rpmE Resolved · high auto-curated
H37Rv Rv1298 · MTBC0 mtbc0_001390 ·
80 aa · 1464202–1464444 (+) ·
RefSeq NP_215814.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L31 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L31 |
| Revised (this work) | 50S ribosomal protein L31. Pfam: Ribosomal_L31 (PF01197.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHA1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL31 |
| Curated function | Binds 23S rRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rpmE |
| eggNOG description | 50S ribosomal protein L31 |
| Orthologous group | COG0254 |
| KEGG orthology |
K02909
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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_L31 | PF01197.24 | 3.3e-32 | 1–66 | Ribosomal protein L31 |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 | coexpression:724 experimental:999 |
Rv0703 rplW |
50S ribosomal protein L23 | 999 | 1000 | coexpression:541 experimental:999 |
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 1000 | coexpression:814 experimental:999 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 1000 | coexpression:554 experimental:999 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:653 experimental:999 |
Rv0055 rpsR1 |
30S ribosomal protein S18 | 999 | 1000 | coexpression:701 experimental:999 textmining:693 |
Rv2904c rplS |
50S ribosomal protein L19 | 999 | 1000 | coexpression:860 experimental:999 |
Rv0709 rpmC |
50S ribosomal protein L29 | 999 | 1000 | coexpression:595 experimental:999 |
Rv2412 rpsT |
30S ribosomal protein S20 | 999 | 1000 | coexpression:842 experimental:999 textmining:653 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 | coexpression:734 experimental:999 textmining:700 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 | coexpression:865 experimental:999 |
Rv1642 rpmI |
50S ribosomal protein L35 | 999 | 1000 | coexpression:791 experimental:999 textmining:457 |
Rv2909c rpsP |
30S ribosomal protein S16 | 999 | 1000 | coexpression:859 experimental:999 textmining:653 |
Rv0701 rplC |
50S ribosomal protein L3 | 999 | 1000 | coexpression:708 experimental:999 |
Rv0682 rpsL |
30S ribosomal protein S12 | 999 | 1000 | coexpression:758 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 L31
- MTBC0 PGAP product: 50S ribosomal protein L31
- Pfam (hmmscan --cut_ga): Ribosomal_L31 PF01197.24 (E=3e-32)
- (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_215814.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L31 (PF01197.24)
- 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
COG0254 - Curated reference: UniProt P9WHA1 (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 — 176 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001390|Rv1298|rpmE MKSDIHPAYEETTVVCGCGNTFQTRSTKPGGRIVVEVCSQCHPFYTGKQKILDSGGRVARFEKRYGKRKVGADKAVSTGK