Rv0493c Family assigned · medium auto-curated
H37Rv Rv0493c · MTBC0 - ·
329 aa · 583701–584690 (-) ·
RefSeq NP_215007.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Tocopherol_cycl (PF14249.13) domain(s); putative function inferred from the domain architecture. |
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 |
P9WKU7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0493c |
UniProt still lists this protein as Uncharacterized protein Rv0493c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2CDI5 |
|---|
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 | 0.971 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.38% of strains (555) · 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 |
|---|---|---|---|---|
Tocopherol_cycl | PF14249.13 | 3.6e-29 | 33–302 | Tocopherol cyclase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0492c (GMC-type oxidoreductase), high confidence from genomic context alone (score 976 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) |
|---|---|---|---|---|
Rv0492c |
GMC-type oxidoreductase | 976 | 976 ctx | neighborhood:881 cooccurence:770 |
Rv0492A hyp |
hypothetical protein | 957 | 957 ctx | neighborhood:882 coexpression:651 |
Rv0494 |
HTH-type transcriptional regulator | 823 | 823 ctx | neighborhood:622 cooccurence:549 |
Rv1648 |
transmembrane protein | 716 | 716 ctx | cooccurence:716 |
Rv1775 hyp |
hypothetical protein | 700 | 700 ctx | cooccurence:699 |
Rv1270c lprA |
lipoprotein LprA | 680 | 681 ctx | cooccurence:676 |
Rv3413c rsdA |
anti-sigma-D factor RsdA | 648 | 648 ctx | cooccurence:648 |
Rv0538 |
membrane protein | 636 | 636 ctx | cooccurence:634 |
Rv3788 hyp |
hypothetical protein | 634 | 634 ctx | cooccurence:629 |
Rv2113 |
integral membrane protein | 609 | 609 ctx | cooccurence:607 |
Rv1966 mce3A |
Mce family protein Mce3A | 605 | 606 ctx | cooccurence:602 |
Rv3903c cpnT hyp |
hypothetical protein | 595 | 595 ctx | cooccurence:595 |
Rv3071 hyp |
hypothetical protein | 586 | 587 ctx | cooccurence:583 |
Rv1024 |
membrane protein | 582 | 583 ctx | cooccurence:580 |
Rv2761c hsdS |
type I restriction/modification system specificity determinant HsdS | 522 | 522 ctx | cooccurence:522 |
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): hypothetical protein
- Pfam (hmmscan --cut_ga): Tocopherol_cycl PF14249.13 (E=4e-29)
- (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_215007.1)
- Domains: Pfam-A via hmmscan --cut_ga — Tocopherol_cycl (PF14249.13)
- 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
2CDI5 - Curated reference: UniProt P9WKU7 (SwissProt, reviewed; 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 —
29 functional partner(s); context anchor
Rv0492c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0493c| MGESTTQPAGGAAVDDETRSAALPRWRGAAGRLEVWYATLSDPLTRTGLWVHCETVAPTTGGPYAHGWVTWFPPDAPPGTERFGPQPAQPAAGPAWFDIAGVRMAPAELTGRTRSLAWELSWKDTAAPLWTFPRVAWERELLPGAQVVIAPTAVFAGSLAVGETTHRVDSWRGSVAHIYGHGNAKRWGWIHADLGDGDVLEVVTAVSHKPGLRRLAPLAFVRFRIDGKDWPASPLPSLRMRTTLGVRHWQLEGRIGGREALIRVDQPPERCVSLGYTDPDGAKAVCTNTEQADIHIELGGRHWSVLGTGHAEVGLRGTAAPAIKEGTPA