Rv3272 Resolved · high auto-curated
H37Rv Rv3272 · MTBC0 mtbc0_003480 ·
394 aa · 3675591–3676775 (+) ·
RefSeq NP_217789.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | CoA transferase |
| Revised (this work) | CoA transferase. Pfam: CoA_transf_3 (PF02515.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96877
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable fatty acyl-CoA transferase Rv3272 |
| EC (curated) |
EC 2.8.3.-
|
| Curated function | Probably involved in fatty acid metabolism. Binds to fatty acyl-CoAs of varying carbon chain lengths, with the highest binding affinity for palmitoyl-CoA (C16:0). In vitro, alters the cell wall lipid profile and protects mycobacteria from acidic, oxidative and antibiotic stress. May play a significant role in host-pathogen interaction. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | CoA-transferase family III |
| Orthologous group | COG1804 |
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 | 2.061 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 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 |
|---|---|---|---|---|
CoA_transf_3 | PF02515.23 | 4.0e-118 | 10–387 | CoA-transferase family III |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3273 (transmembrane carbonic anhydrase), high confidence from genomic context alone (score 820 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) |
|---|---|---|---|---|
Rv3273 |
transmembrane carbonic anhydrase | 820 | 820 ctx | neighborhood:810 |
Rv3271c |
integral membrane protein | 782 | 782 ctx | neighborhood:781 |
Rv0400c fadE7 |
acyl-CoA dehydrogenase FadE7 | 559 | 543 | |
Rv0118c oxcA |
oxalyl-CoA decarboxylase OxcA | 549 | 527 | |
Rv0983 pepD |
serine protease PepD | 489 | 490 | database:482 |
Rv1223 htrA |
serine protease HtrA | 489 | 490 | database:482 |
Rv3671c marP |
serine protease | 489 | 489 | database:482 |
Rv0125 pepA |
serine protease PepA | 487 | 487 | database:482 |
Rv1679 fadE16 |
acyl-CoA dehydrogenase FadE16 | 503 | 485 | |
Rv1043c hyp |
hypothetical protein | 485 | 485 | database:482 |
Rv2499c |
oxidase regulatory-like protein | 489 | 470 | |
Rv1346 mbtN |
acyl-[acyl-carrier-protein | 486 | 468 | |
Rv0636 hadB |
(3R)-hydroxyacyl-ACP dehydratase subunit HadB | 483 | 463 | |
Rv2524c fas |
fatty acid synthase | 608 | 452 | |
Rv3672c hyp |
hypothetical protein | 451 | 451 |
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: CoA transferase
- Pfam (hmmscan --cut_ga): CoA_transf_3 PF02515.23 (E=4e-118)
- (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_217789.1)
- Domains: Pfam-A via hmmscan --cut_ga — CoA_transf_3 (PF02515.23)
- 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
COG1804 - Curated reference: UniProt P96877 (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 —
26 functional partner(s); context anchor
Rv3273 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003480|Rv3272| MPTSNPAKPLDGFRVLDFTQNVAGPLAGQVLVDLGAEVIKVEAPGGEAARQITSVLPGRPPLATYFLPNNRGKKSVTVDLTTEQAKQQMLRLADTADVVLEAFRPGTMEKLGLGPDDLRSRNPNLIYARLTAYGGNGPHGSRPGIDLVVAAEAGMTTGMPTPEGKPQIIPFQLVDNASGHVLAQAVLAALLHRERNGVADVVQVAMYDVAVGLQANQLMMHLNRAASDQPKPEPAPKAKRRKGVGFATQPSDAFRTADGYIVISAYVPKHWQKLCYLIGRPDLVEDQRFAEQRSRSINYAELTAELELALASKTATEWVQLLQANGLMACLAHTWKQVVDTPLFAENDLTLEVGRGADTITVIRTPARYASFRAVVTDPPPTAGEHNAVFLARP