rpsI Resolved · high auto-curated
H37Rv Rv3442c · MTBC0 mtbc0_003661 ·
151 aa · 3887381–3887836 (-) ·
RefSeq NP_217959.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S9 |
|---|---|
| MTBC0 PGAP re-annotation | 30S ribosomal protein S9 |
| Revised (this work) | 30S ribosomal protein S9. Pfam: Ribosomal_S9 (PF00380.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH25
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Small ribosomal subunit protein uS9 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpsI |
| eggNOG description | Belongs to the universal ribosomal protein uS9 family |
| Orthologous group | COG0103 |
| KEGG orthology |
K02996
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (77) |
GO:0000462, GO:0003674, GO:0003676, GO:0003723, GO:0003735, GO:0005198, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +65 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 | 0.267 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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_S9 | PF00380.26 | 1.8e-45 | 31–151 | Ribosomal protein S9/S16 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplM (50S ribosomal protein L13), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 | coexpression:873 experimental:999 database:540 textmining:595 |
Rv2442c rplU |
50S ribosomal protein L21 | 999 | 1000 | coexpression:891 experimental:999 |
Rv0056 rplI |
50S ribosomal protein L9 | 999 | 1000 | coexpression:866 experimental:999 |
Rv0722 rpmD |
50S ribosomal protein L30 | 999 | 1000 | coexpression:797 experimental:999 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 1000 | coexpression:944 experimental:999 textmining:584 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 1000 ctx | neighborhood:881 cooccurence:593 coexpression:991 experimental:999 textmining:612 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 | coexpression:880 experimental:999 textmining:584 |
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 | coexpression:866 experimental:999 textmining:843 |
Rv2441c rpmA |
50S ribosomal protein L27 | 999 | 1000 | coexpression:912 experimental:999 textmining:618 |
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 | coexpression:883 experimental:999 |
Rv1298 rpmE |
50S ribosomal protein L31 | 999 | 1000 | coexpression:789 experimental:999 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 999 | 1000 | coexpression:727 experimental:999 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 999 | 1000 | coexpression:890 experimental:999 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 999 | 1000 | coexpression:717 experimental:999 database:662 |
Rv0682 rpsL |
30S ribosomal protein S12 | 999 | 1000 | coexpression:861 experimental:999 database:844 textmining:516 |
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 S9
- MTBC0 PGAP product: 30S ribosomal protein S9
- Pfam (hmmscan --cut_ga): Ribosomal_S9 PF00380.26 (E=2e-45)
- (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_217959.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_S9 (PF00380.26)
- 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
COG0103 - Curated reference: UniProt P9WH25 (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 —
230 functional partner(s); context anchor
rplM - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003661|Rv3442c|rpsI MTETTPAPQTPAAPAGPAQSFVLERPIQTVGRRKEAVVRVRLVPGTGKFDLNGRSLEDYFPNKVHQQLIKAPLVTVDRVESFDIFAHLGGGGPSGQAGALRLGIARALILVSPEDRPALKKAGFLTRDPRATERKKYGLKKARKAPQYSKR