Rv0913c Family assigned · medium auto-curated
H37Rv Rv0913c · MTBC0 mtbc0_000969 ·
502 aa · 1020432–1021940 (-) ·
RefSeq NP_215428.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dioxygenase |
|---|---|
| MTBC0 PGAP re-annotation | carotenoid oxygenase family protein |
| Revised (this work) | Carotenoid oxygenase family protein. 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 |
I6Y551
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Dioxygenase |
| EC (curated) |
EC 1.13.11.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | dioxygenase |
| Orthologous group | COG3670 |
| KEGG orthology |
K11159
|
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 | 0.773 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 missense, 2 nonsense, 0 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.45% of strains (649) · 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 | 7.5e-120 | 27–483 | Retinal pigment epithelial membrane protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0914c (lipid carrier protein or keto acyl-CoA thiolase), high confidence from genomic context alone (score 977 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0914c |
lipid carrier protein or keto acyl-CoA thiolase | 977 | 977 ctx | neighborhood:881 cooccurence:756 |
Rv1389 gmk |
guanylate kinase | 576 | 577 | database:573 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 568 | 568 | database:563 |
Rv1819c bacA |
vitamin B12 transport ATP-binding protein BacA | 565 | 565 | database:563 |
Rv3418c groES |
chaperonin GroES | 563 | 563 | database:563 |
Rv1362c |
membrane protein | 573 | 557 | |
Rv1488 hyp |
hypothetical protein | 554 | 554 | database:552 |
Rv0915c PPE14 |
PPE family protein PPE14 | 548 | 548 ctx | neighborhood:546 |
Rv2213 pepB |
cytosol aminopeptidase | 561 | 544 | database:544 |
Rv1770 hyp |
hypothetical protein | 541 | 541 | database:528 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 539 | 540 | database:528 |
Rv0916c PE7 |
PE family protein PE7 | 528 | 528 ctx | neighborhood:528 |
Rv1363c |
membrane protein | 536 | 518 | |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 493 | 493 | database:492 |
Rv3492c |
Mce associated protein | 457 | 437 |
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: dioxygenase
- MTBC0 PGAP product: carotenoid oxygenase family protein
- Pfam (hmmscan --cut_ga): RPE65 PF03055.22 (E=8e-120)
- (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_215428.1)
- 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 I6Y551 (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 —
43 functional partner(s); context anchor
Rv0914c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000969|Rv0913c| MDITIVGKYLSTLPEDDDHPYRTGPWRPQTTEWDADDLTTVTGEVPADLDGIYLRNTENPLHPAFATYHPFDGDGMIHVVGFRDGKAFYRNRFIRTDGFLAENEAGGPLWPGLAEPVQLAKREHGWGARGLMKDASSTDVIVHRGIALTSFYQCGDLYRIDPYSANTLGKESWHGRFPFDWGVSAHPKVDNKTGELLFFNYSKQEPYMRYGVVDQNNELVHYVDVPLPGPRLPHDMAFTENYVILNDFPLFWDPRLLERDVHLPRFYPEIPSRFAVVARRGNDIRWFEADPTFVLHFTNAYEQGDEIVLDGFYEGDPQPLDTGGTKWEKLFRFLALDRLQSRLHRWRLNMVTGAVHEEQLSESITEFGTINADYAASSYRYTYAATGKPSWFLFDGLVKHDLLTGNHECYSFGDGVYGSETAMAPRVGSSAEDDGYLVTLTTDMNDDASYCLVFDAARPGDGPICKLALPERISSGTHSAWVPGAELRRWDHAESPAAAVGL