relJ Resolved · high auto-curated
H37Rv Rv3357 · MTBC0 mtbc0_003572 ·
91 aa · 3797481–3797756 (+) ·
RefSeq NP_217874.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin RelJ |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system antitoxin RelJ |
| Revised (this work) | Type II toxin-antitoxin system antitoxin RelJ. 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 |
P9WF25
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Antitoxin RelJ |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. A probable antitoxin for the putative mRNA interferase RelK. Upon expression in E.coli but not in M.smegmatis this protein neutralizes E.coli YoeB.; FUNCTION: Binds to and represses its own promoter, in combination with RelK repression is somewhat lessened. Several DNA-protein complexes are formed in vitro depending on the RelJ:RelK ratio. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | relJ |
| eggNOG description | Antitoxin component of a toxin-antitoxin (TA) module |
| Orthologous group | COG2161 |
| KEGG orthology |
K19159
|
| Gene Ontology (19) |
GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0019219, GO:0019222, GO:0031323, GO:0031326, GO:0050789, GO:0050794, GO:0051171 +7 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 | 0.312 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
PhdYeFM_antitox | PF02604.27 | 4.8e-22 | 2–72 | Antitoxin Phd_YefM, type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: relK (toxin RelK), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3358 relK |
toxin RelK | 999 | 999 ctx | neighborhood:882 cooccurence:773 experimental:966 textmining:929 |
Rv3359 |
oxidoreductase | 665 | 664 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 | 429 | 429 ctx | neighborhood:426 |
Rv2866 relG |
toxin RelG | 764 | 295 | textmining:680 |
Rv1246c relE |
toxin RelE | 897 | 194 | textmining:878 |
Rv2461c clpP1 |
ATP-dependent CLP protease proteolytic subunit 1 | 483 | 77 | textmining:464 |
Rv3749c vapC50 hyp |
hypothetical protein | 655 | 73 | textmining:644 |
Rv1495 mazF4 |
mRNA interferase MazF4 | 577 | 68 | textmining:565 |
Rv2720 lexA |
repressor LexA | 451 | 62 | textmining:439 |
Rv1991c mazF6 |
mRNA interferase MazF6 | 467 | 61 | textmining:456 |
Rv2801c mazF9 |
mRNA interferase MazF9 | 540 | 58 | textmining:532 |
Rv2063A mazF7 |
mRNA interferase MazF7 | 645 | 55 | textmining:640 |
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 RelJ
- MTBC0 PGAP product: type II toxin-antitoxin system antitoxin RelJ
- Pfam (hmmscan --cut_ga): PhdYeFM_antitox PF02604.27 (E=5e-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_217874.1)
- 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 P9WF25 (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
relK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003572|Rv3357|relJ MSISASEARQRLFPLIEQVNTDHQPVRITSRAGDAVLMSADDYDAWQETVYLLRSPENARRLMEAVARDKAGHSAFTKSVDELREMAGGEE