rplE Resolved · high auto-curated
H37Rv Rv0716 · MTBC0 mtbc0_000758 ·
187 aa · 816252–816815 (+) ·
RefSeq NP_215230.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L5 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L5 |
| Revised (this work) | 50S ribosomal protein L5. Pfam: Ribosomal_L5 (PF00281.25), Ribosomal_L5_C (PF00673.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH83
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL5 |
| Curated function | This is one of the proteins that bind and probably mediate the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplE |
| eggNOG description | This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits |
| Orthologous group | COG0094 |
| KEGG orthology |
K02931
|
| 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 | 0.327 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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_L5 | PF00281.25 | 1.1e-26 | 31–87 | Ribosomal protein L5 |
Ribosomal_L5_C | PF00673.27 | 1.0e-38 | 91–184 | ribosomal L5P family C-terminus |
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) |
|---|---|---|---|---|
Rv0055 rpsR1 |
30S ribosomal protein S18 | 999 | 1000 | coexpression:733 experimental:999 |
Rv0704 rplB |
50S ribosomal protein L2 | 999 | 1000 ctx | cooccurence:748 coexpression:972 experimental:999 database:617 textmining:847 |
Rv2904c rplS |
50S ribosomal protein L19 | 999 | 1000 | coexpression:827 experimental:999 textmining:594 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 1000 ctx | neighborhood:746 cooccurence:749 coexpression:973 experimental:999 textmining:519 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:864 experimental:999 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 1000 ctx | cooccurence:609 coexpression:886 experimental:999 database:461 textmining:702 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 1000 ctx | cooccurence:732 coexpression:946 experimental:999 textmining:602 |
Rv0703 rplW |
50S ribosomal protein L23 | 999 | 1000 | coexpression:967 experimental:999 database:597 textmining:858 |
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 1000 ctx | cooccurence:607 coexpression:865 experimental:999 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 ctx | cooccurence:423 coexpression:864 experimental:999 |
Rv0714 rplN |
50S ribosomal protein L14 | 999 | 1000 ctx | neighborhood:881 cooccurence:747 coexpression:981 experimental:999 database:638 textmining:777 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 | coexpression:860 experimental:999 textmining:579 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 ctx | cooccurence:663 coexpression:960 experimental:999 database:620 textmining:721 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 | coexpression:836 experimental:999 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 1000 ctx | cooccurence:763 coexpression:755 experimental:999 textmining:592 |
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 L5
- MTBC0 PGAP product: 50S ribosomal protein L5
- Pfam (hmmscan --cut_ga): Ribosomal_L5 PF00281.25 (E=1e-26), Ribosomal_L5_C PF00673.27 (E=1e-38)
- (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_215230.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L5 (PF00281.25), Ribosomal_L5_C (PF00673.27)
- 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
COG0094 - Curated reference: UniProt P9WH83 (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 —
245 functional partner(s); context anchor
rplB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000758|Rv0716|rplE MTTAQKVQPRLKERYRSEIRDALRKQFGYGNVMQIPTVTKVVVNMGVGEAARDAKLINGAVNDLALITGQKPEVRRARKSIAQFKLREGMPVGVRVTLRGDRMWEFLDRLTSIALPRIRDFRGLSPKQFDGVGNYTFGLAEQAVFHEVDVDKIDRVRGMDINVVTSAATDDEGRALLRALGFPFKEN