Rv3519 Family assigned · medium auto-curated
H37Rv Rv3519 · MTBC0 mtbc0_003735 ·
236 aa · 3979227–3979937 (+) ·
RefSeq NP_218036.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | acetoacetate decarboxylase family protein |
| Revised (this work) | Acetoacetate decarboxylase family protein. Pfam: ADC (PF06314.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53564
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Acetoacetate decarboxylase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Acetoacetate decarboxylase |
| Orthologous group | COG4689 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 4 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.33% of strains (475) · 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 |
|---|---|---|---|---|
ADC | PF06314.17 | 2.7e-32 | 17–221 | Acetoacetate decarboxylase (ADC) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cyp142 (cytochrome P450 monooxygenase Cyp142), high confidence from genomic context alone (score 793 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) |
|---|---|---|---|---|
Rv3518c cyp142 |
cytochrome P450 monooxygenase Cyp142 | 805 | 793 ctx | neighborhood:790 |
Rv3061c fadE22 |
acyl-CoA dehydrogenase FadE22 | 597 | 581 ctx | cooccurence:580 |
Rv3412 hyp |
hypothetical protein | 569 | 570 ctx | cooccurence:555 |
Rv0771 |
4-carboxymuconolactone decarboxylase | 562 | 562 ctx | cooccurence:562 |
Rv0763c |
ferredoxin | 555 | 555 ctx | cooccurence:541 |
Rv1059 hyp |
hypothetical protein | 508 | 509 ctx | cooccurence:507 |
Rv0271c fadE6 |
acyl-CoA dehydrogenase FadE6 | 523 | 505 ctx | cooccurence:502 |
Rv1786 |
ferredoxin | 495 | 495 ctx | cooccurence:479 |
Rv0585c |
integral membrane protein | 457 | 457 | |
Rv3803c fbpD |
MPT51/MPB51 antigen | 437 | 438 ctx | cooccurence:434 |
Rv0320 hyp |
hypothetical protein | 435 | 435 ctx | cooccurence:435 |
Rv1362c |
membrane protein | 431 | 432 ctx | cooccurence:428 |
Rv0498 hyp |
hypothetical protein | 411 | 411 | coexpression:410 |
Rv3521 hyp |
hypothetical protein | 631 | 335 | textmining:469 |
Rv3522 ltp4 |
lipid transfer protein | 416 | 323 |
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: acetoacetate decarboxylase family protein
- Pfam (hmmscan --cut_ga): ADC PF06314.17 (E=3e-32)
- (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_218036.1)
- Domains: Pfam-A via hmmscan --cut_ga — ADC (PF06314.17)
- 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
COG4689 - Curated reference: UniProt O53564 (TrEMBL, unreviewed; 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 —
18 functional partner(s); context anchor
cyp142 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003735|Rv3519| MPVSQHTIAGTVLTMPVRIRTANLHSAMFSVPADPAQRLIDYSGLRVCEYLPGKAIVMQMLVRYVDGDLGRYHEYGTAIMVNPPGTQRRGPRALTRAAAFIHHLPVDQVFTLEAGRTIWGFPKIMADFNVTDGRRFGFDVSADGRLIAGIEFSTGLPVPTLGWQMLKTYSHHDGVTREIPWEMKVSGLRARLGGARLRLGDHPYAKELASLGLPKRALLSQSAANVEMTFGDGHPI