pdxH Resolved · high auto-curated
H37Rv Rv2607 · MTBC0 mtbc0_002775 ·
224 aa · 2957751–2958425 (+) ·
RefSeq NP_217123.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pyridoxine/pyridoxamine 5'-phosphate oxidase |
|---|---|
| MTBC0 PGAP re-annotation | pyridoxamine 5'-phosphate oxidase |
| Revised (this work) | Pyridoxamine 5'-phosphate oxidase. Pfam: PNPOx_N (PF01243.28), PNP_phzG_C (PF10590.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIJ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pyridoxine 5'-phosphate oxidase |
| EC (curated) |
EC 1.4.3.5
|
| Curated function | Catalyzes the oxidation of pyridoxine 5'-phosphate (PNP) into pyridoxal 5'-phosphate (PLP). Unlike many PNPOx enzymes, Rv2607 does not recognize pyridoxamine 5'-phosphate (PMP) as a substrate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | pdxH |
| eggNOG description | Catalyzes the oxidation of either pyridoxine 5'- phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP) |
| Orthologous group | COG0259 |
| EC number |
EC 1.4.3.5
|
| KEGG orthology |
K00275
|
| KEGG pathways |
map00750, map01100, map01120
|
| KEGG modules |
M00124
|
| Gene Ontology (67) |
GO:0000166, GO:0003674, GO:0003824, GO:0005488, GO:0005515, GO:0006081, GO:0006725, GO:0006732, GO:0006766, GO:0006767, GO:0006793, GO:0006796 +55 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)
| pN/pS | 0.308 · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
PNPOx_N | PF01243.28 | 2.7e-20 | 50–172 | Pyridoxamine 5'-phosphate oxidase |
PNP_phzG_C | PF10590.15 | 1.1e-13 | 188–224 | Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: snzP (pyridoxine biosynthesis protein), high confidence from genomic context alone (score 953 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2606c snzP |
pyridoxine biosynthesis protein | 988 | 953 ctx | neighborhood:550 database:900 textmining:757 |
Rv2604c snoP |
glutamine amidotransferase SnoP | 994 | 947 ctx | neighborhood:496 database:900 textmining:898 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 583 | 567 ctx | fusion:539 |
Rv0896 gltA2 |
citrate synthase 1 | 570 | 551 ctx | neighborhood:544 |
Rv0889c citA |
citrate synthase 2 | 568 | 548 ctx | neighborhood:544 |
Rv0887c hyp |
hypothetical protein | 545 | 546 ctx | neighborhood:544 |
Rv2605c tesB2 |
acyl-CoA thioesterase II | 499 | 499 ctx | neighborhood:496 |
Rv2608 PPE42 |
PPE family protein PPE42 | 491 | 491 ctx | neighborhood:488 |
Rv0038 hyp |
hypothetical protein | 438 | 438 | |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 462 | 415 ctx | fusion:401 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 436 | 355 | |
Rv1832 gcvB |
glycine dehydrogenase | 524 | 328 | |
Rv2139 pyrD |
dihydroorotate dehydrogenase | 445 | 274 | |
Rv0121c hyp |
hypothetical protein | 817 | 73 | textmining:811 |
Rv1875 hyp |
hypothetical protein | 572 | 69 | textmining:559 |
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: pyridoxine/pyridoxamine 5'-phosphate oxidase
- MTBC0 PGAP product: pyridoxamine 5'-phosphate oxidase
- Pfam (hmmscan --cut_ga): PNPOx_N PF01243.28 (E=3e-20), PNP_phzG_C PF10590.15 (E=1e-13)
- (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_217123.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNPOx_N (PF01243.28), PNP_phzG_C (PF10590.15)
- 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
COG0259 - Curated reference: UniProt P9WIJ1 (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 —
28 functional partner(s); context anchor
snzP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002775|Rv2607|pdxH MDDDAQMVAIDKDQLARMRGEYGPEKDGCGDLDFDWLDDGWLTLLRRWLNDAQRAGVSEPNAMVLATVADGKPVTRSVLCKILDESGVAFFTSYTSAKGEQLAVTPYASATFPWYQLGRQAHVQGPVSKVSTEEIFTYWSMRPRGAQLGAWASQQSRPVGSRAQLDNQLAEVTRRFADQDQIPVPPGWGGYRIAPEIVEFWQGRENRMHNRIRVANGRLERLQP