kdpB Family assigned · medium auto-curated
H37Rv Rv1030 · MTBC0 mtbc0_001109 ·
709 aa · 1161061–1163190 (+) ·
RefSeq NP_215546.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | potassium-transporting ATPase subunit B |
|---|---|
| MTBC0 PGAP re-annotation | potassium-transporting ATPase subunit KdpB |
| Revised (this work) | Potassium-transporting ATPase subunit KdpB. Pfam: E1-E2_ATPase (PF00122.26), Hydrolase (PF00702.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPU3
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Potassium-transporting ATPase ATP-binding subunit |
| EC (curated) |
EC 7.2.2.6
|
| 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 is responsible for energy coupling to the transport system and for the release of the potassium ions to the cytoplasm. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | kdpB |
| 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 is responsible for energy coupling to the transport system |
| Orthologous group | COG2216 |
| EC number |
EC 3.6.3.12
|
| KEGG orthology |
K01547
|
| KEGG pathways |
map02020
|
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 | 0.368 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 11 missense, 0 nonsense, 0 frameshift |
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 |
|---|---|---|---|---|
E1-E2_ATPase | PF00122.26 | 1.7e-21 | 126–225 | P-type ATPase actuator domain |
Hydrolase | PF00702.33 | 2.5e-22 | 319–557 | haloacid dehalogenase-like hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: kdpA (potassium-transporting ATPase subunit A), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1029 kdpA |
potassium-transporting ATPase subunit A | 999 | 1000 ctx | neighborhood:881 cooccurence:774 coexpression:976 experimental:895 database:900 textmining:926 |
Rv1031 kdpC |
potassium-transporting ATPase subunit C | 999 | 1000 ctx | neighborhood:882 cooccurence:774 coexpression:865 experimental:837 database:900 textmining:871 |
Rv1028c kdpD |
sensor protein KdpD | 992 | 983 ctx | neighborhood:747 cooccurence:771 coexpression:724 textmining:568 |
Rv1027c kdpE |
transcriptional regulator KdpE | 900 | 850 ctx | neighborhood:747 |
Rv1028A kdpF |
membrane protein KdpF | 962 | 819 ctx | neighborhood:818 textmining:803 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 416 | 416 | coexpression:416 |
Rv1595 nadB |
L-aspartate oxidase | 409 | 409 | coexpression:401 |
Rv1033c trcR |
two component transcriptional regulator TrcR | 413 | 380 | |
Rv0584 |
glycosidase | 662 | 47 | textmining:660 |
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 B
- MTBC0 PGAP product: potassium-transporting ATPase subunit KdpB
- Pfam (hmmscan --cut_ga): E1-E2_ATPase PF00122.26 (E=2e-21), Hydrolase PF00702.33 (E=2e-22)
- (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_215546.1)
- Domains: Pfam-A via hmmscan --cut_ga — E1-E2_ATPase (PF00122.26), Hydrolase (PF00702.33)
- 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
COG2216 - Curated reference: UniProt P9WPU3 (SwissProt, reviewed; Inferred from homology)
- 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 —
9 functional partner(s); context anchor
kdpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001109|Rv1030|kdpB MMIARMETSATAAAATSAPRLRLAKRSLFDPMIVRSALPQSLRKLAPRVQARNPVMLVVLVGAVITTLAFLRDLASSTAQENVFNGLVAAFLWFTVLFANFAEAMAEGRGKAQAAALRKVRSETMANRRTAAGNIESVPSSRLDLDDVVEVSAGETIPSDGEIIEGIASVDESAITGESAPVIRESGGDRSAVTGGTVVLSDRIVVRITAKQGQTFIDRMIALVEGAARQQTPNEIALNILLAGLTIIFLLAVVTLQPFAIYSGGGQRVVVLVALLVCLIPTTIGALLSAIGIAGMDRLVQHNVLATSGRAVEAAGDVNTLLLDKTGTITLGNRQATEFVPINGVSAEAVADAAQLSSLADETPEGRSIVVLAKDEFGLRARDEGVMSHARFVPFTAETRMSGVDLAEVSGIRRIRKGAAAAVMKWVRDHGGHPTEEVGAIVDGISSGGGTPLVVAEWTDNSSARAIGVVHLKDIVKVGIRERFDEMRRMSIRTVMITGDNPATAKAIAQEAGVDDFLAEATPEDKLALIKREQQGGRLVAMTGDGTNDAPALAQADVGVAMNTGTQAAREAGNMVDLDSDPTKLIEVVEIGKQLLITRGALTTFSIANDVAKYFAIIPAMFVGLYPVLDKLNVMALHSPRSAILSAVIFNALVIVALIPLALRGVRFRAESASAMLRRNLLIYGLGGLVVPFIGIKLVDLVIVALGVS