vapC5 Family assigned · medium auto-curated
H37Rv Rv0627 · MTBC0 mtbc0_000651 ·
28 aa · 715088–715171 (+) ·
RefSeq NP_215141.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease VapC5 |
|---|---|
| MTBC0 PGAP re-annotation | galactose-1-phosphate uridylyltransferase |
| Revised (this work) | Type II toxin-antitoxin system VapC family toxin. Pfam: PIN (PF01850.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96917
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease VapC5 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Probable toxic component of a type II toxin-antitoxin (TA) system. The cognate antitoxin is VapB5. Has limited RNase activity on substrates; activity is seen with a VapC5-VapB5 complex. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | galT |
| eggNOG description | galactose-1-phosphate uridylyltransferase |
| Orthologous group | COG1085 |
| EC number |
EC 2.7.7.12
|
| KEGG orthology |
K00965
|
| KEGG pathways |
map00052, map00520, map01100, map04917
|
| KEGG modules |
M00362, M00554, M00632
|
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, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.79% of strains (1147) · 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 | PF01850.28 | 1.1e-17 | 9–125 | PIN domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapB5 (antitoxin VapB5), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0626 vapB5 |
antitoxin VapB5 | 999 | 1000 ctx | neighborhood:882 cooccurence:769 experimental:999 textmining:818 |
Rv0596c vapB4 |
antitoxin VapB4 | 805 | 797 | experimental:784 |
Rv3384c vapC46 |
ribonuclease VapC46 | 590 | 580 ctx | cooccurence:510 |
Rv0625c |
transmembrane protein | 581 | 580 ctx | neighborhood:579 |
Rv3408 vapC47 |
ribonuclease VapC47 | 622 | 548 ctx | cooccurence:540 |
Rv1871c hyp |
hypothetical protein | 500 | 500 ctx | cooccurence:496 |
Rv3385c vapB46 |
antitoxin VapB46 | 498 | 498 | |
Rv3407 vapB47 |
antitoxin VapB47 | 481 | 481 | |
Rv0300 vapB2 |
antitoxin VapB2 | 925 | 449 | experimental:412 textmining:870 |
Rv1560 vapB11 |
antitoxin VapB11 | 438 | 438 | |
Rv1952 vapB14 |
antitoxin VapB14 | 437 | 415 | |
Rv2601A vapB41 |
antitoxin VapB41 | 432 | 410 | |
Rv0065 vapC1 |
ribonuclease VapC1 | 666 | 321 | textmining:529 |
Rv0549c vapC3 |
ribonuclease VapC3 | 637 | 266 | textmining:526 |
Rv0582 vapC26 |
ribonuclease VapC26 | 646 | 252 | textmining:546 |
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: ribonuclease VapC5
- MTBC0 PGAP product: type II toxin-antitoxin system VapC family toxin
- Pfam (hmmscan --cut_ga): PIN PF01850.28 (E=1e-17)
- (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_215141.1)
- Domains: Pfam-A via hmmscan --cut_ga — PIN (PF01850.28)
- 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
COG1085 - Curated reference: UniProt P96917 (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 —
33 functional partner(s); context anchor
vapB5 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000651|Rv0627|vapC5 MSATPPPGGLDASVFIANERGRQLDEAL