Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cation-transporter P-type ATPase B |
|---|
| MTBC0 PGAP re-annotation | cation-translocating P-type ATPase |
|---|
| Revised (this work) | Cation-translocating P-type ATPase. Pfam: HMA (PF00403.33), 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 |
P9WPT9
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Cation-transporting P-type ATPase B |
|---|
| EC (curated) |
EC 7.2.2.-
|
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|
| Preferred name | ctpB |
|---|
| eggNOG description | ATPase, P-type (transporting), HAD superfamily, subfamily IC |
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| Orthologous group | COG2217 |
|---|
| EC number |
EC 3.6.3.54
|
|---|
| KEGG orthology |
K12949, K17686
|
|---|
| KEGG pathways |
map01524, map04016
|
|---|
| Gene Ontology (11) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0044424, GO:0044444, GO:0044464, GO:0071944
|
|---|
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 |
0.416 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
9 synonymous, 10 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 |
|---|
HMA | PF00403.33 |
3.9e-10 | 19–76 |
Heavy-metal-associated domain |
E1-E2_ATPase | PF00122.26 |
5.6e-20 | 247–345 |
P-type ATPase actuator domain |
Hydrolase | PF00702.33 |
4.6e-34 | 440–658 |
haloacid dehalogenase-like hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0092 ctpA |
cation transporter ATPase A |
904 |
903 |
database:900 |
Rv0104 hyp |
hypothetical protein |
772 |
542 ctx |
neighborhood:537 textmining:524 |
Rv0432 sodC |
superoxide dismutase |
630 |
525 |
database:462 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas |
402 |
402 |
|
Rv1674c |
transcriptional regulator |
422 |
393 |
|
Rv0324 |
transcriptional regulator |
402 |
371 |
|
Rv0425c ctpH |
metal cation transporting ATPase H |
476 |
368 |
|
Rv0846c mmcO |
oxidase |
581 |
364 |
|
Rv0190 ricR hyp |
hypothetical protein |
529 |
326 |
|
Rv0107c ctpI |
cation-transporter ATPase I |
517 |
326 |
|
Rv0967 csoR |
copper-sensing transcriptional repressor CsoR |
620 |
322 |
textmining:463 |
Rv1997 ctpF |
cation transporter ATPase F |
445 |
322 |
|
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase |
465 |
289 |
|
Rv1992c ctpG |
cation transporter ATPase G |
433 |
272 |
|
Rv0908 ctpE |
metal cation transporter ATPase E |
458 |
248 |
|
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 P-type ATPase B
- MTBC0 PGAP product: cation-translocating P-type ATPase
- Pfam (hmmscan --cut_ga): HMA PF00403.33 (E=4e-10), E1-E2_ATPase PF00122.26 (E=6e-20), Hydrolase PF00702.33 (E=5e-34)
- (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_214617.1)
- Domains: Pfam-A via hmmscan --cut_ga — HMA (PF00403.33), 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
COG2217
- Curated reference: UniProt
P9WPT9
(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 —
27 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000112|Rv0103c|ctpB
MAAPVVGDADLQSVRRIRLDVSGMSCAACASRVETKLNKIPGVRASVNFATRVATIDAVGMAADELCGVVEKAGYHAAPHTETTVLDKRTKDPDGAHARRLLRRLLVAAVLFVPLADLSTLFAIVPSARVPGWGYILTALAAPVVTWAAWPFHSVALRNARHRTTSMETLISVGIVAATAWSLSSVFGDQPPREGSGIWRAILNSDSIYLEVAAGVTVFVLAGRYFEARAKSKAGSALRALAELGAKNVAVLLPDGAELVIPASELKKRQRFVTRPGETIAADGVVVDGSAAIDMSAMTGEAKPVRAYPAASVVGGTVVMDGRLVIEATAVGADTQFAAMVRLVEQAQTQKARAQRLADHIAGVFVPVVFVIAGLAGAAWLVSGAGADRAFSVTLGVLVIACPCALGLATPTAMMVASGRGAQLGIFIKGYRALETIRSIDTVVFDKTGTLTVGQLAVSTVTMAGSGTSERDREEVLGLAAAVESASEHAMAAAIVAASPDPGPVNGFVAVAGCGVSGEVGGHHVEVGKPSWITRTTPCHDAALVSARLDGESRGETVVFVSVDGVVRAALTIADTLKDSAAAAVAALRSRGLRTILLTGDNRAAADAVAAQVGIDSAVADMLPEGKVDVIQRLREEGHTVAMVGDGINDGPALVGADLGLAIGRGTDVALGAADIILVRDDLNTVPQALDLARATMRTIRMNMIWAFGYNVAAIPIAAAGLLNPLIAGAAMAFSSFFVVSNSLRLRNFGAQ
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