Rv2876 Resolved · medium auto-curated
H37Rv Rv2876 · MTBC0 - ·
104 aa · 3187663–3187977 (+) ·
RefSeq NP_217392.1
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 |
P9WL39
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2876 |
UniProt still lists this protein as Uncharacterized protein Rv2876; 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 (DUF2631) |
| Orthologous group | 2CAUA |
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 | 0.515 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
DUF2631 | PF10939.14 | 7.1e-30 | 18–85 | Protein of unknown function (DUF2631) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqE (lipoprotein LpqE), high confidence from genomic context alone (score 955 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2200c ctaC |
cytochrome C oxidase subunit II | 999 | 999 | experimental:999 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 999 | 999 | experimental:999 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 999 | 999 | experimental:999 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 999 | 999 | experimental:999 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 999 | 999 | experimental:999 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 999 | 999 | experimental:999 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 999 | 999 | experimental:999 |
Rv0432 sodC |
superoxide dismutase | 997 | 998 | experimental:997 |
Rv0863 hyp |
hypothetical protein | 991 | 991 | experimental:987 |
Rv3584 lpqE |
lipoprotein LpqE | 954 | 955 ctx | cooccurence:541 experimental:902 |
Rv1125 hyp |
hypothetical protein | 770 | 770 ctx | cooccurence:770 |
Rv3035 hyp |
hypothetical protein | 759 | 759 ctx | cooccurence:757 |
Rv0383c ttfA hyp |
hypothetical protein | 759 | 759 ctx | cooccurence:759 |
Rv1836c hyp |
hypothetical protein | 743 | 743 ctx | cooccurence:742 |
Rv1274 lprB |
lipoprotein LprB | 739 | 740 ctx | cooccurence:738 |
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): DUF2631 PF10939.14 (E=7e-30)
- (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_217392.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2631 (PF10939.14)
- 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
2CAUA - Curated reference: UniProt P9WL39 (SwissProt, reviewed; 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 —
101 functional partner(s); context anchor
lpqE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2876| MFGQWEFDVSPTGGIAVASTEVEHFAGSQHEVDTAEVPSAAWGWSRIDHRTWHIVGLCIFGFLLAMLRGNHVGHVEDWFLITFAAVVLFVLARDLWGRRRGWIR