prfB Resolved · high auto-curated
H37Rv Rv3105c · MTBC0 - ·
378 aa · 3472768–3473904 (-) ·
RefSeq NP_217621.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peptide chain release factor PrfB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Peptide chain release factor PrfB. Pfam: PCRF (PF03462.24), RF-1 (PF00472.27). |
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 |
P9WHG1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Peptide chain release factor 2 |
| Curated function | Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | prfB |
| eggNOG description | Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA |
| Orthologous group | COG0216 |
| KEGG orthology |
K02836
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0008150, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.541 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
PCRF | PF03462.24 | 2.5e-56 | 36–228 | PCRF domain |
RF-1 | PF00472.27 | 1.5e-37 | 238–345 | RF-1 domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplL (50S ribosomal protein L7/L12), high confidence from genomic context alone (score 978 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2442c rplU |
50S ribosomal protein L21 | 986 | 987 | coexpression:817 experimental:915 |
Rv2441c rpmA |
50S ribosomal protein L27 | 984 | 982 | coexpression:655 experimental:925 |
Rv0652 rplL |
50S ribosomal protein L7/L12 | 982 | 978 ctx | cooccurence:609 experimental:914 |
Rv0708 rplP |
50S ribosomal protein L16 | 978 | 978 ctx | cooccurence:477 experimental:912 |
Rv3443c rplM |
50S ribosomal protein L13 | 977 | 977 ctx | cooccurence:509 coexpression:498 experimental:914 |
Rv2909c rpsP |
30S ribosomal protein S16 | 977 | 976 | coexpression:670 experimental:915 |
Rv1643 rplT |
50S ribosomal protein L20 | 977 | 974 ctx | cooccurence:507 coexpression:422 experimental:915 |
Rv0702 rplD |
50S ribosomal protein L4 | 976 | 974 ctx | cooccurence:460 coexpression:475 experimental:914 |
Rv3456c rplQ |
50S ribosomal protein L17 | 972 | 973 ctx | cooccurence:457 coexpression:458 experimental:915 |
Rv0682 rpsL |
30S ribosomal protein S12 | 973 | 970 | coexpression:599 experimental:910 |
Rv0683 rpsG |
30S ribosomal protein S7 | 972 | 965 | coexpression:500 experimental:910 |
Rv2904c rplS |
50S ribosomal protein L19 | 966 | 963 | coexpression:417 experimental:923 |
Rv0056 rplI |
50S ribosomal protein L9 | 965 | 960 | experimental:917 |
Rv0715 rplX |
50S ribosomal protein L24 | 960 | 960 | coexpression:448 experimental:913 |
Rv0723 rplO |
50S ribosomal protein L15 | 958 | 956 | experimental:919 |
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): peptide chain release factor PrfB
- Pfam (hmmscan --cut_ga): PCRF PF03462.24 (E=2e-56), RF-1 PF00472.27 (E=1e-37)
- (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_217621.1)
- Domains: Pfam-A via hmmscan --cut_ga — PCRF (PF03462.24), RF-1 (PF00472.27)
- 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
COG0216 - Curated reference: UniProt P9WHG1 (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 —
188 functional partner(s); context anchor
rplL - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3105c|prfB MPVTLAAVDPDRQADIAALDCTLTTVERVLDVEGLRSRIEKLEHEASDPHLWDDQTRAQRVTSELSHTQGELRRVEELRRRLDDLPVLYELAAEEAGAAAADAVAEADAELKSLRADIEATEVRTLLSGEYDEREALVTIRSGAGGVDAADWAEMLMRMYIRWAEQHKYPVEVFDTSYAEEAGIKSATFAVHAPFAYGTLSVEQGTHRLVRISPFDNQSRRQTSFAEVEVLPVVETTDHIDIPEGDVRVDVYRSSGPGGQSVNTTDSAVRLTHIPSGIVVTCQNEKSQLQNKIAAMRVLQAKLLERKRLEERAELDALKADGGSSWGNQMRSYVLHPYQMVKDLRTEYEVGNPAAVLDGDLDGFLEAGIRWRNRRNDD