pheS Family assigned · medium auto-curated
H37Rv Rv1649 · MTBC0 - ·
341 aa · 1858733–1859758 (+) ·
RefSeq NP_216165.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phenylalanine--tRNA ligase subunit alpha |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Phenylalanine--tRNA ligase subunit alpha. Pfam: Phe_tRNA-synt_N (PF02912.24), tRNA-synt_2d (PF01409.26). |
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 |
P9WFU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phenylalanine--tRNA ligase alpha subunit |
| EC (curated) |
EC 6.1.1.20
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | pheS |
| eggNOG description | Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily |
| Orthologous group | COG0016 |
| EC number |
EC 6.1.1.20
|
| KEGG orthology |
K01889
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (61) |
GO:0003674, GO:0003824, GO:0004812, GO:0004826, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006082, GO:0006139, GO:0006399 +49 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 | 0.173 · 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 |
|---|---|---|---|---|
Phe_tRNA-synt_N | PF02912.24 | 8.0e-16 | 23–90 | Aminoacyl tRNA synthetase class II, N-terminal domain |
tRNA-synt_2d | PF01409.26 | 3.9e-95 | 95–334 | tRNA synthetases class II core domain (F) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pheT (phenylalanine--tRNA ligase subunit beta), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 999 | 1000 ctx | neighborhood:892 cooccurence:586 coexpression:998 experimental:999 database:963 textmining:965 |
Rv0708 rplP |
50S ribosomal protein L16 | 820 | 792 | coexpression:433 database:597 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 868 | 741 | coexpression:648 textmining:514 |
Rv1647 |
adenylate cyclase | 738 | 738 ctx | neighborhood:737 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 818 | 702 | coexpression:692 textmining:417 |
Rv2614c thrS |
threonine--tRNA ligase | 753 | 678 | coexpression:432 |
Rv0684 fusA1 |
elongation factor G | 712 | 673 | coexpression:515 |
Rv0683 rpsG |
30S ribosomal protein S7 | 734 | 653 | coexpression:652 |
Rv3419c gcp |
O-sialoglycoprotein endopeptidase | 713 | 623 ctx | cooccurence:590 |
Rv0685 tuf |
elongation factor Tu | 724 | 621 | coexpression:621 |
Rv2524c fas |
fatty acid synthase | 596 | 596 | coexpression:564 |
Rv0721 rpsE |
30S ribosomal protein S5 | 651 | 590 | coexpression:462 |
Rv0716 rplE |
50S ribosomal protein L5 | 690 | 587 | coexpression:514 |
Rv1689 tyrS |
tyrosine--tRNA ligase | 683 | 587 | coexpression:486 |
Rv1643 rplT |
50S ribosomal protein L20 | 659 | 584 |
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): phenylalanine--tRNA ligase subunit alpha
- Pfam (hmmscan --cut_ga): Phe_tRNA-synt_N PF02912.24 (E=8e-16), tRNA-synt_2d PF01409.26 (E=4e-95)
- (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_216165.3)
- Domains: Pfam-A via hmmscan --cut_ga — Phe_tRNA-synt_N (PF02912.24), tRNA-synt_2d (PF01409.26)
- 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
COG0016 - Curated reference: UniProt P9WFU3 (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 —
132 functional partner(s); context anchor
pheT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1649|pheS MLSPEALTTAVDAAQQAIALADTLDVLARVKTEHLGDRSPLALARQALAVLPKEQRAEAGKRVNAARNAAQRSYDERLATLRAERDAAVLVAEGIDVTLPSTRVPAGARHPIIMLAEHVADTFIAMGWELAEGPEVETEQFNFDALNFPADHPARGEQDTFYIAPEDSRQLLRTHTSPVQIRTLLARELPVYIISIGRTFRTDELDATHTPIFHQVEGLAVDRGLSMAHLRGTLDAFARAEFGPSARTRIRPHFFPFTEPSAEVDVWFANKIGGAAWVEWGGCGMVHPNVLRATGIDPDLYSGFAFGMGLERTLQFRNGIPDMRDMVEGDVRFSLPFGVGA