dgt Resolved · high auto-curated
H37Rv Rv2344c · MTBC0 mtbc0_002496 ·
431 aa · 2647207–2648502 (-) ·
RefSeq NP_216860.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | deoxyguanosine triphosphate triphosphohydrolase |
|---|---|
| MTBC0 PGAP re-annotation | deoxyguanosinetriphosphate triphosphohydrolase |
| Revised (this work) | Deoxyguanosinetriphosphate triphosphohydrolase. Pfam: HD (PF01966.29), HD_assoc (PF13286.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNY7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Deoxyguanosinetriphosphate triphosphohydrolase-like protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | dgt |
| eggNOG description | dGTPase family. Type 2 subfamily |
| Orthologous group | COG0232 |
| EC number |
EC 3.1.5.1
|
| KEGG orthology |
K01129
|
| KEGG pathways |
map00230
|
| Gene Ontology (78) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006163, GO:0006195, GO:0006203, GO:0006725, GO:0006753, GO:0006793 +66 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 | 0.285 · 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 |
|---|---|---|---|---|
HD | PF01966.29 | 3.5e-14 | 72–220 | HD domain |
HD_assoc | PF13286.12 | 8.3e-16 | 330–416 | Phosphohydrolase-associated domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dnaG (DNA primase), high confidence from genomic context alone (score 899 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2445c ndkA |
nucleoside diphosphate kinase | 904 | 905 | database:900 |
Rv3307 deoD |
purine nucleoside phosphorylase | 904 | 904 | database:900 |
Rv1617 pykA |
pyruvate kinase | 901 | 901 | database:900 |
Rv2343c dnaG |
DNA primase | 938 | 899 ctx | neighborhood:881 textmining:411 |
Rv2345 |
transmembrane protein | 787 | 787 ctx | neighborhood:785 |
Rv3859c gltB |
glutamate synthase large subunit | 544 | 545 ctx | neighborhood:544 |
Rv1307 atpH |
ATP synthase subunit b/delta | 440 | 441 | |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 430 | 430 | |
Rv1003 rsmI |
rRNA small subunit methyltransferase I | 426 | 426 | coexpression:416 |
Rv2230c |
GTP cyclohydrolase | 417 | 417 | |
Rv1658 argG |
argininosuccinate synthase | 406 | 407 | |
Rv0429c def |
polypeptide deformylase | 593 | 342 | textmining:408 |
Rv2362c recO |
DNA repair protein RecO | 684 | 285 | textmining:576 |
Rv2364c era |
GTPase Era | 487 | 153 | textmining:419 |
Rv3708c asd |
aspartate-semialdehyde dehydrogenase | 563 | 133 | textmining:518 |
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: deoxyguanosine triphosphate triphosphohydrolase
- MTBC0 PGAP product: deoxyguanosinetriphosphate triphosphohydrolase
- Pfam (hmmscan --cut_ga): HD PF01966.29 (E=4e-14), HD_assoc PF13286.12 (E=8e-16)
- (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_216860.1)
- Domains: Pfam-A via hmmscan --cut_ga — HD (PF01966.29), HD_assoc (PF13286.12)
- 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
COG0232 - Curated reference: UniProt P9WNY7 (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 —
22 functional partner(s); context anchor
dnaG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002496|Rv2344c|dgt MSASEHDPYDDFDRQRRVAEAPKTAGLPGTEGQYRSDFARDRARVLHSAALRRLADKTQVVGPREGDTPRTRLTHSLEVAQIGRGMAIGLGCDLDLVELAGLAHDIGHPPYGHNGERALDEVAASHGGFEGNAQNFRILTSLEPKVVDAQGLSAGLNLTRASLDAVTKYPWMRGDGLGSQRRKFGFYDDDRESAVWVRQGAPPERACLEAQVMDWADDVAYSVHDVEDGVVSERIDLRVLAAEEDAAALARLGEREFSRVSADELMAAARRLSRLPVVAAVGKYDATLSASVALKRLTSELVGRFASAAIATTRAAAGPGPLVRFRADLQVPDLVRAEVAVLKILALQFIMSDPRHLETQARQRERIHRVAHRLYSGAPQTLDPVYAAAFNTAADDAARLRVVVDQIASYTEGRLERIDADQLGVSRNALD