Rv3182 Family assigned · medium auto-curated
H37Rv Rv3182 · MTBC0 mtbc0_003383 ·
114 aa · 3575222–3575566 (+) ·
RefSeq NP_217698.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system RelE/ParE family toxin |
| Revised (this work) | Type II toxin-antitoxin system RelE/ParE family toxin. Pfam: Gp49 (PF05973.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53332
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative toxin HigB3 |
| Curated function | Putative toxic component of a type II toxin-antitoxin (TA) system. Its cognate antitoxin would be HigA3. Not toxic upon expression in M.smegmatis. |
UniProt still lists this protein as Putative toxin HigB3; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Phage derived protein Gp49-like (DUF891) |
| Orthologous group | COG4683 |
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, 1 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 |
|---|---|---|---|---|
Gp49 | PF05973.21 | 6.7e-22 | 11–103 | Phage derived protein Gp49-like (DUF891) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: higA3 (transcriptional regulator), high confidence from genomic context alone (score 972 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) |
|---|---|---|---|---|
Rv3183 higA3 |
transcriptional regulator | 991 | 972 ctx | neighborhood:882 cooccurence:771 textmining:701 |
Rv2021c higA2 |
transcriptional regulator | 954 | 781 ctx | cooccurence:768 textmining:800 |
Rv3181c vapB49 |
antitoxin VapB45 | 751 | 476 ctx | neighborhood:474 textmining:545 |
Rv3180c vapC49 |
ribonuclease VapC45 | 752 | 475 ctx | neighborhood:474 textmining:547 |
Rv3184 |
Rv3184, (MTV014.28), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase sub | 427 | 427 ctx | neighborhood:427 |
Rv3185 |
Probable transposase; Rv3185, (MTV014.29), len: 328 aa. Probable IS6110 transposase. Identical to many other M. tuberculosis IS6110 transpos | 427 | 427 ctx | neighborhood:427 |
Rv1956 higA |
antitoxin HigA | 568 | 211 | textmining:475 |
Rv3750c vapB50 |
excisionase | 679 | 169 | textmining:630 |
Rv0298 |
antitoxin | 657 | 50 | textmining:654 |
Rv3357 relJ |
antitoxin RelJ | 534 | 50 | textmining:530 |
Rv3749c vapC50 hyp |
hypothetical protein | 658 | 47 | textmining:656 |
Rv2019 vapC45 hyp |
hypothetical protein | 656 | 47 | textmining:654 |
Rv1955 higB |
toxin HigB | 642 | 47 | textmining:640 |
Rv0299 |
toxin | 651 | 44 | textmining:650 |
Rv1957 secBL |
SecB-like chaperone | 591 | 44 | textmining:590 |
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: type II toxin-antitoxin system RelE/ParE family toxin
- Pfam (hmmscan --cut_ga): Gp49 PF05973.21 (E=7e-22)
- (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_217698.1)
- Domains: Pfam-A via hmmscan --cut_ga — Gp49 (PF05973.21)
- 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
COG4683 - Curated reference: UniProt O53332 (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 —
18 functional partner(s); context anchor
higA3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003383|Rv3182| MAVILLPQVERWFFALNRDAMASVTGAIDLLEMEGPTLGRPVVDKVNDSTFHNMKELRPAGTSIRILFAFDPARQAILLLGGDKAGNWKRWYDNNIPIADQRSENWLASEHGGG