PSEPK ppu00970: Aminoacyl-tRNA biosynthesis
- Module seed:
bacterial_aminoacyl_trna_charging - Candidate genes from membership table: 27
- Primary bucket genes: 24
- Existing review files: 26
- Curated review files: 26
- Selected module proteins: 24
- Selected gene reviews audited in this batch: 24
Curated Boundary
- The reusable module ends when a correctly charged canonical aminoacyl-tRNA
has been formed. Aminoacyl-tRNA use in initiation, elongation, protein
formylation, selenocysteine synthesis, and quality-control hydrolysis is
downstream or adjacent biology. - Direct charging is organized into class I and class II aaRS groups. Each
substrate-specific molecular function is attached to a leaf annoton, with
the exact PSEPK UniProt protein as its representative member. - Bacterial alpha2-beta2 GlyRS (
glyQ,glyS) and PheRS (pheS,pheT) are
represented as complexes with explicit active subunits rather than as four
independent complete synthetases. - Asparaginyl-tRNA formation is a route variant: direct AsnRS where present, or
the two-part indirect route in which a non-discriminating AspRS supplies
Asp-tRNA(Asn) and GatABC transamidates it. KT2440 has no canonicalasnS;
Q88NJ4 AspS and Q88PB9/Q88PC0/Q88PB8 GatABC satisfy the indirect route. - Glutaminyl-tRNA formation is a route variant: direct GlnRS (
glnS) or the
two-part indirect route in which a non-discriminating GluRS supplies
Glu-tRNA(Gln) and GatABC (gatA,gatB,gatC) transamidates it. - KT2440 encodes both GlnS and GatABC. Its direct GlnS route is supported;
use of Q88LF6 GltX on tRNA(Gln) is not established and remains a knowledge
gap. The experimentally resolved homologous system in Pseudomonas aeruginosa
uses direct GlnRS charging and discriminating GluRS alongside the required
indirect AspRS-GatABC Asn route (PMID:14729703). fmtis excluded because it formylates already charged initiator
Met-tRNA(fMet).selAis excluded because it converts already charged
Ser-tRNA(Sec) after SerS aminoacylation.PP_0613/ Q88Q82 is an amidase-family KEGG-map candidate without an aaRS or
GatABC assignment and is excluded from the module pending contrary evidence.
Pathway Satisfiability
| Route or group | KT2440 implementation | Decision |
|---|---|---|
| Direct class I aaRS charging | argS, cysS, gltX, ileS, leuS, metG, trpS, tyrS, valS |
Covered by exact reviewed UniProt identities |
| Direct class II aaRS charging | alaS, aspS, glyQ-glyS, hisS, lysS, pheS-pheT, proS, serS, thrS |
Covered by exact reviewed UniProt identities |
| Direct Asn-tRNA(Asn) route | asnS |
Not present in KT2440; retained as a reusable bacterial alternative with exact ECOLI P0A8M0 exemplar |
| Indirect Asn-tRNA(Asn) route | aspS then gatA-gatB-gatC |
Required in KT2440 and covered by exact PSEPK exemplars plus comparative experimental support (PMID:14729703) |
| Direct Gln-tRNA(Gln) route | glnS / PP_2904 / Q88IU5 |
Covered by the exact reviewed UniProt identity |
| Indirect Gln-tRNA(Gln) route | non-discriminating GluRS then gatA-gatB-gatC |
Retained as a reusable bacterial alternative; not assigned to KT2440 because Q88LF6 recognition of tRNA(Gln) is unestablished |
The module is species-neutral and route-complete as a reusable model. The
required PSEPK indirect Asn route and direct Gln route are covered. KT2440
GatABC has predicted dual-substrate transamidation capacity, but no complete
indirect Gln route is asserted because Glu-tRNA(Gln) precursor production by
Q88LF6 has not been established.
Required Workflow
- [x] Curate or update the species-neutral module.
- [x] Run module-level OpenScientist deep research.
- [ ] Run module + pathway + PSEPK OpenScientist deep research.
