Rv2975a Resolved · high auto-curated
H37Rv Rv2975a · MTBC0 - ·
64 aa · 3331854–3332048 (+) ·
RefSeq YP_009030042.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L28 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 50S ribosomal protein L28. Pfam: Ribosomal_L28 (PF00830.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpmB |
| eggNOG description | Belongs to the bacterial ribosomal protein bL28 family |
| Orthologous group | COG0227 |
| KEGG orthology |
K02902
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (3) |
GO:0003674, GO:0003735, GO:0005198
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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_L28 | PF00830.25 | 5.0e-22 | 4–60 | Ribosomal L28 family |
Evidence
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): 50S ribosomal protein L28
- Pfam (hmmscan --cut_ga): Ribosomal_L28 PF00830.25 (E=5e-22)
- (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 YP_009030042.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L28 (PF00830.25)
- 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
COG0227 - Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2975a| MAAVCDICGKGPGFGKSVSHSHRRTSRRWDPNIQTVHAVTRPGGNKKRLNVCTSCIKAGKITRG