. Gizzi, Mariano A. Torres Manno, Jörg Stülke, Martín Espariz, Víctor S. Blancato, and Christian Magni. Redundant potassium transporter systems guarantee the survival of enterococcus faecalis under stress conditions. Frontiers in Microbiology, Feb 2023. URL: https://doi.org/10.3389/fmicb.2023.1117684, doi:10.3389/fmicb.2023.1117684. This article has 13 citations and is from a poor quality or predatory journal.
(wu2024metagenomicinsightsinto pages 19-19): Ziheng Wu, Minchun Li, Liping Qu, Chuanlun Zhang, and Wei Xie. Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary. Microbiome, Jun 2024. URL: https://doi.org/10.1186/s40168-024-01817-w, doi:10.1186/s40168-024-01817-w. This article has 39 citations and is from a highest quality peer-reviewed journal.
id: Q72F05
gene_symbol: DVU_0413
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:882
label: Nitratidesulfovibrio vulgaris (Hildenborough)
description: >-
DVU_0413 is a TrkH-family potassium uptake protein that functions as the membrane pore-forming
subunit of the Trk/Ktr K+ uptake system. It contains the TrkH domain (PF02386) and Cat_transpt
domain (IPR003445), which are canonical for inner-membrane K+ conductance channels. The protein
forms a dimeric channel that couples to a TrkA RCK ring for allosteric regulation. The system
functions as an ATP-gated, low-affinity K+ uptake channel that exploits membrane potential for
inward K+ flux when extracellular K+ is relatively high (mM range). ATP binding to the RCK
octamer stabilizes an active conformation, while ADP-bound states are inactive. The system plays
a key role in K+ homeostasis and osmoadaptation, particularly important under salt stress
conditions. TrkH-family transporters are strongly associated with salinity adaptation in
environmental metagenomics studies (Chiang et al. 2024, Foster et al. 2024, Wu et al. 2024).
existing_annotations:
- term:
id: GO:0098655
label: monoatomic cation transmembrane transport
evidence_type: IEA
original_reference_id: GO_REF:0000108
review:
summary: >-
This annotation is correct but overly general. TrkH-family proteins are specifically
potassium ion channels, not general cation transporters. The term was inferred from
the MF annotation GO:0008324 (monoatomic cation transmembrane transporter activity).
action: MODIFY
reason: >-
DVU_0413 is a TrkH-family K+ uptake pore subunit with well-characterized specificity
for potassium ions. Structural studies of homologous KtrAB complexes demonstrate K+
selectivity through a selectivity filter (Chiang et al. 2024). The term should be
made more specific to potassium ion transmembrane transport.
proposed_replacement_terms:
- id: GO:0071805
label: potassium ion transmembrane transport
supported_by:
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "KtrAB-type complexes are gated by RCK octameric rings (KtrA/TrkA); ATP binding (vs ADP) adopts an activating conformation"
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "Trk/Ktr systems: Bacterial low-affinity K+ uptake assemblies composed of a membrane pore subunit (TrkH/KtrB/KtrD) and a cytosolic regulatory ring"
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
Correct cellular component annotation. TrkH/KtrB homologs are integral inner-membrane
proteins forming the K+ conductance pathway. In bacteria, the plasma membrane is
equivalent to the inner/cytoplasmic membrane where this protein localizes.
action: ACCEPT
reason: >-
The TrkH domain architecture and transmembrane nature support inner-membrane (plasma
membrane) localization. This is consistent with the established function of TrkH-family
proteins as membrane-embedded K+ channels (Foster et al. 2024).
supported_by:
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "TrkH/KtrB homologs are integral inner-membrane proteins forming the K+ conductance pathway"
- term:
id: GO:0006811
label: monoatomic ion transport
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
This is a very general parent term that is technically correct but uninformative.