- [x] Fetch all 24 selected PSEPK charging genes.
- [x] Use exact UniProt records plus module-level and taxon-aware primary evidence.
- [x] Apply the annotation-reviewer workflow to every GOA row for all 24 selected genes; retain DRAFT status because most local assignments are rule-based rather than direct KT2440 assays.
- [x] Validate the module and all selected gene reviews.
- [ ] Open and shepherd one wave121 PR through formal review.
2026-09-01: A fresh generic OpenScientist run completed after 1,328 seconds and
is included as modules/bacterial_aminoacyl_trna_charging-deep-research-openscientist.md.
No completed module+pathway+taxon OpenScientist report is present in the current
repository or the prior PR history; the KT2440 route decision therefore relies
on exact local records and cached primary evidence, especially PMID:14729703,
rather than claiming a missing report as support.
Candidate Genes
| Done | Gene | Locus | UniProt | Primary bucket | Existing review | Curation | OpenScientist research | Protein |
|---|---|---|---|---|---|---|---|---|
| [x] | glyS |
PP_0060 | Q88RR9 | kegg:ppu00970 | PRESENT | CURATED | module research | Glycine--tRNA ligase beta subunit (EC 6.1.1.14) (Glycyl-tRNA synthetase beta subunit) (GlyRS) |
| [x] | glyQ |
PP_0061 | Q88RR8 | kegg:ppu00970 | PRESENT | CURATED | module research | Glycine--tRNA ligase alpha subunit (EC 6.1.1.14) (Glycyl-tRNA synthetase alpha subunit) (GlyRS) |
| [ ] | fmt |
PP_0067 | Q88RR2 | kegg:ppu00970 | PRESENT | CURATED | MISSING | Methionyl-tRNA formyltransferase (EC 2.1.2.9) |
| [x] | tyrS |
PP_0436 | Q88QQ2 | kegg:ppu00970 | PRESENT | CURATED | module research | Tyrosine--tRNA ligase (EC 6.1.1.1) (Tyrosyl-tRNA synthetase) (TyrRS) |
| [ ] | selA |
PP_0493 | Q88QJ8 | kegg:ppu00450 | PRESENT | CURATED | PRESENT | L-seryl-tRNA(Sec) selenium transferase (EC 2.9.1.1) (Selenocysteine synthase) (Sec synthase) (Selenocysteinyl-tRNA(Sec) |
| [x] | ileS |
PP_0603 | Q88Q92 | kegg:ppu00970 | PRESENT | CURATED | module research | Isoleucine--tRNA ligase (EC 6.1.1.5) (Isoleucyl-tRNA synthetase) (IleRS) |
| [ ] | PP_0613 |
PP_0613 | Q88Q82 | kegg:ppu00970 | MISSING | MISSING | MISSING | Amidase family protein |
| [x] | hisS |
PP_0854 | Q88PJ6 | kegg:ppu00970 | PRESENT | CURATED | module research | Histidine--tRNA ligase (EC 6.1.1.21) (Histidyl-tRNA synthetase) (HisRS) |
| [x] | gatB |
PP_0930 | Q88PC0 | kegg:ppu00970 | PRESENT | CURATED | module research | Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (Asp/Glu-ADT subunit B) (EC 6.3.5.-) |
| [x] | gatA |
PP_0931 | Q88PB9 | kegg:ppu00970 | PRESENT | CURATED | module research | Glutamyl-tRNA(Gln) amidotransferase subunit A (Glu-ADT subunit A) (EC 6.3.5.7) |
| [x] | gatC |
PP_0932 | Q88PB8 | kegg:ppu00970 | PRESENT | CURATED | module research | Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C (Asp/Glu-ADT subunit C) (EC 6.3.5.-) |
| [x] | valS |
