rplF Resolved · high auto-curated
H37Rv Rv0719 · MTBC0 - ·
179 aa · 813398–813937 (+) ·
RefSeq NP_215233.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 50S ribosomal protein L6 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 50S ribosomal protein L6. Pfam: Ribosomal_L6 (PF00347.29). |
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 |
P9WH81
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Large ribosomal subunit protein uL6 |
| Curated function | This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rplF |
| eggNOG description | This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7 L12 stalk, and near the tRNA binding site of the peptidyltransferase center |
| Orthologous group | COG0097 |
| KEGG orthology |
K02933
|
| KEGG pathways |
map03010
|
| KEGG modules |
M00178, M00179
|
| Gene Ontology (63) |
GO:0002181, GO:0003674, GO:0003676, GO:0003723, 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 | 0.172 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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_L6 | PF00347.29 | 7.1e-25 | 91–165 | Ribosomal protein L6 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplB (50S ribosomal protein L2), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3458c rpsD |
30S ribosomal protein S4 | 999 | 1000 | coexpression:892 experimental:999 |
Rv0703 rplW |
50S ribosomal protein L23 | 999 | 1000 | coexpression:973 experimental:999 database:687 |
Rv0683 rpsG |
30S ribosomal protein S7 | 999 | 1000 | coexpression:889 experimental:999 |
Rv2904c rplS |
50S ribosomal protein L19 | 999 | 1000 | coexpression:834 experimental:999 textmining:593 |
Rv0055 rpsR1 |
30S ribosomal protein S18 | 999 | 1000 | coexpression:733 experimental:999 textmining:494 |
Rv0704 rplB |
50S ribosomal protein L2 | 999 | 1000 ctx | cooccurence:678 coexpression:976 experimental:999 database:532 textmining:816 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 1000 ctx | neighborhood:847 fusion:698 cooccurence:600 coexpression:976 experimental:999 textmining:431 |
Rv0053 rpsF |
30S ribosomal protein S6 | 999 | 1000 | coexpression:863 experimental:999 textmining:522 |
Rv0708 rplP |
50S ribosomal protein L16 | 999 | 1000 ctx | cooccurence:636 coexpression:968 experimental:999 database:636 textmining:619 |
Rv0705 rpsS |
30S ribosomal protein S19 | 999 | 1000 ctx | cooccurence:671 coexpression:971 experimental:999 textmining:606 |
Rv2785c rpsO |
30S ribosomal protein S15 | 999 | 1000 | coexpression:861 experimental:999 |
Rv0716 rplE |
50S ribosomal protein L5 | 999 | 1000 ctx | neighborhood:727 cooccurence:748 coexpression:966 experimental:999 database:571 textmining:719 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 999 | 1000 | coexpression:867 experimental:999 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 999 | 1000 ctx | cooccurence:436 coexpression:918 experimental:999 textmining:429 |
Rv0715 rplX |
50S ribosomal protein L24 | 999 | 1000 ctx | neighborhood:727 coexpression:971 experimental:999 database:715 |
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 L6
- Pfam (hmmscan --cut_ga): Ribosomal_L6 PF00347.29 (E=7e-25)
- (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_215233.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribosomal_L6 (PF00347.29)
- 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
COG0097 - Curated reference: UniProt P9WH81 (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 —
331 functional partner(s); context anchor
rplB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0719|rplF MSRIGKQPIPVPAGVDVTIEGQSISVKGPKGTLGLTVAEPIKVARNDDGAIVVTRPDDERRNRSLHGLSRTLVSNLVTGVTQGYTTKMEIFGVGYRVQLKGSNLEFALGYSHPVVIEAPEGITFAVQAPTKFTVSGIDKQKVGQIAANIRRLRRPDPYKGKGVRYEGEQIRRKVGKTGK