Rv0979c Still unknown · low auto-curated
H37Rv Rv0979c · MTBC0 mtbc0_001047 ·
64 aa · 1102006–1102200 (-) ·
RefSeq NP_215494.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 4dqz-assembly1_B Crystal Structure of C-terminal Half of Bacterial Hen (prob 0.20, TM 0.53). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53892
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.665 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 38.4 (very low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
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 |
|---|---|---|---|---|
4dqz-assembly1_B |
0.20 | 0.53 | 2.1e+00 | 4dqz-assembly1_B Crystal Structure of C-terminal Half of Bacterial Hen1 |
3zxu-assembly1_B |
0.16 | 0.46 | 1.4e+00 | 3zxu-assembly1_B Crystal structure of the Ctf19-Mcm21 kinetochore heterodimer from yeast |
3zxu-assembly2_D |
0.16 | 0.49 | 1.4e+00 | 3zxu-assembly2_D Crystal structure of the Ctf19-Mcm21 kinetochore heterodimer from yeast |
4e6n-assembly2_D |
0.16 | 0.45 | 1.6e+00 | 4e6n-assembly2_D Crystal structure of bacterial Pnkp-C/Hen1-N heterodimer |
4drf-assembly2_D |
0.14 | 0.41 | 8.9e-01 | 4drf-assembly2_D Crystal Structure of Bacterial Pnkp-C/Hen1-N Heterodimer |
5mu3-assembly1_B |
0.10 | 0.43 | 2.5e+00 | 5mu3-assembly1_B Crystal structure of Ctf19-Mcm21 kinetochore assembly bound with Ctf19-Mcm21 binding motif of central kinetochore subunit Okp1 |
6wd7-assembly1_8 |
0.09 | 0.33 | 1.3e+00 | 6wd7-assembly1_8 Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-D) |
5tz8-assembly1_B |
0.08 | 0.43 | 4.3e+00 | 5tz8-assembly1_B Crystal structure of S. aureus TarS |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpmF (50S ribosomal protein L32), medium confidence from genomic context alone (score 590 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) |
|---|---|---|---|---|
Rv0979A rpmF |
50S ribosomal protein L32 | 919 | 590 ctx | neighborhood:590 textmining:810 |
Rv0978c PE_PGRS17 |
PE-PGRS family protein PE_PGRS17 | 828 | 405 ctx | neighborhood:405 textmining:723 |
Rv2615c PE_PGRS45 |
PE-PGRS family protein PE_PGRS45 | 860 | 41 | textmining:860 |
Rv0980c PE_PGRS18 |
PE-PGRS family protein PE_PGRS18 | 803 | 41 | textmining:803 |
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
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: hypothetical protein
- Foldseek best: 4dqz-assembly1_B Crystal Structure of C-terminal Half of Bacterial Hen1 (prob 0.20, E=2e+00, TM=0.53)
- (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_215494.2)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt O53892 (TrEMBL, unreviewed; 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)
- Model confidence: ESMFold per-residue pLDDT (mean 38.4, very low)
- 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
rpmF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001047|Rv0979c| MGFRTQVGAATIASTMTWRIPVEDGPAQFRAGVGPGRDRQFTVVAPMVVGLWDRNRRPGWQWPS