pyrE Resolved · high auto-curated
H37Rv Rv0382c · MTBC0 - ·
179 aa · 457841–458380 (-) ·
RefSeq YP_177723.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | orotate phosphoribosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Orotate phosphoribosyltransferase. Pfam: Pribosyltran (PF00156.34). |
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 |
P9WHK9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Orotate phosphoribosyltransferase |
| EC (curated) |
EC 2.4.2.10
|
| Curated function | Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | pyrE |
| eggNOG description | Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP) |
| Orthologous group | COG0461 |
| EC number |
EC 2.4.2.10
|
| KEGG orthology |
K00762
|
| KEGG pathways |
map00240, map01100
|
| KEGG modules |
M00051
|
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 | 0.388 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Pribosyltran | PF00156.34 | 1.6e-08 | 107–157 | Phosphoribosyl transferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0380c (RNA methyltransferase), high confidence from genomic context alone (score 776 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1385 pyrF |
orotidine 5'-phosphate decarboxylase | 993 | 979 | coexpression:734 database:900 textmining:697 |
Rv2139 pyrD |
dihydroorotate dehydrogenase | 990 | 979 | coexpression:734 database:900 textmining:590 |
Rv0381c hyp |
hypothetical protein | 867 | 867 ctx | neighborhood:863 |
Rv1381 pyrC |
dihydroorotase | 912 | 827 | coexpression:731 textmining:518 |
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 841 | 818 | coexpression:732 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 885 | 816 | database:800 textmining:403 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 826 | 800 | coexpression:730 |
Rv0383c ttfA hyp |
hypothetical protein | 785 | 786 ctx | neighborhood:786 |
Rv0380c |
RNA methyltransferase | 775 | 776 ctx | neighborhood:765 |
Rv0385 |
monooxygenase | 790 | 770 | coexpression:671 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 895 | 761 | coexpression:730 textmining:580 |
Rv1937 |
oxygenase | 800 | 730 | coexpression:715 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 819 | 713 | coexpression:697 |
Rv0384c clpB |
chaperone protein ClpB | 762 | 702 ctx | neighborhood:699 |
Rv1382 hyp |
hypothetical protein | 707 | 681 | coexpression:670 |
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): orotate phosphoribosyltransferase
- Pfam (hmmscan --cut_ga): Pribosyltran PF00156.34 (E=2e-08)
- (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_177723.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pribosyltran (PF00156.34)
- 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
COG0461 - Curated reference: UniProt P9WHK9 (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 —
54 functional partner(s); context anchor
Rv0380c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0382c|pyrE MAGPDRAELAELVRRLSVVHGRVTLSSGREADYYVDLRRATLHHRASALIGRLMRELTADWDYSVVGGLTLGADPVATAIMHAPGRPIDAFVVRKSAKAHGMQRLIEGSEVTGQRVLVVEDTSTTGNSALTAVHAVQDVGGEVVGVATVVDRATGAAEAIEAEGLRYRSVLGLADLGLD