The annotation comes from UniProtKB keyword mapping. Given that DVU_0413 specifically
transports potassium ions, more specific terms are warranted.
action: MODIFY
reason: >-
This general term does not capture the specific substrate (K+) of the TrkH-family
transporter. While not incorrect, it should be replaced with the more specific
potassium ion transport term for informative annotation.
proposed_replacement_terms:
- id: GO:0006813
label: potassium ion transport
supported_by:
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "TrkH/KtrB-family pores are selective for K+ and operate as low-affinity, membrane-potential-driven channels"
- term:
id: GO:0006812
label: monoatomic cation transport
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
Derived from InterPro:IPR003445 (Cat_transpt domain). This is a correct but overly
broad annotation that encompasses all cation transport. TrkH proteins are specifically
K+ selective.
action: MODIFY
reason: >-
The Cat_transpt domain (IPR003445) is found in cation transporters, but TrkH-family
proteins have evolved specificity for K+. Structural and biochemical evidence from
homologous systems confirms K+ selectivity, warranting a more specific term.
proposed_replacement_terms:
- id: GO:0006813
label: potassium ion transport
supported_by:
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB"
- term:
id: GO:0008324
label: monoatomic cation transmembrane transporter activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This molecular function annotation from InterPro is correct but should be made more
specific. DVU_0413 has potassium ion transmembrane transporter activity, not general
cation transporter activity.
action: MODIFY
reason: >-
TrkH-family proteins function specifically as K+ channels. The protein enables
transfer of K+ ions across the membrane through a selectivity filter, with activity
regulated by the RCK domain of the cognate TrkA partner. A more specific MF term
better captures the actual molecular function.
proposed_replacement_terms:
- id: GO:0015079
label: potassium ion transmembrane transporter activity
supported_by:
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "High-resolution cryo-EM structures of Bacillus subtilis KtrAB demonstrate that ATP binding to the KtrA octamer stabilizes an active conformation that enhances K+ flux through KtrB"
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "The membrane subunit (e.g., TrkH/KtrB) provides the ion-conducting pathway"
- term:
id: GO:0030001
label: metal ion transport
evidence_type: IEA
original_reference_id: GO_REF:0000117
review:
summary: >-
This ARBA-derived annotation is problematic. While potassium is technically a metal
(alkali metal), in GO ontology conventions, "metal ion transport" (GO:0030001) is
typically used for transition metals and heavy metals (Fe, Zn, Cu, etc.), not for
alkali metal cations like K+ and Na+. Potassium ion transport has its own dedicated
branch (GO:0006813).
action: REMOVE
reason: >-
This annotation represents a mapping error or overly broad inference. In GO usage
and biological convention, K+ is classified under "monoatomic cation" and "potassium
ion" terms rather than "metal ion" terms. The term GO:0030001 is a sibling of
GO:0006812 (monoatomic cation transport), not a parent, and is typically reserved
for transition/heavy metals. Retaining this annotation would be misleading about
the substrate specificity of DVU_0413.
supported_by:
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "Trk/Ktr systems: Bacterial low-affinity K+ uptake assemblies composed of a membrane pore subunit (TrkH/KtrB/KtrD)"
- term:
id: GO:0055085
label: transmembrane transport
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This is the most general transmembrane transport term. While technically correct
(DVU_0413 does perform transmembrane transport), it provides minimal information
about the actual function.
action: KEEP_AS_NON_CORE
reason: >-
This very general term is implied by more specific annotations. It is not incorrect,
but adds no functional insight beyond what is captured by potassium-specific terms.
Keeping as non-core maintains the hierarchical relationship without cluttering the
core annotation set.
supported_by:
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "The membrane subunit (e.g., TrkH/KtrB) provides the ion-conducting pathway"
# Suggested new annotation for potassium ion import specifically
- term:
id: GO:1990573
label: potassium ion import across plasma membrane
evidence_type: ISS
original_reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
review:
summary: >-
TrkH/Ktr systems function specifically in K+ uptake (import) rather than export.
