upp Resolved · high auto-curated
H37Rv Rv3309c · MTBC0 mtbc0_003517 ·
207 aa · 3718608–3719231 (-) ·
RefSeq NP_217826.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | uracil phosphoribosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | uracil phosphoribosyltransferase |
| Revised (this work) | Uracil phosphoribosyltransferase. Pfam: UPRTase (PF14681.13), Pribosyltran (PF00156.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFF3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uracil phosphoribosyltransferase |
| EC (curated) |
EC 2.4.2.9
|
| Curated function | Catalyzes the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | upp |
| eggNOG description | Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate |
| Orthologous group | COG0035 |
| EC number |
EC 2.4.2.9
|
| KEGG orthology |
K00761
|
| KEGG pathways |
map00240, map01100
|
| Gene Ontology (92) |
GO:0003674, GO:0003824, GO:0004849, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006139, GO:0006206, GO:0006213 +80 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 | 0.51 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
UPRTase | PF14681.13 | 2.3e-66 | 5–205 | Uracil phosphoribosyltransferase |
Pribosyltran | PF00156.34 | 1.5e-09 | 67–175 | Phosphoribosyl transferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpiB (ribose-5-phosphate isomerase B), high confidence from genomic context alone (score 916 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3314c deoA |
thymidine phosphorylase | 994 | 952 | coexpression:415 database:900 textmining:895 |
Rv2883c pyrH |
uridylate kinase | 962 | 951 | coexpression:453 database:900 |
Rv1385 pyrF |
orotidine 5'-phosphate decarboxylase | 996 | 930 | database:900 textmining:951 |
Rv2465c rpiB |
ribose-5-phosphate isomerase B | 920 | 916 ctx | fusion:899 |
Rv3307 deoD |
purine nucleoside phosphorylase | 976 | 911 | database:900 textmining:747 |
Rv3396c guaA |
GMP synthase | 943 | 907 | coexpression:895 textmining:418 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 989 | 900 | database:900 textmining:895 |
Rv3310 sapM |
acid phosphatase | 780 | 780 ctx | neighborhood:780 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 724 | 688 | coexpression:662 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 724 | 688 | coexpression:662 |
Rv2890c rpsB |
30S ribosomal protein S2 | 649 | 649 | coexpression:648 |
Rv3311 hyp |
hypothetical protein | 594 | 593 ctx | neighborhood:592 |
Rv2889c tsf |
elongation factor EF-Ts | 573 | 574 | coexpression:572 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 538 | 538 | coexpression:536 |
Rv1712 cmk |
cytidylate kinase | 607 | 535 | database:500 |
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: uracil phosphoribosyltransferase
- MTBC0 PGAP product: uracil phosphoribosyltransferase
- Pfam (hmmscan --cut_ga): UPRTase PF14681.13 (E=2e-66), Pribosyltran PF00156.34 (E=1e-09)
- (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_217826.1)
- Domains: Pfam-A via hmmscan --cut_ga — UPRTase (PF14681.13), 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
COG0035 - Curated reference: UniProt P9WFF3 (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 —
58 functional partner(s); context anchor
rpiB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003517|Rv3309c|upp MQVHVVDHPLAAARLTTLRDERTDNAGFRAALRELTLLLIYEATRDAPCEPVPIRTPLAETVGSRLTKPPLLVPVLRAGLGMVDEAHAALPEAHVGFVGVARDEQTHQPVPYLDSLPDDLTDVPVMVLDPMVATGGSMTHTLGLLISRGAADITVLCVVAAPEGIAALQKAAPNVRLFTAAIDEGLNEVAYIVPGLGDAGDRQFGPR