kdpA Family assigned · medium auto-curated
H37Rv Rv1029 · MTBC0 mtbc0_001108 ·
571 aa · 1159349–1161064 (+) ·
RefSeq NP_215545.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | potassium-transporting ATPase subunit A |
|---|---|
| MTBC0 PGAP re-annotation | potassium-transporting ATPase subunit KdpA |
| Revised (this work) | Potassium-transporting ATPase subunit KdpA. Pfam: KdpA (PF03814.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKF3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Potassium-transporting ATPase potassium-binding subunit |
| Curated function | 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. This subunit binds the extracellular potassium ions and delivers the ions to the membrane domain of KdpB through an intramembrane tunnel. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | kdpA |
| eggNOG description | 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. This subunit binds and transports the potassium across the cytoplasmic membrane |
| Orthologous group | COG2060 |
| EC number |
EC 3.6.3.12
|
| KEGG orthology |
K01546
|
| KEGG pathways |
map02020
|
| Gene Ontology (62) |
GO:0003674, GO:0003824, GO:0005215, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006810, GO:0006811, GO:0006812, GO:0006813 +50 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.446 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 9 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.24% of strains (349) · clonal |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
KdpA | PF03814.22 | 8.0e-240 | 11–568 | Potassium-transporting ATPase A subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: kdpC (potassium-transporting ATPase subunit C), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1031 kdpC |
potassium-transporting ATPase subunit C | 999 | 1000 ctx | neighborhood:881 fusion:817 cooccurence:774 coexpression:843 experimental:895 database:900 textmining:833 |
Rv1030 kdpB |
potassium-transporting ATPase subunit B | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:976 experimental:895 database:900 textmining:926 |
Rv1028c kdpD |
sensor protein KdpD | 989 | 978 ctx | neighborhood:747 cooccurence:772 coexpression:653 textmining:522 |
Rv1028A kdpF |
membrane protein KdpF | 944 | 883 ctx | neighborhood:882 textmining:541 |
Rv1027c kdpE |
transcriptional regulator KdpE | 927 | 876 ctx | neighborhood:747 textmining:437 |
Rv1033c trcR |
two component transcriptional regulator TrcR | 423 | 391 | |
Rv0410c pknG |
serine/threonine-protein kinase PknG | 680 | 63 | textmining:673 |
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase | 494 | 52 | textmining:488 |
Rv0425c ctpH |
metal cation transporting ATPase H | 521 | 51 | textmining:517 |
Rv0103c ctpB |
cation-transporter P-type ATPase B | 466 | 50 | textmining:461 |
Rv2109c prcA |
proteasome subunit alpha | 430 | 44 | textmining:429 |
Rv0812 |
4-amino-4-deoxychorismate lyase | 701 | 41 | textmining:701 |
Rv0561c menJ |
oxidoreductase | 583 | 41 | textmining:584 |
Rv0107c ctpI |
cation-transporter ATPase I | 515 | 41 | textmining:516 |
Rv2110c prcB |
proteasome subunit beta | 434 | 41 | textmining:435 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: potassium-transporting ATPase subunit A
- MTBC0 PGAP product: potassium-transporting ATPase subunit KdpA
- Pfam (hmmscan --cut_ga): KdpA PF03814.22 (E=8e-240)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215545.1)
- Domains: Pfam-A via hmmscan --cut_ga — KdpA (PF03814.22)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG2060 - Curated reference: UniProt P9WKF3 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
15 functional partner(s); context anchor
kdpC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001108|Rv1029|kdpA MSGTSWLQFAALIAVLLLTAPALGGYLAKIYGDEAKKPGDRVFGPIERVIYQVCRVDPGSEQRWSTYALSVLAFSVMSFLLLYGIARFQGVLPFNPTDKPAVTDHVAFNAAVSFMTNTNWQSYSGEATMSHFTQMTGLAVQNFVSASAGMCVLAALIRGLARKRASTLGNFWVDLARTVLRIMFPLSFVVAILLVSQGVIQNLHGFIVANTLEGAPQLIPGGPVASQVAIKQLGTNGGGFFNVNSAHPFENYTPIGNFVENWAILIIPFALCFAFGKMVHDRRQGWAVLAIMGIIWIGMSVAAMSFEAKGNPRLDALGVTQQTTVDQSGGNLEGKEVRFGVGASGLWAASTTGTSNGSVNSMHDSYTPLGGMVPLAHMMLGEVSPGGTGVGLNGLLVMAILAVFIAGLMVGRTPEYLGKKIQATEMKLVTLYILAMPIALLSFAAASVLISSALASRNNPGPHGLSEILYAYTSGANNNGSAFAGLTASTWSYDTTIGVAMLIGRFFLIIPVLAIAGSLARKGTTPVTAATFPTHKPLFVGLVIGVVLIVGGLTFFPALALGPIVEQLSTQ