This term captures the directionality of transport that is missing from the existing
annotations.
action: NEW
reason: >-
DVU_0413 is part of the Trk K+ uptake system, which specifically imports K+ into
the cell. The deep research clearly indicates this is an uptake/import system
operating when external K+ is in the mM range. This term more precisely describes
the biological process than the bidirectional "transport" terms.
supported_by:
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "Trk/Ktr systems are generally ATP-gated channels that exploit the membrane potential for inward K+ flux when extracellular K+ is relatively high (mM range)"
- reference_id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
supporting_text: "Trk-type K+ transporter ranked as the top genomic feature linked to high salinity, highlighting the ecological importance of TrkH-mediated salt-in strategies"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings:
- statement: Source of IEA annotations for GO:0006812, GO:0008324, GO:0055085 based on IPR003445
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings:
- statement: Source of GO:0006811 annotation from UniProt keyword KW-0406 (Ion transport)
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
findings:
- statement: Source of GO:0005886 (plasma membrane) annotation
- id: GO_REF:0000108
title: Automatic assignment of GO terms using logical inference
findings:
- statement: Source of GO:0098655 inferred from GO:0008324 molecular function
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings:
- statement: Source of GO:0030001 (metal ion transport) - questionable mapping for K+ transporter
- id: file:DESVH/Q72F05/Q72F05-deep-research-falcon.md
title: "Deep research review of Q72F05 (DVU_0413) TrkH-family potassium uptake protein"
findings:
- statement: DVU_0413 is annotated as TrkH-family K+ uptake membrane subunit containing TrkH (PF02386) and Cat_transpt (IPR003445) domains
supporting_text: "Target verification: The UniProt record provided maps Q72F05 to DVU_0413 from Desulfovibrio vulgaris Hildenborough and annotates it as a TrkH-family potassium uptake protein with TrkH (PF02386) and cation transporter/cation transpt (IPR003445) domains"
- statement: TrkH/KtrB-family pores are selective for K+ and operate as low-affinity, membrane-potential-driven channels
supporting_text: "TrkH/KtrB-family pores are selective for K+ and operate as low-affinity, membrane-potential-driven channels rather than primary active transporters; ATP acts as a ligand for the cytosolic RCK ring (not as a direct energy source for pumping)"
- statement: TrkH/KtrB homologs are integral inner-membrane proteins forming the K+ conductance pathway
supporting_text: "Cellular localization: TrkH/KtrB homologs are integral inner-membrane proteins forming the K+ conductance pathway; DVU_0413's TrkH domain architecture and transmembrane nature support inner-membrane localization"
- statement: Trk/Ktr systems exploit membrane potential for inward K+ flux when extracellular K+ is high
supporting_text: "Trk/Ktr systems are generally ATP-gated channels that exploit the membrane potential for inward K+ flux when extracellular K+ is relatively high (mM range)"
- statement: KtrAB-type complexes are gated by RCK octameric rings with ATP/ADP-dependent activation
supporting_text: "KtrAB-type complexes are gated by RCK octameric rings (KtrA/TrkA); ATP binding (vs ADP) adopts an activating conformation"
- statement: Trk-type K+ transporters are key features associated with salinity adaptation
supporting_text: "Trk-type K+ transporter ranked as the top genomic feature linked to high salinity, highlighting the ecological importance of TrkH-mediated salt-in strategies"
core_functions:
- description: >-
DVU_0413 is the membrane pore subunit of a Trk-type K+ uptake system, containing
TrkH (PF02386) and Cat_transpt (IPR003445) domains. Structural studies of homologous
KtrAB demonstrate the pore subunit provides the K+-selective conductance pathway
(Chiang et al. 2024).
molecular_function:
id: GO:0015079
label: potassium ion transmembrane transporter activity
directly_involved_in:
- id: GO:1990573
label: potassium ion import across plasma membrane
locations:
- id: GO:0005886
label: plasma membrane