Rv3067 Still unknown · low auto-curated
H37Rv Rv3067 · MTBC0 - ·
136 aa · 3431428–3431838 (+) ·
RefSeq NP_217583.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF732. Function unknown. Foldseek best (non-significant) hit: 3j9x-assembly1_A A Virus that Infects a Hyperthermophile Encapsidates (prob 0.16, TM 0.56). |
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 |
I6YB21
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3067 |
UniProt still lists this protein as Uncharacterized protein Rv3067; 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 (DUF732) |
| Orthologous group | 2AY8K |
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 | 1.096 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 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 |
|---|---|---|---|---|
DUF732 | PF05305.20 | 1.1e-15 | 58–126 | Protein of unknown function (DUF732) |
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 |
|---|---|---|---|---|
3j9x-assembly1_A |
0.16 | 0.56 | 5.1e+00 | 3j9x-assembly1_A A Virus that Infects a Hyperthermophile Encapsidates A-Form DNA |
8pv8-assembly1_CS |
0.04 | 0.24 | 5.1e+00 | 8pv8-assembly1_CS Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3066 (DeoR family transcriptional regulator), medium confidence from genomic context alone (score 558 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) |
|---|---|---|---|---|
Rv3066 |
DeoR family transcriptional regulator | 559 | 558 ctx | neighborhood:556 |
Rv3091 hyp |
hypothetical protein | 544 | 544 ctx | neighborhood:544 |
Rv3065 mmr |
multidrug resistance protein Mmr | 534 | 534 ctx | neighborhood:527 |
Rv0711 atsA |
arylsulfatase AtsA | 803 | 45 | textmining:803 |
Rv3537 kstD |
3-oxosteroid 1-dehydrogenase | 438 | 44 | textmining:437 |
Rv0145 |
S-adenosylmethionine-dependent methyltransferase | 759 | 42 | textmining:759 |
Rv2466c hyp |
hypothetical protein | 654 | 42 | textmining:654 |
Rv3001c ilvC |
ketol-acid reductoisomerase | 652 | 42 | textmining:652 |
Rv0140 hyp |
hypothetical protein | 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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DUF732 PF05305.20 (E=1e-15)
- Foldseek best: 3j9x-assembly1_A A Virus that Infects a Hyperthermophile Encapsidates A-Form DNA (prob 0.16, E=5e+00, TM=0.56)
- (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_217583.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF732 (PF05305.20)
- 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
2AY8K - Curated reference: UniProt I6YB21 (SwissProt, reviewed; 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 —
9 functional partner(s); context anchor
Rv3066 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3067| MLTVGVGIGAAILLGWFTLAHRHPDQPGAAATPPPAGLTTRSAPTAAPPSTLQSPDLDSVFLGNLHDRGISFTNPDAAVYNGKMVCTNLGGGMTVQQVVEALQSSSPALGDRTTAYVAVSIRTYCPKYDAVLPPGS