rplA Resolved · high auto-curated
H37Rv Rv0641 · MTBC0 mtbc0_000679 ·
235 aa · 739070–739777 (+) ·
RefSeq NP_215155.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L1 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L1 |
| Revised (this work) | 50S ribosomal protein L1. Pfam: Ribosomal_L1 (PF00687.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHC7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL1 |
| Curated function | Binds directly to 23S rRNA. The L1 stalk is very mobile in the ribosome, and is involved in E site tRNA release..; FUNCTION: Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplA |
| eggNOG description | Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release |
| Orthologous group | COG0081 |
| KEGG orthology |
K02863
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (76) |
GO:0000470, GO:0003674, GO:0003676, GO:0003723, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840 +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 | 0.342 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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_L1 | PF00687.27 | 1.7e-66 | 31–220 | Ribosomal protein L1p/L10e family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplK (50S ribosomal protein L11), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0723 rplO |
50S ribosomal protein L15 | 999 | 999 | coexpression:957 experimental:928 database:571 |
Rv0640 rplK |
50S ribosomal protein L11 | 999 | 999 ctx | neighborhood:795 cooccurence:476 coexpression:893 experimental:928 textmining:677 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 998 | coexpression:955 experimental:928 database:495 textmining:596 |
Rv0651 rplJ |
50S ribosomal protein L10 | 998 | 998 | coexpression:861 experimental:928 database:693 textmining:415 |
Rv0706 rplV |
50S ribosomal protein L22 | 998 | 998 | coexpression:882 experimental:928 database:774 |
Rv0709 rpmC |
50S ribosomal protein L29 | 998 | 998 | coexpression:894 experimental:928 database:693 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 997 | coexpression:863 experimental:928 database:582 textmining:732 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 997 | coexpression:875 experimental:928 database:651 textmining:766 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 997 | coexpression:864 experimental:928 database:571 textmining:724 |
Rv0722 rpmD |
50S ribosomal protein L30 | 998 | 997 | coexpression:860 experimental:928 database:678 textmining:498 |
Rv3456c rplQ |
50S ribosomal protein L17 | 998 | 997 | coexpression:959 experimental:928 |
Rv0719 rplF |
50S ribosomal protein L6 | 998 | 997 | coexpression:877 experimental:928 database:597 textmining:620 |
Rv0701 rplC |
50S ribosomal protein L3 | 998 | 997 | coexpression:896 experimental:928 database:616 textmining:614 |
Rv0703 rplW |
50S ribosomal protein L23 | 998 | 997 | coexpression:875 experimental:928 database:693 textmining:585 |
Rv0704 rplB |
50S ribosomal protein L2 | 998 | 997 | coexpression:908 experimental:928 database:546 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 L1
- MTBC0 PGAP product: 50S ribosomal protein L1
- Pfam (hmmscan --cut_ga): Ribosomal_L1 PF00687.27 (E=2e-66)
- (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_215155.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L1 (PF00687.27)
- 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
COG0081 - Curated reference: UniProt P9WHC7 (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 —
232 functional partner(s); context anchor
rplK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000679|Rv0641|rplA MSKTSKAYRAAAAKVDRTNLYTPLQAAKLAKETSSTKQDATVEVAIRLGVDPRKADQMVRGTVNLPHGTGKTARVAVFAVGEKADAAVAAGADVVGSDDLIERIQGGWLEFDAAIATPDQMAKVGRIARVLGPRGLMPNPKTGTVTADVAKAVADIKGGKINFRVDKQANLHFVIGKASFDEKLLAENYGAAIDEVLRLKPSSSKGRYLKKITVSTTTGPGIPVDPSITRNFAGE