P. putida Gene Annotation Review Project
Overview
Systematic AI-assisted review of GO annotations for Pseudomonas putida, focusing primarily on the well-characterized KT2440 strain (UniProt: PSEPK). P. putida is a metabolically versatile soil bacterium of significant interest for bioremediation, industrial biotechnology, and plant growth promotion. Its annotations are predominantly from automated pipelines (InterPro2GO, UniProtKB-KW, TreeGrafter), with very few experimental annotations (~50 from PMIDs), making careful review essential.
Organism Details
- Species: Pseudomonas putida
- Primary strain: KT2440 (UniProt taxon code: PSEPK)
- Other strains: PSEPU (general P. putida)
- Genome: ~6.2 Mb, ~5,350 protein-coding genes
- Key biology: Aromatic compound degradation, solvent tolerance, plant root colonization, polyhydroxyalkanoate (PHA) biosynthesis, rare earth element utilization
Completed Reviews
PSEPK (P. putida KT2440) — 18 genes reviewed
| Gene |
Annotations |
Function |
Notes |
PR |
| BenR |
8 |
Transcriptional regulator, benzoate catabolism |
AraC/XylS family |
— |
| PP_0635 |
9 |
Uncharacterized protein |
DUF domain analysis |
— |
| ada |
16 |
Methyltransferase, DNA repair |
Adaptive response to alkylation |
— |
| ampC |
5 |
Beta-lactamase |
Antibiotic resistance |
— |
| ftsY |
11 |
Signal recognition particle receptor |
Sec-dependent protein targeting |
— |
| hglS |
2 |
Hydroxyglutarate synthase |
Rare enzymatic function |
— |
| mrcA |
16 |
Penicillin-binding protein 1a |
Peptidoglycan biosynthesis |
— |
| pedH |
14 |
PQQ-dependent alcohol dehydrogenase |
REE/lanthanide utilization |
— |
| quiC1_qsuB |
8 |
Quinate/shikimate dehydrogenase |
Aromatic compound catabolism |
— |
| rpoS |
— |
Stationary phase sigma factor |
GO:0016987 core; added starvation/biofilm terms; DRAFT |
#159 |
| fleQ |
— |
Flagellar/biofilm master regulator |
Sigma-54 associated; added flagellum assembly/biofilm terms |
#162 |
| pvdA |
— |
L-ornithine N5-monooxygenase |
Pyoverdine biosynthesis; COMPLETE |
#163 |
| algD |
— |
GDP-mannose 6-dehydrogenase |
Alginate biosynthesis |
#157 |
| gacA |
— |
GacS/GacA response regulator |
Phosphorelay; biofilm/T6SS regulation |
#155 |
| pcaG |
— |
Protocatechuate 3,4-dioxygenase α subunit |
Iron-binding terms corrected (β subunit) |
#160 |
| phaC |
— |
PHA synthase (phaC-II, Q88D23) |
Corrected to PHA biosynthetic process |
#161 |
| cbrB |
— |
CbrA/CbrB response regulator |
Carbon catabolite repression; COMPLETE |
#158 |
| xylR |
— |
TOL plasmid regulator (P06519) |
Not native KT2440; organism mismatch noted |
#156 |
PSEPU (general P. putida) — 1 gene
| Gene |
Annotations |
Function |
| Q88CC1 |
reviewed |
Uncharacterized |
Batch 2 — Selected for Review (50 new genes)
Fifty additional well-characterized KT2440 (taxon 160488) genes selected to broaden
functional coverage beyond the initial aromatic-catabolism/biotechnology focus, into
central carbon metabolism, stress response, DNA repair, motility, and membrane transport.
All were seeded via fetch-gene (UniProt + GOA). None overlap with previously present
gene folders.
Status: reviews complete. Each gene has a Falcon (Edison Scientific) deep-research
report (*-deep-research-falcon.md) and a fully reviewed *-ai-review.yaml — all GOA
annotations adjudicated (no PENDING), with descriptions, core_functions, and
references. The review pass corrected a number of mis-annotations and citation errors
surfaced in the raw reports (e.g. wrong PMIDs in exbB/fur/relA/pilA/hpd; cofactor terms
in fur (Zn→Fe(II)) and icd (NADP-specific); TreeGrafter/InterPro2GO over-propagations in
mdh, sdhA, groES, hfq, pvdQ; sigma-factor GO convention for rpoD/rpoH).
