pyrF Resolved · high auto-curated
H37Rv Rv1385 · MTBC0 mtbc0_001486 ·
274 aa · 1569789–1570613 (+) ·
RefSeq NP_215901.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | orotidine 5'-phosphate decarboxylase |
|---|---|
| MTBC0 PGAP re-annotation | orotidine-5'-phosphate decarboxylase |
| Revised (this work) | Orotidine-5'-phosphate decarboxylase. Pfam: OMPdecase (PF00215.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Orotidine 5'-phosphate decarboxylase |
| EC (curated) |
EC 4.1.1.23
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | pyrF |
| eggNOG description | Belongs to the OMP decarboxylase family. Type 2 subfamily |
| Orthologous group | COG0284 |
| EC number |
EC 4.1.1.23
|
| KEGG orthology |
K01591
|
| 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 | 0.132 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
OMPdecase | PF00215.31 | 4.3e-40 | 17–259 | Orotidine 5'-phosphate decarboxylase / HUMPS family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: carB (carbamoyl-phosphate synthase large subunit), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1384 carB |
carbamoyl-phosphate synthase large subunit | 998 | 997 ctx | neighborhood:881 fusion:653 coexpression:918 textmining:419 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 997 | 997 ctx | neighborhood:881 coexpression:776 database:900 |
Rv1383 carA |
carbamoyl-phosphate synthase small subunit | 989 | 988 ctx | neighborhood:881 coexpression:864 |
Rv1381 pyrC |
dihydroorotase | 991 | 987 ctx | neighborhood:881 coexpression:863 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 992 | 983 ctx | neighborhood:881 coexpression:859 textmining:588 |
Rv0382c pyrE |
orotate phosphoribosyltransferase | 993 | 979 | coexpression:734 database:900 textmining:697 |
Rv1382 hyp |
hypothetical protein | 974 | 971 ctx | neighborhood:881 coexpression:764 |
Rv3309c upp |
uracil phosphoribosyltransferase | 996 | 930 | database:900 textmining:951 |
Rv2883c pyrH |
uridylate kinase | 945 | 909 | database:900 textmining:431 |
Rv2139 pyrD |
dihydroorotate dehydrogenase | 945 | 881 | coexpression:861 textmining:563 |
Rv1937 |
oxygenase | 819 | 780 | coexpression:731 |
Rv0385 |
monooxygenase | 792 | 779 | coexpression:733 |
Rv0383c ttfA hyp |
hypothetical protein | 822 | 751 | coexpression:730 |
Rv1389 gmk |
guanylate kinase | 775 | 739 ctx | fusion:517 |
Rv1377c |
transferase | 619 | 619 ctx | neighborhood:614 |
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: orotidine 5'-phosphate decarboxylase
- MTBC0 PGAP product: orotidine-5'-phosphate decarboxylase
- Pfam (hmmscan --cut_ga): OMPdecase PF00215.31 (E=4e-40)
- (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_215901.1)
- Domains: Pfam-A via hmmscan --cut_ga — OMPdecase (PF00215.31)
- 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
COG0284 - Curated reference: UniProt P9WIU3 (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 —
85 functional partner(s); context anchor
carB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001486|Rv1385|pyrF MTGFGLRLAEAKARRGPLCLGIDPHPELLRGWDLATTADGLAAFCDICVRAFADFAVVKPQVAFFESYGAAGFAVLERTIAELRAADVLVLADAKRGDIGATMSAYATAWVGDSPLAADAVTASPYLGFGSLRPLLEVAAAHGRGVFVLAATSNPEGAAVQNAAADGRSVAQLVVDQVGAANEAAGPGPGSIGVVVGATAPQAPDLSAFTGPVLVPGVGVQGGRPEALGGLGGAASSQLLPAVAREVLRAGPGVPELRAAGERMRDAVAYLAAV