Rv2367c Resolved · high auto-curated
H37Rv Rv2367c · MTBC0 - ·
182 aa · 2648364–2648912 (-) ·
RefSeq NP_216883.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | endoribonuclease |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Endoribonuclease. Pfam: YbeY (PF02130.25). |
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 |
P9WGX9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Endoribonuclease YbeY |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | ybeY |
| eggNOG description | Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA |
| Orthologous group | COG0319 |
| KEGG orthology |
K07042
|
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 | 0.197 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
YbeY | PF02130.25 | 2.9e-38 | 17–153 | Endoribonuclease YbeY |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: phoH1 (phosphate starvation-inducible protein PhoH), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2368c phoH1 |
phosphate starvation-inducible protein PhoH | 996 | 996 ctx | neighborhood:881 coexpression:967 |
Rv2366c |
transmembrane protein | 988 | 988 ctx | neighborhood:882 coexpression:887 |
Rv2365c hyp |
hypothetical protein | 977 | 976 ctx | neighborhood:882 coexpression:807 |
Rv2364c era |
GTPase Era | 976 | 973 ctx | neighborhood:791 coexpression:877 |
Rv3846 sodA |
superoxide dismutase | 919 | 907 | experimental:903 |
Rv3456c rplQ |
50S ribosomal protein L17 | 896 | 891 | experimental:869 |
Rv2442c rplU |
50S ribosomal protein L21 | 886 | 880 | experimental:836 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 881 | 873 | experimental:870 |
Rv0640 rplK |
50S ribosomal protein L11 | 870 | 864 | experimental:860 |
Rv0723 rplO |
50S ribosomal protein L15 | 821 | 812 | experimental:796 |
Rv3443c rplM |
50S ribosomal protein L13 | 817 | 809 | experimental:796 |
Rv0715 rplX |
50S ribosomal protein L24 | 816 | 806 | experimental:796 |
Rv0701 rplC |
50S ribosomal protein L3 | 807 | 796 | experimental:791 |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 787 | 774 ctx | neighborhood:476 experimental:533 |
Rv2369c hyp |
hypothetical protein | 775 | 774 ctx | neighborhood:773 |
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): endoribonuclease
- Pfam (hmmscan --cut_ga): YbeY PF02130.25 (E=3e-38)
- (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_216883.1)
- Domains: Pfam-A via hmmscan --cut_ga — YbeY (PF02130.25)
- 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
COG0319 - Curated reference: UniProt P9WGX9 (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 —
129 functional partner(s); context anchor
phoH1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2367c| MREHLMSIEVANESGIDVSEAELVSVARFVIAKMDVNPCAELSMLLLDTAAMADLHMRWMDLPGPTDVMSFPMDELEPGGRPDAPEPGPSMLGDIVLCPEFAAEQAAAAGHSLGHELALLTIHGVLHLLGYDHAEPDEEKEMFALQDRLLEEWVADQVEAYQHDRQDEKDRRLLDKSRYFDL