Rv0108c Family assigned · low
H37Rv Rv0108c · MTBC0 - ·
69 aa · 130895–131104 (-) ·
RefSeq NP_214622.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Small OB-fold / twisted beta-sandwich protein; ambiguous fold-level match (phage head-to-tail joining gpFII-like and/or EF-P/eIF5A OB-fold); function undetermined RefSeq leaves this locus uncharacterised. |
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 |
O53630
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2AYND |
|---|
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 | 0.318 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 81.2 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
1yby-assembly1_A |
1.00 | 0.71 | 1.6e-02 | 1yby-assembly1_A Conserved hypothetical protein Cth-95 from Clostridium thermocellum |
1yby-assembly1_B |
1.00 | 0.69 | 4.4e-02 | 1yby-assembly1_B Conserved hypothetical protein Cth-95 from Clostridium thermocellum |
1ueb-assembly1_A |
1.00 | 0.63 | 1.5e-02 | 1ueb-assembly1_A Crystal structure of translation elongation factor P from Thermus thermophilus HB8 |
4v6a-assembly2_CV |
1.00 | 0.70 | 5.4e-02 | 4v6a-assembly2_CV Structure of EF-P bound to the 70S ribosome. |
5wxk-assembly1_B |
1.00 | 0.66 | 4.9e-02 | 5wxk-assembly1_B EarP bound with domain I of EF-P |
3a5z-assembly1_B |
1.00 | 0.70 | 8.0e-02 | 3a5z-assembly1_B Crystal structure of Escherichia coli GenX in complex with elongation factor P |
8qzv-assembly1_A |
1.00 | 0.71 | 1.3e-01 | 8qzv-assembly1_A Crystal structure of translation factor eIF5A from Trichomonas vaginalis |
1ueb-assembly2_B |
1.00 | 0.60 | 2.5e-02 | 1ueb-assembly2_B Crystal structure of translation elongation factor P from Thermus thermophilus HB8 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0110 (integral membrane protein), medium confidence from genomic context alone (score 620 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) |
|---|---|---|---|---|
Rv0110 |
integral membrane protein | 619 | 620 ctx | neighborhood:618 |
Rv0109 PE_PGRS1 |
PE-PGRS family protein PE_PGRS1 | 445 | 446 ctx | neighborhood:446 |
Rv0107c ctpI |
cation-transporter ATPase I | 417 | 418 ctx | neighborhood:412 |
Rv0863 hyp |
hypothetical protein | 871 | 50 | textmining:870 |
Rv0546c hyp |
hypothetical protein | 497 | 47 | textmining:494 |
Rv3279c birA |
bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase | 653 | 46 | textmining:652 |
Rv2814c |
Probable transposase; Rv2814c, (MTCY16B7.29), len: 328 aa. Probable transposase subunit for IS6110. Identical to many other M. tuberculosis | 511 | 44 | textmining:510 |
Rv0180c |
transmembrane protein | 806 | 41 | textmining:806 |
Rv1779c |
integral membrane protein | 446 | 41 | textmining:446 |
Rv2961 |
transposase | 430 | 41 | textmining:430 |
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
- HHpred (Neff 1.85 low, no significant E): phage head-tail joining 92% E0.65 + EF-P/eIF5A 84-68%; fold-level only, weak profile
- HHpred web (MPI Bioinformatics Toolkit, profile-profile remote homology), interpreted in project 'Still unknown gene function', 2026-06-10. A fold/family-level assignment, 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_214622.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2AYND - Curated reference: UniProt O53630 (TrEMBL, unreviewed; 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)
- Model confidence: ESMFold per-residue pLDDT (mean 81.2, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
10 functional partner(s); context anchor
Rv0110 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0108c| MVPVETLHSGDPITDVNGGGQRYIVLESKTVGDSCVVLELESRVNHQLQVIEKSFPAGYHVGRAHHRIL