Rv0441c Family assigned · low auto-curated
H37Rv Rv0441c · MTBC0 mtbc0_000463 ·
142 aa · 533661–534089 (-) ·
RefSeq NP_214955.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | pyridoxamine 5'-phosphate oxidase family protein |
| Revised (this work) | Pyridoxamine 5'-phosphate oxidase family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKW3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0441c |
UniProt still lists this protein as Uncharacterized protein Rv0441c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2DI8M |
|---|
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 | 0.374 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PPE10 (PPE family protein PPE10), high confidence from genomic context alone (score 885 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) |
|---|---|---|---|---|
Rv0442c PPE10 |
PPE family protein PPE10 | 918 | 885 ctx | neighborhood:846 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 810 | 802 ctx | cooccurence:523 database:549 |
Rv1551 plsB1 |
acyltransferase PlsB | 697 | 684 | database:549 |
Rv2721c hyp |
hypothetical protein | 679 | 680 ctx | cooccurence:679 |
Rv2015c hyp |
hypothetical protein | 669 | 670 ctx | cooccurence:668 |
Rv3810 pirG |
cell surface protein | 665 | 666 ctx | cooccurence:664 |
Rv1765c hyp |
hypothetical protein | 635 | 636 ctx | cooccurence:633 |
Rv3071 hyp |
hypothetical protein | 622 | 623 ctx | cooccurence:622 |
Rv0443 hyp |
hypothetical protein | 615 | 615 ctx | neighborhood:610 |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 588 | 567 | database:552 |
Rv0479c |
membrane protein | 562 | 563 ctx | cooccurence:560 |
Rv1310 atpD |
ATP synthase subunit beta | 572 | 556 | database:538 |
Rv1305 atpE |
ATP synthase subunit C | 539 | 540 | database:526 |
Rv1610 |
membrane protein | 533 | 534 ctx | cooccurence:531 |
Rv2042c hyp |
hypothetical protein | 531 | 532 ctx | cooccurence:523 |
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: pyridoxamine 5'-phosphate oxidase family protein
- (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_214955.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2DI8M - Curated reference: UniProt P9WKW3 (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 —
60 functional partner(s); context anchor
PPE10 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000463|Rv0441c| MGAKKVDLKRLAAALPDYPFAYLITVDDGHRVHTVAVEPVLRELPDGPDGPRAVVDVGLIGGRTRQNLAHRSEVTLLWPPSDPSGYSLIVDGRAQASDAGPDDDTARCGVVPIRALLHRDAAPDSPTAAKGCLHDCVVFSVP