tagA Resolved · high auto-curated
H37Rv Rv1210 · MTBC0 mtbc0_001298 ·
204 aa · 1361964–1362578 (+) ·
RefSeq NP_215726.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA-3-methyladenine glycosylase I TagA |
|---|---|
| MTBC0 PGAP re-annotation | DNA-3-methyladenine glycosylase I |
| Revised (this work) | DNA-3-methyladenine glycosylase I. Pfam: Adenine_glyco (PF03352.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05311
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable DNA-3-methyladenine glycosylase I TagA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | tag |
| eggNOG description | DNA-3-methyladenine glycosylase I |
| Orthologous group | COG2818 |
| EC number |
EC 3.2.2.20
|
| KEGG orthology |
K01246
|
| KEGG pathways |
map03410
|
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 | 0.167 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.38% of strains (555) · 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 |
|---|---|---|---|---|
Adenine_glyco | PF03352.19 | 7.6e-67 | 20–187 | Methyladenine glycosylase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: folP2 (dihydropteroate synthase), high confidence from genomic context alone (score 831 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1209 hyp |
hypothetical protein | 887 | 887 ctx | neighborhood:881 |
Rv1207 folP2 |
dihydropteroate synthase | 830 | 831 ctx | neighborhood:825 |
Rv1208 gpgS |
glucosyl-3-phosphoglycerate synthase | 826 | 827 ctx | neighborhood:825 |
Rv1316c ogt |
methylated-DNA--protein-cysteine methyltransferase | 793 | 785 ctx | fusion:667 |
Rv1211 hyp |
hypothetical protein | 949 | 756 ctx | neighborhood:755 textmining:803 |
Rv1206 fadD6 |
fatty-acid--CoA ligase FadD6 | 756 | 756 ctx | neighborhood:756 |
Rv1205 log hyp |
hypothetical protein | 558 | 559 ctx | neighborhood:559 |
Rv1629 polA |
DNA polymerase I | 693 | 446 | textmining:470 |
Rv0995 rimJ |
ribosomal-protein-alanine acetyltransferase RimJ | 446 | 446 ctx | cooccurence:417 |
Rv1657 argR |
arginine repressor | 426 | 427 | coexpression:400 |
Rv1537 dinX |
DNA polymerase IV | 611 | 241 | textmining:509 |
Rv1317c alkA |
bifunctional regulatory protein/DNA repair enzyme AlkA | 632 | 236 | textmining:539 |
Rv3056 dinP |
DNA polymerase IV 2 | 646 | 191 | textmining:581 |
Rv3589 mutY |
A/G-specific adenine glycosylase | 741 | 117 | textmining:719 |
Rv1638 uvrA |
excinuclease ABC subunit UvrA | 410 | 113 |
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: DNA-3-methyladenine glycosylase I TagA
- MTBC0 PGAP product: DNA-3-methyladenine glycosylase I
- Pfam (hmmscan --cut_ga): Adenine_glyco PF03352.19 (E=8e-67)
- (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_215726.1)
- Domains: Pfam-A via hmmscan --cut_ga — Adenine_glyco (PF03352.19)
- 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
COG2818 - Curated reference: UniProt O05311 (TrEMBL, unreviewed; 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 —
36 functional partner(s); context anchor
folP2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001298|Rv1210|tagA MSGDGLVRCPWAEVRPGPDAQLYRDYHDNEWGRPLYGRVALFERMSLEAFQSGLSWLIILRKRENFRRAFSGFDIDKIARYTDTDVRRLLADDGIVRNRAKIEATIANARAAADLGSSEDLSELLWSFAPPPRPRPVDGSEIPSVSTESKAMSRELKRRGFRFVGPTTAYALMQATGMVDDHIQACWVPTERPFDQPGCPMAAR