Rv3236c Resolved · high auto-curated
H37Rv Rv3236c · MTBC0 - ·
385 aa · 3611959–3613116 (-) ·
RefSeq YP_177949.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane transport protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Integral membrane transport protein. Pfam: Na_H_Exchanger (PF00999.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
L7N665
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable conserved integral membrane transport protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | Probably involved in transport of undeterminated substrate (possibly cations Na H) across the membrane. thought to be responsible for the translocation of the substrate across the membrane |
| Orthologous group | COG0475 |
| KEGG orthology |
K03455
|
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 | 0.354 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 7 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 |
|---|---|---|---|---|
Na_H_Exchanger | PF00999.27 | 2.0e-40 | 15–369 | Sodium/hydrogen exchanger, transmembrane |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mddA (integral membrane protein), high confidence from genomic context alone (score 718 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3237c hyp |
hypothetical protein | 985 | 984 ctx | neighborhood:881 cooccurence:774 coexpression:439 |
Rv3238c mddA |
integral membrane protein | 718 | 718 ctx | neighborhood:706 |
Rv3240c secA1 |
protein translocase subunit SecA | 694 | 694 ctx | neighborhood:694 |
Rv3241c raiA hyp |
hypothetical protein | 687 | 687 ctx | neighborhood:659 |
Rv3239c |
transmembrane transport protein | 596 | 501 ctx | neighborhood:485 |
Rv0425c ctpH |
metal cation transporting ATPase H | 448 | 412 | |
Rv0107c ctpI |
cation-transporter ATPase I | 538 | 388 | |
Rv0908 ctpE |
metal cation transporter ATPase E | 457 | 302 | |
Rv3242c hyp |
hypothetical protein | 539 | 299 | |
Rv2287 yjcE |
Na(+)/H(+) transporter | 407 | 226 | |
Rv0994 moeA1 |
molybdopterin molybdenumtransferase 1 | 415 | 208 | |
Rv3659c |
conjugal transfer protein | 806 | 50 | textmining:805 |
Rv3654c hyp |
hypothetical protein | 513 | 41 | textmining:513 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): integral membrane transport protein
- Pfam (hmmscan --cut_ga): Na_H_Exchanger PF00999.27 (E=2e-40)
- (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 YP_177949.1)
- Domains: Pfam-A via hmmscan --cut_ga — Na_H_Exchanger (PF00999.27)
- 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
COG0475 - Curated reference: UniProt L7N665 (TrEMBL, unreviewed; 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 —
13 functional partner(s); context anchor
mddA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3236c| MEVSRALLFELGVLLAVLAVLGAVARRFALSPIPVYLLAGLSLGNGGILGVAAAGEFIATGAPIGVVLLLLALGLEFSATEFASSLRHHLPSAGVDIVLNATPGAVAGWLLGLDGVAILGLAGVTYISSSGVIARLLEDLRRLGNRETPAVLSVLVLEDFAMAAYLPLFAVLATDGSWLEAVVGMTVAIAALLGAFAASYRWGHHVGRLVTHPDSEQLLLRVLGITLIVAAVAESLHASAAVGAFLVGLTLTGETADRARMVLTPLRDLFATIFFLGIGLSVDPGKLVSMLPVALALAAVTAATKVATGMFAARREGVARRGQLRAGTALVARGEFSLIIIGLAGASIPGVAALATAYVFVMAIVGPILARYTGGGLPAAAVASN