rpsL Resolved · high auto-curated
H37Rv Rv0682 · MTBC0 mtbc0_000721 ·
124 aa · 785646–786020 (+) ·
RefSeq NP_215196.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S12 |
|---|---|
| MTBC0 PGAP re-annotation | 30S ribosomal protein S12 |
| Revised (this work) | 30S ribosomal protein S12. Pfam: Ribosom_S12_S23 (PF00164.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH63
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Small ribosomal subunit protein uS12 |
| Curated function | With S4 and S5 plays an important role in translational accuracy..; FUNCTION: Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpsL |
| eggNOG description | Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit |
| Orthologous group | COG0048 |
| KEGG orthology |
K02950
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (44) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005840, GO:0006412, GO:0006518, GO:0006807, GO:0008150 +32 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 | 0.335 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Ribosom_S12_S23 | PF00164.32 | 3.9e-41 | 18–123 | Ribosomal protein S12/S23 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsK (30S ribosomal protein S11), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0717 rpsN1 |
30S ribosomal protein S14 | 999 | 1000 | coexpression:734 experimental:999 database:662 |
Rv1643 rplT |
50S ribosomal protein L20 | 999 | 1000 | coexpression:861 experimental:999 |
Rv3442c rpsI |
30S ribosomal protein S9 | 999 | 1000 | coexpression:861 experimental:999 database:844 textmining:516 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 999 | 1000 | coexpression:967 experimental:999 database:844 textmining:614 |
Rv0706 rplV |
50S ribosomal protein L22 | 999 | 1000 | coexpression:888 experimental:999 |
Rv3459c rpsK |
30S ribosomal protein S11 | 999 | 1000 ctx | cooccurence:512 coexpression:968 experimental:999 database:844 |
Rv0723 rplO |
50S ribosomal protein L15 | 999 | 1000 | coexpression:865 experimental:999 |
Rv2442c rplU |
50S ribosomal protein L21 | 999 | 1000 | coexpression:864 experimental:999 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 ctx | cooccurence:473 coexpression:864 experimental:999 database:844 textmining:512 |
Rv0722 rpmD |
50S ribosomal protein L30 | 999 | 1000 | coexpression:863 experimental:999 textmining:451 |
Rv0056 rplI |
50S ribosomal protein L9 | 999 | 1000 | coexpression:794 experimental:999 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 1000 | coexpression:958 experimental:999 database:844 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 ctx | cooccurence:422 coexpression:905 experimental:999 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 1000 | coexpression:863 experimental:999 textmining:625 |
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 | coexpression:946 experimental:999 |
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: 30S ribosomal protein S12
- MTBC0 PGAP product: 30S ribosomal protein S12
- Pfam (hmmscan --cut_ga): Ribosom_S12_S23 PF00164.32 (E=4e-41)
- (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_215196.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosom_S12_S23 (PF00164.32)
- 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
COG0048 - Curated reference: UniProt P9WH63 (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 —
308 functional partner(s); context anchor
rpsK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000721|Rv0682|rpsL MPTIQQLVRKGRRDKISKVKTAALKGSPQRRGVCTRVYTTTPKKPNSALRKVARVKLTSQVEVTAYIPGEGHNLQEHSMVLVRGGRVKDLPGVRYKIIRGSLDTQGVKNRKQARSRYGAKKEKG