rplW Resolved · high auto-curated
H37Rv Rv0703 · MTBC0 mtbc0_000745 ·
100 aa · 806218–806520 (+) ·
RefSeq NP_215217.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L23 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L23 |
| Revised (this work) | 50S ribosomal protein L23. Pfam: Ribosomal_L23 (PF00276.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHB9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL23 |
| Curated function | One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplW |
| eggNOG description | One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome |
| Orthologous group | COG0089 |
| KEGG orthology |
K02892
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (76) |
GO:0000027, GO:0003674, GO:0003676, GO:0003723, GO:0003735, GO:0005198, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +64 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, 3 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_L23 | PF00276.26 | 5.1e-31 | 9–91 | Ribosomal protein L23 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplB (50S ribosomal protein L2), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 1000 | coexpression:904 experimental:999 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 | coexpression:875 experimental:999 |
Rv2904c rplS |
50S ribosomal protein L19 | 999 | 1000 | coexpression:871 experimental:999 |
Rv0704 rplB |
50S ribosomal protein L2 | 999 | 1000 ctx | neighborhood:776 coexpression:995 experimental:999 database:571 textmining:845 |
Rv0055 rpsR1 |
30S ribosomal protein S18 | 999 | 1000 | coexpression:734 experimental:999 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 1000 ctx | cooccurence:445 coexpression:963 experimental:999 database:404 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:861 experimental:999 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 1000 ctx | neighborhood:739 coexpression:995 experimental:999 textmining:823 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 1000 ctx | neighborhood:739 coexpression:968 experimental:999 database:652 textmining:528 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 1000 | coexpression:967 experimental:999 database:597 textmining:858 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 | coexpression:863 experimental:999 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 | coexpression:920 experimental:999 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 1000 ctx | neighborhood:739 cooccurence:406 coexpression:894 experimental:999 textmining:429 |
Rv0715 rplX |
50S ribosomal protein L24 | 999 | 1000 | coexpression:971 experimental:999 database:818 textmining:594 |
Rv0721 rpsE |
30S ribosomal protein S5 | 999 | 1000 | coexpression:957 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 L23
- MTBC0 PGAP product: 50S ribosomal protein L23
- Pfam (hmmscan --cut_ga): Ribosomal_L23 PF00276.26 (E=5e-31)
- (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_215217.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L23 (PF00276.26)
- 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
COG0089 - Curated reference: UniProt P9WHB9 (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 —
209 functional partner(s); context anchor
rplB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000745|Rv0703|rplW MATLADPRDIILAPVISEKSYGLLDDNVYTFLVRPDSNKTQIKIAVEKIFAVKVASVNTANRQGKRKRTRTGYGKRKSTKRAIVTLAPGSRPIDLFGAPA