dut Resolved · high auto-curated
H37Rv Rv2697c · MTBC0 - ·
154 aa · 3013683–3014147 (-) ·
RefSeq NP_217213.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | deoxyuridine 5'-triphosphate nucleotidohydrolase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Deoxyuridine 5'-triphosphate nucleotidohydrolase. Pfam: dUTPase (PF00692.25), DCD (PF22769.2). |
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 |
P9WNS5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Deoxyuridine 5'-triphosphate nucleotidohydrolase |
| EC (curated) |
EC 3.6.1.23
|
| Curated function | This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | dut |
| eggNOG description | This enzyme is involved in nucleotide metabolism it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA |
| Orthologous group | COG0756 |
| EC number |
EC 3.6.1.23
|
| KEGG orthology |
K01520
|
| KEGG pathways |
map00240, map00983, map01100
|
| KEGG modules |
M00053
|
| Gene Ontology (100) |
GO:0000287, GO:0003674, GO:0003824, GO:0004170, GO:0005488, GO:0006139, GO:0006220, GO:0006221, GO:0006226, GO:0006244, GO:0006725, GO:0006753 +88 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 | 0.389 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
dUTPase | PF00692.25 | 8.9e-27 | 15–149 | dUTPase |
DCD | PF22769.2 | 2.4e-13 | 32–118 | dCTP deaminase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2698 (transmembrane protein), high confidence from genomic context alone (score 793 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1252c lprE |
lipoprotein LprE | 964 | 963 | experimental:837 database:782 |
Rv2764c thyA |
thymidylate synthase ThyA | 986 | 951 | coexpression:445 database:900 textmining:739 |
Rv3247c tmk |
thymidylate kinase | 949 | 929 | database:900 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 956 | 914 | database:900 textmining:513 |
Rv2754c thyX |
thymidylate synthase ThyX | 993 | 908 | database:900 textmining:934 |
Rv0321 dcd |
deoxycytidine triphosphate deaminase | 930 | 908 | database:900 |
Rv2698 |
transmembrane protein | 793 | 793 ctx | neighborhood:790 |
Rv2696c hyp |
hypothetical protein | 793 | 793 ctx | neighborhood:790 |
Rv2116 lppK |
lipoprotein LppK | 743 | 718 | coexpression:709 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 743 | 718 | coexpression:709 |
Rv2737c recA |
recombinase A | 792 | 707 | coexpression:414 database:457 |
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 716 | 699 | coexpression:674 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 685 | 673 ctx | fusion:673 |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 703 | 663 | coexpression:644 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 703 | 663 | coexpression:644 |
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): deoxyuridine 5'-triphosphate nucleotidohydrolase
- Pfam (hmmscan --cut_ga): dUTPase PF00692.25 (E=9e-27), DCD PF22769.2 (E=2e-13)
- (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_217213.1)
- Domains: Pfam-A via hmmscan --cut_ga — dUTPase (PF00692.25), DCD (PF22769.2)
- 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
COG0756 - Curated reference: UniProt P9WNS5 (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 —
37 functional partner(s); context anchor
Rv2698 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2697c|dut MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL