Rv0268c Family assigned · medium auto-curated
H37Rv Rv0268c · MTBC0 - ·
169 aa · 322764–323273 (-) ·
RefSeq NP_214782.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains PhdYeFM_antitox (PF02604.27) domain(s); putative function inferred from the domain architecture. |
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 |
P95225
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative antitoxin Rv0268c |
| Curated function | Putative antitoxin component of a type II toxin-antitoxin (TA) system; however the expected toxin coding sequence is not found adjacent to this gene. |
UniProt still lists this protein as Putative antitoxin Rv0268c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
D Cell cycle control, cell division, chromosome partitioning
|
|---|---|
| eggNOG description | toxin-antitoxin pair type II binding |
| Orthologous group | COG2161 |
| KEGG orthology |
K19159
|
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, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (167) · 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 |
|---|---|---|---|---|
PhdYeFM_antitox | PF02604.27 | 7.8e-13 | 90–140 | Antitoxin Phd_YefM, type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadD2 (fatty-acid--CoA ligase FadD2), medium confidence from genomic context alone (score 448 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) |
|---|---|---|---|---|
Rv3358 relK |
toxin RelK | 793 | 756 | experimental:748 |
Rv0269c hyp |
hypothetical protein | 941 | 597 ctx | neighborhood:596 textmining:860 |
Rv0270 fadD2 |
fatty-acid--CoA ligase FadD2 | 448 | 448 ctx | neighborhood:441 |
Rv0366c hyp |
hypothetical protein | 672 | 78 | textmining:659 |
Rv1103c mazE3 |
antitoxin MazE3 | 810 | 76 | textmining:803 |
Rv2017 |
transcriptional regulator | 664 | 72 | textmining:653 |
Rv0229c vapC51 hyp |
hypothetical protein | 470 | 69 | textmining:454 |
Rv2515c hyp |
hypothetical protein | 817 | 67 | textmining:812 |
Rv2514c hyp |
hypothetical protein | 868 | 63 | textmining:865 |
Rv2022c higB2 hyp |
hypothetical protein | 541 | 59 | textmining:533 |
Rv0207c hyp |
hypothetical protein | 732 | 58 | textmining:728 |
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 761 | 51 | textmining:759 |
Rv3641c fic |
cell filamentation protein Fic | 438 | 49 | textmining:434 |
Rv0367c hyp |
hypothetical protein | 804 | 47 | textmining:803 |
Rv0078A hyp |
hypothetical protein | 804 | 47 | 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): PhdYeFM_antitox PF02604.27 (E=8e-13)
- (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_214782.1)
- Domains: Pfam-A via hmmscan --cut_ga — PhdYeFM_antitox (PF02604.27)
- 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
COG2161 - Curated reference: UniProt P95225 (SwissProt, reviewed; Inferred from homology)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
17 functional partner(s); context anchor
fadD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0268c| MGTRSKSRTRQLKQSNGCTATTSGASDRRRRARRRTAPAWLREDEWLRHHLPHPPRQLSRCLHRRRRSACHHRYSRRTPKGGLPMTSSLVPISEARAHLSRLVRESADDDVVLMNHGRPAAILISAERYESLMEELEDLRDRLSVHEREHVTMPLDKLGAELGVDIGRV