Rv3237c Family assigned · medium auto-curated
H37Rv Rv3237c · MTBC0 mtbc0_003445 ·
160 aa · 3635264–3635746 (-) ·
RefSeq NP_217754.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | cation:proton antiporter regulatory subunit |
| Revised (this work) | Cation:proton antiporter regulatory subunit. Pfam: KhtT_N (PF25991.1), TrkA_C (PF02080.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05882
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | regulatory, ligand-binding protein related to C-terminal domains of K channels |
| Orthologous group | COG0490 |
| KEGG orthology |
K07228
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 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 |
|---|---|---|---|---|
KhtT_N | PF25991.1 | 1.4e-25 | 1–70 | K(+)/H(+) antiporter subunit KhtT, N-terminal domain |
TrkA_C | PF02080.27 | 5.9e-15 | 92–155 | TrkA-C domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3236c (integral membrane transport protein), high confidence from genomic context alone (score 984 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3236c |
integral membrane transport protein | 985 | 984 ctx | neighborhood:881 cooccurence:774 coexpression:439 |
Rv3238c mddA |
integral membrane protein | 760 | 761 ctx | neighborhood:759 |
Rv3240c secA1 |
protein translocase subunit SecA | 696 | 696 ctx | neighborhood:694 |
Rv3241c raiA hyp |
hypothetical protein | 668 | 669 ctx | neighborhood:659 |
Rv3239c |
transmembrane transport protein | 483 | 474 ctx | neighborhood:471 |
Rv0806c cpsY |
exopolysaccharide phosphotransferase CpsY | 426 | 426 ctx | cooccurence:421 |
Rv2692 ceoC |
TRK system potassium uptake protein CeoC | 508 | 91 | textmining:481 |
Rv3200c |
transmembrane cation transporter | 515 | 90 | textmining:489 |
Rv2691 ceoB |
TRK system potassium uptake protein CeoB | 510 | 89 | textmining:485 |
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: hypothetical protein
- MTBC0 PGAP product: cation:proton antiporter regulatory subunit
- Pfam (hmmscan --cut_ga): KhtT_N PF25991.1 (E=1e-25), TrkA_C PF02080.27 (E=6e-15)
- (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_217754.1)
- Domains: Pfam-A via hmmscan --cut_ga — KhtT_N (PF25991.1), TrkA_C (PF02080.27)
- 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
COG0490 - Curated reference: UniProt O05882 (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 —
9 functional partner(s); context anchor
Rv3236c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003445|Rv3237c| MDVKEVLLPGVGLRYEFTSYRGDRIGIVARRSGGFDVVLYGRDDPDEARPVLRLTDEEAEAVAQILGAPRIAERFTELTREVPGLKAGQIHIRAGSLFVDRPLGDTRARTRTGASIVAIVRDEDVLASPGPTDVLRAGDVLIVIGTEDGIAGVEQIVEKG