rpsH Resolved · high auto-curated
H37Rv Rv0718 · MTBC0 - ·
132 aa · 812976–813374 (+) ·
RefSeq NP_215232.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S8 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 30S ribosomal protein S8. Pfam: Ribosomal_S8 (PF00410.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WH27
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Small ribosomal subunit protein uS8 |
| Curated function | One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpsH |
| eggNOG description | One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit |
| Orthologous group | COG0096 |
| KEGG orthology |
K02994
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (27) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0008150, GO:0015935, GO:0022626 +15 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 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_S8 | PF00410.25 | 2.8e-49 | 5–132 | Ribosomal protein S8 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplF (50S ribosomal protein L6), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 | coexpression:958 experimental:999 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 ctx | neighborhood:847 fusion:698 cooccurence:600 coexpression:976 experimental:999 textmining:431 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 1000 | coexpression:875 experimental:999 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 1000 | coexpression:968 experimental:999 database:844 |
Rv0056 rplI |
50S ribosomal protein L9 | 999 | 1000 | coexpression:864 experimental:999 |
Rv0722 rpmD |
50S ribosomal protein L30 | 999 | 1000 ctx | neighborhood:825 coexpression:958 experimental:999 |
Rv2442c rplU |
50S ribosomal protein L21 | 999 | 1000 | coexpression:868 experimental:999 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 ctx | cooccurence:727 coexpression:968 experimental:999 database:925 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 999 | 1000 | coexpression:736 experimental:999 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 999 | 1000 | coexpression:735 experimental:999 |
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 ctx | neighborhood:847 cooccurence:635 coexpression:967 experimental:999 |
Rv2441c rpmA |
50S ribosomal protein L27 | 999 | 1000 | coexpression:844 experimental:999 |
Rv3442c rpsI |
30S ribosomal protein S9 | 999 | 1000 | coexpression:907 experimental:999 database:540 |
Rv1643 rplT |
50S ribosomal protein L20 | 999 | 1000 | coexpression:840 experimental:999 |
Rv0682 rpsL |
30S ribosomal protein S12 | 999 | 1000 ctx | cooccurence:521 coexpression:875 experimental:999 database:844 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): 30S ribosomal protein S8
- Pfam (hmmscan --cut_ga): Ribosomal_S8 PF00410.25 (E=3e-49)
- (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_215232.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_S8 (PF00410.25)
- 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
COG0096 - Curated reference: UniProt P9WH27 (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 —
255 functional partner(s); context anchor
rplF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0718|rpsH MTMTDPIADFLTRLRNANSAYHDEVSLPHSKLKANIAQILKNEGYISDFRTEDARVGKSLVIQLKYGPSRERSIAGLRRVSKPGLRVYAKSTNLPRVLGGLGVAIISTSSGLLTDRQAARQGVGGEVLAYVW