rnj Resolved · high auto-curated
H37Rv Rv2752c · MTBC0 mtbc0_002929 ·
558 aa · 3086930–3088606 (-) ·
RefSeq NP_217268.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease J |
|---|---|
| MTBC0 PGAP re-annotation | ribonuclease J |
| Revised (this work) | Ribonuclease J. Pfam: Lactamase_B (PF00753.34), Lactamase_B_2 (PF12706.14), RNase_J_b_CASP (PF22505.2), RMMBL (PF07521.18), RNase_J_C (PF17770.8). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGZ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease J |
| EC (curated) |
EC 3.1.-.-, EC 3.5.2.6
|
| Curated function | An RNase that has 5'-3' exonuclease and possible endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay (By similarity). Has both beta-lactamase and RNase activity, but the physiological relevance of the beta-lactamase activity, i.e. whether it confers antibiotic resistance, has not been shown. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rnj |
| eggNOG description | An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay |
| Orthologous group | COG0595 |
| KEGG orthology |
K12574
|
| KEGG pathways |
map03018
|
| Gene Ontology (44) |
GO:0003674, GO:0003824, GO:0004518, GO:0004519, GO:0004521, GO:0004527, GO:0004532, GO:0004534, GO:0004540, GO:0006139, GO:0006364, GO:0006396 +32 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 | 0.983 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 10 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.32% of strains (465) · 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 |
|---|---|---|---|---|
Lactamase_B | PF00753.34 | 2.0e-09 | 29–182 | Metallo-beta-lactamase superfamily |
Lactamase_B_2 | PF12706.14 | 4.1e-11 | 58–172 | Beta-lactamase superfamily domain |
RNase_J_b_CASP | PF22505.2 | 2.6e-48 | 231–355 | Ribonuclease J, beta-CASP domain |
RMMBL | PF07521.18 | 3.4e-10 | 369–414 | Zn-dependent metallo-hydrolase RNA specificity domain |
RNase_J_C | PF17770.8 | 3.5e-12 | 461–558 | Ribonuclease J C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dapA (4-hydroxy-tetrahydrodipicolinate synthase), high confidence from genomic context alone (score 885 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 934 | 885 ctx | neighborhood:839 textmining:449 |
Rv2754c thyX |
thymidylate synthase ThyX | 866 | 796 ctx | neighborhood:766 |
Rv2756c hsdM |
type I restriction/modification system DNA methylase HsdM | 650 | 650 ctx | neighborhood:644 |
Rv2762c hyp |
hypothetical protein | 788 | 640 ctx | neighborhood:635 textmining:436 |
Rv3241c raiA hyp |
hypothetical protein | 580 | 574 ctx | cooccurence:452 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 533 | 534 | coexpression:518 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 533 | 534 | coexpression:518 |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 529 | 530 | coexpression:514 |
Rv3398c idsA1 |
multifunctional dimethylallyltransferase/geranyltranstransferase/farnesyltranstransferase | 527 | 528 | coexpression:512 |
Rv0989c grcC2 |
polyprenyl-diphosphate synthase GrcC | 526 | 527 | coexpression:511 |
Rv3459c rpsK |
30S ribosomal protein S11 | 512 | 512 | coexpression:407 |
Rv1295 thrC |
threonine synthase | 508 | 490 | coexpression:488 |
Rv0702 rplD |
50S ribosomal protein L4 | 484 | 484 | |
Rv0703 rplW |
50S ribosomal protein L23 | 492 | 434 | coexpression:416 |
Rv0704 rplB |
50S ribosomal protein L2 | 429 | 430 | coexpression:412 |
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: ribonuclease J
- MTBC0 PGAP product: ribonuclease J
- Pfam (hmmscan --cut_ga): Lactamase_B PF00753.34 (E=2e-09), Lactamase_B_2 PF12706.14 (E=4e-11), RNase_J_b_CASP PF22505.2 (E=3e-48), RMMBL PF07521.18 (E=3e-10), RNase_J_C PF17770.8 (E=4e-12)
- (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_217268.1)
- Domains: Pfam-A via hmmscan --cut_ga — Lactamase_B (PF00753.34), Lactamase_B_2 (PF12706.14), RNase_J_b_CASP (PF22505.2), RMMBL (PF07521.18), RNase_J_C (PF17770.8)
- 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
COG0595 - Curated reference: UniProt P9WGZ9 (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 —
48 functional partner(s); context anchor
dapA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002929|Rv2752c|rnj MDVDLPPPGPLTSGGLRVTALGGINEIGRNMTVFEHLGRLLIIDCGVLFPGHDEPGVDLILPDMRHVEDRLDDIEALVLTHGHEDHIGAIPFLLKLRPDIPVVGSKFTLALVAEKCREYRITPVFVEVREGQSTRHGVFECEYFAVNHSTPDALAIAVYTGAGTILHTGDIKFDQLPPDGRPTDLPGMSRLGDTGVDLLLCDSTNAEIPGVGPSESEVGPTLHRLIRGADGRVIVACFASNVDRVQQIIDAAVALGRRVSFVGRSMVRNMRVARQLGFLRVADSDLIDIAAAETMAPDQVVLITTGTQGEPMSALSRMSRGEHRSITLTAGDLIVLSSSLIPGNEEAVFGVIDALSKIGARVVTNAQARVHVSGHAYAGELLFLYNGVRPRNVMPVHGTWRMLRANAKLAASTGVPQESILLAENGVSVDLVAGKASISGAVPVGKMFVDGLIAGDVGDITLGERLILSSGFVAVTVVVRRGTGQPLAAPHLHSRGFSEDPKALEPAVRKVEAELESLVAANVTDPIRIAQGVRRTVGKWVGETYRRQPMIVPTVIEV