end Resolved · high auto-curated
H37Rv Rv0670 · MTBC0 mtbc0_000709 ·
252 aa · 773878–774636 (+) ·
RefSeq NP_215184.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | endonuclease IV |
|---|---|
| MTBC0 PGAP re-annotation | deoxyribonuclease IV |
| Revised (this work) | Deoxyribonuclease IV. Pfam: AP_endonuc_2 (PF01261.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ13
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable endonuclease 4 |
| EC (curated) |
EC 3.1.21.2
|
| Curated function | Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic (AP) sites, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | nfo |
| eggNOG description | Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin |
| Orthologous group | COG0648 |
| EC number |
EC 3.1.21.2
|
| KEGG orthology |
K01151
|
| KEGG pathways |
map03410
|
| Gene Ontology (31) |
GO:0003674, GO:0003824, GO:0003906, GO:0006139, GO:0006259, GO:0006281, GO:0006284, GO:0006725, GO:0006807, GO:0006950, GO:0006974, GO:0008081 +19 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) pseudogene candidate
| pN/pS | 1.348 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 7.70% of strains (11179) · 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 |
|---|---|---|---|---|
AP_endonuc_2 | PF01261.31 | 3.1e-43 | 14–248 | Xylose isomerase-like TIM barrel |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqP (lipoprotein LpqP), high confidence from genomic context alone (score 844 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0671 lpqP |
lipoprotein LpqP | 844 | 844 ctx | neighborhood:835 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 951 | 826 | experimental:825 textmining:732 |
Rv0672 fadE8 |
acyl-CoA dehydrogenase FadE8 | 769 | 769 ctx | neighborhood:768 |
Rv0674 hyp |
hypothetical protein | 766 | 766 ctx | neighborhood:764 |
Rv0673 echA4 |
enoyl-CoA hydratase EchA4 | 766 | 766 ctx | neighborhood:764 |
Rv0675 echA5 |
enoyl-CoA hydratase EchA5 | 765 | 765 ctx | neighborhood:764 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 622 | 599 ctx | neighborhood:544 |
Rv0669c |
neutral ceramidase | 577 | 576 ctx | neighborhood:558 |
Rv1156 hyp |
hypothetical protein | 605 | 562 | experimental:441 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 545 | 545 ctx | neighborhood:544 |
Rv3010c pfkA |
6-phosphofructokinase | 509 | 510 | coexpression:494 |
Rv2529 hyp |
hypothetical protein | 547 | 486 | experimental:462 |
Rv0114 gmhB |
D-glycero-alpha-D-manno-heptose-1,7-bisphosphate 7-phosphatase | 530 | 483 | |
Rv3674c nth |
endonuclease III | 768 | 480 | experimental:441 textmining:572 |
Rv1870c hyp |
hypothetical protein | 530 | 480 | experimental:441 |
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: endonuclease IV
- MTBC0 PGAP product: deoxyribonuclease IV
- Pfam (hmmscan --cut_ga): AP_endonuc_2 PF01261.31 (E=3e-43)
- (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_215184.1)
- Domains: Pfam-A via hmmscan --cut_ga — AP_endonuc_2 (PF01261.31)
- 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
COG0648 - Curated reference: UniProt P9WQ13 (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 —
46 functional partner(s); context anchor
lpqP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000709|Rv0670|end MLIGSHVSPTDPLAAAEAEGADVVQIFLGNPQSWKAPKPRDDAAALKAATLPIYVHAPYLINLASANNRVRIPSRKILQETCAAAADIGAAAVIVHGGHVADDNDIDKGFQRWRKALDRLETEVPVYLENTAGGDHAMARRFDTIARLWDVIGDTGIGFCLDTCHTWAAGEALTDAVDRIKAITGRIDLVHCNDSRDEAGSGRDRHANLGSGQIDPDLLVAAVKAAGAPVICETADQGRKDDIAFLRERTGS