Rv2019 Family assigned · medium auto-curated
H37Rv Rv2019 · MTBC0 mtbc0_002149 ·
138 aa · 2289602–2290018 (+) ·
RefSeq NP_216535.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains PIN_10 (PF18478.8) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53465
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative ribonuclease VapC45 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. An RNase. The cognate antitoxin is VapB45. |
UniProt still lists this protein as Putative ribonuclease VapC45; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2CNI4 |
|---|
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 | 0.252 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (372) · 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 |
|---|---|---|---|---|
PIN_10 | PF18478.8 | 9.2e-14 | 13–94 | PIN like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2017 (transcriptional regulator), medium confidence from genomic context alone (score 434 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2018 vapB45 hyp |
hypothetical protein | 890 | 803 ctx | neighborhood:802 textmining:464 |
Rv2017 |
transcriptional regulator | 434 | 434 ctx | neighborhood:432 |
Rv2016 hyp |
hypothetical protein | 577 | 430 ctx | neighborhood:427 |
Rv1246c relE |
toxin RelE | 425 | 76 | textmining:404 |
Rv3749c vapC50 hyp |
hypothetical protein | 816 | 47 | textmining:816 |
Rv3182 higB3 hyp |
hypothetical protein | 656 | 47 | textmining:654 |
Rv3358 relK |
toxin RelK | 643 | 47 | textmining:641 |
Rv0065 vapC1 |
ribonuclease VapC1 | 566 | 47 | textmining:564 |
Rv3697c vapC48 |
ribonuclease VapC48 | 520 | 47 | textmining:517 |
Rv1838c vapC13 |
ribonuclease VapC13 | 513 | 47 | textmining:510 |
Rv2022c higB2 hyp |
hypothetical protein | 631 | 46 | textmining:630 |
Rv3357 relJ |
antitoxin RelJ | 536 | 46 | textmining:534 |
Rv0549c vapC3 |
ribonuclease VapC3 | 459 | 46 | textmining:456 |
Rv0624 vapC30 |
ribonuclease VapC30 | 655 | 45 | textmining:654 |
Rv2021c higA2 |
transcriptional regulator | 544 | 45 | textmining:543 |
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: hypothetical protein
- MTBC0 PGAP product: hypothetical protein
- Pfam (hmmscan --cut_ga): PIN_10 PF18478.8 (E=9e-14)
- (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_216535.1)
- Domains: Pfam-A via hmmscan --cut_ga — PIN_10 (PF18478.8)
- 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
2CNI4 - Curated reference: UniProt O53465 (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
Rv2017 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002149|Rv2019| MQPDRNLLADLDHIFVDRSLGAVQVPQLLRDAGFRLTTMREHYGETQAQSVSDHKWIAMTAECGWIGFHKDANIRRNAVERRTVLDTGARLFCVPRADILAEQVAARYIASLAAIARAARFPGPFIYTVHPSKIVRVL