rplO Resolved · high auto-curated
H37Rv Rv0723 · MTBC0 mtbc0_000765 ·
146 aa · 819383–819823 (+) ·
RefSeq NP_215237.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L15 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L15 |
| Revised (this work) | 50S ribosomal protein L15. Pfam: Ribosomal_L27A (PF00828.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHD7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL15 |
| Curated function | Binds to the 23S rRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplO |
| eggNOG description | Binds to the 23S rRNA |
| Orthologous group | COG0200 |
| KEGG orthology |
K02876
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (28) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0005886, GO:0015934, GO:0016020 +16 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, 1 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_L27A | PF00828.26 | 1.0e-18 | 76–144 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplN (50S ribosomal protein L14), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0714 rplN |
50S ribosomal protein L14 | 999 | 1000 ctx | neighborhood:714 coexpression:875 experimental:999 database:635 textmining:456 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 1000 ctx | cooccurence:520 coexpression:745 experimental:999 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 ctx | cooccurence:579 coexpression:911 experimental:999 database:758 textmining:582 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 | coexpression:863 experimental:999 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 | coexpression:844 experimental:999 |
Rv0715 rplX |
50S ribosomal protein L24 | 999 | 1000 ctx | neighborhood:714 coexpression:887 experimental:999 database:546 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 1000 ctx | cooccurence:438 coexpression:968 experimental:999 textmining:470 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 | coexpression:865 experimental:999 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 1000 ctx | neighborhood:714 cooccurence:532 coexpression:906 experimental:999 database:635 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 ctx | cooccurence:502 coexpression:862 experimental:999 |
Rv0709 rpmC |
50S ribosomal protein L29 | 999 | 1000 | coexpression:969 experimental:999 database:635 |
Rv0721 rpsE |
30S ribosomal protein S5 | 999 | 1000 ctx | neighborhood:882 cooccurence:485 coexpression:976 experimental:999 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 1000 ctx | neighborhood:825 cooccurence:477 coexpression:964 experimental:999 |
Rv0704 rplB |
50S ribosomal protein L2 | 999 | 1000 ctx | cooccurence:412 coexpression:969 experimental:999 database:613 |
Rv0055 rpsR1 |
30S ribosomal protein S18 | 999 | 1000 | coexpression:733 experimental:999 |
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: 50S ribosomal protein L15
- MTBC0 PGAP product: 50S ribosomal protein L15
- Pfam (hmmscan --cut_ga): Ribosomal_L27A PF00828.26 (E=1e-18)
- (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_215237.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L27A (PF00828.26)
- 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
COG0200 - Curated reference: UniProt P9WHD7 (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 —
314 functional partner(s); context anchor
rplN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000765|Rv0723|rplO MTLKLHDLRPARGSKTARTRVGRGDGSKGKTAGRGTKGTRARKQVPVTFEGGQMPIHMRLPKLKGFRNRFRTEYEIVNVGDINRLFPQGGAVGVDDLVAKGAVRKNALVKVLGDGKLTAKVDVSAHKFSGSARAKITAAGGSATEL