Stress response, chaperones & global regulation (12)
| Gene |
UniProt |
Function |
| dnaK |
Q88DU2 |
Hsp70 chaperone (protein folding) |
| groEL |
Q88N55 |
GroEL chaperonin |
| groES |
Q88N56 |
GroES co-chaperonin |
| grpE |
Q88DU1 |
DnaK nucleotide-exchange factor |
| htpG |
Q88FB9 |
Hsp90 chaperone |
| rpoH |
Q7CCA6 |
Heat-shock sigma factor (σ32) |
| rpoD |
Q88QU7 |
Primary/housekeeping sigma factor (σ70) |
| fur |
Q88DT9 |
Ferric uptake regulator |
| oxyR |
Q88C74 |
Peroxide-responsive transcription regulator |
| relA |
Q88MB8 |
(p)ppGpp synthetase (stringent response) |
| hfq |
Q88DD3 |
RNA chaperone / sRNA-mediated regulation |
| ppk |
Q88CG4 |
Polyphosphate kinase |
DNA repair & recombination (7)
| Gene |
UniProt |
Function |
| recA |
Q88ME4 |
Recombinase / SOS response |
| recB |
Q88DZ5 |
Exonuclease V β subunit |
| ruvB |
Q88NJ0 |
Holliday junction branch-migration helicase |
| uvrB |
Q88LF9 |
Excinuclease ABC subunit B (NER) |
| uvrC |
Q88FJ7 |
Excinuclease ABC subunit C (NER) |
| mutL |
Q88DD1 |
DNA mismatch repair (MutL) |
| mutS |
Q88ME7 |
DNA mismatch repair (MutS) |
| Gene |
UniProt |
Function |
| gltA |
Q88FA4 |
Citrate synthase |
| acnB |
Q88KF1 |
Aconitase B |
| icd |
Q88FS2 |
Isocitrate dehydrogenase |
| sucA |
Q88FA9 |
2-oxoglutarate dehydrogenase E1 |
| sucC |
Q88FB2 |
Succinyl-CoA synthetase β |
| sdhA |
Q88FA7 |
Succinate dehydrogenase flavoprotein |
| fumC |
Q88M20 |
Fumarase C |
| mdh |
Q88Q44 |
Malate dehydrogenase |
| Gene |
UniProt |
Function |
| gapA |
Q88P44 |
Glyceraldehyde-3-phosphate dehydrogenase |
| pgk |
Q88D64 |
Phosphoglycerate kinase |
| eno |
Q88MF9 |
Enolase |
| tpiA |
Q88DV4 |
Triosephosphate isomerase |
| pykA |
Q88N54 |
Pyruvate kinase |
| ppc |
Q88MR4 |
PEP carboxylase (anaplerotic) |
| pgl |
Q88P30 |
6-phosphogluconolactonase (ED/PPP) |
| aceA |
Q88FI0 |
Isocitrate lyase (glyoxylate shunt) |
| pta |
Q88PS4 |
Phosphate acetyltransferase (acetate overflow) |
Chemotaxis & motility (4)
| Gene |
UniProt |
Function |
| cheY |
Q88EW2 |
Chemotaxis response regulator |
| cheZ |
Q88EW3 |
CheY-P phosphatase |
| fliG |
Q88ET5 |
Flagellar motor switch (C-ring) |
| pilA |
Q88Q62 |
Type IV pilin |
Membrane transport, iron & nitrogen acquisition (8)
| Gene |
UniProt |
Function |
| oprD |
Q88NK1 |
Outer-membrane porin D |
| oprE |
Q88R99 |
Outer-membrane porin E (anaerobically induced) |
| tonB |
Q88C75 |
TonB (energization of OM transport) |
| exbB |
Q88C77 |
ExbB (TonB system) |
| amtB |
Q88CE8 |
Ammonium transporter |
| glnK |
Q88CE7 |
PII nitrogen-regulatory protein |
| pvdQ |
Q88IU8 |
Pyoverdine maturation acylase |
| fpvA |
Q88F81 |
Ferripyoverdine TonB-dependent receptor |
Aromatic / aromatic-amino-acid catabolism (2)
| Gene |
UniProt |
Function |
| hpd |
Q88HC7 |
4-hydroxyphenylpyruvate dioxygenase |
| fcs |
Q88HK0 |
Feruloyl-CoA synthetase (ferulate catabolism) |
Batch 3 — Aromatic Amino Acid (AAA) Biosynthesis Pathway (16 genes)
The shikimate → chorismate → Trp/Phe/Tyr biosynthetic pathway in KT2440 (taxon
160488). Complements the existing aromatic catabolism coverage (ben/cat/pca) with the
anabolic route to aromatic amino acids. Seeded via fetch-gene; Falcon (Edison)
deep-research reports generated per gene. Status: reviews complete — all
annotations adjudicated, descriptions/core_functions/references populated (e.g. trpC and
aroQ over-propagation fixes; aroA bifunctional EPSPS/TyrA module captured). Name variants not resolving as primary UniProt
symbols in KT2440 are covered by a resolved paralog (aroD→aroQ, aroF/aroG→aroH, aroL→aroK)
or are differently named / fused in Pseudomonas (trpG, pheC, tyrA).