PP_0977 | Q88P76 | kegg:ppu00970 | PRESENT | CURATED | module research | Valine--tRNA ligase (EC 6.1.1.9) (Valyl-tRNA synthetase) (ValRS) |
| [x] | metG |
PP_1097 | Q88NV7 | kegg:ppu00450 | PRESENT | CURATED | module research | Methionine--tRNA ligase (EC 6.1.1.10) (Methionyl-tRNA synthetase) (MetRS) |
| [x] | proS |
PP_1205 | Q88NK2 | kegg:ppu00970 | PRESENT | CURATED | module research | Proline--tRNA ligase (EC 6.1.1.15) (Prolyl-tRNA synthetase) (ProRS) |
| [x] | aspS |
PP_1213 | Q88NJ4 | kegg:ppu00970 | PRESENT | CURATED | module research | Aspartate--tRNA(Asp/Asn) ligase (EC 6.1.1.23) (Aspartyl-tRNA synthetase) (AspRS) (Non-discriminating aspartyl-tRNA synth |
| [x] | trpS |
PP_1311 | Q88NA1 | kegg:ppu00970 | PRESENT | CURATED | module research | Tryptophan--tRNA ligase (EC 6.1.1.2) (Tryptophanyl-tRNA synthetase) (TrpRS) |
| [x] | lysS |
PP_1496 | Q88MS3 | kegg:ppu00970 | PRESENT | CURATED | module research | Lysine--tRNA ligase (EC 6.1.1.6) (Lysyl-tRNA synthetase) (LysRS) |
| [x] | gltX |
PP_1977 | Q88LF6 | kegg:ppu00860 | PRESENT | CURATED | module research | Glutamate--tRNA ligase (EC 6.1.1.17) (Glutamyl-tRNA synthetase) (GluRS) |
| [x] | thrS |
PP_2465 | Q88K27 | kegg:ppu00970 | PRESENT | CURATED | module research | Threonine--tRNA ligase (EC 6.1.1.3) (Threonyl-tRNA synthetase) (ThrRS) |
| [x] | pheS |
PP_2469 | Q88K23 | kegg:ppu00970 | PRESENT | CURATED | module research | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase alpha subunit) (PheRS) |
| [x] | pheT |
PP_2470 | Q88K22 | kegg:ppu00970 | PRESENT | CURATED | module research | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase beta subunit) (PheRS) |
| [x] | glnS |
PP_2904 | Q88IU5 | kegg:ppu00970 | PRESENT | CURATED | module research | Glutamine--tRNA ligase (EC 6.1.1.18) (Glutaminyl-tRNA synthetase) (GlnRS) |
| [x] | cysS |
PP_2905 | Q88IU4 | kegg:ppu00970 | PRESENT | CURATED | module research | Cysteine--tRNA ligase (EC 6.1.1.16) (Cysteinyl-tRNA synthetase) (CysRS) |
| [x] | serS |
PP_4000 | Q88FT2 | kegg:ppu00970 | PRESENT | CURATED | module research | Serine--tRNA ligase (EC 6.1.1.11) (Seryl-tRNA synthetase) (SerRS) (Seryl-tRNA(Ser/Sec) synthetase) |
| [x] | alaS |
PP_4474 | Q88EI8 | kegg:ppu00970 | PRESENT | CURATED | module research | Alanine--tRNA ligase (EC 6.1.1.7) (Alanyl-tRNA synthetase) (AlaRS) |
| [x] | leuS |
PP_4794 | Q88DN1 | kegg:ppu00970 | PRESENT | CURATED | module research | Leucine--tRNA ligase (EC 6.1.1.4) (Leucyl-tRNA synthetase) (LeuRS) |
| [x] | argS |
PP_5089 | Q88CU1 | kegg:ppu00970 | PRESENT | CURATED | module research | Arginine--tRNA ligase (EC 6.1.1.19) (Arginyl-tRNA synthetase) (ArgRS) |
Notes
The TSV is the machine-readable 27-protein KEGG candidate snapshot. The 24
checked charging genes have row-complete annotation-reviewer audits. fmt,
selA, and PP_0613 are retained only to document boundary exclusions and are
not counted as selected module proteins.