ubiA Resolved · high auto-curated
H37Rv Rv3806c · MTBC0 mtbc0_004034 ·
302 aa · 4293035–4293943 (-) ·
RefSeq NP_218323.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | decaprenyl-phosphate phosphoribosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | decaprenyl-phosphate phosphoribosyltransferase |
| Revised (this work) | Decaprenyl-phosphate phosphoribosyltransferase. Pfam: UbiA (PF01040.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFR5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Decaprenyl-phosphate phosphoribosyltransferase |
| EC (curated) |
EC 2.4.2.45
|
| Curated function | Involved in the biosynthesis of decaprenylphosphoryl arabinose (DPA) a precursor for arabinan synthesis in mycobacterial cell wall biosynthesis. Catalyzes the transfer of a 5-phosphoribosyl residue from phosphoribose diphosphate (PRPP) to decaprenyl phosphate (DP) to form decaprenylphosphoryl-5-phosphoribose (DPPR). The enzyme favors polyprenyl phosphate with 50-60 carbon atoms, is unable to use C-20 polyprenyl phosphate, and uses C-75 polyprenyl phosphate less efficiently than C-50 or C-60. Cannot use UDP-galactose or GDP-mannose as a sugar donor. May play a role in ethambutol (EMB) resistanc. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | ubiA |
| eggNOG description | Catalyzes the formation of decaprenylphosphoryl-5-phosphoribose from phosphoribose diphosphate and decaprenyl phosphate |
| Orthologous group | COG0382 |
| EC number |
EC 2.4.2.45
|
| KEGG orthology |
K14136
|
| Gene Ontology (43) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0006629, GO:0006643, GO:0006664, GO:0008150 +31 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 | 0.637 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 9 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 |
|---|---|---|---|---|
UbiA | PF01040.24 | 1.8e-21 | 53–265 | UbiA prenyltransferase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3807c (decaprenylphosphoryl-5-phosphoribose phosphatase), high confidence from genomic context alone (score 970 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3807c |
decaprenylphosphoryl-5-phosphoribose phosphatase | 994 | 970 ctx | neighborhood:882 database:500 textmining:818 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 981 | 968 ctx | neighborhood:780 coexpression:801 textmining:464 |
Rv3808c glfT2 |
galactofuranosyl transferase GlfT | 970 | 963 ctx | neighborhood:843 coexpression:772 |
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 965 | 899 ctx | cooccurence:774 database:552 textmining:675 |
Rv3809c glf |
UDP-galactopyranose mutase | 880 | 847 ctx | neighborhood:843 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 808 | 808 | coexpression:797 |
Rv1797 eccE5 |
ESX-5 type VII secretion system protein EccE | 797 | 797 | coexpression:797 |
Rv3791 dprE2 |
decaprenylphosphoryl-D-2-keto erythropentose reductase | 896 | 788 ctx | cooccurence:773 textmining:531 |
Rv2073c |
oxidoreductase | 794 | 786 ctx | cooccurence:772 |
Rv0513 |
transmembrane protein | 783 | 783 | coexpression:783 |
Rv1310 atpD |
ATP synthase subunit beta | 791 | 781 | database:731 |
Rv0176 |
Mce associated transmembrane protein | 780 | 780 | coexpression:780 |
Rv0178 |
Mce associated membrane protein | 773 | 773 | coexpression:746 |
Rv3789 |
GtrA family protein | 798 | 756 ctx | cooccurence:742 |
Rv1836c hyp |
hypothetical protein | 777 | 754 | coexpression:752 |
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: decaprenyl-phosphate phosphoribosyltransferase
- MTBC0 PGAP product: decaprenyl-phosphate phosphoribosyltransferase
- Pfam (hmmscan --cut_ga): UbiA PF01040.24 (E=2e-21)
- (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_218323.1)
- Domains: Pfam-A via hmmscan --cut_ga — UbiA (PF01040.24)
- 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
COG0382 - Curated reference: UniProt P9WFR5 (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 —
79 functional partner(s); context anchor
Rv3807c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004034|Rv3806c|ubiA MSEDVVTQPPANLVAGVVKAIRPRQWVKNVLVLAAPLAALGGGVRYDYVEVLSKVSMAFVVFSLAASAVYLVNDVRDVEADREHPTKRFRPIAAGVVPEWLAYTVAVVLGVTSLAGAWMLTPNLALVMVVYLAMQLAYCFGLKHQAVVDICVVSSAYLIRAIAGGVATKIPLSKWFLLIMAFGSLFMVAGKRYAELHLAERTGAAIRKSLESYTSTYLRFVWTLSATAVVLCYGLWAFERDGYSGSWFAVSMIPFTIAILRYAVDVDGGLAGEPEDIALRDRVLQLLALAWIATVGAAVAFG