ung Resolved · high auto-curated
H37Rv Rv2976c · MTBC0 mtbc0_003161 ·
227 aa · 3353244–3353927 (-) ·
RefSeq NP_217492.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | uracil-DNA glycosylase |
|---|---|
| MTBC0 PGAP re-annotation | uracil-DNA glycosylase |
| 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.
Curated reference (UniProt)
| UniProt |
P9WFQ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uracil-DNA glycosylase |
| EC (curated) |
EC 3.2.2.27
|
| Curated function | Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ung |
| eggNOG description | Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine |
| Orthologous group | COG0692 |
| EC number |
EC 3.2.2.27
|
| KEGG orthology |
K03648
|
| KEGG pathways |
map03410, map05340
|
| Gene Ontology (34) |
GO:0003674, GO:0003824, GO:0004844, GO:0006139, GO:0006259, GO:0006281, GO:0006284, GO:0006285, GO:0006725, GO:0006807, GO:0006950, GO:0006974 +22 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 | 0.271 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
UDG | PF03167.26 | 1.9e-15 | 57–214 | Uracil DNA glycosylase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: thiL (thiamine-monophosphate kinase), high confidence from genomic context alone (score 852 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2977c thiL |
thiamine-monophosphate kinase | 851 | 852 ctx | neighborhood:836 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 852 | 807 | database:743 |
Rv2979c |
resolvase | 737 | 737 ctx | neighborhood:721 |
Rv2978c tnpB |
transposase | 730 | 729 ctx | neighborhood:721 |
Rv2980 hyp |
hypothetical protein | 728 | 728 ctx | neighborhood:728 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 638 | 616 | experimental:457 |
Rv2116 lppK |
lipoprotein LppK | 636 | 613 | experimental:457 |
Rv2192c trpD |
anthranilate phosphoribosyltransferase | 592 | 592 ctx | fusion:555 |
Rv3674c nth |
endonuclease III | 613 | 571 ctx | fusion:508 |
Rv0670 end |
endonuclease IV | 566 | 434 | |
Rv2737c recA |
recombinase A | 500 | 345 | |
Rv2467 pepN |
aminopeptidase PepN | 591 | 294 | textmining:446 |
Rv2697c dut |
deoxyuridine 5'-triphosphate nucleotidohydrolase | 442 | 271 | |
Rv1080c greA |
transcription elongation factor GreA | 428 | 197 | |
Rv3752c tadA |
cytidine/deoxycytidylate deaminase | 434 | 190 |
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: uracil-DNA glycosylase
- MTBC0 PGAP product: uracil-DNA glycosylase
- Pfam (hmmscan --cut_ga): UDG PF03167.26 (E=2e-15)
- (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_217492.1)
- 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
COG0692 - Curated reference: UniProt P9WFQ9 (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 —
19 functional partner(s); context anchor
thiL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003161|Rv2976c|ung MTARPLSELVERGWAAALEPVADQVAHMGQFLRAEIAAGRRYLPAGSNVLRAFTFPFDNVRVLIVGQDPYPTPGHAVGLSFSVAPDVRPWPRSLANIFDEYTADLGYPLPSNGDLTPWAQRGVLLLNRVLTVRPSNPASHRGKGWEAVTECAIRALAARAAPLVAILWGRDASTLKPMLAAGNCVAIESPHPSPLSASRGFFGSRPFSRANELLVGMGAEPIDWRLP