tyrS Resolved · high auto-curated
H37Rv Rv1689 · MTBC0 mtbc0_001797 ·
424 aa · 1925617–1926891 (+) ·
RefSeq NP_216205.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tyrosine--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | tyrosine--tRNA ligase |
| Revised (this work) | Tyrosine--tRNA ligase. Pfam: tRNA-synt_1b (PF00579.32), SYY_C-terminal (PF22421.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFT1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Tyrosine--tRNA ligase |
| EC (curated) |
EC 6.1.1.1
|
| Curated function | Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | tyrS |
| eggNOG description | Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr) |
| Orthologous group | COG0162 |
| EC number |
EC 6.1.1.1
|
| KEGG orthology |
K01866
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (47) |
GO:0003674, GO:0003824, GO:0004812, GO:0004831, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006082 +35 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 | 0.337 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
tRNA-synt_1b | PF00579.32 | 2.0e-84 | 30–325 | tRNA synthetases class I (W and Y) |
SYY_C-terminal | PF22421.2 | 4.3e-14 | 354–415 | Tyrosine--tRNA ligase SYY-like C-terminal domain |
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 907 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 956 | 907 ctx | neighborhood:544 coexpression:804 textmining:554 |
Rv1688 mpg |
3-methyladenine DNA glycosylase | 884 | 872 ctx | neighborhood:872 |
Rv2889c tsf |
elongation factor EF-Ts | 760 | 697 | coexpression:511 |
Rv2524c fas |
fatty acid synthase | 691 | 690 | coexpression:645 |
Rv1292 argS |
arginine--tRNA ligase | 972 | 680 | coexpression:655 textmining:919 |
Rv1299 prfA |
peptide chain release factor PrfA | 849 | 645 | coexpression:560 textmining:593 |
Rv1687c |
ABC transporter ATP-binding protein | 644 | 644 ctx | neighborhood:600 |
Rv1536 ileS |
isoleucine--tRNA ligase | 934 | 634 | coexpression:544 textmining:829 |
Rv1686c |
ABC transporter permease | 631 | 631 ctx | neighborhood:631 |
Rv0041 leuS |
leucine--tRNA ligase | 966 | 609 | coexpression:406 textmining:917 |
Rv2793c truB |
tRNA pseudouridine synthase B | 640 | 592 | |
Rv1649 pheS |
phenylalanine--tRNA ligase subunit alpha | 683 | 587 | coexpression:486 |
Rv2357c glyS |
glycine--tRNA ligase | 674 | 575 | coexpression:468 |
Rv1643 rplT |
50S ribosomal protein L20 | 571 | 572 | coexpression:403 |
Rv1279 |
GMC-type oxidoreductase | 555 | 555 ctx | fusion:505 |
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: tyrosine--tRNA ligase
- MTBC0 PGAP product: tyrosine--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA-synt_1b PF00579.32 (E=2e-84), SYY_C-terminal PF22421.2 (E=4e-14)
- (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_216205.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA-synt_1b (PF00579.32), SYY_C-terminal (PF22421.2)
- 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
COG0162 - Curated reference: UniProt P9WFT1 (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 —
70 functional partner(s); context anchor
pheT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001797|Rv1689|tyrS MSGMILDELSWRGLIAQSTDLDTLAAEAQRGPMTVYAGFDPTAPSLHAGHLVPLLTLRRFQRAGHRPIVLAGGATGMIGDPRDVGERSLNEADTVAEWTERIRGQLERFVDFDDSPMGAIVENNLEWTGSLSAIEFLRDIGKHFSVNVMLARDTIRRRLAGEGISYTEFSYLLLQANDYVELHRRHGCTLQIGGADQWGNIIAGVRLVRQKLGATVHALTVPLVTAADGTKFGKSTGGGSLWLDPQMTSPYAWYQYFVNTADADVIRYLRWFTFLSADELAELEQATAQRPQQRAAQRRLASELTVLVHGEAATAAVEHASRALFGRGELARLDEATLAAALRETTVAELKPGSPDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDFLHGRWLVLRRGKRSIAGVERIG