Rv1321 Resolved · high auto-curated
H37Rv Rv1321 · MTBC0 - ·
226 aa · 1484279–1484959 (+) ·
RefSeq NP_215837.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | endonuclease NucS |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Endonuclease NucS. Pfam: NucS_N (PF21003.3), NucS_C (PF01939.22). |
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 |
P9WIY5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Endonuclease NucS |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Cleaves both 3' and 5' ssDNA extremities of branched DNA structures. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | nucS |
| eggNOG description | Cleaves both 3' and 5' ssDNA extremities of branched DNA structures |
| Orthologous group | COG1637 |
| KEGG orthology |
K07503
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
NucS_N | PF21003.3 | 2.7e-43 | 1–99 | Endonuclease NucS N-terminal PH-like domain |
NucS_C | PF01939.22 | 6.0e-53 | 106–226 | Endonuclease NucS C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: whiB1 (transcriptional regulator WhiB1), high confidence from genomic context alone (score 736 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1322 hyp |
hypothetical protein | 959 | 888 ctx | neighborhood:849 textmining:649 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 735 | 736 ctx | cooccurence:732 |
Rv1830 |
HTH-type transcriptional regulator | 734 | 735 ctx | cooccurence:731 |
Rv1318c |
adenylate cyclase | 723 | 724 ctx | neighborhood:724 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 722 | 723 ctx | cooccurence:720 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 714 | 714 ctx | cooccurence:713 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 691 | 692 ctx | cooccurence:689 |
Rv1317c alkA |
bifunctional regulatory protein/DNA repair enzyme AlkA | 715 | 682 ctx | neighborhood:678 |
Rv3195 hyp |
hypothetical protein | 658 | 659 ctx | cooccurence:657 |
Rv1440 secG |
protein-export membrane protein SecG | 639 | 639 ctx | cooccurence:634 |
Rv1316c ogt |
methylated-DNA--protein-cysteine methyltransferase | 724 | 637 ctx | neighborhood:634 |
Rv2699c hyp |
hypothetical protein | 636 | 637 ctx | cooccurence:633 |
Rv3332 nagA |
N-acetylglucosamine-6-phosphate deacetylase NagA | 617 | 618 ctx | fusion:549 |
Rv2708c hyp |
hypothetical protein | 611 | 611 ctx | cooccurence:610 |
Rv2413c hyp |
hypothetical protein | 711 | 607 ctx | cooccurence:598 |
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): endonuclease NucS
- Pfam (hmmscan --cut_ga): NucS_N PF21003.3 (E=3e-43), NucS_C PF01939.22 (E=6e-53)
- (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_215837.1)
- Domains: Pfam-A via hmmscan --cut_ga — NucS_N (PF21003.3), NucS_C (PF01939.22)
- 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
COG1637 - Curated reference: UniProt P9WIY5 (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 —
52 functional partner(s); context anchor
whiB1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1321| MSRVRLVIAQCTVDYIGRLTAHLPSARRLLLFKADGSVSVHADDRAYKPLNWMSPPCWLTEESGGQAPVWVVENKAGEQLRITIEGIEHDSSHELGVDPGLVKDGVEAHLQALLAEHIQLLGEGYTLVRREYMTAIGPVDLLCSDERGGSVAVEIKRRGEIDGVEQLTRYLELLNRDSVLAPVKGVFAAQQIKPQARILATDRGIRCLTLDYDTMRGMDSGEYRLF