rpsF Resolved · high auto-curated
H37Rv Rv0053 · MTBC0 mtbc0_000058 ·
96 aa · 58300–58590 (+) ·
RefSeq NP_214567.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S6 |
|---|---|
| MTBC0 PGAP re-annotation | 30S ribosomal protein S6 |
| Revised (this work) | 30S ribosomal protein S6. Pfam: Ribosomal_S6 (PF01250.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH31
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Small ribosomal subunit protein bS6 |
| Curated function | Binds together with bS18 to 16S ribosomal RNA. In the 70S ribosome of this organism interacts with an extended helix of 23S rRNA, forming intersubunit bridge B9. This protein moves when the 70S ribosome undergoes rotation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpsF |
| eggNOG description | Binds together with S18 to 16S ribosomal RNA |
| Orthologous group | COG0360 |
| KEGG orthology |
K02990
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (37) |
GO:0003674, GO:0003676, GO:0003723, GO:0003735, GO:0005198, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +25 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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_S6 | PF01250.23 | 2.4e-31 | 4–92 | Ribosomal protein S6 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsR1 (30S ribosomal protein S18), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 1000 | coexpression:861 experimental:999 |
Rv0703 rplW |
50S ribosomal protein L23 | 999 | 1000 | coexpression:861 experimental:999 |
Rv2890c rpsB |
30S ribosomal protein S2 | 999 | 1000 | coexpression:864 experimental:999 database:844 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 | coexpression:859 experimental:999 database:844 |
Rv2904c rplS |
50S ribosomal protein L19 | 999 | 1000 | coexpression:859 experimental:999 |
Rv0055 rpsR1 |
30S ribosomal protein S18 | 999 | 1000 ctx | neighborhood:733 cooccurence:502 coexpression:736 experimental:999 textmining:582 |
Rv0704 rplB |
50S ribosomal protein L2 | 999 | 1000 | coexpression:863 experimental:999 textmining:427 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 1000 | coexpression:863 experimental:999 |
Rv0640 rplK |
50S ribosomal protein L11 | 999 | 1000 | coexpression:859 experimental:999 database:404 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 1000 | coexpression:861 experimental:999 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 1000 | coexpression:860 experimental:999 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 1000 | coexpression:864 experimental:999 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 | coexpression:812 experimental:999 database:844 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 | coexpression:849 experimental:999 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 1000 | coexpression:859 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 S6
- MTBC0 PGAP product: 30S ribosomal protein S6
- Pfam (hmmscan --cut_ga): Ribosomal_S6 PF01250.23 (E=2e-31)
- (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_214567.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_S6 (PF01250.23)
- 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
COG0360 - Curated reference: UniProt P9WH31 (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 —
236 functional partner(s); context anchor
rpsR1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000058|Rv0053|rpsF MRPYEIMVILDPTLDERTVAPSLETFLNVVRKDGGKVEKVDIWGKRRLAYEIAKHAEGIYVVIDVKAAPATVSELDRQLSLNESVLRTKVMRTDKH