rplS Resolved · high auto-curated
H37Rv Rv2904c · MTBC0 mtbc0_003086 ·
113 aa · 3234741–3235082 (-) ·
RefSeq NP_217420.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L19 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L19 |
| Revised (this work) | 50S ribosomal protein L19. Pfam: Ribosomal_L19 (PF01245.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHC9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL19 |
| Curated function | This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplS |
| eggNOG description | This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site |
| Orthologous group | COG0335 |
| KEGG orthology |
K02884
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (30) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0005886, 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 | 0.634 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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_L19 | PF01245.27 | 1.5e-50 | 5–112 | Ribosomal protein L19 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsP (30S ribosomal protein S16), 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 | coexpression:877 experimental:999 textmining:616 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 1000 | coexpression:836 experimental:999 |
Rv3924c rpmH |
50S ribosomal protein L34 | 999 | 1000 | coexpression:646 experimental:999 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:859 experimental:999 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 1000 | coexpression:810 experimental:999 textmining:604 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 1000 | coexpression:775 experimental:999 textmining:601 |
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 1000 | coexpression:894 experimental:999 |
Rv0703 rplW |
50S ribosomal protein L23 | 999 | 1000 | coexpression:871 experimental:999 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 | coexpression:904 experimental:999 |
Rv0714 rplN |
50S ribosomal protein L14 | 999 | 1000 | coexpression:936 experimental:999 textmining:594 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 ctx | cooccurence:446 coexpression:864 experimental:999 textmining:420 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 | coexpression:871 experimental:999 textmining:589 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 | coexpression:866 experimental:999 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 1000 | coexpression:920 experimental:999 textmining:595 |
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 L19
- MTBC0 PGAP product: 50S ribosomal protein L19
- Pfam (hmmscan --cut_ga): Ribosomal_L19 PF01245.27 (E=1e-50)
- (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_217420.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L19 (PF01245.27)
- 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
COG0335 - Curated reference: UniProt P9WHC9 (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 —
243 functional partner(s); context anchor
rpsP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003086|Rv2904c|rplS MNRLDFVDKPSLRDDIPAFNPGDTINVHVKVIEGAKERLQVFKGVVIRRQGGGIRETFTVRKESYGVGVERTFPVHSPNIDHIEVVTRGDVRRAKLYYLRELRGKKAKIKEKR