rplY Resolved · high auto-curated
H37Rv Rv1015c · MTBC0 mtbc0_001090 ·
215 aa · 1141258–1141905 (-) ·
RefSeq NP_215531.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L25/general stress protein Ctc |
|---|---|
| MTBC0 PGAP re-annotation | 50S ribosomal protein L25/general stress protein Ctc |
| Revised (this work) | 50S ribosomal protein L25/general stress protein Ctc. Pfam: Ribosomal_L25p (PF01386.25), Ribosomal_TL5_C (PF14693.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHB5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein bL25 |
| Curated function | This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | ctc |
| eggNOG description | This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance |
| Orthologous group | COG1825 |
| KEGG orthology |
K02897
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178
|
| Gene Ontology (56) |
GO:0003674, GO:0003676, GO:0003723, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005840, GO:0006412, GO:0006518 +44 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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_L25p | PF01386.25 | 2.1e-23 | 9–95 | Ribosomal L25p family |
Ribosomal_TL5_C | PF14693.12 | 6.2e-17 | 103–181 | Ribosomal protein TL5, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0056 rplI |
50S ribosomal protein L9 | 999 | 1000 | coexpression:829 experimental:999 textmining:568 |
Rv0722 rpmD |
50S ribosomal protein L30 | 999 | 1000 | coexpression:706 experimental:999 |
Rv0707 rpsC |
30S ribosomal protein S3 | 999 | 1000 | coexpression:789 experimental:999 |
Rv2442c rplU |
50S ribosomal protein L21 | 999 | 1000 | coexpression:833 experimental:999 textmining:650 |
Rv3456c rplQ |
50S ribosomal protein L17 | 999 | 1000 | coexpression:834 experimental:999 |
Rv0702 rplD |
50S ribosomal protein L4 | 999 | 1000 | coexpression:786 experimental:999 |
Rv3443c rplM |
50S ribosomal protein L13 | 999 | 1000 | coexpression:957 experimental:999 |
Rv0719 rplF |
50S ribosomal protein L6 | 999 | 1000 | coexpression:677 experimental:999 |
Rv1298 rpmE |
50S ribosomal protein L31 | 999 | 1000 | coexpression:684 experimental:999 |
Rv2441c rpmA |
50S ribosomal protein L27 | 999 | 1000 | coexpression:821 experimental:999 |
Rv0720 rplR |
50S ribosomal protein L18 | 999 | 1000 | coexpression:753 experimental:999 |
Rv0634B rpmG2 |
50S ribosomal protein L33 | 999 | 1000 | coexpression:650 experimental:999 |
Rv1643 rplT |
50S ribosomal protein L20 | 999 | 1000 | coexpression:678 experimental:999 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 999 | 1000 | coexpression:707 experimental:999 |
Rv0682 rpsL |
30S ribosomal protein S12 | 999 | 1000 | coexpression:742 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 L25/general stress protein Ctc
- MTBC0 PGAP product: 50S ribosomal protein L25/general stress protein Ctc
- Pfam (hmmscan --cut_ga): Ribosomal_L25p PF01386.25 (E=2e-23), Ribosomal_TL5_C PF14693.12 (E=6e-17)
- (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_215531.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L25p (PF01386.25), Ribosomal_TL5_C (PF14693.12)
- 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
COG1825 - Curated reference: UniProt P9WHB5 (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 — 179 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001090|Rv1015c|rplY MAKSASNQLRVTVRTETGKGASRRARRAGKIPAVLYGHGAEPQHLELPGHDYAAVLRHSGTNAVLTLDIAGKEQLALTKALHIHPIRRTIQHADLLVVRRGEKVVVEVSVVVEGQAGPDTLVTQETNSIEIEAEALSIPEQLTVSIEGAEPGTQLTAGQIALPAGVSLISDPDLLVVNVVKAPTAEELEGEVAGAEEAEEAAVEAGEAEAAGESE