rplM Resolved · high auto-curated
H37Rv Rv3443c · MTBC0 mtbc0_003662 ·
147 aa · 3887833–3888276 (-) ·
RefSeq NP_217960.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L13 |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L13 |
| Revised (this work) | 50S ribosomal protein L13. Pfam: Ribosomal_L13 (PF00572.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHE1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL13 |
| Curated function | This protein is one of the early assembly proteins of the 50S ribosomal subunit. It is important during the early stages of 50S assembly. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplM |
| eggNOG description | This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly |
| Orthologous group | COG0102 |
| KEGG orthology |
K02871
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (63) |
GO:0003674, GO:0003676, GO:0003723, GO:0003729, GO:0003735, GO:0005198, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737 +51 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 | 0.08 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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_L13 | PF00572.25 | 2.1e-45 | 13–131 | Ribosomal protein L13 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpmA (50S ribosomal protein L27), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 999 | 1000 | coexpression:957 experimental:999 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 999 | 1000 | coexpression:731 experimental:999 |
Rv1298 rpmE |
50S ribosomal protein L31 | 999 | 1000 | coexpression:824 experimental:999 |
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 | coexpression:885 experimental:999 database:801 |
Rv2441c rpmA |
50S ribosomal protein L27 | 999 | 1000 ctx | cooccurence:566 coexpression:944 experimental:999 textmining:615 |
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 ctx | cooccurence:606 coexpression:866 experimental:999 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 | coexpression:875 experimental:999 database:660 textmining:610 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 1000 ctx | cooccurence:601 coexpression:886 experimental:999 database:582 textmining:686 |
Rv0056 rplI |
50S ribosomal protein L9 | 999 | 1000 | coexpression:864 experimental:999 textmining:597 |
Rv0722 rpmD |
50S ribosomal protein L30 | 999 | 1000 | coexpression:874 experimental:999 database:747 |
Rv2442c rplU |
50S ribosomal protein L21 | 999 | 1000 | coexpression:944 experimental:999 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 | coexpression:879 experimental:999 textmining:619 |
Rv0723 rplO |
50S ribosomal protein L15 | 999 | 1000 ctx | cooccurence:622 coexpression:864 experimental:999 database:790 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 999 | 1000 | coexpression:864 experimental:999 textmining:591 |
Rv3459c rpsK |
30S ribosomal protein S11 | 999 | 1000 | coexpression:863 experimental:999 textmining:672 |
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 L13
- MTBC0 PGAP product: 50S ribosomal protein L13
- Pfam (hmmscan --cut_ga): Ribosomal_L13 PF00572.25 (E=2e-45)
- (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_217960.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L13 (PF00572.25)
- 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
COG0102 - Curated reference: UniProt P9WHE1 (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 —
355 functional partner(s); context anchor
rpmA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003662|Rv3443c|rplM MPTYAPKAGDTTRSWYVIDATDVVLGRLAVAAANLLRGKHKPTFAPNVDGGDFVIVINADKVAISGDKLQHKMVYRHSGYPGGLHKRTIGELMQRHPDRVVEKAILGMLPKNRLSRQIQRKLRVYAGPEHPHSAQQPVPYELKQVAQ