Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S1 |
|---|
| MTBC0 PGAP re-annotation | 30S ribosomal protein S1 |
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| Revised (this work) | 30S ribosomal protein S1. Pfam: S1 (PF00575.30), S1_RRP5 (PF23459.2). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH43
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Small ribosomal subunit protein bS1 |
|---|
| Curated function | Binds mRNA, facilitating recognition of most mRNAs by the 30S ribosomal subunit during translation initiation (By similarity). Probably plays a role in trans-translation; binds tmRNA (the product of the ssrA gene). In trans-translation Ala-aminoacylated transfer-messenger RNA (tmRNA, product of the ssrA gene; the 2 termini fold to resemble tRNA(Ala) while it encodes a short internal open reading frame (the tag peptide)) acts like a tRNA, entering the A-site of the ribosome and displacing the stalled mRNA (which is subsequently degraded). The ribosome then switches to translate the ORF on the t. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|
| Preferred name | rpsA |
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| eggNOG description | Ribosomal protein S1 |
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| Orthologous group | COG0539 |
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| KEGG orthology |
K02945
|
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| KEGG pathways |
map03010
|
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| KEGG modules |
M00178
|
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| Gene Ontology (15) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, GO:0044424 +3 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 |
0.496 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
5 synonymous, 8 missense, 0 nonsense, 1 frameshift
|
|---|
| Disruption |
1 distinct premature-stop/frameshift site(s); most common in
0.24% of strains
(346) · clonal
|
|---|
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 |
|---|
S1 | PF00575.30 |
6.0e-27 | 206–277 |
S1 RNA binding domain |
S1_RRP5 | PF23459.2 |
2.2e-06 | 206–276 |
RRP5 S1 domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0718 rpsH |
30S ribosomal protein S8 |
999 |
1000 |
coexpression:968 experimental:928 database:816 |
Rv0702 rplD |
50S ribosomal protein L4 |
999 |
999 |
coexpression:962 experimental:920 database:599 |
Rv3459c rpsK |
30S ribosomal protein S11 |
999 |
999 |
coexpression:856 experimental:923 database:925 |
Rv0721 rpsE |
30S ribosomal protein S5 |
999 |
999 |
coexpression:936 experimental:888 database:925 |
Rv0682 rpsL |
30S ribosomal protein S12 |
999 |
998 |
coexpression:948 experimental:922 database:600 textmining:646 |
Rv3458c rpsD |
30S ribosomal protein S4 |
999 |
998 |
coexpression:875 experimental:922 database:844 textmining:452 |
Rv0683 rpsG |
30S ribosomal protein S7 |
998 |
998 |
coexpression:875 experimental:922 database:809 textmining:457 |
Rv0710 rpsQ |
30S ribosomal protein S17 |
998 |
997 |
coexpression:784 experimental:923 database:816 textmining:427 |
Rv0701 rplC |
50S ribosomal protein L3 |
997 |
996 |
coexpression:969 experimental:873 textmining:407 |
Rv0704 rplB |
50S ribosomal protein L2 |
997 |
996 |
coexpression:967 experimental:878 textmining:403 |
Rv0719 rplF |
50S ribosomal protein L6 |
996 |
995 |
coexpression:961 experimental:865 |
Rv0700 rpsJ |
30S ribosomal protein S10 |
995 |
995 |
coexpression:948 experimental:903 |
Rv2890c rpsB |
30S ribosomal protein S2 |
996 |
994 |
coexpression:854 experimental:915 database:540 textmining:498 |
Rv0715 rplX |
50S ribosomal protein L24 |
995 |
994 |
coexpression:951 experimental:879 |
Rv0716 rplE |
50S ribosomal protein L5 |
995 |
993 |
coexpression:943 experimental:882 |
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 S1
- MTBC0 PGAP product: 30S ribosomal protein S1
- Pfam (hmmscan --cut_ga): S1 PF00575.30 (E=6e-27), S1_RRP5 PF23459.2 (E=2e-06)
- (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_216146.1)
- Domains: Pfam-A via hmmscan --cut_ga — S1 (PF00575.30), S1_RRP5 (PF23459.2)
- 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
COG0539
- Curated reference: UniProt
P9WH43
(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)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001738|Rv1630|rpsA
MPSPTVTSPQVAVNDIGSSEDFLAAIDKTIKYFNDGDIVEGTIVKVDRDEVLLDIGYKTEGVIPARELSIKHDVDPNEVVSVGDEVEALVLTKEDKEGRLILSKKRAQYERAWGTIEALKEKDEAVKGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLQPYIGKEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNNLQKGTIRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVQVGDEVTVEVLDVDMDRERVSLSLKATQEDPWRHFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPDQVVAVGDDAMVKVIDIDLERRRISLSLKQANEDYTEEFDPAKYGMADSYDEQGNYIFPEGFDAETNEWLEGFEKQRAEWEARYAEAERRHKMHTAQMEKFAAAEAAGRGADDQSSASSAPSEKTAGGSLASDAQLAALREKLAGSA
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