rplT Resolved · high auto-curated
H37Rv Rv1643 · MTBC0 mtbc0_001752 ·
129 aa · 1865205–1865594 (+) ·
RefSeq NP_216159.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L20 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L20 |
| Revised (this work) | 50S ribosomal protein L20. Pfam: Ribosomal_L20 (PF00453.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHC5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL20 |
| Curated function | Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplT |
| eggNOG description | Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit |
| Orthologous group | COG0292 |
| KEGG orthology |
K02887
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (46) |
GO:0000027, GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0005886, GO:0006996 +34 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_L20 | PF00453.24 | 1.7e-41 | 3–109 | Ribosomal protein L20 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplX (50S ribosomal protein L24), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0709 rpmC |
50S ribosomal protein L29 | 999 | 1000 | coexpression:815 experimental:999 |
Rv0721 rpsE |
30S ribosomal protein S5 | 999 | 1000 | coexpression:831 experimental:999 textmining:596 |
Rv0715 rplX |
50S ribosomal protein L24 | 999 | 1000 ctx | cooccurence:442 coexpression:795 experimental:999 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 1000 | coexpression:840 experimental:999 |
Rv2412 rpsT |
30S ribosomal protein S20 | 999 | 1000 | coexpression:683 experimental:999 textmining:422 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 | coexpression:839 experimental:999 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 1000 | coexpression:853 experimental:999 textmining:688 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 | coexpression:855 experimental:999 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 1000 | coexpression:803 experimental:999 textmining:545 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 | coexpression:902 experimental:999 textmining:687 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 | coexpression:862 experimental:999 textmining:733 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 ctx | neighborhood:800 coexpression:976 experimental:999 textmining:760 |
Rv0714 rplN |
50S ribosomal protein L14 | 999 | 1000 | coexpression:856 experimental:999 textmining:593 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 | coexpression:830 experimental:999 textmining:850 |
Rv0703 rplW |
50S ribosomal protein L23 | 999 | 1000 | coexpression:853 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 L20
- MTBC0 PGAP product: 50S ribosomal protein L20
- Pfam (hmmscan --cut_ga): Ribosomal_L20 PF00453.24 (E=2e-41)
- (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_216159.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L20 (PF00453.24)
- 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
COG0292 - Curated reference: UniProt P9WHC5 (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 —
222 functional partner(s); context anchor
rplX - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001752|Rv1643|rplT MARVKRAVNAHKKRRSILKASRGYRGQRSRLYRKAKEQQLHSLNYAYRDRRARKGEFRKLWIARINAAARLNDITYNRLIQGLKAAGVEVDRKNLADIAISDPAAFTALVDVARAALPEDVNAPSGEAA