Rv0307c Family assigned · low
H37Rv Rv0307c · MTBC0 mtbc0_000327 ·
160 aa · 379896–380378 (-) ·
RefSeq NP_214821.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | PH/GRAM-superfamily fold (pleckstrin-homology-like beta-sandwich, typically lipid/membrane-binding); specific function undetermined RefSeq leaves this locus uncharacterised. |
Curated reference (UniProt)
| UniProt |
O07234
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 | 29ZRI |
|---|
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 | 0.182 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 89.4 (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 |
|---|---|---|---|---|
8ujw-assembly1_A |
0.33 | 0.33 | 6.3e-02 | 8ujw-assembly1_A Crystal structure of the KETc7 antigen from Taenia solium |
2dtc-assembly1_B |
0.30 | 0.30 | 7.0e-02 | 2dtc-assembly1_B Crystal structure of MS0666 |
2lfu-assembly1_A |
0.13 | 0.30 | 1.8e-01 | 2lfu-assembly1_A The structure of a N. meningitides protein targeted for vaccine development |
1r0u-assembly1_A |
0.10 | 0.33 | 1.2e+00 | 1r0u-assembly1_A Crystal structure of ywiB protein from Bacillus subtilis |
7cso-assembly2_B |
0.07 | 0.29 | 1.0e+00 | 7cso-assembly2_B Structure of Ephexin4 DH-PH-SH3 |
3o12-assembly1_A |
0.04 | 0.21 | 5.3e-01 | 3o12-assembly1_A The crystal structure of a functionally unknown protein from Saccharomyces cerevisiae. |
2vdu-assembly2_B |
0.04 | 0.34 | 3.0e+00 | 2vdu-assembly2_B Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex |
8j07-assembly1_3G |
0.04 | 0.27 | 1.9e+00 | 8j07-assembly1_3G 96nm repeat of human respiratory doublet microtubule and associated axonemal complexes |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0308 (integral membrane protein), high confidence from genomic context alone (score 789 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) |
|---|---|---|---|---|
Rv0308 |
integral membrane protein | 788 | 789 ctx | neighborhood:787 |
Rv0309 hyp |
hypothetical protein | 685 | 685 ctx | neighborhood:684 |
Rv0306 bluB |
oxidoreductase | 554 | 554 ctx | neighborhood:544 |
Rv0296c |
sulfatase | 546 | 547 ctx | neighborhood:544 |
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 5.76): convergent PH-superfamily hits - GRAM domain 93% (E1), methylosome pICln PH-domain 87%, Vps36 GLUE/PH-domain (ESCRT-II lipid-binding) 78%; fold-level assignment
- 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_214821.1)
- 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
29ZRI - Curated reference: UniProt O07234 (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 89.4, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
4 functional partner(s); context anchor
Rv0308 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000327|Rv0307c| MAVIVRKWFGLGRLPADLRCQVEAEGLIYLAEYVAVTRRFTGVIPGLRASHSIASYVGALAFTEQRVLGTLSMVPKLAGRVVDARWDGPQAGAATAEISPTGLQLDLDVADVDPKFSGQLALHFKATIGEDVLSRLPRRSLAFDVPAEYVNLAVGVTYSP