rnpA Resolved · high auto-curated
H37Rv Rv3923c · MTBC0 - ·
125 aa · 4410412–4410789 (-) ·
RefSeq NP_218440.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease P protein component |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Ribonuclease P protein component. Pfam: Ribonuclease_P (PF00825.25). |
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 |
P9WGZ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease P protein component |
| EC (curated) |
EC 3.1.26.5
|
| Curated function | RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rnpA |
| eggNOG description | RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme |
| Orthologous group | COG0594 |
| EC number |
EC 3.1.26.5
|
| KEGG orthology |
K03536
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.739 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Ribonuclease_P | PF00825.25 | 8.5e-22 | 12–117 | Ribonuclease P |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: yidD (membrane protein insertion efficiency factor), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3922c yidD |
membrane protein insertion efficiency factor | 999 | 996 ctx | neighborhood:881 coexpression:968 textmining:885 |
Rv3921c yidC |
membrane protein insertase YidC | 997 | 993 ctx | neighborhood:881 coexpression:947 textmining:683 |
Rv3920c hyp |
hypothetical protein | 961 | 960 ctx | neighborhood:792 coexpression:814 |
Rv3924c rpmH |
50S ribosomal protein L34 | 994 | 936 ctx | neighborhood:816 coexpression:667 textmining:923 |
Rv0682 rpsL |
30S ribosomal protein S12 | 920 | 921 | coexpression:921 |
Rv0702 rplD |
50S ribosomal protein L4 | 929 | 914 | coexpression:914 |
Rv0701 rplC |
50S ribosomal protein L3 | 914 | 902 | coexpression:902 |
Rv0719 rplF |
50S ribosomal protein L6 | 900 | 900 | coexpression:900 |
Rv1297 rho |
transcription termination factor Rho | 902 | 873 | coexpression:869 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 874 | 869 | coexpression:869 |
Rv1630 rpsA |
30S ribosomal protein S1 | 868 | 855 | coexpression:847 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 859 | 841 | coexpression:840 |
Rv0704 rplB |
50S ribosomal protein L2 | 846 | 839 | coexpression:839 |
Rv0703 rplW |
50S ribosomal protein L23 | 833 | 833 | coexpression:833 |
Rv0684 fusA1 |
elongation factor G | 805 | 806 | coexpression:806 |
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): ribonuclease P protein component
- Pfam (hmmscan --cut_ga): Ribonuclease_P PF00825.25 (E=9e-22)
- (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_218440.3)
- Domains: Pfam-A via hmmscan --cut_ga — Ribonuclease_P (PF00825.25)
- 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
COG0594 - Curated reference: UniProt P9WGZ3 (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 —
135 functional partner(s); context anchor
yidD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3923c|rnpA MIATPGLFAVLRARNRMRRSADFETTVKHGMRTVRSDMVVYWWRGSGGGPRVGLIIAKSVGSAVERHRVARRLRHVAGSIVKELHPSDHVVIRALPSSRHVSSARLEQQLRCGLRRAVELAGSDR