rplU Resolved · high auto-curated
H37Rv Rv2442c · MTBC0 mtbc0_002601 ·
104 aa · 2764295–2764609 (-) ·
RefSeq NP_216958.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L21 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L21 |
| Revised (this work) | 50S ribosomal protein L21. Pfam: Ribosomal_L21p (PF00829.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHC3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL21 |
| Curated function | This protein binds to 23S rRNA in the presence of protein bL20. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplU |
| eggNOG description | This protein binds to 23S rRNA in the presence of protein L20 |
| Orthologous group | COG0261 |
| KEGG orthology |
K02888
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (11) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 0 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_L21p | PF00829.27 | 1.2e-32 | 5–103 | Ribosomal prokaryotic L21 protein |
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) |
|---|---|---|---|---|
Rv0634B rpmG2 |
50S ribosomal protein L33 | 999 | 1000 | coexpression:733 experimental:999 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 999 | 1000 | coexpression:833 experimental:999 textmining:650 |
Rv1298 rpmE |
50S ribosomal protein L31 | 999 | 1000 | coexpression:841 experimental:999 |
Rv2441c rpmA |
50S ribosomal protein L27 | 999 | 1000 ctx | neighborhood:869 coexpression:976 experimental:999 textmining:513 |
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 | coexpression:849 experimental:999 |
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 | coexpression:852 experimental:999 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 1000 | coexpression:864 experimental:999 textmining:441 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 1000 | coexpression:944 experimental:999 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 | coexpression:862 experimental:999 textmining:513 |
Rv0722 rpmD |
50S ribosomal protein L30 | 999 | 1000 | coexpression:817 experimental:999 |
Rv0056 rplI |
50S ribosomal protein L9 | 999 | 1000 | coexpression:849 experimental:999 textmining:486 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 | coexpression:851 experimental:999 |
Rv0723 rplO |
50S ribosomal protein L15 | 999 | 1000 | coexpression:826 experimental:999 |
Rv0706 rplV |
50S ribosomal protein L22 | 999 | 1000 | coexpression:860 experimental:999 |
Rv3459c rpsK |
30S ribosomal protein S11 | 999 | 1000 | coexpression:863 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 L21
- MTBC0 PGAP product: 50S ribosomal protein L21
- Pfam (hmmscan --cut_ga): Ribosomal_L21p PF00829.27 (E=1e-32)
- (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_216958.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L21p (PF00829.27)
- 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
COG0261 - Curated reference: UniProt P9WHC3 (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 —
297 functional partner(s); context anchor
rpmA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002601|Rv2442c|rplU MMATYAIVKTGGKQYKVAVGDVVKVEKLESEQGEKVSLPVALVVDGATVTTDAKALAKVAVTGEVLGHTKGPKIRIHKFKNKTGYHKRQGHRQQLTVLKVTGIA