rplD Resolved · high auto-curated
H37Rv Rv0702 · MTBC0 mtbc0_000744 ·
223 aa · 805547–806218 (+) ·
RefSeq NP_215216.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L4 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L4 |
| Revised (this work) | 50S ribosomal protein L4. Pfam: Ribosomal_L4 (PF00573.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH85
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL4 |
| Curated function | One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome..; FUNCTION: Forms part of the polypeptide exit tunnel. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplD |
| eggNOG description | 50S ribosomal protein L4 |
| Orthologous group | COG0088 |
| KEGG orthology |
K02926
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (55) |
GO:0003674, GO:0003676, GO:0003723, GO:0003735, GO:0005198, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840 +43 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 | 1.051 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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_L4 | PF00573.28 | 2.6e-67 | 24–209 | Ribosomal protein L4/L1 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplC (50S ribosomal protein L3), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 ctx | neighborhood:882 cooccurence:717 coexpression:975 experimental:999 database:585 textmining:924 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 | coexpression:863 experimental:999 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 | coexpression:902 experimental:999 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 1000 | coexpression:932 experimental:999 database:662 textmining:587 |
Rv0714 rplN |
50S ribosomal protein L14 | 999 | 1000 | coexpression:958 experimental:999 database:571 textmining:687 |
Rv0709 rpmC |
50S ribosomal protein L29 | 999 | 1000 ctx | neighborhood:739 coexpression:957 experimental:999 database:658 |
Rv0721 rpsE |
30S ribosomal protein S5 | 999 | 1000 | coexpression:967 experimental:999 database:844 textmining:597 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 | coexpression:848 experimental:999 database:844 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 1000 | coexpression:970 experimental:999 database:571 textmining:811 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 | coexpression:884 experimental:999 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 1000 ctx | neighborhood:739 coexpression:886 experimental:999 database:844 |
Rv0715 rplX |
50S ribosomal protein L24 | 999 | 1000 | coexpression:967 experimental:999 database:623 |
Rv2412 rpsT |
30S ribosomal protein S20 | 999 | 1000 | coexpression:677 experimental:999 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:861 experimental:999 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 1000 ctx | neighborhood:739 cooccurence:648 coexpression:967 experimental:999 database:434 textmining:621 |
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 L4
- MTBC0 PGAP product: 50S ribosomal protein L4
- Pfam (hmmscan --cut_ga): Ribosomal_L4 PF00573.28 (E=3e-67)
- (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_215216.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L4 (PF00573.28)
- 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
COG0088 - Curated reference: UniProt P9WH85 (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
rplC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000744|Rv0702|rplD MAAQEQKTLKIDVKTPAGKVDGAIELPAELFDVPANIALMHQVVTAQRAAARQGTHSTKTRGEVSGGGRKPYRQKGTGRARQGSTRAPQFTGGGVVHGPKPRDYSQRTPKKMIAAALRGALSDRARNGRIHAITELVEGQNPSTKSARAFLASLTERKQVLVVIGRSDEAGAKSVRNLPGVHILAPDQLNTYDVLRADDVVFSVEALNAYIAANTTTSEEVSA