prfA Resolved · high auto-curated
H37Rv Rv1299 · MTBC0 mtbc0_001391 ·
357 aa ·
1464534–1465607 MTBC0
(+) ·
RefSeq NP_215815.1
Genomic neighbourhood (genome browser)
Open in full genome browser →This gene (outlined) in its genomic context; arrows are neighbouring genes coloured by verdict. Click any gene to navigate. Pan and zoom in the full browser.
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). |
| Functional category (TubercuList) | information pathways |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
In the literature (TB corpus sweep) 4 publications
4 TB publications mention this gene. 4 publication(s) discuss this gene (4 in a M. tuberculosis context).
This layer CITES the literature and adds context; it does not change the verdict or the function stated elsewhere in this fiche. This distinguishes a gene that is dark because nobody has looked from one that is dark despite having been studied. Source: PubMed (whole): H37Rv locus tag + GENE NAME + ortholog identifiers (Mb…, MMAR_…, MSMEG_…, ML…, MAB_…), under a mycobacterial context filter; hits verified against the abstract text. Species-context counts distinguish M. tuberculosis literature from literature on other mycobacteria. phase76/phase77, 2026-07-13.
Genomic-neighbour overlap (structural caveat) co-directional · 0 % of gene
| Neighbour | prmC (Rv1300, + strand) |
|---|---|
| Overlap | 4 bp, 0 % of this gene's length |
co-directional overlap: ordinary (e.g. shared stop/start codons in an operon), not the Rv2438A-type artefact P20.1, derived from GFF3 gene coordinates, 2026-08-03.
Post-translational modifications
2 reported modified residue(s):
N-acetylthreonine @2, N5-methylglutamine @236.
Experimentally reported post-translational modification(s). A phosphosite indicates the protein is expressed and is a substrate of the M. tuberculosis Ser/Thr/Tyr kinase signalling network — a regulatory context, NOT a molecular function. Source: UniProt (Modified residue features; PTM sites curated from the M. tuberculosis literature).
CRISPRi vulnerability
Vulnerability index -8.59 (95% CI -9.85 to -7.33). A more negative index = more vulnerable to knockdown (better drug-target quality); indicative threshold VI ≤ -6 = highly vulnerable.
Quantitative CRISPRi knockdown, graded (finer than binary Tn-seq essentiality). Source: CRISPRi vulnerability index (Bosch 2021, pebble.rockefeller.edu).
Legacy record & comparison (Mycobrowser)
| Mycobrowser function | Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA |
|---|
The legacy Mycobrowser record is shown for verification. Mycobrowser is no longer maintained; its EC numbers predate recent nomenclature revisions, so a class change usually reflects re-numbering, not a conflict.
Orthologues (reciprocal best hits across mycobacteria)
| M. bovis |
Mb1331
· 100.0% identity |
|---|---|
| M. leprae |
ML1134
· 89.4% identity |
| M. marinum |
MMAR_4098
· 84.0% identity |
| M. smegmatis |
MSMEG_4950
· 82.6% identity |
| M. orygis |
RJtmp_001369
· 100.0% identity |
| M. abscessus |
MAB_1442
· 83.7% identity |
Reciprocal-best-hit orthologues (DIAMOND) against the Mycobrowser reference proteomes. A missing species is informative: e.g. a gene absent from M. leprae was likely lost in its reductive genome evolution. Locus tags link to Mycobrowser.
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.
Outgroup conservation (beyond the MTBC) Bacteria
| M. canettii dN/dS (deep-divergence selection) |
inf (low power)
· 1 consensus substitution(s) low power (1 canettii-consensus substitution(s)); present in M. canettii but dN/dS not reliable |
|---|---|
| Genus-wide presence (~53 non-MTBC Mycobacterium) |
present in 53/53 (100%) · mean identity 90.1%
· 4/4 closest MTBAP relatives conserved across the genus (present in 53/53 non-MTBC Mycobacterium genomes, incl. distant relatives) — an ancient core gene predating the genus radiation |
| Phylostratum (deepest detected homolog) |
MTBC-specific → Mycobacterium → Mycobacteriaceae → Corynebacteriales → Actinomycetia → Bacteria detected in 13/13 non-Mycobacterium reference genomes (down to Bacteria) · mean identity 66.5% detected down to outside the phylum (Proteobacteria/Firmicutes controls) — a universally conserved, ancient bacterial gene |
Two orthogonal outgroup signals. M. canettii (the immediate outgroup) gives a deep-divergence dN/dS (a low value confirms a constrained, real gene; shown as confident only at ≥8 substitutions, else flagged low-power). Genus-wide presence/absence (tblastn vs assembled non-MTBC genomes) places the gene on the ancient-core ↔ MTBC-specific axis: a gene absent even from the closest MTBAP relatives is a candidate MTBC-specific innovation (possible host-adaptation factor, to confirm by synteny). The phylostratum extends that axis outside the genus (tblastn vs 13 reference genomes spanning Mycobacteriaceae → Corynebacteriales → Actinomycetia → outside the phylum): it is the deepest clade in which a homolog is still detected, i.e. a proxy for gene age. Read it with the null model in mind: a shallow (young) stratum can also reflect homology-detection failure for short or fast-evolving ORFs, so it is a descriptive axis, not a proof of novelty.
