rplL Resolved · high auto-curated
H37Rv Rv0652 · MTBC0 mtbc0_000690 ·
130 aa · 752935–753327 (+) ·
RefSeq NP_215166.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L7/L12 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L7/L12 |
| Revised (this work) | 50S ribosomal protein L7/L12. Pfam: Ribosomal_L12_N (PF16320.11), Ribosomal_L12 (PF00542.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHE3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL12 |
| Curated function | Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplL |
| eggNOG description | Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation |
| Orthologous group | COG0222 |
| KEGG orthology |
K02935
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (15) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044424 +3 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, 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_L12_N | PF16320.11 | 3.1e-19 | 6–53 | Ribosomal protein L7/L12 dimerisation domain |
Ribosomal_L12 | PF00542.25 | 7.3e-28 | 63–130 | Ribosomal protein L7/L12 C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplJ (50S ribosomal protein L10), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0651 rplJ |
50S ribosomal protein L10 | 999 | 1000 ctx | neighborhood:827 cooccurence:501 coexpression:967 experimental:969 textmining:775 |
Rv3443c rplM |
50S ribosomal protein L13 | 998 | 997 ctx | cooccurence:496 coexpression:913 experimental:928 textmining:672 |
Rv3442c rpsI |
30S ribosomal protein S9 | 998 | 997 | coexpression:959 experimental:928 textmining:585 |
Rv0640 rplK |
50S ribosomal protein L11 | 998 | 996 ctx | cooccurence:568 coexpression:863 experimental:928 textmining:623 |
Rv0708 rplP |
50S ribosomal protein L16 | 998 | 995 | coexpression:875 experimental:928 textmining:662 |
Rv2441c rpmA |
50S ribosomal protein L27 | 997 | 994 | coexpression:875 experimental:928 textmining:604 |
Rv0721 rpsE |
30S ribosomal protein S5 | 997 | 994 | coexpression:917 experimental:928 textmining:591 |
Rv0682 rpsL |
30S ribosomal protein S12 | 996 | 994 | coexpression:864 experimental:927 textmining:420 |
Rv1643 rplT |
50S ribosomal protein L20 | 996 | 994 | coexpression:863 experimental:928 textmining:535 |
Rv0683 rpsG |
30S ribosomal protein S7 | 995 | 994 | coexpression:863 experimental:928 |
Rv2890c rpsB |
30S ribosomal protein S2 | 997 | 993 | coexpression:889 experimental:928 textmining:587 |
Rv0641 rplA |
50S ribosomal protein L1 | 997 | 993 | coexpression:864 experimental:913 textmining:621 |
Rv0702 rplD |
50S ribosomal protein L4 | 996 | 993 | coexpression:875 experimental:928 textmining:583 |
Rv3456c rplQ |
50S ribosomal protein L17 | 995 | 993 | coexpression:871 experimental:928 |
Rv0707 rpsC |
30S ribosomal protein S3 | 996 | 992 | coexpression:875 experimental:921 textmining:602 |
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 L7/L12
- MTBC0 PGAP product: 50S ribosomal protein L7/L12
- Pfam (hmmscan --cut_ga): Ribosomal_L12_N PF16320.11 (E=3e-19), Ribosomal_L12 PF00542.25 (E=7e-28)
- (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_215166.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L12_N (PF16320.11), Ribosomal_L12 (PF00542.25)
- 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
COG0222 - Curated reference: UniProt P9WHE3 (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 —
188 functional partner(s); context anchor
rplJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000690|Rv0652|rplL MAKLSTDELLDAFKEMTLLELSDFVKKFEETFEVTAAAPVAVAAAGAAPAGAAVEAAEEQSEFDVILEAAGDKKIGVIKVVREIVSGLGLKEAKDLVDGAPKPLLEKVAKEAADEAKAKLEAAGATVTVK