rplV Resolved · high auto-curated
H37Rv Rv0706 · MTBC0 mtbc0_000748 ·
197 aa · 807882–808475 (+) ·
RefSeq NP_215220.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L22 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L22 |
| Revised (this work) | 50S ribosomal protein L22. Pfam: Ribosomal_L22 (PF00237.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHC1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL22 |
| Curated function | This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity)..; FUNCTION: The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplV |
| eggNOG description | The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome |
| Orthologous group | COG0091 |
| KEGG orthology |
K02890
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (30) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0008150, GO:0015934 +18 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 | 0.37 · 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_L22 | PF00237.25 | 6.1e-38 | 15–118 | Ribosomal protein L22p/L17e |
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:734 experimental:999 |
Rv0704 rplB |
50S ribosomal protein L2 | 999 | 1000 ctx | neighborhood:822 cooccurence:537 coexpression:995 experimental:999 database:639 textmining:856 |
Rv2904c rplS |
50S ribosomal protein L19 | 999 | 1000 | coexpression:866 experimental:999 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 1000 ctx | cooccurence:685 coexpression:968 experimental:999 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:860 experimental:999 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 1000 ctx | neighborhood:882 cooccurence:612 coexpression:995 experimental:999 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 1000 ctx | neighborhood:882 cooccurence:500 coexpression:995 experimental:999 database:651 textmining:634 |
Rv0703 rplW |
50S ribosomal protein L23 | 999 | 1000 ctx | neighborhood:739 coexpression:990 experimental:999 database:844 textmining:718 |
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 1000 ctx | cooccurence:612 coexpression:892 experimental:999 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 | coexpression:865 experimental:999 textmining:887 |
Rv0714 rplN |
50S ribosomal protein L14 | 999 | 1000 ctx | cooccurence:402 coexpression:880 experimental:999 database:654 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 | coexpression:894 experimental:999 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 | coexpression:862 experimental:999 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 ctx | neighborhood:739 cooccurence:519 coexpression:958 experimental:999 database:749 textmining:850 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 1000 ctx | cooccurence:609 coexpression:785 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: 50S ribosomal protein L22
- MTBC0 PGAP product: 50S ribosomal protein L22
- Pfam (hmmscan --cut_ga): Ribosomal_L22 PF00237.25 (E=6e-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_215220.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L22 (PF00237.25)
- 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
COG0091 - Curated reference: UniProt P9WHC1 (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 —
274 functional partner(s); context anchor
rplB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000748|Rv0706|rplV MTAATKATEYPSAVAKARFVRVSPRKARRVIDLVRGRSVSDALDILRWAPQAASGPVAKVIASAAANAQNNGGLDPATLVVATVYADQGPTAKRIRPRAQGRAFRIRRRTSHITVVVESRPAKDQRSAKSSRARRTEASKAASKVGATAPAKKAAAKAPAKKAPASSGVKKTPAKKAPAKKAPAKASETSAAKGGSD