Rv3633 Family assigned · medium auto-curated
H37Rv Rv3633 · MTBC0 mtbc0_003850 ·
291 aa · 4095495–4096370 (+) ·
RefSeq NP_218150.1
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 |
P9WI89
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3633 |
UniProt still lists this protein as Uncharacterized protein Rv3633; 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 |
| Orthologous group | COG5285 |
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 1.697 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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 |
|---|---|---|---|---|
PhyH | PF05721.20 | 3.2e-38 | 15–213 | Phytanoyl-CoA dioxygenase (PhyH) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipL (esterase LipL), medium confidence from genomic context alone (score 533 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) |
|---|---|---|---|---|
Rv1867 hyp |
hypothetical protein | 705 | 694 ctx | cooccurence:400 database:497 |
Rv3351c hyp |
hypothetical protein | 630 | 617 | database:463 |
Rv2280 |
Rv2280, (MTCY339.30c), len: 459 aa. Probable dehydrogenase. Similar to D-lactate dehydrogenase (cytochrome) precursor e.g. G1061264 (587 aa) | 604 | 590 | database:463 |
Rv1774 |
oxidoreductase | 602 | 588 | database:463 |
Rv1257c |
oxidoreductase | 554 | 538 | database:463 |
Rv1771 |
L-gulono-1,4-lactone dehydrogenase | 549 | 533 | database:463 |
Rv1497 lipL |
esterase LipL | 533 | 533 ctx | cooccurence:527 |
Rv3107c agpS |
alkyldihydroxyacetonephosphate synthase | 547 | 531 | database:463 |
Rv2251 |
flavoprotein | 547 | 531 | database:463 |
Rv0161 |
oxidoreductase | 547 | 531 | database:463 |
Rv1923 lipD |
lipase LipD | 530 | 531 ctx | cooccurence:524 |
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 545 | 529 | database:463 |
Rv3719 hyp |
hypothetical protein | 545 | 529 | database:463 |
Rv1726 |
oxidoreductase | 545 | 529 | database:463 |
Rv2250A |
Possible flavoprotein; Rv2250A, len: 139 aa. Conserved hypothetical protein, possibly flavoprotein. Similar to N-terminus of SCF91.28c|AL132 | 544 | 528 | 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=3e-38)
- (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_218150.1)
- 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 P9WI89 (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 —
59 functional partner(s); context anchor
lipL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003850|Rv3633| MTQSSSVERLVGEIDEFGYTVVEDVLDADSVAAYLADTRRLERELPTVIANSTTVVKGLARPGHVPVDRVDHDWVRIDNLLLHGTRYEALPVHPKLLPVIEGVLGRDCLLSWCMTSNQLPGAVAQRLHCDDEMYPLPRPHQPLLCNALIALCDFTADNGATQVVPGSHRWPERPSPPYPEGKPVEINAGDALIWNGSLWHTAAANRTDAPRPALTINFCVGFVRQQVNQQLSIPRELVRCFEPRLQELIGYGLYAGKMGRIDWRPPADYLDADRHPFLDAVADRLQTSVRL