relE Resolved · high auto-curated
H37Rv Rv1246c · MTBC0 mtbc0_001335 ·
97 aa · 1397129–1397422 (-) ·
RefSeq NP_215762.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | toxin RelE |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system mRNA interferase RelE |
| Revised (this work) | Type II toxin-antitoxin system mRNA interferase RelE. Pfam: ParE_toxin (PF05016.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50461
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Toxin RelE |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Has RNase activity (By similarity). Overexpression in M.tuberculosis or M.smegmatis inhibits colony formation in a bacteriostatic rather than bacteriocidal fashion. Its toxic effect is neutralized by coexpression with cognate antitoxin RelB (shown only for M.smegmatis)..; FUNCTION: In combination with RelB represses its own promoter. Has been seen to bind DNA in complex with cognate antitoxin RelB but not alone. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | relE |
| eggNOG description | ParE toxin of type II toxin-antitoxin system, parDE |
| Orthologous group | COG2026 |
| Gene Ontology (39) |
GO:0003674, GO:0003824, GO:0004518, GO:0004519, GO:0006139, GO:0006401, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009056, GO:0009057 +27 more
|
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, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (380) · 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 |
|---|---|---|---|---|
ParE_toxin | PF05016.22 | 1.8e-10 | 9–88 | ParE toxin of type II toxin-antitoxin system, parDE |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: relB (antitoxin RelB), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1247c relB |
antitoxin RelB | 997 | 983 ctx | neighborhood:882 cooccurence:774 textmining:878 |
Rv2865 relF |
antitoxin RelF | 975 | 872 ctx | cooccurence:774 textmining:815 |
Rv1245c |
short-chain type dehydrogenase/reductase | 654 | 653 ctx | neighborhood:651 |
Rv0659c mazF2 |
toxin MazF2 | 755 | 644 ctx | cooccurence:633 |
Rv1942c mazF5 |
toxin MazF5 | 705 | 584 ctx | cooccurence:572 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 576 | 576 ctx | neighborhood:564 |
Rv2017 |
transcriptional regulator | 511 | 449 ctx | cooccurence:413 |
Rv3387 |
transposase | 439 | 440 ctx | cooccurence:436 |
Rv2961 |
transposase | 431 | 432 ctx | cooccurence:428 |
Rv1034c |
Probable transposase (fragment); Rv1034c, (MTCY10G2.15), len: 129 aa. Probable IS1560 transposase fragment, similar to part of Rv3387|E12023 | 406 | 407 ctx | cooccurence:405 |
Rv3749c vapC50 hyp |
hypothetical protein | 492 | 314 | |
Rv0595c vapC4 |
ribonuclease VapC4 | 600 | 297 | textmining:455 |
Rv1102c mazF3 |
mRNA interferase MazF3 | 732 | 281 | textmining:643 |
Rv3750c vapB50 |
excisionase | 452 | 264 | |
Rv1495 mazF4 |
mRNA interferase MazF4 | 582 | 228 | textmining:482 |
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: toxin RelE
- MTBC0 PGAP product: type II toxin-antitoxin system mRNA interferase RelE
- Pfam (hmmscan --cut_ga): ParE_toxin PF05016.22 (E=2e-10)
- (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_215762.1)
- Domains: Pfam-A via hmmscan --cut_ga — ParE_toxin (PF05016.22)
- 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
COG2026 - Curated reference: UniProt O50461 (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 —
37 functional partner(s); context anchor
relB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001335|Rv1246c|relE MSDDHPYHVAITATAARDLQRLPEKIAAACVEFVFGPLLNNPHRLGKPLRNDLEGLHSARRGDYRVVYAIDDGHHRVEIIHIARRSASYRMNPCRPR