ogt Resolved · high auto-curated
H37Rv Rv1316c · MTBC0 mtbc0_001411 ·
165 aa · 1486162–1486659 (-) ·
RefSeq NP_215832.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methylated-DNA--protein-cysteine methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | methylated-DNA--protein-cysteine methyltransferase |
| Revised (this work) | Methylated-DNA--protein-cysteine methyltransferase. Pfam: Methyltransf_1N (PF02870.22), DNA_binding_1 (PF01035.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJW5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methylated-DNA--protein-cysteine methyltransferase |
| EC (curated) |
EC 2.1.1.63
|
| Curated function | Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction: the enzyme is irreversibly inactivated. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ogt |
| eggNOG description | Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated |
| Orthologous group | COG0350 |
| EC number |
EC 2.1.1.63
|
| KEGG orthology |
K00567
|
| Gene Ontology (41) |
GO:0003674, GO:0003824, GO:0003908, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006259, GO:0006281, GO:0006304, GO:0006307, GO:0006725 +29 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 | 0.221 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 2 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 |
|---|---|---|---|---|
Methyltransf_1N | PF02870.22 | 2.8e-16 | 2–71 | 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain |
DNA_binding_1 | PF01035.27 | 8.5e-38 | 75–154 | 6-O-methylguanine DNA methyltransferase, DNA binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: alkA (bifunctional regulatory protein/DNA repair enzyme AlkA), high confidence from genomic context alone (score 954 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1317c alkA |
bifunctional regulatory protein/DNA repair enzyme AlkA | 987 | 954 ctx | neighborhood:881 coexpression:567 textmining:742 |
Rv1318c |
adenylate cyclase | 785 | 786 ctx | neighborhood:786 |
Rv1210 tagA |
DNA-3-methyladenine glycosylase I TagA | 793 | 785 ctx | fusion:667 |
Rv1321 nucS |
endonuclease NucS | 724 | 637 ctx | neighborhood:634 |
Rv1322 hyp |
hypothetical protein | 492 | 491 ctx | neighborhood:478 |
Rv1319c |
adenylate cyclase | 466 | 466 ctx | neighborhood:466 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 594 | 459 ctx | neighborhood:459 |
Rv1320c |
adenylate cyclase | 450 | 450 ctx | neighborhood:450 |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 469 | 449 | experimental:418 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 480 | 446 | experimental:418 |
Rv2623 TB31.7 |
universal stress protein | 427 | 428 | coexpression:419 |
Rv1636 TB15.3 |
iron-regulated universal stress protein | 427 | 428 | coexpression:419 |
Rv1996 |
universal stress protein | 427 | 428 | coexpression:419 |
Rv2624c |
universal stress protein | 427 | 427 | coexpression:418 |
Rv3134c |
universal stress protein | 427 | 427 | coexpression:418 |
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: methylated-DNA--protein-cysteine methyltransferase
- MTBC0 PGAP product: methylated-DNA--protein-cysteine methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_1N PF02870.22 (E=3e-16), DNA_binding_1 PF01035.27 (E=9e-38)
- (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_215832.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_1N (PF02870.22), DNA_binding_1 (PF01035.27)
- 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
COG0350 - Curated reference: UniProt P9WJW5 (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 —
32 functional partner(s); context anchor
alkA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001411|Rv1316c|ogt MIHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTYEPSRTHWTPDPGAFSGAVDQLNAYFAGELTEFDVELDLRGTDFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEKSRAPADLTLFD