rpsM Resolved · high auto-curated
H37Rv Rv3460c · MTBC0 mtbc0_003678 ·
124 aa · 3905579–3905953 (-) ·
RefSeq NP_217977.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S13 |
|---|---|
| MTBC0 PGAP re-annotation | 30S ribosomal protein S13 |
| Revised (this work) | 30S ribosomal protein S13. Pfam: Ribosomal_S13 (PF00416.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH61
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Small ribosomal subunit protein uS13 |
| Curated function | Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpsM |
| eggNOG description | Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits |
| Orthologous group | COG0099 |
| KEGG orthology |
K02952
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (55) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0005886, GO:0006412, GO:0006518 +43 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 | 0.516 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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_S13 | PF00416.28 | 2.0e-35 | 3–109 | Ribosomal protein S13/S18 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplO (50S ribosomal protein L15), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0723 rplO |
50S ribosomal protein L15 | 999 | 1000 ctx | cooccurence:520 coexpression:745 experimental:999 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 999 | 1000 ctx | cooccurence:452 coexpression:943 experimental:999 database:662 textmining:583 |
Rv0706 rplV |
50S ribosomal protein L22 | 999 | 1000 ctx | cooccurence:609 coexpression:785 experimental:999 |
Rv3459c rpsK |
30S ribosomal protein S11 | 999 | 1000 ctx | neighborhood:882 fusion:498 cooccurence:712 coexpression:941 experimental:999 database:662 textmining:594 |
Rv3442c rpsI |
30S ribosomal protein S9 | 999 | 1000 ctx | cooccurence:459 coexpression:730 experimental:999 textmining:601 |
Rv1643 rplT |
50S ribosomal protein L20 | 999 | 1000 | coexpression:803 experimental:999 textmining:545 |
Rv0682 rpsL |
30S ribosomal protein S12 | 999 | 1000 ctx | cooccurence:571 coexpression:944 experimental:999 database:662 textmining:512 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 999 | 1000 | coexpression:675 experimental:999 database:632 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 999 | 1000 | coexpression:693 experimental:999 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 999 | 1000 | coexpression:668 experimental:999 |
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 ctx | cooccurence:658 coexpression:743 experimental:999 |
Rv2441c rpmA |
50S ribosomal protein L27 | 999 | 1000 | coexpression:791 experimental:999 textmining:612 |
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 ctx | neighborhood:726 coexpression:808 experimental:999 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 ctx | cooccurence:759 coexpression:827 experimental:999 textmining:586 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 1000 ctx | cooccurence:493 coexpression:767 experimental:999 textmining:616 |
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 S13
- MTBC0 PGAP product: 30S ribosomal protein S13
- Pfam (hmmscan --cut_ga): Ribosomal_S13 PF00416.28 (E=2e-35)
- (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_217977.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_S13 (PF00416.28)
- 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
COG0099 - Curated reference: UniProt P9WH61 (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
rplO - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003678|Rv3460c|rpsM MARLVGVDLPRDKRMEVALTYIFGIGRTRSNEILAATGIDRDLRTRDLTEEQLIHLRDYIEANLKVEGDLRREVQADIRRKIEIGCYQGLRHRRGMPVRGQRTKTNARTRKGPKRTIAGKKKAR