deoD Resolved · high auto-curated
H37Rv Rv3307 · MTBC0 mtbc0_003515 ·
268 aa · 3716192–3716998 (+) ·
RefSeq NP_217824.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | purine nucleoside phosphorylase |
|---|---|
| MTBC0 PGAP re-annotation | purine-nucleoside phosphorylase |
| Revised (this work) | Purine-nucleoside phosphorylase. Pfam: PNP_UDP_1 (PF01048.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP01
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Purine nucleoside phosphorylase |
| EC (curated) |
EC 2.4.2.1
|
| Curated function | The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate. Cleaves guanosine, inosine, 2'-deoxyguanosine and 2'-deoxyinosine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | punA |
| eggNOG description | The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta- (deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate |
| Orthologous group | COG0005 |
| EC number |
EC 2.4.2.1
|
| KEGG orthology |
K03783
|
| KEGG pathways |
map00230, map00240, map00760, map01100, map01110
|
| Gene Ontology (48) |
GO:0003674, GO:0003824, GO:0004731, GO:0006139, GO:0006152, GO:0006161, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009056, GO:0009116 +36 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 | 0.81 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
PNP_UDP_1 | PF01048.27 | 9.8e-46 | 30–266 | Phosphorylase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cdd (cytidine deaminase), high confidence from genomic context alone (score 971 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3315c cdd |
cytidine deaminase | 971 | 971 ctx | cooccurence:600 database:924 |
Rv3308 pmmB |
phosphomannomutase PmmB | 958 | 956 ctx | neighborhood:881 cooccurence:438 |
Rv3314c deoA |
thymidine phosphorylase | 991 | 951 ctx | cooccurence:478 database:900 textmining:826 |
Rv2584c apt |
adenine phosphoribosyltransferase | 991 | 950 | database:938 textmining:831 |
Rv3313c add |
adenosine deaminase | 953 | 938 | database:922 |
Rv3624c hpt |
hypoxanthine-guanine phosphoribosyltransferase | 975 | 925 | database:900 textmining:693 |
Rv3393 iunH |
nucleoside hydrolase | 963 | 917 | database:900 textmining:583 |
Rv2202c adoK |
adenosine kinase | 938 | 914 | database:900 |
Rv3309c upp |
uracil phosphoribosyltransferase | 976 | 911 | database:900 textmining:747 |
Rv1151c cobB |
NAD-dependent protein deacylase | 935 | 904 | database:900 |
Rv0573c pncB2 |
nicotinic acid phosphoribosyltransferase PncB2 | 909 | 904 | database:900 |
Rv1330c pncB1 |
nicotinic acid phosphoribosyltransferase PncB1 | 908 | 904 | database:900 |
Rv2344c dgt |
deoxyguanosine triphosphate triphosphohydrolase | 904 | 904 | database:900 |
Rv0212c nadR |
transcriptional regulator NadR | 903 | 904 | database:900 |
Rv2043c pncA |
pyrazinamidase/nicotinamidase PncA | 908 | 903 | database:900 |
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: purine nucleoside phosphorylase
- MTBC0 PGAP product: purine-nucleoside phosphorylase
- Pfam (hmmscan --cut_ga): PNP_UDP_1 PF01048.27 (E=1e-45)
- (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_217824.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNP_UDP_1 (PF01048.27)
- 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
COG0005 - Curated reference: UniProt P9WP01 (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 —
38 functional partner(s); context anchor
cdd - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003515|Rv3307|deoD MADPRPDPDELARRAAQVIADRTGIGEHDVAVVLGSGWLPAVAALGSPTTVLPQAELPGFVPPTAAGHAGELLSVPIGAHRVLVLAGRIHAYEGHDLRYVVHPVRAARAAGAQIMVLTNAAGGLRADLQVGQPVLISDHLNLTARSPLVGGEFVDLTDAYSPRLRELARQSDPQLAEGVYAGLPGPHYETPAEIRMLQTLGADLVGMSTVHETIAARAAGAEVLGVSLVTNLAAGITGEPLSHAEVLAAGAASATRMGALLADVIARF