mazF9 Resolved · high auto-curated
H37Rv Rv2801c · MTBC0 mtbc0_002980 ·
118 aa · 3132582–3132938 (-) ·
RefSeq NP_217317.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | mRNA interferase MazF9 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system toxin endoribonuclease MazF9 |
| Revised (this work) | Type II toxin-antitoxin system toxin endoribonuclease MazF9. 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.
Curated reference (UniProt)
| UniProt |
P71650
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Endoribonuclease MazF9 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli and M.smegmatis inhibits cell growth and colony formation. Its toxic effect is neutralized by coexpression with cognate antitoxin MazE9. Acts as an mRNA interferase, specifically cleaving between U and C in UAC sequences. May cleave its cognate antitoxin's gene. In E.coli expression with non-cognate antitoxins VapB27 and VapB40 partially neutralizes the toxin. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | toxic component of a |
| Orthologous group | COG2337 |
| KEGG orthology |
K07171
|
| Gene Ontology (52) |
GO:0003674, GO:0003824, GO:0004518, GO:0004519, GO:0004521, GO:0004540, GO:0006139, GO:0006401, GO:0006402, GO:0006725, GO:0006807, GO:0008150 +40 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) pseudogene candidate
| pN/pS | 0.272 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 2 missense, 2 nonsense, 0 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 2.58% of strains (3748) · 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 |
|---|---|---|---|---|
PemK_toxin | PF02452.24 | 1.4e-28 | 3–113 | PemK-like, MazF-like toxin of type II toxin-antitoxin system |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mazE9 (antitoxin MazE9), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2801A mazE9 |
antitoxin MazE9 | 999 | 1000 ctx | neighborhood:882 cooccurence:767 experimental:999 textmining:655 |
Rv2063 mazE7 |
antitoxin MazE7 | 828 | 808 | experimental:793 |
Rv2802c |
arginine/hypothetical protein | 694 | 693 ctx | neighborhood:676 |
Rv1991A mazE6 |
antitoxin MazE6 | 860 | 616 | experimental:434 textmining:652 |
Rv2803 hyp |
hypothetical protein | 491 | 491 ctx | neighborhood:491 |
Rv1942c mazF5 |
toxin MazF5 | 881 | 449 ctx | cooccurence:449 textmining:793 |
Rv3095 |
HTH-type transcriptional regulator | 416 | 417 | coexpression:417 |
Rv1725c hyp |
hypothetical protein | 415 | 415 | coexpression:415 |
Rv1103c mazE3 |
antitoxin MazE3 | 664 | 333 | textmining:518 |
Rv1102c mazF3 |
mRNA interferase MazF3 | 855 | 297 | textmining:803 |
Rv1991c mazF6 |
mRNA interferase MazF6 | 445 | 275 | |
Rv2549c vapC20 |
ribonuclease VapC20 | 459 | 271 | |
Rv0659c mazF2 |
toxin MazF2 | 616 | 250 | textmining:510 |
Rv2829c vapC22 |
ribonuclease VapC22 | 508 | 245 | |
Rv1495 mazF4 |
mRNA interferase MazF4 | 887 | 170 | textmining:870 |
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: mRNA interferase MazF9
- MTBC0 PGAP product: type II toxin-antitoxin system toxin endoribonuclease MazF9
- Pfam (hmmscan --cut_ga): PemK_toxin PF02452.24 (E=1e-28)
- (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_217317.1)
- 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 P71650 (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 —
24 functional partner(s); context anchor
mazE9 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002980|Rv2801c|mazF9 MMRRGEIWQVDLDPARGSEANNQRPAVVVSNDRANATATRLGRGVITVVPVTSNIAKVYPFQVLLSATTTGLQVDCKAQAEQIRSIATERLLRPIGRVSAAELAQLDEALKLHLDLWS