Rv0739 Still unknown · low auto-curated
H37Rv Rv0739 · MTBC0 - ·
268 aa · 830855–831661 (+) ·
RefSeq NP_215253.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF4226. Function unknown. Foldseek best (non-significant) hit: 8e4g-assembly1_a Remodeling of the bacteriophage T7 during initial inf (prob 0.99, TM 0.69). |
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 |
P9WKS1
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv0739 |
UniProt still lists this protein as Uncharacterized protein Rv0739; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2F1S8 |
|---|
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 | 1.21 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 60.18% of strains (87386) · reference-fixed |
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 |
|---|---|---|---|---|
DUF4226 | PF10774.16 | 4.8e-27 | 5–110 | Domain of unknown function (DUF4226) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 80.4 (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 |
|---|---|---|---|---|
8e4g-assembly1_a |
0.99 | 0.69 | 3.0e-01 | 8e4g-assembly1_a Remodeling of the bacteriophage T7 during initial infection |
7ey7-assembly1_A |
0.94 | 0.75 | 1.1e+00 | 7ey7-assembly1_A bacteriophage T7 tail complex |
6zw4-assembly1_F |
0.25 | 0.50 | 3.6e+00 | 6zw4-assembly1_F C14 symmetry: Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. |
6nct-assembly1_B |
0.23 | 0.38 | 1.3e+00 | 6nct-assembly1_B Structure of p110alpha/niSH2 - vector data collection |
6zw6-assembly1_G |
0.21 | 0.50 | 4.6e+00 | 6zw6-assembly1_G C16 symmetry: Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. |
8qbs-assembly1_A |
0.20 | 0.45 | 3.6e+00 | 8qbs-assembly1_A Cryo-EM structure of Vipp1-F197K/L200K helical filament with lattice 1 (Vipp1-F197K/L200K_L1) |
8v8i-assembly1_B |
0.16 | 0.38 | 2.0e+00 | 8v8i-assembly1_B PI3Ka H1047R co-crystal structure with inhibitor in cryptic pocket (compound 5). |
8i7r-assembly1_F4 |
0.14 | 0.49 | 5.8e+00 | 8i7r-assembly1_F4 In situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0740 hyp |
hypothetical protein | 531 | 531 ctx | neighborhood:524 |
Rv0738 hyp |
hypothetical protein | 448 | 448 ctx | neighborhood:443 |
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): DUF4226 PF10774.16 (E=5e-27)
- Foldseek best: 8e4g-assembly1_a Remodeling of the bacteriophage T7 during initial infection (prob 0.99, E=3e-01, TM=0.69)
- (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_215253.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4226 (PF10774.16)
- 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
2F1S8 - Curated reference: UniProt P9WKS1 (SwissProt, reviewed; 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 80.4, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 2 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0739| MVLTRRAREVALTQHIGVSAETDRAVVPKLRQAYDSLVCGRRRLGAIGAEIENAVAHQRALGLDTPAGARNFSRFLATKAHDITRVLAATAAESQAGAARLRSLASSYQAVGFGPKPQEPPPDPVPFPPYQPKVWAACRARGQDPDKVVRTFHHAPMSARFRSLPAGDSVLYCGNDKYGLLHIQAKHGRQWHDIADARWPSAGNWRYLADYAIGATLAYPERVEYNQDNDTFAVYRRMSLPDGRYVFTTRVIISARDGKIITAFPQTT