Rv3271c Resolved · high auto-curated
H37Rv Rv3271c · MTBC0 mtbc0_003479 ·
222 aa · 3674822–3675490 (-) ·
RefSeq NP_217788.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | cation transporter |
| Revised (this work) | Cation transporter. Pfam: Cation_efflux (PF01545.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96876
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | Cation efflux family |
| Orthologous group | COG0053 |
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) | 1 synonymous, 1 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 |
|---|---|---|---|---|
Cation_efflux | PF01545.27 | 8.0e-06 | 37–213 | Cation efflux transmembrane domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3273 (transmembrane carbonic anhydrase), medium confidence from genomic context alone (score 603 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3272 hyp |
hypothetical protein | 782 | 782 ctx | neighborhood:781 |
Rv1240 mdh |
malate dehydrogenase | 682 | 683 | coexpression:672 |
Rv3273 |
transmembrane carbonic anhydrase | 619 | 603 ctx | neighborhood:597 |
Rv0648 |
alpha-mannosidase | 510 | 510 | coexpression:411 |
Rv2159c hyp |
hypothetical protein | 427 | 427 | |
Rv1712 cmk |
cytidylate kinase | 423 | 424 | coexpression:405 |
Rv1994c cmtR |
HTH-type transcriptional regulator CmtR | 419 | 391 | |
Rv2683 hyp |
hypothetical protein | 410 | 384 | |
Rv3483c hyp |
hypothetical protein | 671 | 147 | textmining:630 |
Rv1275 lprC |
lipoprotein LprC | 630 | 85 | textmining:613 |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 461 | 84 | textmining:436 |
Rv1457c |
antibiotic ABC transporter permease | 476 | 77 | textmining:457 |
Rv0625c |
transmembrane protein | 669 | 73 | textmining:658 |
Rv1337 |
integral membrane protein | 638 | 63 | textmining:630 |
Rv0227c |
membrane protein | 552 | 55 | textmining:546 |
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: integral membrane protein
- MTBC0 PGAP product: cation transporter
- Pfam (hmmscan --cut_ga): Cation_efflux PF01545.27 (E=8e-06)
- (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_217788.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cation_efflux (PF01545.27)
- 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
COG0053 - Curated reference: UniProt P96876 (TrEMBL, unreviewed; 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 —
23 functional partner(s); context anchor
Rv3273 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003479|Rv3271c| METTTEHRDESTLDSPVSVAREAEWQRNVRWARWLAWVSLAVLLTEGAVGLWQGIAVGSVALTGWALGGGSEGLASAMVLWRFTGDRTWSATAEHRAQRGVAVSFWLTAPYLVAESIRHLAGEHRAETSVIGIGLTAIALLLMPVLGWANHRVGERLGSGATAGEGTQNYLCAAQAAAVLLGLAITAVWSNGWWIDPAIGLAIAGIAVWQGIRTWRGHGCGC