rplK Resolved · high auto-curated
H37Rv Rv0640 · MTBC0 mtbc0_000678 ·
142 aa · 738575–739003 (+) ·
RefSeq NP_215154.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L11 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L11 |
| Revised (this work) | 50S ribosomal protein L11. Pfam: Ribosomal_L11_N (PF03946.20), Ribosomal_L11 (PF00298.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHE5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL11 |
| Curated function | Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplK |
| eggNOG description | Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors |
| Orthologous group | COG0080 |
| KEGG orthology |
K02867
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (77) |
GO:0000027, GO:0003674, GO:0003676, GO:0003723, GO:0003735, GO:0005198, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737 +65 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 | 0.16 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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_L11_N | PF03946.20 | 8.0e-30 | 11–68 | Ribosomal protein L11, N-terminal domain |
Ribosomal_L11 | PF00298.25 | 2.1e-30 | 73–141 | Ribosomal protein L11, RNA binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplA (50S ribosomal protein L1), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 | coexpression:864 experimental:999 database:556 textmining:572 |
Rv0651 rplJ |
50S ribosomal protein L10 | 999 | 1000 | coexpression:859 experimental:997 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 999 | 1000 | coexpression:858 experimental:997 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:859 experimental:999 database:404 |
Rv0500B |
Rv0500B, len: 33 aa. Conserved hypothetical protein. Basic protein 18 of the 33 aa are Arg or Lys, with strong similarity to AL079345|SCE68_ | 999 | 999 | experimental:999 |
Rv0641 rplA |
50S ribosomal protein L1 | 999 | 999 ctx | neighborhood:795 cooccurence:476 coexpression:893 experimental:928 textmining:677 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 998 | coexpression:915 experimental:928 database:532 textmining:791 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 998 | coexpression:885 experimental:928 database:766 textmining:516 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 999 | 998 ctx | neighborhood:809 cooccurence:449 coexpression:967 experimental:446 textmining:569 |
Rv0706 rplV |
50S ribosomal protein L22 | 998 | 997 | coexpression:889 experimental:928 database:588 textmining:587 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 998 | 997 ctx | cooccurence:621 coexpression:918 experimental:908 |
Rv0704 rplB |
50S ribosomal protein L2 | 998 | 997 | coexpression:890 experimental:928 database:512 textmining:667 |
Rv0714 rplN |
50S ribosomal protein L14 | 998 | 997 | coexpression:864 experimental:928 database:556 textmining:614 |
Rv0722 rpmD |
50S ribosomal protein L30 | 998 | 996 | coexpression:862 experimental:928 database:564 textmining:647 |
Rv3443c rplM |
50S ribosomal protein L13 | 998 | 996 | coexpression:866 experimental:928 database:571 textmining:620 |
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 L11
- MTBC0 PGAP product: 50S ribosomal protein L11
- Pfam (hmmscan --cut_ga): Ribosomal_L11_N PF03946.20 (E=8e-30), Ribosomal_L11 PF00298.25 (E=2e-30)
- (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_215154.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L11_N (PF03946.20), Ribosomal_L11 (PF00298.25)
- 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
COG0080 - Curated reference: UniProt P9WHE5 (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 —
349 functional partner(s); context anchor
rplA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000678|Rv0640|rplK MAPKKKVAGLIKLQIVAGQANPAPPVGPALGQHGVNIMEFCKAYNAATENQRGNVIPVEITVYEDRSFTFTLKTPPAAKLLLKAAGVAKGSAEPHKTKVAKVTWDQVREIAETKKTDLNANDVDAAAKIIAGTARSMGITVE