prfA Resolved · high auto-curated
H37Rv Rv1299 · MTBC0 mtbc0_001391 ·
357 aa · 1464534–1465607 (+) ·
RefSeq NP_215815.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peptide chain release factor PrfA |
|---|---|
| MTBC0 PGAP re-annotation | peptide chain release factor 1 |
| Revised (this work) | Peptide chain release factor 1. 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.
Curated reference (UniProt)
| UniProt |
P9WHG3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Peptide chain release factor 1 |
| Curated function | Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | prfA |
| eggNOG description | Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA |
| Orthologous group | COG0216 |
| KEGG orthology |
K02835
|
| 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 | 0.674 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.38% of strains (548) · clonal |
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 | 2.9e-60 | 13–204 | PCRF domain |
RF-1 | PF00472.27 | 5.6e-41 | 215–322 | RF-1 domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hemK (release factor glutamine methyltransferase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1300 hemK |
release factor glutamine methyltransferase | 999 | 999 ctx | neighborhood:881 coexpression:896 experimental:890 textmining:551 |
Rv3443c rplM |
50S ribosomal protein L13 | 979 | 979 ctx | cooccurence:683 experimental:908 |
Rv1643 rplT |
50S ribosomal protein L20 | 979 | 977 ctx | cooccurence:582 coexpression:411 experimental:913 |
Rv1298 rpmE |
50S ribosomal protein L31 | 979 | 977 ctx | neighborhood:778 coexpression:434 experimental:830 |
Rv2441c rpmA |
50S ribosomal protein L27 | 978 | 973 ctx | cooccurence:610 experimental:913 |
Rv0683 rpsG |
30S ribosomal protein S7 | 976 | 969 ctx | cooccurence:544 experimental:907 |
Rv0702 rplD |
50S ribosomal protein L4 | 968 | 966 ctx | cooccurence:567 experimental:908 |
Rv3442c rpsI |
30S ribosomal protein S9 | 967 | 964 ctx | cooccurence:501 experimental:907 |
Rv2785c rpsO |
30S ribosomal protein S15 | 964 | 961 ctx | cooccurence:555 experimental:907 |
Rv0701 rplC |
50S ribosomal protein L3 | 964 | 960 ctx | cooccurence:535 experimental:908 |
Rv3456c rplQ |
50S ribosomal protein L17 | 964 | 959 ctx | cooccurence:486 experimental:913 |
Rv0708 rplP |
50S ribosomal protein L16 | 961 | 957 ctx | cooccurence:521 experimental:908 |
Rv2890c rpsB |
30S ribosomal protein S2 | 958 | 956 | experimental:907 |
Rv2909c rpsP |
30S ribosomal protein S16 | 950 | 946 | experimental:907 |
Rv0682 rpsL |
30S ribosomal protein S12 | 957 | 945 | experimental:907 |
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: peptide chain release factor PrfA
- MTBC0 PGAP product: peptide chain release factor 1
- Pfam (hmmscan --cut_ga): PCRF PF03462.24 (E=3e-60), RF-1 PF00472.27 (E=6e-41)
- (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_215815.1)
- 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 P9WHG3 (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 —
167 functional partner(s); context anchor
hemK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001391|Rv1299|prfA MTQPVQTIDVLLAEHAELELALADPALHSNPAEARRVGRRFARLAPIVATHRKLTSARDDLETARELVASDESFAAEVAALEARVGELDAQLTDMLAPRDPHDADDIVLEVKSGEGGEESALFAADLARMYIRYAERHGWAVTVLDETTSDLGGYKDATLAIASKADTPDGVWSRMKFEGGVHRVQRVPVTESQGRVHTSAAGVLVYPEPEEVGQVQIDESDLRIDVFRSSGKGGQGVNTTDSAVRITHLPTGIVVTCQNERSQLQNKTRALQVLAARLQAMAEEQALADASADRASQIRTVDRSERIRTYNFPENRITDHRIGYKSHNLDQVLDGDLDALFDALSAADKQSRLRQS