rplB Resolved · high auto-curated
H37Rv Rv0704 · MTBC0 mtbc0_000746 ·
280 aa · 806721–807563 (+) ·
RefSeq NP_215218.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L2 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L2 |
| Revised (this work) | 50S ribosomal protein L2. Pfam: Ribosomal_L2_N (PF00181.31), Ribosomal_L2_C (PF03947.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHA5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL2 |
| Curated function | One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplB |
| eggNOG description | One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity |
| Orthologous group | COG0090 |
| KEGG orthology |
K02886
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (61) |
GO:0002181, GO:0003674, GO:0003676, GO:0003723, GO:0003735, GO:0005198, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829 +49 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 | 0.169 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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_L2_N | PF00181.31 | 1.2e-37 | 30–119 | Ribosomal Proteins L2, RNA binding N-terminal domain |
Ribosomal_L2_C | PF03947.25 | 4.6e-55 | 126–251 | Ribosomal Proteins L2, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplE (50S ribosomal protein L5), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 | coexpression:833 experimental:999 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 1000 ctx | cooccurence:748 coexpression:972 experimental:999 database:617 textmining:847 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 | coexpression:880 experimental:999 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 1000 ctx | neighborhood:822 coexpression:963 experimental:999 |
Rv0715 rplX |
50S ribosomal protein L24 | 999 | 1000 | coexpression:968 experimental:999 database:570 |
Rv0721 rpsE |
30S ribosomal protein S5 | 999 | 1000 ctx | cooccurence:738 coexpression:971 experimental:999 textmining:596 |
Rv0709 rpmC |
50S ribosomal protein L29 | 999 | 1000 ctx | neighborhood:822 coexpression:970 experimental:999 database:617 |
Rv0714 rplN |
50S ribosomal protein L14 | 999 | 1000 ctx | cooccurence:740 coexpression:957 experimental:999 database:617 textmining:676 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 | coexpression:882 experimental:999 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 ctx | neighborhood:776 cooccurence:734 coexpression:973 experimental:999 database:616 textmining:865 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 | coexpression:864 experimental:999 textmining:571 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 1000 ctx | cooccurence:736 coexpression:843 experimental:999 textmining:585 |
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 1000 | coexpression:957 experimental:999 textmining:416 |
Rv0703 rplW |
50S ribosomal protein L23 | 999 | 1000 ctx | neighborhood:776 coexpression:995 experimental:999 database:571 textmining:845 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 ctx | cooccurence:491 coexpression:878 experimental:999 textmining:858 |
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 L2
- MTBC0 PGAP product: 50S ribosomal protein L2
- Pfam (hmmscan --cut_ga): Ribosomal_L2_N PF00181.31 (E=1e-37), Ribosomal_L2_C PF03947.25 (E=5e-55)
- (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_215218.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L2_N (PF00181.31), Ribosomal_L2_C (PF03947.25)
- 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
COG0090 - Curated reference: UniProt P9WHA5 (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 —
351 functional partner(s); context anchor
rplE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000746|Rv0704|rplB MAIRKYKPTTPGRRGASVSDFAEITRSTPEKSLVRPLHGRGGRNAHGRITTRHKGGGHKRAYRMIDFRRNDKDGVNAKVAHIEYDPNRTARIALLHYLDGEKRYIIAPNGLSQGDVVESGANADIKPGNNLPLRNIPAGTLIHAVELRPGGGAKLARSAGSSIQLLGKEASYASLRMPSGEIRRVDVRCRATVGEVGNAEQANINWGKAGRMRWKGKRPSVRGVVMNPVDHPHGGGEGKTSGGRHPVSPWGKPEGRTRNANKSSNKFIVRRRRTGKKHSR