Rv3188 Family assigned · low auto-curated
H37Rv Rv3188 · MTBC0 mtbc0_003385 ·
115 aa · 3576430–3576777 (+) ·
RefSeq NP_217704.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | antitoxin Xre/MbcA/ParS toxin-binding domain-containing protein |
| Revised (this work) | Antitoxin Xre/MbcA/ParS toxin-binding domain-containing protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53334
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable mycobacterial cidal antitoxin Rv3188 |
| Curated function | Probable antitoxin component of a type II toxin-antitoxin (TA) system. Neutralizes the activity of cognate toxin Rv3189 by blocking access to the toxin active site. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2384) |
| Orthologous group | 2A9J7 |
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 | 0.722 · 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).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3186 (Rv3186, (MTV014.30), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase sub), medium confidence from genomic context alone (score 414 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) |
|---|---|---|---|---|
Rv1989c mbcT hyp |
hypothetical protein | 985 | 959 | experimental:956 textmining:652 |
Rv3189 hyp |
hypothetical protein | 976 | 888 ctx | neighborhood:882 textmining:802 |
Rv3186 |
Rv3186, (MTV014.30), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase sub | 414 | 414 ctx | neighborhood:414 |
Rv3187 |
Probable transposase; Rv3187, (MTV014.31), len: 328 aa. Probable IS6110 transposase. Identical to many other M. tuberculosis IS6110 transpos | 414 | 414 ctx | neighborhood:414 |
Rv2035 hyp |
hypothetical protein | 659 | 64 | textmining:651 |
Rv2022c higB2 hyp |
hypothetical protein | 445 | 55 | textmining:437 |
Rv2865 relF |
antitoxin RelF | 445 | 54 | textmining:438 |
Rv0549c vapC3 |
ribonuclease VapC3 | 439 | 53 | textmining:432 |
Rv2034 |
ArsR family HTH-type transcriptional repressor | 519 | 50 | textmining:515 |
Rv0550c vapB3 |
antitoxin VapB3 | 443 | 50 | textmining:438 |
Rv1044 hyp |
hypothetical protein | 442 | 50 | textmining:437 |
Rv0837c hyp |
hypothetical protein | 515 | 47 | textmining:512 |
Rv2866 relG |
toxin RelG | 514 | 47 | textmining:511 |
Rv0918 hyp |
hypothetical protein | 681 | 46 | textmining:680 |
Rv1045 hyp |
hypothetical protein | 436 | 46 | textmining:434 |
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
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: antitoxin Xre/MbcA/ParS toxin-binding domain-containing protein
- (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_217704.1)
- 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
2A9J7 - Curated reference: UniProt O53334 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
25 functional partner(s); context anchor
Rv3186 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003385|Rv3188| MAVTLDRAVEASEIVDALKPFGVTQVDVAAVIQVSDRAVRGWRTGDIRPERYDRLAQLRDLVLLLSDSLTPRGVGQWLHAKNRLLDGQRPVDLLAKDRYEDVRSAAESFIDGAYV