Rv0048c Family assigned · low
H37Rv Rv0048c · MTBC0 mtbc0_000053 ·
289 aa · 51927–52796 (-) ·
RefSeq NP_214562.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF1707 domain-containing protein |
| Revised (this work) | Lipoprotein of the EnvF-like family (cell-envelope). RefSeq leaves it 'membrane protein'. |
Curated reference (UniProt)
| UniProt |
P9WM87
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0048c |
UniProt still lists this protein as Uncharacterized protein Rv0048c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF1707) |
| Orthologous group | 2FB62 |
| Gene Ontology (14) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226, GO:0044425, GO:0044459 +2 more
|
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 | 2.135 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 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 |
|---|---|---|---|---|
DUF1707 | PF08044.17 | 2.4e-16 | 17–69 | DUF1707 SHOCT-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3779 (transmembrane protein), high confidence from genomic context alone (score 773 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3779 |
transmembrane protein | 773 | 773 ctx | cooccurence:767 |
Rv1171 hyp |
hypothetical protein | 767 | 767 ctx | cooccurence:767 |
Rv0875c hyp |
hypothetical protein | 756 | 756 ctx | cooccurence:756 |
Rv2423 hyp |
hypothetical protein | 752 | 753 ctx | cooccurence:751 |
Rv0188 |
transmembrane protein | 746 | 747 ctx | cooccurence:746 |
Rv3773c hyp |
hypothetical protein | 744 | 744 ctx | cooccurence:744 |
Rv2079 hyp |
hypothetical protein | 739 | 739 ctx | cooccurence:739 |
Rv3202c adnA |
ATP-dependent DNA helicase | 738 | 738 ctx | cooccurence:718 |
Rv0517 |
acyltransferase | 737 | 738 ctx | cooccurence:734 |
Rv3899c hyp |
hypothetical protein | 727 | 718 ctx | cooccurence:706 |
Rv1075c hyp |
hypothetical protein | 715 | 716 ctx | cooccurence:649 |
Rv3435c |
transmembrane protein | 715 | 715 ctx | cooccurence:714 |
Rv1635c |
mannosyltransferase | 713 | 713 ctx | cooccurence:713 |
Rv3481c |
integral membrane protein | 707 | 708 ctx | cooccurence:707 |
Rv2525c hyp |
hypothetical protein | 704 | 703 ctx | cooccurence:697 |
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
- Foldseek vs AFDB-SwissProt: lipoprotein EnvF, TM 0.50, E 3e-6
- Structural homology vs AlphaFold-Swiss-Prot (Foldseek; 542k curated SwissProt structures), project 'Still unknown gene function' phase13, 2026-06-10. Fold/family-level, not a demonstrated function.
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_214562.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1707 (PF08044.17)
- 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
2FB62 - Curated reference: UniProt P9WM87 (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 —
80 functional partner(s); context anchor
Rv3779 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000053|Rv0048c| MAKWLGAPLARGVSTATRAKDSDRQDACRILDDALRDGELSMEEHRERVSAATKAVTLGDLQRLVADLQVESAPAQMPALKSRAKRTELGLLAAAFVASVLLGVGIGWGVYGNTRSPLDFTSDPGAKPDGIAPVVLTPPRQLHSLGGLTGLLEQTRKRFGDTMGYRLVIYPEYASLDRVDPADDRRVLAYTYRGGWGDATSSAKSIADVSVVDLSKFDAKTAVGIMRGAPETLGLKQSDVKSMYLIVEPAKDPTTPAALSLSLYVSSDYGGGYLVFAGDGTIKHVSYPS