rpsD Resolved · high auto-curated
H37Rv Rv3458c · MTBC0 mtbc0_003676 ·
201 aa · 3904542–3905147 (-) ·
RefSeq NP_217975.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S4 |
|---|---|
| MTBC0 PGAP re-annotation | 30S ribosomal protein S4 |
| Revised (this work) | 30S ribosomal protein S4. Pfam: Ribosomal_S4 (PF00163.25), S4 (PF01479.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH35
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Small ribosomal subunit protein uS4 |
| Curated function | One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit..; FUNCTION: With S5 and S12 plays an important role in translational accuracy. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpsD |
| eggNOG description | One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit |
| Orthologous group | COG0522 |
| KEGG orthology |
K02986
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (70) |
GO:0003674, GO:0003676, GO:0003723, GO:0003735, GO:0005198, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +58 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 | 0.093 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 2 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_S4 | PF00163.25 | 3.8e-30 | 3–90 | Ribosomal protein S4/S9 N-terminal domain |
S4 | PF01479.31 | 6.4e-16 | 92–136 | S4 domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsM (30S ribosomal protein S13), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 1000 ctx | neighborhood:882 cooccurence:468 coexpression:982 experimental:999 database:662 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 | coexpression:885 experimental:999 textmining:408 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 | coexpression:866 experimental:999 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 | coexpression:875 experimental:999 |
Rv0714 rplN |
50S ribosomal protein L14 | 999 | 1000 ctx | cooccurence:410 coexpression:865 experimental:999 |
Rv0709 rpmC |
50S ribosomal protein L29 | 999 | 1000 | coexpression:864 experimental:999 |
Rv0721 rpsE |
30S ribosomal protein S5 | 999 | 1000 ctx | cooccurence:489 coexpression:877 experimental:999 database:844 textmining:902 |
Rv0715 rplX |
50S ribosomal protein L24 | 999 | 1000 | coexpression:875 experimental:999 textmining:504 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 1000 | coexpression:861 experimental:999 database:844 |
Rv2412 rpsT |
30S ribosomal protein S20 | 999 | 1000 | coexpression:769 experimental:999 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 ctx | neighborhood:546 coexpression:888 experimental:999 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 | coexpression:859 experimental:999 database:844 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 1000 ctx | cooccurence:607 coexpression:865 experimental:999 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 1000 ctx | cooccurence:496 coexpression:865 experimental:999 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 1000 | coexpression:888 experimental:999 database:844 |
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 S4
- MTBC0 PGAP product: 30S ribosomal protein S4
- Pfam (hmmscan --cut_ga): Ribosomal_S4 PF00163.25 (E=4e-30), S4 PF01479.31 (E=6e-16)
- (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_217975.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_S4 (PF00163.25), S4 (PF01479.31)
- 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
COG0522 - Curated reference: UniProt P9WH35 (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 —
278 functional partner(s); context anchor
rpsM - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003676|Rv3458c|rpsD MARYTGPVTRKSRRLRTDLVGGDQAFEKRPYPPGQHGRARIKESEYLLQLQEKQKARFTYGVMEKQFRRYYEEAVRQPGKTGEELLKILESRLDNVIYRAGLARTRRMARQLVSHGHFNVNGVHVNVPSYRVSQYDIVDVRDKSLNTVPFQIARETAGERPIPSWLQVVGERQRVLIHQLPERAQIDVPLTEQLIVEYYSK