Rv1155 Resolved · high auto-curated
H37Rv Rv1155 · MTBC0 mtbc0_001241 ·
147 aa · 1289870–1290313 (+) ·
RefSeq NP_215671.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pyridoxine/pyridoxamine 5'-phosphate oxidase |
|---|---|
| MTBC0 PGAP re-annotation | PPOX class F420-dependent oxidoreductase |
| Revised (this work) | PPOX class F420-dependent oxidoreductase. Pfam: PNPOx_N (PF01243.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06553
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | F420H(2)-dependent reductase Rv1155 |
| EC (curated) |
EC 1.-.-.-
|
| Curated function | F420H(2)-dependent reductase able to catalyze the reduction of biliverdin-IXalpha to bilirubin-IXalpha in vitro. However, kinetic parameters show that it is less efficient than the biliverdin reductase Rv2074 and suggest biliverdin-IXalpha is unlikely to be the native substrate of Rv1155, which probably catalyzes the reduction of an alternative molecule in vivo. Binds coenzyme F420, but does not bind FMN or other flavins. Cannot use pyridoxine 5'-phosphate, pyridoxamine 5'-phosphate, pyridoxal 5'-phosphate (PLP), the anti-tuberculosis drug PA-824 or aflatoxin analogs as substrates. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | PFAM pyridoxamine 5'-phosphate |
| Orthologous group | COG3467 |
| KEGG orthology |
K07005
|
| Gene Ontology (41) |
GO:0000166, GO:0003674, GO:0005488, GO:0005515, GO:0006766, GO:0006767, GO:0006807, GO:0008144, GO:0008150, GO:0008152, GO:0009987, GO:0010181 +29 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 | 0.343 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 3 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 | 9.1e-13 | 6–132 | Pyridoxamine 5'-phosphate oxidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: omt (O-methyltransferase), medium confidence from genomic context alone (score 574 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1875 hyp |
hypothetical protein | 919 | 603 ctx | cooccurence:601 textmining:805 |
Rv1154c hyp |
hypothetical protein | 589 | 589 ctx | neighborhood:585 |
Rv3463 hyp |
hypothetical protein | 586 | 587 ctx | cooccurence:585 |
Rv1153c omt |
O-methyltransferase | 574 | 574 ctx | neighborhood:573 |
Rv1156 hyp |
hypothetical protein | 528 | 529 ctx | neighborhood:521 |
Rv2216 |
epimerase family protein | 517 | 517 | coexpression:513 |
Rv0044c |
oxidoreductase | 514 | 501 ctx | cooccurence:498 |
Rv1558 hyp |
hypothetical protein | 821 | 500 ctx | cooccurence:493 textmining:658 |
Rv1001 arcA |
arginine deiminase | 446 | 446 | coexpression:446 |
Rv0513 |
transmembrane protein | 431 | 431 ctx | cooccurence:424 |
Rv2323c hyp |
hypothetical protein | 418 | 418 | coexpression:416 |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 408 | 409 | coexpression:409 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 407 | 408 | coexpression:408 |
Rv3268 hyp |
hypothetical protein | 406 | 407 ctx | cooccurence:402 |
Rv1364c |
sigma factor regulatory protein | 401 | 402 | coexpression:402 |
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: PPOX class F420-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): PNPOx_N PF01243.28 (E=9e-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_215671.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNPOx_N (PF01243.28)
- 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
COG3467 - Curated reference: UniProt O06553 (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 —
24 functional partner(s); context anchor
omt - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001241|Rv1155| MARQVFDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPPAAAPDDDTVEALIALYRNIAGEHPDWDDYRQAMVTDRRVLLTLPISHVYGLPPGMR