Rv3122 Still unknown · low auto-curated
H37Rv Rv3122 · MTBC0 - ·
156 aa · 3488089–3488559 (+) ·
RefSeq NP_217638.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF6788. Function unknown. Foldseek best (non-significant) hit: 2w9j-assembly1_A The crystal structure of SRP14 from the Schizosacchar (prob 0.41, TM 0.31). |
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 |
O07033
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DUF6788 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2C62F |
|---|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (291) · clonal |
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 |
|---|---|---|---|---|
DUF6788 | PF20586.4 | 1.3e-16 | 21–98 | Domain of unknown function (DUF6788) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 90.6 (very high). 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 |
|---|---|---|---|---|
2w9j-assembly1_A |
0.41 | 0.31 | 9.7e-02 | 2w9j-assembly1_A The crystal structure of SRP14 from the Schizosaccharomyces pombe signal recognition particle |
3v47-assembly1_C |
0.14 | 0.42 | 1.6e+00 | 3v47-assembly1_C Crystal structure of the N-terminal fragment of zebrafish TLR5 in complex with Salmonella flagellin |
5m3k-assembly1_E |
0.11 | 0.40 | 3.4e+00 | 5m3k-assembly1_E A multi-component acyltransferase PhlABC from Pseudomonas protegens |
7qcd-assembly1_A |
0.11 | 0.43 | 2.5e+00 | 7qcd-assembly1_A CryoEM structure of the Smc5/6-holocomplex (composite structure) |
6vy1-assembly1_G |
0.09 | 0.33 | 2.1e+00 | 6vy1-assembly1_G Cryo-EM structure of filamentous PFD from Methanocaldococcus jannaschii |
4rbr-assembly1_B |
0.07 | 0.40 | 5.0e+00 | 4rbr-assembly1_B Crystal structure of Repressor of Toxin (Rot), a central regulator of Staphylococcus aureus virulence |
4r79-assembly1_B |
0.05 | 0.18 | 9.8e-01 | 4r79-assembly1_B Mos1 transposase paired-end complex with left transposon end |
2pmz-assembly2_V |
0.04 | 0.23 | 3.2e+00 | 2pmz-assembly2_V Archaeal RNA polymerase from Sulfolobus solfataricus |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3123 hyp |
hypothetical protein | 773 | 773 ctx | neighborhood:770 |
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): DUF6788 PF20586.4 (E=1e-16)
- Foldseek best: 2w9j-assembly1_A The crystal structure of SRP14 from the Schizosaccharomyces pom (prob 0.41, E=1e-01, TM=0.31)
- (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_217638.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF6788 (PF20586.4)
- 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
2C62F - Curated reference: UniProt O07033 (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 90.6, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 1 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3122| MYSGCWINNQNGETRVGEDSLEDLEQRRARLYDQLAATGDFRRGSISENYRRCGKPNCVCAQEGHPGHGPRYLWTRTVAGRGTKGRQLSVEEVDKVRAELANYHRFAQVSEQIVAVNEAICEARPPNPAATAPPAGTTGHKKGGSATRSRRSSPPR