pth Resolved · high auto-curated
H37Rv Rv1014c · MTBC0 mtbc0_001089 ·
191 aa · 1140670–1141245 (-) ·
RefSeq NP_215530.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peptidyl-tRNA hydrolase |
|---|---|
| MTBC0 PGAP re-annotation | aminoacyl-tRNA hydrolase |
| Revised (this work) | Aminoacyl-tRNA hydrolase. Pfam: Pept_tRNA_hydro (PF01195.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHN7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Peptidyl-tRNA hydrolase |
| EC (curated) |
EC 3.1.1.29
|
| Curated function | Hydrolyzes ribosome-free peptidyl-tRNAs (with 1 or more amino acids incorporated), which drop off the ribosome during protein synthesis, or as a result of ribosome stalling..; FUNCTION: Catalyzes the release of premature peptidyl moieties from peptidyl-tRNA molecules trapped in stalled 50S ribosomal subunits, and thus maintains levels of free tRNAs and 50S ribosomes..; FUNCTION: Important for recycling peptidyl-tRNA(Pro) that has dropped off during the incorporation of proline into a growing peptide. Probably cleaves the acetyl group off acetylated aminoacylated-tRNA (produced by TacT for exam. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | pth |
| eggNOG description | The natural substrate for this enzyme may be peptidyl- tRNAs which drop off the ribosome during protein synthesis |
| Orthologous group | COG0193 |
| EC number |
EC 3.1.1.29
|
| KEGG orthology |
K01056
|
| Gene Ontology (16) |
GO:0003674, GO:0003824, GO:0004045, GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0016787, GO:0016788, GO:0040007, GO:0044464 +4 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 | 1.037 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
Pept_tRNA_hydro | PF01195.26 | 4.8e-67 | 6–189 | Peptidyl-tRNA hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplY (50S ribosomal protein L25/general stress protein Ctc), high confidence from genomic context alone (score 940 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 942 | 940 ctx | neighborhood:874 coexpression:486 |
Rv1112 ychF |
GTP-binding protein | 862 | 820 | coexpression:710 |
Rv1020 mfd |
transcription-repair coupling factor | 775 | 742 | coexpression:644 |
Rv1016c lpqT |
lipoprotein LpqT | 730 | 729 ctx | neighborhood:728 |
Rv3625c mesJ |
tRNA(Ile)-lysidine synthase | 692 | 673 | coexpression:646 |
Rv1307 atpH |
ATP synthase subunit b/delta | 675 | 656 | coexpression:648 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 663 | 648 ctx | neighborhood:498 |
Rv2404c lepA |
GTP-binding protein LepA | 668 | 627 ctx | cooccurence:562 |
Rv2882c frr |
ribosome recycling factor | 709 | 621 ctx | cooccurence:612 |
Rv3443c rplM |
50S ribosomal protein L13 | 612 | 613 ctx | cooccurence:515 |
Rv3105c prfB |
peptide chain release factor PrfB | 693 | 612 | coexpression:493 |
Rv3456c rplQ |
50S ribosomal protein L17 | 665 | 607 ctx | cooccurence:585 |
Rv0690c hyp |
hypothetical protein | 574 | 573 ctx | fusion:538 |
Rv1402 priA |
primosomal protein N' | 535 | 536 | coexpression:512 |
Rv1299 prfA |
peptide chain release factor PrfA | 833 | 535 ctx | cooccurence:494 textmining:656 |
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: peptidyl-tRNA hydrolase
- MTBC0 PGAP product: aminoacyl-tRNA hydrolase
- Pfam (hmmscan --cut_ga): Pept_tRNA_hydro PF01195.26 (E=5e-67)
- (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_215530.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pept_tRNA_hydro (PF01195.26)
- 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
COG0193 - Curated reference: UniProt P9WHN7 (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 —
101 functional partner(s); context anchor
rplY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001089|Rv1014c|pth MAEPLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLAKPRCYMNESGRQIGPLAKFYSVAPANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVVAALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGMEPAQNRVHAW