relK Family assigned · medium auto-curated
H37Rv Rv3358 · MTBC0 mtbc0_003573 ·
85 aa · 3797753–3798010 (+) ·
RefSeq NP_217875.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | toxin RelK |
|---|---|
| MTBC0 PGAP re-annotation | Txe/YoeB family addiction module toxin |
| Revised (this work) | Txe/YoeB family addiction module toxin. Pfam: YoeB_toxin (PF06769.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WF09
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Toxin RelK |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Has RNase activity and preferentially cleaves at the 3'-end of purine ribonucleotides (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 antitoxin RelJ (shown only for M.smegmatis). Overexpression also increases the number of rifampcin-tolerant persister cells..; FUNCTION: In combination with RelJ represses its own promoter. Several DNA-protein complexes are formed in vitro depending on the . |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | relK |
| eggNOG description | YoeB-like toxin of bacterial type II toxin-antitoxin system |
| Orthologous group | COG4115 |
| KEGG orthology |
K19158
|
| Gene Ontology (68) |
GO:0003674, GO:0003824, GO:0004518, GO:0004519, GO:0006139, GO:0006355, GO:0006401, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009056 +56 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 | 0.896 · 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 |
|---|---|---|---|---|
YoeB_toxin | PF06769.21 | 9.1e-40 | 6–85 | YoeB-like toxin of bacterial type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: relJ (antitoxin RelJ), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3357 relJ |
antitoxin RelJ | 999 | 999 ctx | neighborhood:882 cooccurence:773 experimental:966 textmining:929 |
Rv1247c relB |
antitoxin RelB | 956 | 765 | experimental:748 textmining:824 |
Rv2865 relF |
antitoxin RelF | 923 | 763 | experimental:748 textmining:690 |
Rv0268c hyp |
hypothetical protein | 793 | 756 | experimental:748 |
Rv3359 |
oxidoreductase | 666 | 666 ctx | neighborhood:661 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 588 | 589 ctx | neighborhood:589 |
Rv3355c |
integral membrane protein | 556 | 557 ctx | neighborhood:557 |
Rv2788 sirR |
transcriptional repressor SirR | 499 | 500 | experimental:500 |
Rv3360 hyp |
hypothetical protein | 426 | 426 ctx | neighborhood:426 |
Rv2866 relG |
toxin RelG | 832 | 77 | textmining:826 |
Rv1246c relE |
toxin RelE | 889 | 76 | textmining:885 |
Rv1991c mazF6 |
mRNA interferase MazF6 | 579 | 55 | textmining:573 |
Rv1955 higB |
toxin HigB | 661 | 49 | textmining:659 |
Rv2019 vapC45 hyp |
hypothetical protein | 643 | 47 | textmining:641 |
Rv1495 mazF4 |
mRNA interferase MazF4 | 542 | 47 | textmining:540 |
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 RelK
- MTBC0 PGAP product: Txe/YoeB family addiction module toxin
- Pfam (hmmscan --cut_ga): YoeB_toxin PF06769.21 (E=9e-40)
- (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_217875.1)
- Domains: Pfam-A via hmmscan --cut_ga — YoeB_toxin (PF06769.21)
- 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
COG4115 - Curated reference: UniProt P9WF09 (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
relJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003573|Rv3358|relK MRSVNFDPDAWEDFLFWLAADRKTARRITRLIGEIQRDPFSGIGKPEPLQGELSGYWSRRIDDEHRLVYRAGDDEVTMLKARYHY