mutY Resolved · high auto-curated
H37Rv Rv3589 · MTBC0 mtbc0_003808 ·
304 aa · 4054170–4055084 (+) ·
RefSeq NP_218106.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | A/G-specific adenine glycosylase |
|---|---|
| MTBC0 PGAP re-annotation | A/G-specific adenine glycosylase |
| Revised (this work) | A/G-specific adenine glycosylase. Pfam: HhH-GPD (PF00730.32), HHH (PF00633.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ09
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Adenine DNA glycosylase |
| EC (curated) |
EC 3.2.2.31
|
| Curated function | Adenine glycosylase active on G:A and C:A mispairs, as well as processing 7,8-dihydro-8-oxoguanine:A (8-oxoG) mismatches. Minor activity against 8-oxoG:G and 8-oxo:T mismatches is also seen. Bind dsDNA oligonucleotides containing the above mismatches. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | mutY |
| eggNOG description | adenine glycosylase |
| Orthologous group | COG1194 |
| KEGG orthology |
K03575
|
| KEGG pathways |
map03410
|
| Gene Ontology (32) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006259, GO:0006281, GO:0006284, GO:0006725, GO:0006807, GO:0006950 +20 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 | 0.367 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.27% of strains (386) · clonal |
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 |
|---|---|---|---|---|
HhH-GPD | PF00730.32 | 1.2e-16 | 46–159 | HhH-GPD superfamily base excision DNA repair protein |
HHH | PF00633.30 | 6.2e-07 | 111–139 | Helix-hairpin-helix motif |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: canB (carbonic anhydrase), high confidence from genomic context alone (score 793 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 903 | 865 | experimental:428 database:771 |
Rv3588c canB |
carbonic anhydrase | 857 | 793 ctx | neighborhood:792 |
Rv3587c |
membrane protein | 721 | 721 ctx | neighborhood:713 |
Rv2116 lppK |
lipoprotein LppK | 490 | 422 | experimental:412 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 531 | 420 | experimental:412 |
Rv3674c nth |
endonuclease III | 939 | 382 | textmining:906 |
Rv1316c ogt |
methylated-DNA--protein-cysteine methyltransferase | 441 | 294 | |
Rv1537 dinX |
DNA polymerase IV | 609 | 210 | textmining:526 |
Rv1108c xseA |
exodeoxyribonuclease VII large subunit | 462 | 189 | |
Rv3585 radA |
DNA repair protein RadA | 418 | 177 | |
Rv3671c marP |
serine protease | 409 | 164 | |
Rv2191 hyp |
hypothetical protein | 479 | 157 | textmining:408 |
Rv2985 mutT1 |
8-oxo-dGTP diphosphatase | 651 | 140 | textmining:611 |
Rv2464c nei1 |
DNA glycosylase | 839 | 126 | textmining:824 |
Rv0944 fpg2 |
formamidopyrimidine-DNA glycosylase | 776 | 125 | textmining:755 |
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: A/G-specific adenine glycosylase
- MTBC0 PGAP product: A/G-specific adenine glycosylase
- Pfam (hmmscan --cut_ga): HhH-GPD PF00730.32 (E=1e-16), HHH PF00633.30 (E=6e-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_218106.1)
- Domains: Pfam-A via hmmscan --cut_ga — HhH-GPD (PF00730.32), HHH (PF00633.30)
- 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
COG1194 - Curated reference: UniProt P9WQ09 (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 —
50 functional partner(s); context anchor
canB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003808|Rv3589|mutY MPHILPEPSVTGPRHISDTNLLAWYQRSHRDLPWREPGVSPWQILVSEFMLQQTPAARVLAIWPDWVRRWPTPSATATASTADVLRAWGKLGYPRRAKRLHECATVIARDHNDVVPDDIEILVTLPGVGSYTARAVACFAYRQRVPVVDTNVRRVVARAVHGRADAGAPSVPRDHADVLALLPHRETAPEFSVALMELGATVCTARTPRCGLCPLDWCAWRHAGYPPSDGPPRRGQAYTGTDRQVRGRLLDVLRAAEFPVTRAELDVAWLTDTAQRDRALESLLADALVTRTVDGRFALPGEGF