Rv0476 Resolved · medium auto-curated
H37Rv Rv0476 · MTBC0 - ·
87 aa · 566508–566771 (+) ·
RefSeq NP_214990.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transmembrane protein. |
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 |
P9WKW1
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized protein Rv0476 |
UniProt still lists this protein as Uncharacterized protein Rv0476; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2516) |
| Orthologous group | 2EHMU |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
DUF2516 | PF10724.15 | 6.2e-26 | 1–84 | Protein of unknown function (DUF2516) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: deoC (2-deoxyribose-5-phosphate aldolase), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 884 | 884 ctx | neighborhood:882 |
Rv0477 hyp |
hypothetical protein | 882 | 882 ctx | neighborhood:882 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 827 | 827 ctx | neighborhood:766 |
Rv0474 |
HTH-type transcriptional regulator | 709 | 709 ctx | neighborhood:661 |
Rv0473 |
transmembrane protein | 696 | 697 ctx | neighborhood:622 |
Rv0472c |
HTH-type transcriptional regulator | 584 | 584 | |
Rv2700 cei hyp |
hypothetical protein | 475 | 475 ctx | cooccurence:475 |
Rv3050c |
AsnC family transcriptional regulator | 472 | 472 | |
Rv2360c hyp |
hypothetical protein | 454 | 455 ctx | cooccurence:452 |
Rv0556 |
transmembrane protein | 451 | 452 ctx | cooccurence:449 |
Rv2772c |
transmembrane protein | 436 | 437 ctx | cooccurence:434 |
Rv1382 hyp |
hypothetical protein | 431 | 431 ctx | cooccurence:431 |
Rv3212 hyp |
hypothetical protein | 422 | 423 ctx | cooccurence:416 |
Rv3438 hyp |
hypothetical protein | 422 | 422 ctx | cooccurence:422 |
Rv1486c hyp |
hypothetical protein | 421 | 422 ctx | cooccurence:418 |
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): transmembrane protein
- Pfam (hmmscan --cut_ga): DUF2516 PF10724.15 (E=6e-26)
- (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_214990.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2516 (PF10724.15)
- 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
2EHMU - Curated reference: UniProt P9WKW1 (SwissProt, reviewed; 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 —
17 functional partner(s); context anchor
deoC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0476| MLVLLVAVLVTAVYAFVHAALQRPDAYTAADKLTKPVWLVILGAAVALASILYPVLGVLGMAMSACASGVYLVDVRPKLLEIQGKSR