Rv0944 Resolved · high auto-curated
H37Rv Rv0944 · MTBC0 - ·
158 aa · 1053765–1054241 (+) ·
RefSeq NP_215459.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | formamidopyrimidine-DNA glycosylase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Formamidopyrimidine-DNA glycosylase. Pfam: H2TH (PF06831.20), zf-FPG_IleRS (PF06827.21). |
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 |
L0T864
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized formamidopyrimidine-DNA glycosylase-like protein |
UniProt still lists this protein as Uncharacterized formamidopyrimidine-DNA glycosylase-like protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | mutM1 |
| eggNOG description | Belongs to the FPG family |
| Orthologous group | COG0266 |
| EC number |
EC 3.2.2.23, EC 4.2.99.18
|
| KEGG orthology |
K10563
|
| 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 | 0.721 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 |
|---|---|---|---|---|
H2TH | PF06831.20 | 5.4e-18 | 11–91 | Formamidopyrimidine-DNA glycosylase H2TH domain |
zf-FPG_IleRS | PF06827.21 | 1.9e-07 | 115–143 | Zinc finger found in FPG and IleRS |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0945 (oxidoreductase), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2924c fpg |
formamidopyrimidine-DNA glycosylase | 946 | 926 | database:900 |
Rv0945 |
oxidoreductase | 976 | 883 ctx | neighborhood:881 textmining:808 |
Rv1629 polA |
DNA polymerase I | 864 | 815 | coexpression:790 |
Rv3297 nei |
endonuclease VIII | 968 | 766 ctx | cooccurence:766 textmining:870 |
Rv0943c |
monooxygenase | 924 | 620 ctx | neighborhood:618 textmining:808 |
Rv1903 |
membrane protein | 556 | 557 ctx | neighborhood:544 |
Rv2090 |
5'-3' exonuclease | 552 | 524 | coexpression:428 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 554 | 512 | coexpression:470 |
Rv1156 hyp |
hypothetical protein | 530 | 503 | coexpression:414 |
Rv3674c nth |
endonuclease III | 548 | 418 | coexpression:418 |
Rv1870c hyp |
hypothetical protein | 449 | 418 | coexpression:418 |
Rv2464c nei1 |
DNA glycosylase | 428 | 282 | |
Rv2737c recA |
recombinase A | 437 | 253 | |
Rv3589 mutY |
A/G-specific adenine glycosylase | 776 | 125 | textmining:755 |
Rv2926c hyp |
hypothetical protein | 526 | 73 | textmining:510 |
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): formamidopyrimidine-DNA glycosylase
- Pfam (hmmscan --cut_ga): H2TH PF06831.20 (E=5e-18), zf-FPG_IleRS PF06827.21 (E=2e-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_215459.1)
- Domains: Pfam-A via hmmscan --cut_ga — H2TH (PF06831.20), zf-FPG_IleRS (PF06827.21)
- 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
COG0266 - Curated reference: UniProt L0T864 (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
Rv0945 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0944| MAGTPQPRALGPDALDVSTDDLAGLLAGNTGRIKTVITDQKVIAGIGNAYSDEILHVAKISPFATAGKLSGAQLTCLHEAMASVLSDAVRRSVGQGAAMLKGEKRSGLRVHARTGLPCPVCGDTVREVSFADKSFQYCPTCQTGGKALADRRMSRLLK