rpsB Resolved · high auto-curated
H37Rv Rv2890c · MTBC0 mtbc0_003072 ·
287 aa · 3219948–3220811 (-) ·
RefSeq NP_217406.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 30S ribosomal protein S2 |
|---|---|
| MTBC0 PGAP re-annotation | 30S ribosomal protein S2 |
| Revised (this work) | 30S ribosomal protein S2. Pfam: Ribosomal_S2 (PF00318.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH39
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Small ribosomal subunit protein uS2 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpsB |
| eggNOG description | Belongs to the universal ribosomal protein uS2 family |
| Orthologous group | COG0052 |
| KEGG orthology |
K02967
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (57) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0005886, GO:0006412 +45 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 | 0.653 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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_S2 | PF00318.26 | 1.2e-99 | 9–224 | Ribosomal protein S2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsG (30S ribosomal protein S7), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2055c rpsR2 |
30S ribosomal protein S18 | 999 | 1000 | coexpression:732 experimental:997 database:540 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 ctx | cooccurence:442 coexpression:875 experimental:928 database:925 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 1000 | coexpression:865 experimental:997 database:925 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:864 experimental:999 database:844 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 ctx | cooccurence:450 coexpression:864 experimental:928 database:925 textmining:841 |
Rv3442c rpsI |
30S ribosomal protein S9 | 999 | 1000 | coexpression:886 experimental:928 database:925 textmining:588 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 999 | coexpression:861 experimental:928 database:925 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 999 | coexpression:855 experimental:928 database:925 textmining:629 |
Rv0721 rpsE |
30S ribosomal protein S5 | 999 | 999 | coexpression:864 experimental:928 database:925 textmining:591 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 999 | coexpression:888 experimental:928 database:844 textmining:502 |
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 999 | coexpression:885 experimental:928 database:844 textmining:415 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 999 | coexpression:864 experimental:928 database:925 textmining:619 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 999 | coexpression:874 experimental:928 database:844 textmining:622 |
Rv0500B |
Rv0500B, len: 33 aa. Conserved hypothetical protein. Basic protein 18 of the 33 aa are Arg or Lys, with strong similarity to AL079345|SCE68_ | 999 | 999 | experimental:999 |
Rv0682 rpsL |
30S ribosomal protein S12 | 999 | 999 | coexpression:864 experimental:928 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 S2
- MTBC0 PGAP product: 30S ribosomal protein S2
- Pfam (hmmscan --cut_ga): Ribosomal_S2 PF00318.26 (E=1e-99)
- (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_217406.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_S2 (PF00318.26)
- 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
COG0052 - Curated reference: UniProt P9WH39 (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 —
294 functional partner(s); context anchor
rpsG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003072|Rv2890c|rpsB MAVVTMKQLLDSGTHFGHQTRRWNPKMKRFIFTDRNGIYIIDLQQTLTFIDKAYEFVKETVAHGGSVLFVGTKKQAQESVAAEATRVGMPYVNQRWLGGMLTNFSTVHKRLQRLKELEAMEQTGGFEGRTKKEILGLTREKNKLERSLGGIRDMAKVPSAIWVVDTNKEHIAVGEARKLGIPVIAILDTNCDPDEVDYPIPGNDDAIRSAALLTRVIASAVAEGLQARAGLGRADGKPEAEAAEPLAEWEQELLASATASATPSATASTTALTDAPAGATEPTTDAS