mutT3 Resolved · high auto-curated
H37Rv Rv0413 · MTBC0 - ·
217 aa · 499713–500366 (+) ·
RefSeq NP_214927.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 8-oxo-dGTP diphosphatase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 8-oxo-dGTP diphosphatase. Pfam: NUDIX (PF00293.35). |
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 |
P9WIX9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative 8-oxo-dGTP diphosphatase 3 |
| EC (curated) |
EC 3.6.1.55
|
| Curated function | May be involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine, 8-oxo-dGTP) from DNA and the nucleotide pool. 8-oxo-dGTP is inserted opposite dA and dC residues of template DNA with almost equal efficiency thus leading to A.T to G.C transversions. MutT specifically degrades 8-oxo-dGTP to the monophosphate (By similarity). |
UniProt still lists this protein as Putative 8-oxo-dGTP diphosphatase 3; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | mutT3 |
| eggNOG description | Belongs to the NUDIX hydrolase family |
| Orthologous group | COG0494 |
| EC number |
EC 3.6.1.55
|
| KEGG orthology |
K03574
|
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 | 1.45 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
NUDIX | PF00293.35 | 1.9e-17 | 45–155 | NUDIX domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glnH (glutamine-binding lipoprotein GlnH), medium confidence from genomic context alone (score 644 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3282 hyp |
hypothetical protein | 823 | 823 ctx | fusion:809 |
Rv0411c glnH |
glutamine-binding lipoprotein GlnH | 644 | 644 ctx | neighborhood:635 |
Rv0410c pknG |
serine/threonine-protein kinase PknG | 738 | 640 ctx | neighborhood:635 |
Rv0412c glnX |
membrane protein | 640 | 640 ctx | neighborhood:635 |
Rv0531 |
membrane protein | 456 | 457 ctx | cooccurence:406 |
Rv0904c accD3 |
acetyl-CoAcarboxylase carboxyl transferase subunit beta | 427 | 345 | |
Rv3251c rubA |
rubredoxin RubA | 494 | 46 | textmining:492 |
Rv0097 |
oxidoreductase | 411 | 44 | textmining:410 |
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): 8-oxo-dGTP diphosphatase
- Pfam (hmmscan --cut_ga): NUDIX PF00293.35 (E=2e-17)
- (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_214927.1)
- Domains: Pfam-A via hmmscan --cut_ga — NUDIX (PF00293.35)
- 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
COG0494 - Curated reference: UniProt P9WIX9 (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 —
8 functional partner(s); context anchor
glnH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0413|mutT3 MPSCPPAYSEQVRGDGDGWVVSDSGVAYWGRYGAAGLLLRAPRPDGTPAVLLQHRALWSHQGGTWGLPGGARDSHETPEQTAVRESSEEAGLSAERLEVRATVVTAEVCGVDDTHWTYTTVVADAGELLDTVPNRESAELRWVAENEVADLPLHPGFAASWQRLRTAPATVPLARCDERRQRLPRTIQIEAGVFLWCTPGDADQAPSPLGRRISSLL