rpmB2 Resolved · high auto-curated
H37Rv Rv2058c · MTBC0 mtbc0_002191 ·
78 aa · 2343438–2343674 (-) ·
RefSeq NP_216574.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L28 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L28 |
| 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.
Curated reference (UniProt)
| UniProt |
P9WHA9
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL28B |
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 (25) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0015934, GO:0022625, GO:0022626 +13 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 | 0.367 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 | 8.2e-26 | 4–61 | Ribosomal L28 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsN2 (30S ribosomal protein S14), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2056c rpsN2 |
30S ribosomal protein S14 | 999 | 999 ctx | neighborhood:882 coexpression:927 experimental:789 textmining:575 |
Rv2057c rpmG1 |
50S ribosomal protein L33 | 999 | 999 ctx | neighborhood:882 cooccurence:671 coexpression:906 experimental:789 textmining:787 |
Rv2055c rpsR2 |
30S ribosomal protein S18 | 999 | 995 ctx | neighborhood:882 coexpression:731 experimental:789 textmining:887 |
Rv0056 rplI |
50S ribosomal protein L9 | 988 | 987 | coexpression:708 experimental:956 |
Rv0979A rpmF |
50S ribosomal protein L32 | 974 | 966 | coexpression:731 experimental:829 |
Rv0053 rpsF |
30S ribosomal protein S6 | 963 | 959 | coexpression:728 experimental:829 |
Rv3443c rplM |
50S ribosomal protein L13 | 959 | 954 | coexpression:732 experimental:829 |
Rv2442c rplU |
50S ribosomal protein L21 | 959 | 954 | coexpression:732 experimental:829 |
Rv2904c rplS |
50S ribosomal protein L19 | 959 | 954 | coexpression:731 experimental:829 |
Rv2785c rpsO |
30S ribosomal protein S15 | 959 | 954 | coexpression:729 experimental:829 |
Rv2412 rpsT |
30S ribosomal protein S20 | 959 | 954 | coexpression:731 experimental:829 |
Rv2909c rpsP |
30S ribosomal protein S16 | 959 | 954 | coexpression:731 experimental:829 |
Rv0682 rpsL |
30S ribosomal protein S12 | 958 | 954 | coexpression:727 experimental:829 |
Rv1298 rpmE |
50S ribosomal protein L31 | 965 | 953 | coexpression:720 experimental:829 |
Rv2441c rpmA |
50S ribosomal protein L27 | 958 | 953 | coexpression:727 experimental:829 |
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: 50S ribosomal protein L28
- MTBC0 PGAP product: 50S ribosomal protein L28
- Pfam (hmmscan --cut_ga): Ribosomal_L28 PF00830.25 (E=8e-26)
- (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_216574.1)
- 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 - Curated reference: UniProt P9WHA9 (SwissProt, reviewed; Inferred from homology)
- 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 —
203 functional partner(s); context anchor
rpsN2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002191|Rv2058c|rpmB2 MSAHCQVTGRKPGFGNTVSHSHRRSRRRWSPNIQQRTYYLPSEGRRIRLRVSTKGIKVIDRDGIEAVVARLRRQGQRI