Rv1875 Resolved · high auto-curated
H37Rv Rv1875 · MTBC0 mtbc0_001988 ·
147 aa · 2142420–2142863 (+) ·
RefSeq NP_216391.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| 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 |
O07754
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Pyridoxamine 5-phosphate |
| Orthologous group | COG3467 |
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 | 0.363 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (377) · 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 |
|---|---|---|---|---|
PNPOx_N | PF01243.28 | 8.2e-10 | 11–94 | Pyridoxamine 5'-phosphate oxidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lldD2 (L-lactate dehydrogenase), medium confidence from genomic context alone (score 620 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) |
|---|---|---|---|---|
Rv1874 hyp |
hypothetical protein | 877 | 878 ctx | neighborhood:874 |
Rv1872c lldD2 |
L-lactate dehydrogenase | 620 | 620 ctx | neighborhood:438 |
Rv3463 hyp |
hypothetical protein | 605 | 606 ctx | cooccurence:546 |
Rv1155 |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 919 | 603 ctx | cooccurence:601 textmining:805 |
Rv2428 ahpC |
alkyl hydroperoxide reductase subunit AhpC | 588 | 589 ctx | neighborhood:521 |
Rv1873 hyp |
hypothetical protein | 582 | 583 ctx | neighborhood:580 |
Rv0121c hyp |
hypothetical protein | 940 | 559 ctx | cooccurence:552 textmining:870 |
Rv3368c |
oxidoreductase | 481 | 481 ctx | cooccurence:450 |
Rv3060c |
GntR family transcriptional regulator | 481 | 481 ctx | cooccurence:478 |
Rv2125 hyp |
hypothetical protein | 449 | 449 | coexpression:449 |
Rv2714 hyp |
hypothetical protein | 447 | 447 | coexpression:447 |
Rv3268 hyp |
hypothetical protein | 443 | 444 ctx | cooccurence:443 |
Rv1870c hyp |
hypothetical protein | 431 | 431 | |
Rv0774c hyp |
hypothetical protein | 424 | 424 ctx | cooccurence:424 |
Rv0519c |
membrane protein | 422 | 422 ctx | cooccurence:422 |
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: PPOX class F420-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): PNPOx_N PF01243.28 (E=8e-10)
- (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_216391.1)
- 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 O07754 (TrEMBL, unreviewed; 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 —
33 functional partner(s); context anchor
lldD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001988|Rv1875| MTTLNEAAALAAAERGLAVVSTVRADGTVQASLVNVGLLPHPVSGEPSLGFTTYGKVKLGNLRARPQLAVTFRNGWQWATVEGRAQLVGPDDPRPWLVDGERLRLLLREVFTAAGGTHDDWDEYDRVMAQEQRAVVLITPTRIYSNG