dcd Resolved · high auto-curated
H37Rv Rv0321 · MTBC0 mtbc0_000342 ·
190 aa · 391905–392477 (+) ·
RefSeq NP_214835.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | deoxycytidine triphosphate deaminase |
|---|---|
| MTBC0 PGAP re-annotation | dCTP deaminase |
| Revised (this work) | DCTP deaminase. Pfam: DCD (PF22769.2), DCD_N (PF06559.17), DCD_C (PF22569.2), dUTPase (PF00692.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP17
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | dCTP deaminase, dUMP-forming |
| EC (curated) |
EC 3.5.4.30
|
| Curated function | Bifunctional enzyme that catalyzes both the deamination of dCTP to dUTP and the hydrolysis of dUTP to dUMP without releasing the toxic dUTP intermediate. It also acts as a dUTP diphosphatase. Affinity for dCTP and dUTP are very similar. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | dcd |
| eggNOG description | Belongs to the dCTP deaminase family |
| Orthologous group | COG0717 |
| EC number |
EC 3.5.4.13
|
| KEGG orthology |
K01494
|
| KEGG pathways |
map00240, map01100
|
| KEGG modules |
M00053
|
| Gene Ontology (12) |
GO:0003674, GO:0003824, GO:0004170, GO:0016462, GO:0016787, GO:0016810, GO:0016814, GO:0016817, GO:0016818, GO:0019239, GO:0033973, GO:0047429
|
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 | 1.038 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
DCD | PF22769.2 | 8.4e-43 | 2–151 | dCTP deaminase-like |
DCD_N | PF06559.17 | 5.2e-07 | 3–151 | 2'-deoxycytidine 5'-triphosphate deaminase (DCD) N-terminal domain |
DCD_C | PF22569.2 | 4.5e-08 | 64–175 | 2'-deoxycytidine 5'-triphosphate deaminase (DCD), C-terminal domain |
dUTPase | PF00692.25 | 1.5e-07 | 72–163 | dUTPase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: udgA (UDP-glucose 6-dehydrogenase UdgA), medium confidence from genomic context alone (score 611 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1699 pyrG |
CTP synthase | 927 | 920 | database:900 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 926 | 915 | database:900 |
Rv2697c dut |
deoxyuridine 5'-triphosphate nucleotidohydrolase | 930 | 908 | database:900 |
Rv0320 hyp |
hypothetical protein | 702 | 703 ctx | neighborhood:700 |
Rv3266c rmlD |
dTDP-4-dehydrorhamnose reductase | 645 | 645 | coexpression:645 |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 612 | 611 ctx | neighborhood:611 |
Rv0319 pcp |
pyrrolidone-carboxylate peptidase | 560 | 560 ctx | neighborhood:560 |
Rv3628 ppa |
inorganic pyrophosphatase | 494 | 465 | |
Rv2965c kdtB |
phosphopantetheine adenylyltransferase | 455 | 456 | coexpression:456 |
Rv0318c |
integral membrane protein | 413 | 413 ctx | neighborhood:410 |
Rv0382c pyrE |
orotate phosphoribosyltransferase | 463 | 248 | |
Rv2754c thyX |
thymidylate synthase ThyX | 517 | 156 | textmining:452 |
Rv2764c thyA |
thymidylate synthase ThyA | 486 | 154 | textmining:418 |
Rv3247c tmk |
thymidylate kinase | 477 | 123 | textmining:428 |
Rv0524 hemL |
glutamate-1-semialdehyde 2,1-aminomutase | 677 | 97 | textmining:658 |
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: deoxycytidine triphosphate deaminase
- MTBC0 PGAP product: dCTP deaminase
- Pfam (hmmscan --cut_ga): DCD PF22769.2 (E=8e-43), DCD_N PF06559.17 (E=5e-07), DCD_C PF22569.2 (E=4e-08), dUTPase PF00692.25 (E=1e-07)
- (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_214835.1)
- Domains: Pfam-A via hmmscan --cut_ga — DCD (PF22769.2), DCD_N (PF06559.17), DCD_C (PF22569.2), dUTPase (PF00692.25)
- 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
COG0717 - Curated reference: UniProt P9WP17 (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 —
23 functional partner(s); context anchor
udgA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000342|Rv0321|dcd MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRST