Rv3098A Family assigned · medium auto-curated
H37Rv Rv3098A · MTBC0 - ·
106 aa · 3467606–3467926 (+) ·
RefSeq YP_007411812.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PemK-like protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | PemK-like protein. Pfam: PemK_toxin (PF02452.24). |
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 |
V5QRX7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative toxin Rv3098A/RVBD_3098A |
| Curated function | Putative toxic component of a possible type II toxin-antitoxin (TA) system. Its toxic effect may be neutralized by cognate antitoxin Rv3098B/RVBD_3098B. |
UniProt still lists this protein as Putative toxin Rv3098A/RVBD_3098A; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | PemK-like, MazF-like toxin of type II toxin-antitoxin system |
| Orthologous group | COG2337 |
| KEGG orthology |
K07171
|
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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
PemK_toxin | PF02452.24 | 5.6e-16 | 4–103 | PemK-like, MazF-like toxin of type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC3 (ribonuclease VapC3), high confidence from genomic context alone (score 761 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0549c vapC3 |
ribonuclease VapC3 | 769 | 761 ctx | cooccurence:761 |
Rv0960 vapC9 |
ribonuclease VapC9 | 762 | 754 ctx | cooccurence:753 |
Rv1720c vapC12 |
ribonuclease VapC12 | 753 | 745 ctx | cooccurence:744 |
Rv0065 vapC1 |
ribonuclease VapC1 | 748 | 740 ctx | cooccurence:739 |
Rv2801A mazE9 |
antitoxin MazE9 | 676 | 672 ctx | cooccurence:528 |
Rv3180c vapC49 |
ribonuclease VapC45 | 660 | 660 ctx | cooccurence:659 |
Rv3407 vapB47 |
antitoxin VapB47 | 614 | 615 ctx | cooccurence:614 |
Rv1991A mazE6 |
antitoxin MazE6 | 630 | 607 | experimental:434 |
Rv3098c hyp |
hypothetical protein | 572 | 572 ctx | neighborhood:572 |
Rv0582 vapC26 |
ribonuclease VapC26 | 564 | 564 ctx | cooccurence:564 |
Rv3384c vapC46 |
ribonuclease VapC46 | 562 | 546 ctx | cooccurence:545 |
Rv2018 vapB45 hyp |
hypothetical protein | 488 | 488 ctx | cooccurence:488 |
Rv0456A mazF1 |
toxin MazF1 | 482 | 482 ctx | cooccurence:482 |
Rv2548 vapC19 |
ribonuclease VapC19 | 480 | 479 ctx | cooccurence:476 |
Rv3408 vapC47 |
ribonuclease VapC47 | 465 | 465 ctx | cooccurence:463 |
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): PemK-like protein
- Pfam (hmmscan --cut_ga): PemK_toxin PF02452.24 (E=6e-16)
- (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 YP_007411812.1)
- Domains: Pfam-A via hmmscan --cut_ga — PemK_toxin (PF02452.24)
- 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
COG2337 - Curated reference: UniProt V5QRX7 (SwissProt, reviewed; Evidence at protein level)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
22 functional partner(s); context anchor
vapC3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3098A| MVIRGAVYRVDFGDAKRGHEQRGRRYAVVISPGSMPWSVVTVVPTSTSAQPAVFRPELEVMGTKTRFLVDQIRTIGIVYVHGDPVDYLDRDQMAKVEHAVARYLGL