Essentiality (transposon mutagenesis) essential
| DeJesus 2017 call | ES · essential |
|---|---|
| What the call means | essential: insertions absent across the whole ORF |
| TA sites (Himar1) | 14 in the ORF — 14 in the essential state, 0 growth-defect, 0 non-essential, 0 growth-advantage. Saturation 0.000, mean read count 0. A region of the protein devoid of TA sites is invisible to this assay: nothing can be inferred about it, in either direction. |
Genome-wide Himar1 transposon essentiality in H37Rv (DeJesus 2017). An essential call (ES/ESD/GD) is strong, independent evidence that a "hypothetical" locus encodes a functional, selectively required gene — orthogonal to intra-species conservation.
Chemical-genetic target & druggability (PROSPECT) hypomorph tool strain
This gene is part of the PROSPECT collection of TetON transcriptional-knockdown (hypomorph) strains of essential M. tuberculosis genes, built as a sensitised background for chemical-genetic mechanism-of-action deconvolution. Being in the panel means the gene is an essential / vulnerable target for which a validated knockdown tool strain exists.
| Hypomorph strain | prfA-FLAG-tetOn-2 (TetON promoter 2) |
|---|---|
| Baseline knockdown fitness | 2.257 median doublings (across 6 screen pool(s)) — fewer doublings = stronger growth defect on knockdown |
| Used in target deconvolution | yes (informs phenotypic-cluster / MOA assignment) |
Panel membership reflects essentiality/vulnerability and the availability of a genetic tool, not a specific molecular function; it never changes the verdict here. Source: Bond AN et al., Nat Commun 2025;16:9673 (doi:10.1038/s41467-025-64662-x); PROSPECT chemical-genetic platform.
Proteomics (mass spectrometry) detected
| MS detection | detected in 14 of 16 independent MS datasets |
|---|---|
| Integrated abundance | 167.0 ppm · rank 940/3519 (73.3th percentile) |
Detection by mass spectrometry is direct, experimental evidence that the protein product exists — orthogonal to sequence conservation and to Tn-seq essentiality, and especially decisive for a "hypothetical" locus. Reproducible detection across several independent datasets (PaxDb) makes the existence claim robust; the integrated abundance places the protein in the proteome's dynamic range.
Physico-chemical properties (computed, ProtParam)
| Length | 357 aa |
|---|---|
| Molecular weight | 39.0 kDa |
| Theoretical pI | 5.06 |
| GRAVY | -0.406 (hydrophilic) |
| Aliphatic index | 88.3 |
| Aromaticity | 0.042 |
| Instability index | 36.5 (stable) |
Computed from the ancestral MTBC0 sequence with the ExPASy ProtParam method (Biopython). Descriptive biophysical context: a positive GRAVY flags a hydrophobic (often membrane) protein, a high instability index (>40) predicts a short in-vitro half-life, an extreme pI hints at compartment or binding partner.
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 |
Structural search (AlphaFold DB model, Foldseek vs PDB — genome-wide) pLDDT 87.8
| PDB hit | prob | TM-score | E-value | Description |
|---|---|---|---|---|
9d7s-assembly2_2w |
1.00 | 0.90 | 4.2e-29 sig | 9d7s-assembly2_2w Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Api antimicrobial peptide, mRNA, A-site release factor 1, and deacylated P-site and E-site tRNAphe at 2.85A resolution |
8akn-assembly1_W |
1.00 | 0.67 | 9.9e-35 sig | 8akn-assembly1_W Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome |
4v63-assembly1_AX |
1.00 | 0.70 | 1.5e-31 sig | 4v63-assembly1_AX Structural basis for translation termination on the 70S ribosome. |
6bok-assembly2_HD |
1.00 | 0.87 | 6.4e-27 sig | 6bok-assembly2_HD E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome |
8fze-assembly1_w |
1.00 | 0.68 | 4.9e-31 sig | 8fze-assembly1_w Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State I-A) |
Foldseek search of the AlphaFold DB model (mean pLDDT 87.8, gated at 70) against the PDB — a genome-wide extension of the ESMFold dark-gene search that also covers proteins beyond the single-sequence length limit. Confident structural neighbours (E < 0.01) shown.
Genomic context (neighbours & predicted operon) operon of 3
| Upstream (5' on genome) | rpmE (+ strand, 89 bp gap) |
|---|---|
| Downstream (3' on genome) | hemK (+ strand, -4 bp gap) |
| Predicted operon |
prfA · hemK · Rv1301
|
Neighbours from the H37Rv annotation (+ strand). The operon is predicted by co-directional intergenic distance (same strand, gaps ≤50 bp) — a transcription-unit hypothesis, not a mapped TSS. For a "hypothetical", co-transcription with a characterised operon is a concrete functional lead (complements the STRING neighborhood channel below).
