Rv1990c Family assigned · medium auto-curated
H37Rv Rv1990c · MTBC0 mtbc0_002114 ·
113 aa · 2256909–2257250 (-) ·
RefSeq NP_216506.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | antitoxin Xre/MbcA/ParS toxin-binding domain-containing protein |
| Revised (this work) | Antitoxin Xre/MbcA/ParS toxin-binding domain-containing protein. Pfam: Xre_MbcA_ParS_C (PF09722.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLP7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Mycobacterial cidal antitoxin MbcA |
| Curated function | Antitoxin component of a type II toxin-antitoxin (TA) system. Neutralizes the activity of cognate toxin MbcT by blocking access to the toxin active site. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2384) |
| Orthologous group | 2AF64 |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
Xre_MbcA_ParS_C | PF09722.16 | 1.7e-07 | 63–110 | Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1990A (Rv1990A, len: 111 aa. Possible dehydrogenase (fragment), similar to N-terminal part of several dehydrogenases and hypothetical proteins, e.g), medium confidence from genomic context alone (score 430 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1989c mbcT hyp |
hypothetical protein | 999 | 1000 ctx | neighborhood:882 experimental:999 textmining:870 |
Rv1990A |
Rv1990A, len: 111 aa. Possible dehydrogenase (fragment), similar to N-terminal part of several dehydrogenases and hypothetical proteins, e.g | 430 | 430 ctx | neighborhood:425 |
Rv2034 |
ArsR family HTH-type transcriptional repressor | 644 | 85 | textmining:627 |
Rv2021c higA2 |
transcriptional regulator | 533 | 85 | textmining:511 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 440 | 55 | textmining:432 |
Rv0238 |
transcriptional regulator | 653 | 47 | textmining:651 |
Rv1423 whiA |
transcriptional regulator WhiA | 433 | 45 | textmining:431 |
Rv0023 |
transcriptional regulator | 861 | 42 | textmining:861 |
Rv2862A vapB23 |
antitoxin VapB23 | 440 | 41 | textmining:440 |
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: transcriptional regulator
- MTBC0 PGAP product: antitoxin Xre/MbcA/ParS toxin-binding domain-containing protein
- Pfam (hmmscan --cut_ga): Xre_MbcA_ParS_C PF09722.16 (E=2e-07)
- (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_216506.1)
- Domains: Pfam-A via hmmscan --cut_ga — Xre_MbcA_ParS_C (PF09722.16)
- 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
2AF64 - Curated reference: UniProt P9WLP7 (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 —
9 functional partner(s); context anchor
Rv1990A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002114|Rv1990c| MGVNVLASTVSGAIERLGLTYEEVGDIVDASPRSVARWTAGQVVPQRLNKQRLIELAYVADALAEVLPRDQANVWMFSPNRLLEHRKPADLVRDGEYQRVLALIDAMAEGVFV