rpmG1 Resolved · high auto-curated
H37Rv Rv2057c · MTBC0 - ·
54 aa · 2314661–2314825 (-) ·
RefSeq YP_177856.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L33 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 50S ribosomal protein L33. Pfam: Ribosomal_L33 (PF00471.27). |
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).
Curated reference (UniProt)
| UniProt |
P9WH97
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL33A |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpmG |
| eggNOG description | Belongs to the bacterial ribosomal protein bL33 family |
| Orthologous group | COG0267 |
| KEGG orthology |
K02913
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (22) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0015934, GO:0022625, GO:0022626, GO:0032991, GO:0043226, GO:0043228 +10 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 | 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_L33 | PF00471.27 | 8.3e-16 | 9–54 | Ribosomal protein L33 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpmB2 (50S ribosomal protein L28), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 999 | coexpression:671 experimental:997 |
Rv2058c rpmB2 |
50S ribosomal protein L28 | 999 | 999 ctx | neighborhood:882 cooccurence:671 coexpression:906 experimental:789 textmining:787 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 999 | 997 ctx | neighborhood:882 coexpression:771 experimental:870 textmining:831 |
Rv2055c rpsR2 |
30S ribosomal protein S18 | 998 | 995 ctx | neighborhood:882 coexpression:687 experimental:870 textmining:614 |
Rv0105c rpmB1 |
50S ribosomal protein L28 | 993 | 973 ctx | cooccurence:600 coexpression:672 experimental:789 textmining:783 |
Rv0979A rpmF |
50S ribosomal protein L32 | 984 | 969 | coexpression:722 experimental:829 textmining:525 |
Rv2442c rplU |
50S ribosomal protein L21 | 973 | 969 | coexpression:730 experimental:870 |
Rv2441c rpmA |
50S ribosomal protein L27 | 972 | 969 | coexpression:728 experimental:870 |
Rv0708 rplP |
50S ribosomal protein L16 | 971 | 968 | coexpression:645 experimental:870 |
Rv1643 rplT |
50S ribosomal protein L20 | 971 | 968 | coexpression:723 experimental:870 |
Rv0685 tuf |
elongation factor Tu | 969 | 968 | coexpression:706 experimental:829 |
Rv0056 rplI |
50S ribosomal protein L9 | 970 | 966 | coexpression:708 experimental:870 |
Rv0651 rplJ |
50S ribosomal protein L10 | 968 | 966 | coexpression:731 experimental:870 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 968 | 966 | coexpression:731 experimental:870 |
Rv0701 rplC |
50S ribosomal protein L3 | 967 | 966 | coexpression:731 experimental:870 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): 50S ribosomal protein L33
- Pfam (hmmscan --cut_ga): Ribosomal_L33 PF00471.27 (E=8e-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 YP_177856.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L33 (PF00471.27)
- 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
COG0267 - Curated reference: UniProt P9WH97 (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
rpmB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2057c|rpmG1 MARTDIRPIVKLRSTAGTGYTYTTRKNRRNDPDRLILRKYDPILRRHVDFREER