trpS Resolved · high auto-curated
H37Rv Rv3336c · MTBC0 mtbc0_003549 ·
336 aa · 3748606–3749616 (-) ·
RefSeq NP_217853.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tryptophan--tRNA ligase |
|---|---|
| MTBC0 PGAP re-annotation | tryptophan--tRNA ligase |
| Revised (this work) | Tryptophan--tRNA ligase. Pfam: tRNA-synt_1b (PF00579.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFT3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Tryptophan--tRNA ligase |
| EC (curated) |
EC 6.1.1.2
|
| Curated function | Catalyzes the attachment of tryptophan to tRNA(Trp). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | trpS |
| eggNOG description | Tryptophanyl-tRNA synthetase |
| Orthologous group | COG0180 |
| EC number |
EC 6.1.1.2
|
| KEGG orthology |
K01867
|
| KEGG pathways |
map00970
|
| KEGG modules |
M00359, M00360
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 0 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 | 4.2e-79 | 7–289 | tRNA synthetases class I (W and Y) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: yhjD (integral membrane protein), high confidence from genomic context alone (score 861 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3335c yhjD |
integral membrane protein | 861 | 861 ctx | neighborhood:857 |
Rv3308 pmmB |
phosphomannomutase PmmB | 629 | 629 ctx | fusion:611 |
Rv3338 |
Rv3338, (MTV016.38), len: 214 aa. Hypothetical protein, equivalent to C-termini of Q49926|ML0685 TPEA (putative hydrolase) from Mycobacteriu | 619 | 619 ctx | neighborhood:618 |
Rv3337 |
Rv3337, (MTV016.37), len: 128 aa. Conserved hypothetical protein, equivalent to N-terminus of Q49926|ML0685 TPEA (putative hydrolase) from M | 618 | 618 ctx | neighborhood:618 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 837 | 589 | coexpression:421 textmining:621 |
Rv3834c serS |
serine--tRNA ligase | 798 | 547 | coexpression:445 textmining:573 |
Rv2357c glyS |
glycine--tRNA ligase | 648 | 541 | coexpression:412 |
Rv3758c proV |
glycine betaine/carnitine/choline/L-proline ABC transporter ATP-binding protein ProV | 510 | 510 | coexpression:494 |
Rv2448c valS |
valine--tRNA ligase | 751 | 506 | textmining:517 |
Rv2535c pepQ |
cytoplasmic peptidase PepQ | 522 | 502 | |
Rv0041 leuS |
leucine--tRNA ligase | 825 | 498 | textmining:666 |
Rv2089c pepE |
dipeptidase PepE | 519 | 498 | |
Rv1689 tyrS |
tyrosine--tRNA ligase | 700 | 478 | textmining:449 |
Rv1292 argS |
arginine--tRNA ligase | 767 | 456 | coexpression:413 textmining:590 |
Rv0788 purQ |
phosphoribosylformylglycinamidine synthase | 455 | 456 | coexpression:425 |
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: tryptophan--tRNA ligase
- MTBC0 PGAP product: tryptophan--tRNA ligase
- Pfam (hmmscan --cut_ga): tRNA-synt_1b PF00579.32 (E=4e-79)
- (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_217853.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA-synt_1b (PF00579.32)
- 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
COG0180 - Curated reference: UniProt P9WFT3 (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 —
55 functional partner(s); context anchor
yhjD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003549|Rv3336c|trpS MSTPTGSRRIFSGVQPTSDSLHLGNALGAVAQWVGLQDDHDAFFCVVDLHAITIPQDPEALRRRTLITAAQYLALGIDPGRATIFVQSQVPAHTQLAWVLGCFTGFGQASRMTQFKDKSARQGSEATTVGLFTYPVLQAADVLAYDTELVPVGEDQRQHLELARDVAQRFNSRFPGTLVVPDVLIPKMTAKIYDLQDPTSKMSKSAGTDAGLINLLDDPALSAKKIRSAVTDSERDIRYDPDVKPGVSNLLNIQSAVTGTDIDVLVDGYAGHGYGDLKKDTAEAVVEFVNPIQARVDELTADPAELEAVLAAGAQRAHDVASKTVQRVYDRLGFLL