Rv3807c Resolved · high auto-curated
H37Rv Rv3807c · MTBC0 - ·
165 aa · 4269840–4270337 (-) ·
RefSeq NP_218324.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | decaprenylphosphoryl-5-phosphoribose phosphatase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Decaprenylphosphoryl-5-phosphoribose phosphatase. Pfam: PAP2 (PF01569.28). |
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 |
P9WI53
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Decaprenylphosphoryl-5-phosphoribose phosphatase |
| EC (curated) |
EC 3.1.3.111
|
| Curated function | Phosphatase involved in the biosynthesis of decaprenylphosphoryl arabinose (DPA), which serves as the arabinose donor for the biosynthesis of arabinogalactan, the major mycobacterial cell wall polysaccharide (By similarity). Catalyzes the dephosphorylation of decaprenylphosphoryl-5-phosphoribose (DPPR) to decaprenyl-phosphoribose (DPR) (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | Membrane-associated phospholipid phosphatase |
| Orthologous group | COG0671 |
| EC number |
EC 3.6.1.27
|
| KEGG orthology |
K19302
|
| KEGG pathways |
map00550
|
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) pseudogene candidate
| pN/pS | 0.411 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 5.04% of strains (7315) · 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 |
|---|---|---|---|---|
PAP2 | PF01569.28 | 1.7e-13 | 52–152 | PAP2 superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ubiA (decaprenyl-phosphate phosphoribosyltransferase), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 994 | 970 ctx | neighborhood:882 database:500 textmining:818 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 972 | 956 ctx | neighborhood:780 coexpression:770 textmining:408 |
Rv3808c glfT2 |
galactofuranosyl transferase GlfT | 898 | 860 ctx | neighborhood:843 |
Rv3809c glf |
UDP-galactopyranose mutase | 878 | 845 ctx | neighborhood:843 |
Rv0719 rplF |
50S ribosomal protein L6 | 787 | 779 | experimental:405 database:630 |
Rv1252c lprE |
lipoprotein LprE | 763 | 755 | experimental:405 database:599 |
Rv3810 pirG |
cell surface protein | 721 | 721 ctx | neighborhood:714 |
Rv3801c fadD32 |
long-chain-fatty-acid--AMP ligase FadD32 | 662 | 661 | database:500 |
Rv1683 |
bifunctional long-chain acyl-CoA synthase/lipase | 672 | 659 | database:500 |
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 879 | 650 | database:500 textmining:670 |
Rv2276 cyp121 |
cytochrome P450 Cyp121 | 635 | 635 | database:524 |
Rv0778 cyp126 |
cytochrome P450 Cyp126 | 635 | 635 | database:524 |
Rv0568 cyp135B1 |
cytochrome P450 Cyp135B1 | 633 | 633 | database:524 |
Rv3685c cyp137 |
cytochrome P450 Cyp137 | 633 | 633 | database:524 |
Rv3121 cyp141 |
cytochrome P450 Cyp141 | 632 | 632 | database:524 |
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): decaprenylphosphoryl-5-phosphoribose phosphatase
- Pfam (hmmscan --cut_ga): PAP2 PF01569.28 (E=2e-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_218324.1)
- Domains: Pfam-A via hmmscan --cut_ga — PAP2 (PF01569.28)
- 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
COG0671 - Curated reference: UniProt P9WI53 (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 —
94 functional partner(s); context anchor
ubiA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3807c| MVAVQSALVDRPGMLATARGLSHFGEHCIGWLILALLGAIALPRRRREWLVAGAGAFVAHAIAVLIKRLVRRQRPDHPAIAVNVDTPSQLSFPSAHATSTTAAALLMGRATGLPLPVVLVPPMALSRILLGVHYPSDVAVGVALGATVGAIVDSVGGGRQRARKR