Functional interaction network (STRING v12, guilt-by-association)
Explore full network →Node colour = verdict, dashed = hypothetical; edge colour = evidence (green experimental, orange genomic-context, grey co-expression), width ∝ score. Click a partner to open its page; "Explore full network" to walk the graph.
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 exp |
release factor glutamine methyltransferase | 999 | 999 ctx | neighborhood:881 coexpression:896 experimental:890 textmining:551 |
Rv3443c rplM exp |
50S ribosomal protein L13 | 979 | 979 ctx | cooccurence:683 experimental:908 |
Rv1643 rplT exp |
50S ribosomal protein L20 | 979 | 977 ctx | cooccurence:582 coexpression:411 experimental:913 |
Rv1298 rpmE exp |
50S ribosomal protein L31 | 979 | 977 ctx | neighborhood:778 coexpression:434 experimental:830 |
Rv2441c rpmA exp |
50S ribosomal protein L27 | 978 | 973 ctx | cooccurence:610 experimental:913 |
Rv0683 rpsG exp |
30S ribosomal protein S7 | 976 | 969 ctx | cooccurence:544 experimental:907 |
Rv0702 rplD exp |
50S ribosomal protein L4 | 968 | 966 ctx | cooccurence:567 experimental:908 |
Rv3442c rpsI exp |
30S ribosomal protein S9 | 967 | 964 ctx | cooccurence:501 experimental:907 |
Rv2785c rpsO exp |
30S ribosomal protein S15 | 964 | 961 ctx | cooccurence:555 experimental:907 |
Rv0701 rplC exp |
50S ribosomal protein L3 | 964 | 960 ctx | cooccurence:535 experimental:908 |
Rv3456c rplQ exp |
50S ribosomal protein L17 | 964 | 959 ctx | cooccurence:486 experimental:913 |
Rv0708 rplP exp |
50S ribosomal protein L16 | 961 | 957 ctx | cooccurence:521 experimental:908 |
Rv2890c rpsB exp |
30S ribosomal protein S2 | 958 | 956 | experimental:907 |
Rv2909c rpsP exp |
30S ribosomal protein S16 | 950 | 946 | experimental:907 |
Rv0682 rpsL exp |
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 exp badge marks an experimentally-supported partner (measured interaction, experimental/database channel ≥400) as opposed to a purely predicted one — but note that the M. tuberculosis experimental interactome is dominated by a noisy bacterial-two-hybrid screen, so a strong measured link that contradicts the operon/localisation context is likely a false positive. 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)
- Genome-wide structure: AlphaFold DB model (Jumper et al. 2021, doi:10.1038/s41586-021-03819-2; Varadi et al. 2024, doi:10.1093/nar/gkad1011) searched vs PDB with Foldseek (mean pLDDT 87.8)
- 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 - Essentiality: genome-wide transposon mutagenesis in H37Rv — DeJesus et al. 2017 (mBio, doi:10.1128/mBio.02133-16, CC BY)
- Proteomics: integrated mass-spectrometry abundance from PaxDb 5.0 (Huang et al. 2023, doi:10.1016/j.mcpro.2023.100640), taxon 83332 — weighted average of 16 datasets, incl. Schubert et al. 2013 (doi:10.1016/j.chom.2013.04.008) and Albrethsen et al. 2013 (doi:10.1074/mcp.M112.018846)
- Functional category: TubercuList scheme (Cole et al. 1998, doi:10.1038/31159), via Mycobrowser (Kapopoulou et al. 2011, doi:10.1016/j.tube.2010.09.006)
- Orthologues: reciprocal best hits (DIAMOND, Buchfink et al. 2021, doi:10.1038/s41592-021-01101-x) against Mycobrowser release 5 reference proteomes
- Genomic context / operon: H37Rv annotation; operon predicted by co-directional intergenic distance (Salgado et al. 2000, doi:10.1073/pnas.030539397)
- Physico-chemical properties: ExPASy ProtParam method via Biopython (Gasteiger et al. 2005), computed from the MTBC0 sequence
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001391|Rv1299|prfA MTQPVQTIDVLLAEHAELELALADPALHSNPAEARRVGRRFARLAPIVATHRKLTSARDDLETARELVASDESFAAEVAALEARVGELDAQLTDMLAPRDPHDADDIVLEVKSGEGGEESALFAADLARMYIRYAERHGWAVTVLDETTSDLGGYKDATLAIASKADTPDGVWSRMKFEGGVHRVQRVPVTESQGRVHTSAAGVLVYPEPEEVGQVQIDESDLRIDVFRSSGKGGQGVNTTDSAVRITHLPTGIVVTCQNERSQLQNKTRALQVLAARLQAMAEEQALADASADRASQIRTVDRSERIRTYNFPENRITDHRIGYKSHNLDQVLDGDLDALFDALSAADKQSRLRQS
Spot an error? Suggest an improvement
Found a mistake, a missing reference, or have a better functional hypothesis for prfA? Email the maintainer — the message is pre-filled with this gene's details.