Rv0088 Resolved · high auto-curated
H37Rv Rv0088 · MTBC0 - ·
224 aa · 96927–97601 (+) ·
RefSeq NP_214602.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polyketide cyclase/dehydrase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Polyketide cyclase/dehydrase. Pfam: Polyketide_cyc2 (PF10604.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WM73
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0088 |
UniProt still lists this protein as Uncharacterized protein Rv0088; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Polyketide cyclase / dehydrase and lipid transport |
| Orthologous group | COG3832 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.456 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
Polyketide_cyc2 | PF10604.16 | 1.8e-08 | 77–215 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hycE (formate hydrogenase HycE), medium confidence from genomic context alone (score 673 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0087 hycE |
formate hydrogenase HycE | 673 | 673 ctx | neighborhood:658 |
Rv0086 hycQ |
hydrogenase HycQ | 667 | 668 ctx | neighborhood:658 |
Rv0081 |
HTH-type transcriptional regulator | 751 | 667 ctx | neighborhood:651 |
Rv0085 hycP |
hydrogenase HycP | 666 | 666 ctx | neighborhood:658 |
Rv0084 hycD |
formate hydrogenlyase HycD | 657 | 657 ctx | neighborhood:644 |
Rv0082 |
oxidoreductase | 656 | 656 ctx | neighborhood:644 |
Rv0083 |
oxidoreductase | 653 | 653 ctx | neighborhood:644 |
Rv0089 |
methyltransferase | 564 | 564 ctx | neighborhood:499 |
Rv0080 hyp |
hypothetical protein | 456 | 457 ctx | neighborhood:455 |
Rv0079 hyp |
hypothetical protein | 452 | 452 ctx | neighborhood:452 |
Rv0090 |
membrane protein | 429 | 429 | |
Rv2529 hyp |
hypothetical protein | 406 | 407 ctx | cooccurence:403 |
Rv1117 hyp |
hypothetical protein | 406 | 406 ctx | cooccurence:406 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): polyketide cyclase/dehydrase
- Pfam (hmmscan --cut_ga): Polyketide_cyc2 PF10604.16 (E=2e-08)
- (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_214602.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polyketide_cyc2 (PF10604.16)
- 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
COG3832 - Curated reference: UniProt P9WM73 (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 —
13 functional partner(s); context anchor
hycE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0088| MSVYKHAPSRVRLRQTRSTVVKGRSGSLSWRRVRTGDLGLAVWGGREEYRAVKPGTPGIQPKGDMMTVTVVDAGPGRVSRSVEVAAPAAELFAIVADPRRHRELDGSGTVRGNIKVPAKLVVGSKFSTKMKLFGLPYRITSRVTALKPNELVEWSHPLGHRWRWEFESLSPTLTRVTETFDYHAAGAIKNGLKFYEMTGFAKSNAAGIEATLAKLSDQYARGRA