mpg Resolved · high auto-curated
H37Rv Rv1688 · MTBC0 mtbc0_001796 ·
203 aa · 1924994–1925605 (+) ·
RefSeq NP_216204.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3-methyladenine DNA glycosylase |
|---|---|
| MTBC0 PGAP re-annotation | DNA-3-methyladenine glycosylase |
| Revised (this work) | DNA-3-methyladenine glycosylase. Pfam: Pur_DNA_glyco (PF02245.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJP7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative 3-methyladenine DNA glycosylase |
| EC (curated) |
EC 3.2.2.-
|
UniProt still lists this protein as Putative 3-methyladenine DNA glycosylase; 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 | mpg |
| eggNOG description | Belongs to the DNA glycosylase MPG family |
| Orthologous group | COG2094 |
| EC number |
EC 3.2.2.21
|
| KEGG orthology |
K03652
|
| KEGG pathways |
map03410
|
| Gene Ontology (31) |
GO:0003674, GO:0003824, GO:0003905, GO:0006139, GO:0006259, GO:0006281, GO:0006284, GO:0006725, GO:0006807, GO:0006950, GO:0006974, GO:0008150 +19 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 | 1.12 · 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 |
|---|---|---|---|---|
Pur_DNA_glyco | PF02245.22 | 1.4e-54 | 7–184 | Methylpurine-DNA glycosylase (MPG) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tyrS (tyrosine--tRNA ligase), high confidence from genomic context alone (score 872 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1689 tyrS |
tyrosine--tRNA ligase | 884 | 872 ctx | neighborhood:872 |
Rv1687c |
ABC transporter ATP-binding protein | 788 | 789 ctx | neighborhood:787 |
Rv1686c |
ABC transporter permease | 728 | 728 ctx | neighborhood:726 |
Rv1685c hyp |
hypothetical protein | 724 | 724 ctx | neighborhood:722 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 779 | 673 | database:661 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 566 | 566 ctx | neighborhood:544 |
Rv3859c gltB |
glutamate synthase large subunit | 550 | 529 ctx | neighborhood:529 |
Rv1317c alkA |
bifunctional regulatory protein/DNA repair enzyme AlkA | 535 | 172 | textmining:462 |
Rv3586 disA |
DNA integrity scanning protein DisA | 568 | 156 | textmining:510 |
Rv3674c nth |
endonuclease III | 479 | 104 | textmining:443 |
Rv0950c hyp |
hypothetical protein | 804 | 50 | textmining:803 |
Rv2891 hyp |
hypothetical protein | 658 | 47 | textmining:656 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 658 | 47 | textmining:656 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 801 | 44 | textmining:801 |
Rv3786c hyp |
hypothetical protein | 657 | 44 | textmining:656 |
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: 3-methyladenine DNA glycosylase
- MTBC0 PGAP product: DNA-3-methyladenine glycosylase
- Pfam (hmmscan --cut_ga): Pur_DNA_glyco PF02245.22 (E=1e-54)
- (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_216204.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pur_DNA_glyco (PF02245.22)
- 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
COG2094 - Curated reference: UniProt P9WJP7 (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 —
20 functional partner(s); context anchor
tyrS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001796|Rv1688|mpg MNAEELAIDPVAAAHRLLGATIAGRGVRAMVVEVEAYGGVPDGPWPDAAAHSYRGRNGRNDVMFGPPGRLYTYRSHGIHVCANVACGPDGTAAAVLLRAAAIEDGAELATSRRGQTVRAVALARGPGNLCAALGITMADNGIDLFDPSSPVRLRLNDTHRARSGPRVGVSQAADRPWRLWLTGRPEVSAYRRSSRAPARGASD