Rv1501 Family assigned · medium auto-curated
H37Rv Rv1501 · MTBC0 mtbc0_001606 ·
273 aa · 1701695–1702516 (+) ·
RefSeq NP_216017.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | phytanoyl-CoA dioxygenase family protein |
| Revised (this work) | Phytanoyl-CoA dioxygenase family protein. Pfam: PhyH (PF05721.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI91
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1501 |
UniProt still lists this protein as Uncharacterized protein Rv1501; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Phytanoyl-CoA dioxygenase (PhyH) |
| Orthologous group | COG5285 |
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 | 0.948 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (201) · 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 |
|---|---|---|---|---|
PhyH | PF05721.20 | 4.0e-37 | 21–209 | Phytanoyl-CoA dioxygenase (PhyH) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pimF (glycosyltransferase), high confidence from genomic context alone (score 863 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) |
|---|---|---|---|---|
Rv1500 pimF |
glycosyltransferase | 862 | 863 ctx | neighborhood:783 |
Rv1502 hyp |
hypothetical protein | 766 | 767 ctx | neighborhood:505 cooccurence:469 |
Rv1499 hyp |
hypothetical protein | 625 | 624 ctx | neighborhood:622 |
Rv1867 hyp |
hypothetical protein | 629 | 615 | database:497 |
Rv3351c hyp |
hypothetical protein | 601 | 587 | database:463 |
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 600 | 586 | database:463 |
Rv2209 |
integral membrane protein | 546 | 547 ctx | cooccurence:542 |
Rv3719 hyp |
hypothetical protein | 556 | 540 | database:463 |
Rv1771 |
L-gulono-1,4-lactone dehydrogenase | 548 | 532 | database:463 |
Rv3353c hyp |
hypothetical protein | 545 | 529 | database:463 |
Rv0063 |
oxidoreductase | 545 | 529 | database:463 |
Rv1774 |
oxidoreductase | 545 | 529 | database:463 |
Rv2280 |
Rv2280, (MTCY339.30c), len: 459 aa. Probable dehydrogenase. Similar to D-lactate dehydrogenase (cytochrome) precursor e.g. G1061264 (587 aa) | 544 | 528 | database:463 |
Rv0441c hyp |
hypothetical protein | 544 | 528 | database:463 |
Rv1726 |
oxidoreductase | 543 | 527 | database:463 |
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: phytanoyl-CoA dioxygenase family protein
- Pfam (hmmscan --cut_ga): PhyH PF05721.20 (E=4e-37)
- (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_216017.1)
- Domains: Pfam-A via hmmscan --cut_ga — PhyH (PF05721.20)
- 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
COG5285 - Curated reference: UniProt P9WI91 (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 —
72 functional partner(s); context anchor
pimF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001606|Rv1501| MIPVKVENNTSLDQVQDALNCVGYAVVEDVLDEASLAATRDRMYRVQERILTEIGKERLARAGELGVLRLMMKYDPHFFTFLEIPEVLSIVDRVLSETAILHLQNGFILPSFPPFSTPDVFQNAFHQDFPRVLSGYIASVNIMFAIDPFTRDTGATLVVPGSHQRIEKPDHTYLARNAVPVQCAAGSLFVFDSTLWHAAGRNTSGKDRLAINHQFTRSFFKQQIDYVRALGDAVVLEQPARTQQLLGWYSRVVTNLDEYYQPPDKRLYRKGQG