Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cation transporter ATPase F |
|---|
| MTBC0 PGAP re-annotation | cation-transporting P-type ATPase |
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| Revised (this work) | Cation-transporting P-type ATPase. Pfam: Cation_ATPase_N (PF00690.32), E1-E2_ATPase (PF00122.26), Hydrolase (PF00702.33), Cation_ATPase (PF13246.13), Hydrolase_3 (PF08282.19), Cation_ATPase_C (PF00689.27). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPS9
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable cation-transporting ATPase F |
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| EC (curated) |
EC 7.2.2.-
|
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Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|
| Preferred name | ctpF |
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| eggNOG description | ATPase, P-type (transporting), HAD superfamily, subfamily IC |
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| Orthologous group | COG0474 |
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| EC number |
EC 3.6.3.8
|
|---|
| KEGG orthology |
K01537, K12953
|
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| Gene Ontology (66) |
GO:0003674, GO:0003824, GO:0005215, GO:0005388, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005886, GO:0005887, GO:0006810, GO:0006811 +54 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)
pseudogene candidate
| pN/pS |
0.638 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
8 synonymous, 14 missense, 0 nonsense, 2 frameshift
|
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| Disruption |
2 distinct premature-stop/frameshift site(s); most common in
25.62% of strains
(37208) · clonal
|
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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 |
|---|
Cation_ATPase_N | PF00690.32 |
3.7e-19 | 12–78 |
Cation transporter/ATPase, N-terminus |
E1-E2_ATPase | PF00122.26 |
8.0e-30 | 119–231 |
P-type ATPase actuator domain |
Hydrolase | PF00702.33 |
4.9e-13 | 330–655 |
haloacid dehalogenase-like hydrolase |
Cation_ATPase | PF13246.13 |
6.3e-27 | 389–545 |
P-type ATPase, cytoplasmic domain N |
Hydrolase_3 | PF08282.19 |
1.7e-04 | 627–679 |
haloacid dehalogenase-like hydrolase |
Cation_ATPase_C | PF00689.27 |
1.7e-44 | 726–893 |
Cation transporting ATPase, C-terminus |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2625c rip3 |
zinc metalloprotease Rip3 |
924 |
908 |
coexpression:876 |
Rv2029c pfkB |
6-phosphofructokinase PfkB |
908 |
889 |
coexpression:860 |
Rv2028c |
universal stress protein |
908 |
873 |
coexpression:869 |
Rv2624c |
universal stress protein |
877 |
873 |
coexpression:869 |
Rv2030c hyp |
hypothetical protein |
892 |
871 |
coexpression:815 |
Rv1736c narX |
nitrate reductase-like protein NarX |
892 |
862 |
coexpression:862 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB |
892 |
852 |
coexpression:814 |
Rv2626c hrp1 |
hypoxic response protein |
860 |
830 |
coexpression:804 |
Rv2004c hyp |
hypothetical protein |
899 |
828 |
coexpression:757 textmining:439 |
Rv2032 acg |
NAD(P)H nitroreductase |
909 |
818 |
coexpression:814 textmining:519 |
Rv0574c hyp |
hypothetical protein |
817 |
818 |
coexpression:785 |
Rv2623 TB31.7 |
universal stress protein |
888 |
815 |
coexpression:809 textmining:421 |
Rv2627c hyp |
hypothetical protein |
814 |
814 |
coexpression:810 |
Rv1737c narK2 |
nitrate/nitrite transporter |
903 |
802 |
coexpression:802 textmining:535 |
Rv2005c |
universal stress protein |
829 |
802 |
coexpression:796 |
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: cation transporter ATPase F
- MTBC0 PGAP product: cation-transporting P-type ATPase
- Pfam (hmmscan --cut_ga): Cation_ATPase_N PF00690.32 (E=4e-19), E1-E2_ATPase PF00122.26 (E=8e-30), Hydrolase PF00702.33 (E=5e-13), Cation_ATPase PF13246.13 (E=6e-27), Hydrolase_3 PF08282.19 (E=2e-04), Cation_ATPase_C PF00689.27 (E=2e-44)
- (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_216513.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cation_ATPase_N (PF00690.32), E1-E2_ATPase (PF00122.26), Hydrolase (PF00702.33), Cation_ATPase (PF13246.13), Hydrolase_3 (PF08282.19), Cation_ATPase_C (PF00689.27)
- 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
COG0474
- Curated reference: UniProt
P9WPS9
(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 —
77 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002124|Rv1997|ctpF
MSASVSATTAHHGLPAHEVVLLLESDPYHGLSDGEAAQRLERFGPNTLAVVTRASLLARILRQFHHPLIYVLLVAGTITAGLKEFVDAAVIFGVVVINAIVGFIQESKAEAALQGLRSMVHTHAKVVREGHEHTMPSEELVPGDLVLLAAGDKVPADLRLVRQTGLSVNESALTGESTPVHKDEVALPEGTPVADRRNIAYSGTLVTAGHGAGIVVATGAETELGEIHRLVGAAEVVATPLTAKLAWFSKFLTIAILGLAALTFGVGLLRRQDAVETFTAAIALAVGAIPEGLPTAVTITLAIGMARMAKRRAVIRRLPAVETLGSTTVICADKTGTLTENQMTVQSIWTPHGEIRATGTGYAPDVLLCDTDDAPVPVNANAALRWSLLAGACSNDAALVRDGTRWQIVGDPTEGAMLVVAAKAGFNPERLATTLPQVAAIPFSSERQYMATLHRDGTDHVVLAKGAVERMLDLCGTEMGADGALRPLDRATVLRATEMLTSRGLRVLATGMGAGAGTPDDFDENVIPGSLALTGLQAMSDPPRAAAASAVAACHSAGIAVKMITGDHAGTATAIATEVGLLDNTEPAAGSVLTGAELAALSADQYPEAVDTASVFARVSPEQKLRLVQALQARGHVVAMTGDGVNDAPALRQANIGVAMGRGGTEVAKDAADMVLTDDDFATIEAAVEEGRGVFDNLTKFITWTLPTNLGEGLVILAAIAVGVALPILPTQILWINMTTAIALGLMLAFEPKEAGIMTRPPRDPDQPLLTGWLVRRTLLVSTLLVASAWWLFAWELDNGAGLHEARTAALNLFVVVEAFYLFSCRSLTRSAWRLGMFANRWIILGVSAQAIAQFAITYLPAMNMVFDTAPIDIGVWVRIFAVATAITIVVATDTLLPRIRAQPP
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