relF Resolved · high auto-curated
H37Rv Rv2865 · MTBC0 mtbc0_003047 ·
93 aa · 3198203–3198484 (+) ·
RefSeq NP_217381.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin RelF |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system antitoxin RelF |
| Revised (this work) | Type II toxin-antitoxin system antitoxin RelF. Pfam: PhdYeFM_antitox (PF02604.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33347
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin RelF |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis neutralizes the effect of toxin RelE2.; FUNCTION: Induces its own promoter, in combination with RelG represses its own promoter. Has been seen to bind DNA in complex with toxin RelG but not alone. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | relF |
| eggNOG description | Antitoxin component of a toxin-antitoxin (TA) module |
| Orthologous group | COG2161 |
| Gene Ontology (26) |
GO:0003674, GO:0005488, GO:0005515, GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0019219, GO:0019222, GO:0031323, GO:0031326 +14 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 | 0.978 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
PhdYeFM_antitox | PF02604.27 | 2.0e-21 | 1–72 | Antitoxin Phd_YefM, type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: relG (toxin RelG), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2866 relG |
toxin RelG | 998 | 994 ctx | neighborhood:788 cooccurence:773 experimental:893 textmining:820 |
Rv1246c relE |
toxin RelE | 975 | 872 ctx | cooccurence:774 textmining:815 |
Rv3358 relK |
toxin RelK | 923 | 763 | experimental:748 textmining:690 |
Rv0659c mazF2 |
toxin MazF2 | 674 | 634 ctx | cooccurence:627 |
Rv1942c mazF5 |
toxin MazF5 | 648 | 610 ctx | cooccurence:604 |
Rv2864c |
penicillin-binding lipoprotein | 468 | 469 ctx | neighborhood:464 |
Rv0960 vapC9 |
ribonuclease VapC9 | 521 | 427 ctx | cooccurence:409 |
Rv2017 |
transcriptional regulator | 413 | 411 | |
Rv1720c vapC12 |
ribonuclease VapC12 | 405 | 385 | |
Rv1102c mazF3 |
mRNA interferase MazF3 | 500 | 370 | |
Rv0595c vapC4 |
ribonuclease VapC4 | 469 | 367 | |
Rv1495 mazF4 |
mRNA interferase MazF4 | 421 | 274 | |
Rv0549c vapC3 |
ribonuclease VapC3 | 553 | 217 | textmining:454 |
Rv2021c higA2 |
transcriptional regulator | 428 | 187 | |
Rv2022c higB2 hyp |
hypothetical protein | 510 | 167 | textmining:436 |
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: antitoxin RelF
- MTBC0 PGAP product: type II toxin-antitoxin system antitoxin RelF
- Pfam (hmmscan --cut_ga): PhdYeFM_antitox PF02604.27 (E=2e-21)
- (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_217381.1)
- 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 O33347 (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 —
29 functional partner(s); context anchor
relG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003047|Rv2865|relF MRILPISTIKGKLNEFVDAVSSTQDQITITKNGAPAAVLVGADEWESLQETLYWLAQPGIRESIAEADADIASGRTYGEDEIRAEFGVPRRPH