rpsO Resolved · high auto-curated
H37Rv Rv2785c · MTBC0 - ·
89 aa · 3093479–3093748 (-) ·
RefSeq NP_217301.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S15 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 30S ribosomal protein S15. Pfam: Ribosomal_S15 (PF00312.28). |
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 |
P9WH55
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Small ribosomal subunit protein uS15 |
| Curated function | One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA..; FUNCTION: Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpsO |
| eggNOG description | Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome |
| Orthologous group | COG0184 |
| KEGG orthology |
K02956
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (25) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0005886, GO:0015935, GO:0016020, GO:0022626, GO:0022627, GO:0032991 +13 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 | 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 |
|---|---|---|---|---|
Ribosomal_S15 | PF00312.28 | 8.6e-36 | 8–88 | Ribosomal protein S15 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpmA (50S ribosomal protein L27), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 | coexpression:859 experimental:999 |
Rv2441c rpmA |
50S ribosomal protein L27 | 999 | 1000 ctx | cooccurence:601 coexpression:852 experimental:999 |
Rv1298 rpmE |
50S ribosomal protein L31 | 999 | 1000 | coexpression:865 experimental:999 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 999 | 1000 | coexpression:804 experimental:999 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 999 | 1000 | coexpression:727 experimental:999 |
Rv2442c rplU |
50S ribosomal protein L21 | 999 | 1000 | coexpression:822 experimental:999 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 | coexpression:859 experimental:999 database:925 |
Rv0056 rplI |
50S ribosomal protein L9 | 999 | 1000 | coexpression:775 experimental:999 |
Rv0722 rpmD |
50S ribosomal protein L30 | 999 | 1000 | coexpression:851 experimental:999 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 | coexpression:861 experimental:999 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 1000 ctx | cooccurence:415 coexpression:858 experimental:999 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 1000 | coexpression:848 experimental:999 database:844 |
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 ctx | cooccurence:511 coexpression:856 experimental:999 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 999 | 1000 | coexpression:853 experimental:999 database:844 |
Rv3459c rpsK |
30S ribosomal protein S11 | 999 | 1000 | coexpression:859 experimental:999 database:925 |
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): 30S ribosomal protein S15
- Pfam (hmmscan --cut_ga): Ribosomal_S15 PF00312.28 (E=9e-36)
- (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_217301.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_S15 (PF00312.28)
- 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
COG0184 - Curated reference: UniProt P9WH55 (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 —
266 functional partner(s); context anchor
rpmA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2785c|rpsO MALTAEQKKEILRSYGLHETDTGSPEAQIALLTKRIADLTEHLKVHKHDHHSRRGLLLLVGRRRRLIKYISQIDVERYRSLIERLGLRR