rpmA Resolved · high auto-curated
H37Rv Rv2441c · MTBC0 mtbc0_002600 ·
86 aa · 2764020–2764280 (-) ·
RefSeq NP_216957.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L27 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L27 |
| Revised (this work) | 50S ribosomal protein L27. Pfam: Ribosomal_L27 (PF01016.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHB3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL27 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpmA |
| eggNOG description | Belongs to the bacterial ribosomal protein bL27 family |
| Orthologous group | COG0211 |
| KEGG orthology |
K02899
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (32) |
GO:0003674, GO:0003735, GO:0005198, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0005886, GO:0008150 +20 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 | 1.057 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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_L27 | PF01016.25 | 1.1e-35 | 2–80 | Ribosomal L27 protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplQ (50S ribosomal protein L17), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 ctx | cooccurence:456 coexpression:858 experimental:999 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 1000 | coexpression:869 experimental:999 textmining:595 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 1000 ctx | cooccurence:566 coexpression:944 experimental:999 textmining:615 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 | coexpression:800 experimental:999 textmining:594 |
Rv0722 rpmD |
50S ribosomal protein L30 | 999 | 1000 | coexpression:700 experimental:999 |
Rv0056 rplI |
50S ribosomal protein L9 | 999 | 1000 | coexpression:845 experimental:999 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 | coexpression:810 experimental:999 textmining:610 |
Rv2442c rplU |
50S ribosomal protein L21 | 999 | 1000 ctx | neighborhood:869 coexpression:976 experimental:999 textmining:513 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 999 | 1000 | coexpression:731 experimental:999 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 999 | 1000 | coexpression:821 experimental:999 |
Rv1298 rpmE |
50S ribosomal protein L31 | 999 | 1000 | coexpression:827 experimental:999 |
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 | coexpression:736 experimental:999 |
Rv3442c rpsI |
30S ribosomal protein S9 | 999 | 1000 | coexpression:912 experimental:999 textmining:618 |
Rv1643 rplT |
50S ribosomal protein L20 | 999 | 1000 | coexpression:864 experimental:999 textmining:604 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 999 | 1000 | coexpression:690 experimental:999 |
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 L27
- MTBC0 PGAP product: 50S ribosomal protein L27
- Pfam (hmmscan --cut_ga): Ribosomal_L27 PF01016.25 (E=1e-35)
- (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_216957.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L27 (PF01016.25)
- 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
COG0211 - Curated reference: UniProt P9WHB3 (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 —
249 functional partner(s); context anchor
rplQ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002600|Rv2441c|rpmA MAHKKGASSSRNGRDSAAQRLGVKRYGGQVVKAGEILVRQRGTKFHPGVNVGRGGDDTLFAKTAGAVEFGIKRGRKTVSIVGSTTA