deoA Resolved · high auto-curated
H37Rv Rv3314c · MTBC0 mtbc0_003524 ·
427 aa · 3724322–3725605 (-) ·
RefSeq NP_217831.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | thymidine phosphorylase |
|---|---|
| MTBC0 PGAP re-annotation | thymidine phosphorylase |
| Revised (this work) | Thymidine phosphorylase. Pfam: Glycos_trans_3N (PF02885.23), Glycos_transf_3 (PF00591.28), PYNP_C (PF07831.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFS1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Thymidine phosphorylase |
| EC (curated) |
EC 2.4.2.4
|
| Curated function | The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | deoA |
| eggNOG description | phosphorylase |
| Orthologous group | COG0213 |
| EC number |
EC 2.4.2.2, EC 2.4.2.4
|
| KEGG orthology |
K00756, K00758
|
| KEGG pathways |
map00240, map00983, map01100, map05219
|
| Gene Ontology (16) |
GO:0003674, GO:0003824, GO:0004645, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0009032, GO:0016740, GO:0016757, GO:0016758 +4 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 | 0.299 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
Glycos_trans_3N | PF02885.23 | 1.1e-18 | 10–71 | Glycosyl transferase family, helical bundle domain |
Glycos_transf_3 | PF00591.28 | 1.7e-37 | 83–291 | Glycosyl transferase family, a/b domain |
PYNP_C | PF07831.20 | 3.0e-19 | 339–411 | Pyrimidine nucleoside phosphorylase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cdd (cytidine deaminase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3315c cdd |
cytidine deaminase | 999 | 999 ctx | neighborhood:881 fusion:530 cooccurence:750 coexpression:431 database:900 textmining:885 |
Rv3309c upp |
uracil phosphoribosyltransferase | 994 | 952 | coexpression:415 database:900 textmining:895 |
Rv3307 deoD |
purine nucleoside phosphorylase | 991 | 951 ctx | cooccurence:478 database:900 textmining:826 |
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 955 | 942 ctx | cooccurence:714 coexpression:728 |
Rv3313c add |
adenosine deaminase | 989 | 920 ctx | neighborhood:882 textmining:870 |
Rv1379 pyrR |
bifunctional pyrimidine operon regulatory protein/uracil phosphoribosyltransferase | 913 | 901 | database:900 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 764 | 750 ctx | neighborhood:746 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 749 | 750 ctx | neighborhood:746 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 681 | 682 ctx | neighborhood:677 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 681 | 681 ctx | neighborhood:677 |
Rv0343 iniC |
iIsoniazid inductible protein IniC | 662 | 662 | coexpression:643 |
Rv2364c era |
GTPase Era | 662 | 662 | coexpression:643 |
Rv3312A mtp |
pilin | 707 | 625 ctx | neighborhood:624 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 575 | 575 | coexpression:575 |
Rv3000 |
transmembrane protein | 522 | 523 ctx | neighborhood:520 |
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: thymidine phosphorylase
- MTBC0 PGAP product: thymidine phosphorylase
- Pfam (hmmscan --cut_ga): Glycos_trans_3N PF02885.23 (E=1e-18), Glycos_transf_3 PF00591.28 (E=2e-37), PYNP_C PF07831.20 (E=3e-19)
- (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_217831.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glycos_trans_3N (PF02885.23), Glycos_transf_3 (PF00591.28), PYNP_C (PF07831.20)
- 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
COG0213 - Curated reference: UniProt P9WFS1 (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 —
31 functional partner(s); context anchor
cdd - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003524|Rv3314c|deoA MTDFAFDAPTVIRTKRDGGRLSDAAIDWVVKAYTDGRVADEQMSALLMAIVWRGMDRGEIARWTAAMLASGARLDFTDLPLATVDKHSTGGVGDKITLPLVPVVAACGGAVPQASGRGLGHTGGTLDKLESITGFTANLSNQRVREQLCDVGAAIFAAGQLAPADAKLYALRDITGTVESLPLIASSIMSKKLAEGAGALVLDVKVGSGAFMRSPVQARELAHTMVELGAAHGVPTRALLTEMNCPLGRTVGNALEVAEALEVLAGGGPPDVVELTLRLAGEMLELAGIHGRDPAQTLRDGTAMDRFRRLVAAQGGDLSKPLPIGSHSETVTAGASGTMGDIDAMAVGLAAWRLGAGRSRPGARVQHGAGVRIHRRPGEPVVVGEPLFTLYTNAPERFGAARAELAGGWSIRDSPPQVRPLIVDRIV