Rv0318c Family assigned · medium auto-curated
H37Rv Rv0318c · MTBC0 - ·
264 aa · 386305–387099 (-) ·
RefSeq YP_177716.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Integral membrane protein. Pfam: Zip (PF02535.29). |
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 |
Q6MX47
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | transporter |
| Orthologous group | COG0428 |
| KEGG orthology |
K07238
|
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 | 0.977 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (156) · clonal |
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 |
|---|---|---|---|---|
Zip | PF02535.29 | 2.3e-12 | 131–263 | ZIP Zinc transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pcp (pyrrolidone-carboxylate peptidase), medium confidence from genomic context alone (score 564 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 654 | 641 | coexpression:465 |
Rv0319 pcp |
pyrrolidone-carboxylate peptidase | 563 | 564 ctx | neighborhood:561 |
Rv1749c |
integral membrane protein | 545 | 546 ctx | cooccurence:544 |
Rv1348 irtA |
iron ABC transporter ATP-binding protein/permease IrtA | 516 | 516 | coexpression:447 |
Rv0355c PPE8 |
PPE family protein PPE8 | 516 | 516 ctx | cooccurence:513 |
Rv3846 sodA |
superoxide dismutase | 533 | 512 | coexpression:472 |
Rv2216 |
epimerase family protein | 507 | 508 | coexpression:467 |
Rv0320 hyp |
hypothetical protein | 502 | 502 ctx | neighborhood:496 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 502 | 502 ctx | cooccurence:502 |
Rv3347c PPE55 |
PPE family protein PPE55 | 493 | 494 ctx | cooccurence:491 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 489 | 489 ctx | cooccurence:489 |
Rv3350c PPE56 |
PPE family protein PPE56 | 488 | 488 ctx | cooccurence:485 |
Rv2267c stf3 hyp |
hypothetical protein | 511 | 486 | |
Rv1753c PPE24 |
PPE family protein PPE24 | 468 | 468 ctx | cooccurence:465 |
Rv1917c PPE34 |
PPE family protein PPE34 | 467 | 468 ctx | cooccurence:466 |
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 protein
- Pfam (hmmscan --cut_ga): Zip PF02535.29 (E=2e-12)
- (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_177716.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zip (PF02535.29)
- 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
COG0428 - Curated reference: UniProt Q6MX47 (TrEMBL, unreviewed; Predicted)
- 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 —
53 functional partner(s); context anchor
pcp - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0318c| MSLAVTMFKRARAEIFDRNREVGISNVTTAASLVTFPVLAGILGGVVPSVRTPSAAMVSGVQHFAAGIVMAAVAGEVLPDLRSRGPLWLIVVGFSAGVAVLVALRRFDGHGEHQDGDDVGELPVGFLTVVAVDLFIDGLLVATGATVSSRTAIIITIALTVEVLFLGLAVALRLAGSGMPRIRAAATTSALSLVIAVGGVSGAVALGRAGNTVLTLVLAFAAGALLWLVVEELLVEAHETPERPWMAVMFFAGFLILYGLGVME