rsfS Resolved · high auto-curated
H37Rv Rv2420c · MTBC0 mtbc0_002576 ·
126 aa · 2742064–2742444 (-) ·
RefSeq NP_216936.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | ribosome silencing factor |
| Revised (this work) | Ribosome silencing factor. Pfam: RsfS (PF02410.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86327
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosomal silencing factor RsfS |
| Curated function | Functions as a ribosomal silencing factor. Interacts with ribosomal protein uL14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | rsfS |
| eggNOG description | Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation |
| Orthologous group | COG0799 |
| KEGG orthology |
K09710
|
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 |
|---|---|---|---|---|
RsfS | PF02410.22 | 7.9e-32 | 14–108 | Ribosomal silencing factor during starvation |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nadD (nicotinate-nucleotide adenylyltransferase), high confidence from genomic context alone (score 969 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0714 rplN |
50S ribosomal protein L14 | 991 | 989 | experimental:989 |
Rv2421c nadD |
nicotinate-nucleotide adenylyltransferase | 976 | 969 ctx | neighborhood:882 coexpression:676 |
Rv2442c rplU |
50S ribosomal protein L21 | 944 | 944 | experimental:928 |
Rv2904c rplS |
50S ribosomal protein L19 | 933 | 933 | experimental:928 |
Rv3456c rplQ |
50S ribosomal protein L17 | 933 | 933 | experimental:928 |
Rv2441c rpmA |
50S ribosomal protein L27 | 932 | 933 | experimental:917 |
Rv3443c rplM |
50S ribosomal protein L13 | 932 | 933 | experimental:928 |
Rv0715 rplX |
50S ribosomal protein L24 | 942 | 932 | experimental:928 |
Rv0701 rplC |
50S ribosomal protein L3 | 930 | 931 | experimental:928 |
Rv0723 rplO |
50S ribosomal protein L15 | 929 | 929 | experimental:928 |
Rv0979A rpmF |
50S ribosomal protein L32 | 936 | 927 | experimental:917 |
Rv1643 rplT |
50S ribosomal protein L20 | 932 | 924 | experimental:917 |
Rv0640 rplK |
50S ribosomal protein L11 | 923 | 922 | experimental:921 |
Rv0702 rplD |
50S ribosomal protein L4 | 923 | 921 | experimental:917 |
Rv0706 rplV |
50S ribosomal protein L22 | 922 | 918 | experimental:915 |
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: hypothetical protein
- MTBC0 PGAP product: ribosome silencing factor
- Pfam (hmmscan --cut_ga): RsfS PF02410.22 (E=8e-32)
- (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_216936.1)
- Domains: Pfam-A via hmmscan --cut_ga — RsfS (PF02410.22)
- 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
COG0799 - Curated reference: UniProt O86327 (TrEMBL, unreviewed; 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 —
105 functional partner(s); context anchor
nadD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002576|Rv2420c|rsfS MTANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFYALDRLWGDCPVVPVDLSANSAGAQ