Rv1159A Resolved · high auto-curated
H37Rv Rv1159A · MTBC0 - ·
94 aa · 1286284–1286568 (-) ·
RefSeq YP_177641.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 4a-hydroxytetrahydrobiopterin dehydratase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 4a-hydroxytetrahydrobiopterin dehydratase. Pfam: Pterin_4a (PF01329.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WI93
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative pterin-4-alpha-carbinolamine dehydratase |
| EC (curated) |
EC 4.2.1.96
|
UniProt still lists this protein as Putative pterin-4-alpha-carbinolamine dehydratase; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | phhB |
| eggNOG description | dehydratase |
| Orthologous group | COG2154 |
| EC number |
EC 4.2.1.96
|
| KEGG orthology |
K01724
|
| KEGG pathways |
map00790
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
Pterin_4a | PF01329.25 | 7.5e-30 | 4–90 | Pterin 4 alpha carbinolamine dehydratase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mutT2 (8-oxo-dGTP diphosphatase), medium confidence from genomic context alone (score 669 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3110 moaB1 |
pterin-4-alpha-carbinolamine dehydratase | 918 | 918 | database:900 |
Rv1160 mutT2 |
8-oxo-dGTP diphosphatase | 669 | 669 ctx | neighborhood:622 |
Rv1161 narG |
nitrate reductase subunit alpha | 440 | 441 ctx | neighborhood:437 |
Rv1163 narJ |
nitrate reductase subunit delta | 434 | 435 ctx | neighborhood:431 |
Rv0976c hyp |
hypothetical protein | 480 | 430 | coexpression:410 |
Rv1159 pimE |
polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase | 871 | 49 | textmining:870 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): 4a-hydroxytetrahydrobiopterin dehydratase
- Pfam (hmmscan --cut_ga): Pterin_4a PF01329.25 (E=8e-30)
- (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 YP_177641.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pterin_4a (PF01329.25)
- 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
COG2154 - Curated reference: UniProt P9WI93 (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 —
6 functional partner(s); context anchor
mutT2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1159A| MAVLTDEQVDAALHDLNGWQRAGGVLRRSIKFPTFMAGIDAVRRVAERAEEVNHHPDIDIRWRTVTFALVTHAVGGITENDIAMAHDIDAMFGA