Shikimate trunk (common pathway, 7)
| Gene |
UniProt |
Function |
| aroH |
Q88LR3 |
DAHP synthase (3-deoxy-D-arabino-heptulosonate-7-P synthase) |
| aroB |
Q88CV2 |
3-dehydroquinate synthase |
| aroQ |
Q88IJ6 |
3-dehydroquinate dehydratase (type II) |
| aroE |
Q88IJ7 |
Shikimate dehydrogenase |
| aroK |
Q88CV1 |
Shikimate kinase |
| aroA |
Q88M05 |
EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) |
| aroC |
Q88LU7 |
Chorismate synthase |
Tryptophan branch (6)
| Gene |
UniProt |
Function |
| trpE |
Q88QS1 |
Anthranilate synthase component I |
| trpD |
Q88QR7 |
Anthranilate phosphoribosyltransferase |
| trpC |
Q88QR6 |
Indole-3-glycerol-phosphate synthase |
| trpF |
Q88LE0 |
N-(5'-phosphoribosyl)anthranilate isomerase |
| trpA |
Q88RP7 |
Tryptophan synthase α |
| trpB |
Q88RP6 |
Tryptophan synthase β |
Phe/Tyr branch & aromatic aminotransferases (3)
| Gene |
UniProt |
Function |
| pheA |
Q88M06 |
Chorismate mutase / prephenate dehydratase (P-protein) |
| tyrB |
Q88LG1 |
Aromatic-amino-acid aminotransferase |
| hisC |
Q88P86 |
Histidinol-phosphate / aromatic aminotransferase |
Priority Genes for Future Review
Aromatic Catabolism (core P. putida biology)
- benABCD — Benzoate dioxygenase complex
- catABC — Catechol branch of β-ketoadipate pathway
- pcaGHBDCIJF — Protocatechuate branch
- nahABCDEF — Naphthalene degradation (if present in KT2440 derivatives)
- xylXYZ — Toluene/xylene degradation (TOL plasmid genes)
- phaABCZ — Polyhydroxyalkanoate biosynthesis
- glk, zwf, edd, eda — Glucose catabolism (ED pathway, no EMP)
- gcd — Glucose dehydrogenase (periplasmic oxidation)
- PP_1084 (oleC), PP_1083 (oleD) — Olefin biosynthesis
Rare Earth Element Biology
- pedE — Ca²⁺-dependent ethanol dehydrogenase (counterpart to pedH)
- lanM — Lanmodulin (lanthanide-binding protein)
- lutH/lutABCDEF — Lanthanide uptake and transport
Solvent Tolerance
- ttgABC, ttgDEF, ttgGHI — Toluene efflux pumps (RND family)
- srpABC — Solvent resistance regulon
Plant Interactions
- pvdABCDES — Pyoverdine siderophore biosynthesis
- iaaM/iaaH — Indole-3-acetic acid biosynthesis (auxin)
- algABCDEFG — Alginate biosynthesis
Stress Response & Regulation
- rpoS — Stationary phase sigma factor
- gacA/gacS — Global regulatory two-component system
- fleQ — Flagellar/biofilm master regulator
- cbrA/cbrB — Carbon-nitrogen balance regulation
- SPKW-PSEPK — Analysis of UniProtKB-KW annotation patterns in P. putida
- REE — Rare earth element biology (pedH is a key gene)
- BIOSENSORS — Biosensor applications (BenR is relevant)
Notes
- P. putida KT2440 uses the Entner-Doudoroff pathway exclusively for glucose catabolism (no Embden-Meyerhof-Parnas pathway). This is important for annotation review — glycolysis terms may need careful handling.
- Many genes are annotated by homology to P. aeruginosa (PSEAE), but functional divergence is common — P. putida is non-pathogenic while P. aeruginosa is an opportunistic pathogen. Virulence-associated annotations transferred by homology should be scrutinized.
- The REE/lanthanide biology is relatively recent science (post-2011). Annotations for pedH and related genes may be incomplete or missing entirely.