Rv0122 Still unknown · low
H37Rv Rv0122 · MTBC0 mtbc0_000133 ·
122 aa · 148657–149025 (+) ·
RefSeq NP_214636.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no Pfam domain above threshold. Foldseek gives a suggestive but non-significant fold similarity to a ribonuclease (prob 0.98, E=5e-2, TM=0.61) with weaker hits to HigBA-type toxin-antitoxin RNases: a possible RNase/toxin-like fold, not conclusive. |
Curated reference (UniProt)
| UniProt |
O07172
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 | 296XN |
|---|
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 | 0.671 · 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 58.7 (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 |
|---|---|---|---|---|
3u97-assembly1_A |
0.98 | 0.61 | 5.0e-02 | 3u97-assembly1_A 1.1 Angstrom-resolution crystal structure of the Brucella abortus ribonuclease toxin, BrnT |
7snx-assembly1_A |
0.44 | 0.56 | 5.0e-01 | 7snx-assembly1_A 1.70A Resolution Structure of NanoBiT Complementation Reporter Complex of LgBit and SmBiT Subunits |
5jaa-assembly1_D |
0.38 | 0.55 | 8.3e-01 | 5jaa-assembly1_D Crystal structure of the HigBA2 toxin-antitoxin complex |
5m4y-assembly3_F |
0.38 | 0.67 | 7.8e-01 | 5m4y-assembly3_F Crystal structure of the Sec3/Sso2 complex at 2.20 angstrom resolution |
7sny-assembly1_A |
0.35 | 0.52 | 5.0e-01 | 7sny-assembly1_A 2.10A Resolution Structure of NanoBiT Complementation Reporter Large Subunit LgBiT |
7sns-assembly2_B |
0.35 | 0.53 | 5.3e-01 | 7sns-assembly2_B 1.55A Resolution Structure of NanoLuc Luciferase |
5ibo-assembly2_B |
0.33 | 0.54 | 7.8e-01 | 5ibo-assembly2_B 1.95A resolution structure of NanoLuc luciferase |
5lg4-assembly1_C |
0.33 | 0.67 | 1.1e+00 | 5lg4-assembly1_C Crystal structure of the Sec3/Sso2 complex at 2.9 angstrom resolution |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS2 (PE-PGRS family protein PE_PGRS2), medium confidence from genomic context alone (score 405 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) |
|---|---|---|---|---|
Rv0123 hyp |
hypothetical protein | 887 | 887 ctx | neighborhood:882 |
Rv0121c hyp |
hypothetical protein | 533 | 533 ctx | neighborhood:532 |
Rv0124 PE_PGRS2 |
PE-PGRS family protein PE_PGRS2 | 406 | 405 ctx | neighborhood:405 |
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
- MTBC0 PGAP product: 'hypothetical protein'
- Pfam: no domain above threshold
- Foldseek on the ESMFold model: suggestive, non-significant similarity to a ribonuclease (3U97) and HigBA-type TA RNases
ESM Atlas signal (exploratory)
Ancestral protein hash 5135771dde1bc60ea490cc21e09cb3a3 ·
10 ESM-space neighbours (max similarity 0.867).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 10268 |
1.26 | RNase domains and signal peptides |
| 2 | 5823 |
0.69 | Basic–aromatic ligand-binding cores |
| 3 | 2522 |
0.61 | Arg/Lys-rich N-terminal nucleic-acid-binding patch |
| 4 | 11814 |
0.56 | Bacterial disordered N-terminal tails |
| 5 | 8753 |
0.54 | Basic C-terminal RNA-binding tails |
| 6 | 12874 |
0.48 | C-terminal assembly region |
| 7 | 12227 |
0.48 | Tryptophan residue detector |
| 8 | 1645 |
0.42 | Exposed interaction-processing loop motif |
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_214636.1)
- 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
296XN - Curated reference: UniProt O07172 (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 58.7, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
3 functional partner(s); context anchor
PE_PGRS2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000133|Rv0122| MAGSVSAAAGIGWVGLNVTETNRDQCYRVERTTVDALTHPEYRVHTRGVQRVRVTRNARKHRVSKHRIVAAMRHCGVPVIQEDGSLYYQGRDTSGRLTEVVAVEADDGDLIITHAMPKEWKR