udgB Resolved · high auto-curated
H37Rv Rv1259 · MTBC0 - ·
299 aa · 1407339–1408238 (+) ·
RefSeq NP_215775.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | uracil DNA glycosylase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Uracil DNA glycosylase. Pfam: UDG (PF03167.26). |
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 |
P9WM53
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Type-5 uracil-DNA glycosylase |
| EC (curated) |
EC 3.2.2.-
|
| Curated function | DNA glycosylase with broad substrate specificity. Can remove uracil from double-stranded DNA containing either a U/G, U/A, U/C or U/T base pair. Can also excise ethenocytosine and hypoxanthine from double-stranded DNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | udgB |
| eggNOG description | Uracil-DNA glycosylase |
| Orthologous group | COG1573 |
| EC number |
EC 3.2.2.27
|
| KEGG orthology |
K21929
|
| KEGG pathways |
map03410
|
| Gene Ontology (37) |
GO:0003674, GO:0003824, GO:0004844, GO:0005488, GO:0006139, GO:0006259, GO:0006281, GO:0006284, GO:0006725, GO:0006807, GO:0006950, GO:0006974 +25 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 | 0.612 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
UDG | PF03167.26 | 7.6e-25 | 120–292 | Uracil DNA glycosylase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1260 (oxidoreductase), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1260 |
oxidoreductase | 882 | 883 ctx | neighborhood:881 |
Rv3073c hyp |
hypothetical protein | 625 | 625 ctx | fusion:570 |
Rv1258c tap |
multidrug-efflux transporter | 595 | 595 ctx | neighborhood:585 |
Rv1257c |
oxidoreductase | 588 | 588 ctx | neighborhood:585 |
Rv3421c tsaB hyp |
hypothetical protein | 540 | 541 | coexpression:503 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 491 | 492 | coexpression:478 |
Rv2478c hyp |
hypothetical protein | 465 | 466 | experimental:447 |
Rv0054 ssb |
single-strand DNA-binding protein | 465 | 466 | experimental:447 |
Rv1256c cyp130 |
cytochrome P450 Cyp130 | 438 | 438 ctx | neighborhood:425 |
Rv1255c |
HTH-type transcriptional regulator | 427 | 427 ctx | neighborhood:425 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 421 | 421 | |
Rv3206c moeB1 |
adenylyltransferase/sulfurtransferase MoeZ | 762 | 349 | textmining:651 |
Rv0670 end |
endonuclease IV | 630 | 235 | textmining:537 |
Rv3913 trxB2 |
thioredoxin reductase | 512 | 98 | textmining:482 |
Rv2674 msrB |
peptide methionine sulfoxide reductase MsrB | 662 | 97 | textmining:642 |
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): uracil DNA glycosylase
- Pfam (hmmscan --cut_ga): UDG PF03167.26 (E=8e-25)
- (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_215775.1)
- Domains: Pfam-A via hmmscan --cut_ga — UDG (PF03167.26)
- 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
COG1573 - Curated reference: UniProt P9WM53 (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 —
21 functional partner(s); context anchor
Rv1260 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1259|udgB MNIAAESSAKPVWGPPNFCAAAARMQDVRVLMHPKTGRAFRSPVEPGSGWPGDPATPQTPVAADAAQVSALAGGAGSICELNALISVCRACPRLVSWREEVAVVKRRAFADQPYWGRPVPGWGSKRPRLLILGLAPAAHGANRTGRMFTGDRSGDQLYAALHRAGLVNSPVSVDAADGLRANRIRITAPVRCAPPGNSPTPAERLTCSPWLNAEWRLVSDHIRAIVALGGFAWQVALRLAGASGTPKPRFGHGVVTELGAGVRLLGCYHPSQQNMFTGRLTPTMLDDIFREAKKLAGIE