Rv0654 Resolved · high auto-curated
H37Rv Rv0654 · MTBC0 mtbc0_000692 ·
501 aa · 754086–755591 (+) ·
RefSeq NP_215168.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | carotenoid cleavage oxygenase |
|---|---|
| MTBC0 PGAP re-annotation | carotenoid cleavage oxygenase |
| Revised (this work) | Carotenoid cleavage oxygenase. Pfam: RPE65 (PF03055.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPR5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Carotenoid cleavage oxygenase |
| EC (curated) |
EC 1.13.11.-
|
| Curated function | Catalyzes the oxidative cleavage of several carotenoids and apocarotenoids in vitro. In contrast to other carotenoid oxygenases, cleaves substrates at two different sites, namely the central C15-C15' and an excentric double bond at the C13-C14 position, leading to retinal (C20), beta-apo-14'-carotenal (C22) and beta-apo-13-carotenone (C18) from beta-carotene (C40), as well as the corresponding hydroxylated products from zeaxanthin and lutein. Converts beta-apo-10'-carotenal (C27) into beta-apo-13-carotenone (C18) and to minor amounts of beta-apo-15-carotenal (retinal; C20) from the cleavage at. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | dioxygenase |
| Orthologous group | COG3670 |
| KEGG orthology |
K11159
|
| Gene Ontology (29) |
GO:0003674, GO:0003824, GO:0006629, GO:0006720, GO:0006721, GO:0008150, GO:0008152, GO:0008300, GO:0009056, GO:0009987, GO:0010436, GO:0016042 +17 more
|
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) pseudogene candidate
| pN/pS | 1.711 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 2.43% of strains (3524) · 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 |
|---|---|---|---|---|
RPE65 | PF03055.22 | 6.8e-112 | 19–499 | Retinal pigment epithelial membrane protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0653c (transcriptional regulator), high confidence from genomic context alone (score 785 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0653c |
transcriptional regulator | 785 | 785 ctx | neighborhood:785 |
Rv0655 mkl |
ABC transporter ATP-binding protein | 771 | 772 ctx | neighborhood:772 |
Rv1819c bacA |
vitamin B12 transport ATP-binding protein BacA | 619 | 620 | database:563 |
Rv1389 gmk |
guanylate kinase | 576 | 577 | database:573 |
Rv0914c |
lipid carrier protein or keto acyl-CoA thiolase | 556 | 557 ctx | cooccurence:543 |
Rv2213 pepB |
cytosol aminopeptidase | 561 | 544 | database:544 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 538 | 538 | database:528 |
Rv1770 hyp |
hypothetical protein | 538 | 538 | database:528 |
Rv0178 |
Mce associated membrane protein | 451 | 430 | |
Rv2390c hyp |
hypothetical protein | 451 | 430 | |
Rv1362c |
membrane protein | 451 | 430 | |
Rv1972 |
Mce associated membrane protein | 451 | 430 | |
Rv1973 |
Mce associated membrane protein | 451 | 430 | |
Rv1363c |
membrane protein | 451 | 430 | |
Rv0177 |
Mce associated protein | 451 | 430 |
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: carotenoid cleavage oxygenase
- MTBC0 PGAP product: carotenoid cleavage oxygenase
- Pfam (hmmscan --cut_ga): RPE65 PF03055.22 (E=7e-112)
- (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_215168.1)
- Domains: Pfam-A via hmmscan --cut_ga — RPE65 (PF03055.22)
- 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
COG3670 - Curated reference: UniProt P9WPR5 (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 —
30 functional partner(s); context anchor
Rv0653c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000692|Rv0654| MTTAQAAESQNPYLEGFLAPVSTEVTATDLPVTGRIPEHLDGRYLRNGPNPVAEVDPATYHWFTGDAMVHGVALRDGKARWYRNRWVRTPAVCAALGEPISARPHPRTGIIEGGPNTNVLTHAGRTLALVEAGVVNYELTDELDTVGPCDFDGTLHGGYTAHPQRDPHTGELHAVSYSFARGHRVQYSVIGTDGHARRTVDIEVAGSPMMHSFSLTDNYVVIYDLPVTFDPMQVVPASVPRWLQRPARLVIQSVLGRVRIPDPIAALGNRMQGHSDRLPYAWNPSYPARVGVMPREGGNEDVRWFDIEPCYVYHPLNAYSECRNGAEVLVLDVVRYSRMFDRDRRGPGGDSRPSLDRWTINLATGAVTAECRDDRAQEFPRINETLVGGPHRFAYTVGIEGGFLVGAGAALSTPLYKQDCVTGSSTVASLDPDLLIGEMVFVPNPSARAEDDGILMGYGWHRGRDEGQLLLLDAQTLESIATVHLPQRVPMGFHGNWAPTT