L-arginine biosynthesis via acetylated ornithine (microbial)

De novo microbial L-arginine biosynthesis from L-glutamate through N-acetylated intermediates and L-ornithine. The module includes the linear route, in which ArgA initiates acetylation and ArgE hydrolyses N-acetyl-L-ornithine, and the cyclic route, in which bifunctional ArgJ can initiate the pathway and recycle the acetyl group from N-acetyl-L-ornithine. After ornithine formation, ArgF, ArgG, and ArgH convert it through L-citrulline and argininosuccinate to L-arginine. Carbamoyl-phosphate production is shared with pyrimidine metabolism and is intentionally outside the module boundary. Succinylated-intermediate, N-acetylcitrulline, and LysW-dependent arginine pathways are distinct implementations not expanded in this module.

MODULE:arginine_biosynthesisDRAFTMetabolic Pathwaymodules/arginine_biosynthesis.yaml
L-arginine biosynthetic processGO:0006526
GapMind:aa
GapMind for amino acid biosynthesis
The conserved reaction set and alternative linear and cyclic acetylated-ornithine routes derive from the GapMind arginine pathway definition arg.steps (PaperBLAST, Price & Arkin, LBL).
MetaCyc:ARGSYN-PWY
L-arginine biosynthesis I via L-acetylornithine
Grounds the linear ArgA-to-ArgE acetylated-intermediate route.
MetaCyc:ARGSYNBSUB-PWY
L-arginine biosynthesis II (acetyl cycle)
Grounds the cyclic ArgJ acetyl-transfer implementation.
GO:0006526
L-arginine biosynthetic process
The module is grounded in the GO biological-process term for L-arginine biosynthesis.
PMID:31451546
Arginine Biosynthesis Modulates Pyoverdine Production and Release in Pseudomonas putida as Part of the Mechanism of Adaptation to Oxidative Stress.
KT2440 genetics identifies PP_4481 as argD (= astC) and shows that separate argD, argE, and argJ mutants are not arginine auxotrophs. This supports overlapping aminotransferase and ornithine-release implementations without establishing which route carries dominant flux. In contrast, argA, argB, argF, argG, and argH mutants are auxotrophic, supporting the corresponding required steps in the PSEPK instance.
KEGG:ppu00220
Pseudomonas putida KT2440 arginine biosynthesis map
The PSEPK pathway instance supplies exact UniProt exemplars for all eight reactions while the broader KEGG map also contains catabolic and shared nitrogen-metabolism genes outside this module boundary.
file:projects/P_PUTIDA/data/psepk_pathway_membership.tsv
PSEPK pathway membership table
The local partition provides accession and locus-tag mappings used to distinguish the biosynthetic core from arginine catabolism, urease, and shared carbamoyl-phosphate synthesis.
file:projects/P_PUTIDA/deep-research/PSEPK__arginine_biosynthesis__ppu00220-deep-research-openscientist.md
OpenScientist PSEPK module, pathway, and taxon synthesis
The species-aware retrieval recovers the eight-step pathway outline and flags the KEGG boundary spillover. Its recommendation to promote AST-operon PP_4481 as a biosynthetic step-4 contributor and its unqualified redundancy claims are rejected here in favor of direct KT2440 genetics, local PANTHER subfamilies, and the curated gene reviews.
file:modules/arginine_biosynthesis-deep-research-openscientist.md
OpenScientist reusable acetylated-ornithine pathway synthesis
The species-neutral retrieval supports the eight-reaction boundary, distinguishes linear ArgA/ArgE from cyclic ArgJ acetyl management, and identifies carbamoyl-phosphate supply plus LysW, N-acetylcitrulline, and succinylated routes as neighboring systems. Family and node identifiers remain grounded independently in local UniProt, PANTHER, and PAINT data.
file:PSEPK/argD/argD-deep-research-openscientist.md
OpenScientist synthesis for PSEPK PP_4481 acyl-ornithine aminotransferase
Genomic context and family analysis place PP_4481 in the AST catabolic operon and identify PP_0372 as the stronger PSEPK candidate for the biosynthetic acetylornithine-transaminase step. The report's route-level claims are treated as hypotheses pending direct KT2440 genetics.
15Nodes
8Parts
3Variant Sets
6Variants
11Annotons
8Connections

Derived QC

Recommended-field compliance

55.6% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)

Module deep research

✓ present

  • arginine_biosynthesis-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • glutamate_acetylation_step → acetylglutamate_kinase_step [NOT_CHECKED]
  • acetylglutamate_kinase_step → acetylglutamyl_phosphate_reductase_step [NOT_CHECKED]
  • acetylglutamyl_phosphate_reductase_step → acetylornithine_aminotransferase_step [NOT_CHECKED]
  • acetylornithine_aminotransferase_step → ornithine_release_step [NOT_CHECKED]
  • ornithine_release_step → ornithine_carbamoyltransferase_step [NOT_CHECKED]
  • ornithine_carbamoyltransferase_step → argininosuccinate_synthase_step [NOT_CHECKED]
  • argininosuccinate_synthase_step → argininosuccinate_lyase_step [NOT_CHECKED]

Gene-review completeness (10/20 grounded genes reviewed)

9 complete review(s) · 10 with deep research · 10 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
argA P0A0Z9 ✓ ✓ ✓
argB P59300 ✓ ✓ ✓
argC1 Q88QQ6 ✓ ✓ ✓
argC2 P59308 ✓ ✓ ✓
argE Q88CJ5 ✓ ✓ ✓
argF Q88NX4 ✓ ✓ ✓
argG P59604 ✓ ✓ ✓
argH P59618 ✓ ✓ ✓
argJ P59612 ✓ ✓ ✓
aruC Q88QW2 ✓ 5/6 ✓
Escherichia coli ArgA P0A6C5 ✗ — —
Escherichia coli ArgB P0A6C8 ✗ — —
Escherichia coli ArgC P11446 ✗ — —
Escherichia coli ArgH P11447 ✗ — —
Escherichia coli ArgE P23908 ✗ — —
Bacillus subtilis ArgJ P36843 ✗ — —
Nostoc ArgC2 P54894 ✗ — —
Synechocystis ArgD P73133 ✗ — —
Synechocystis ArgG P77973 ✗ — —
Mycobacterium tuberculosis ArgF P9WIT9 ✗ — —

Details

L-arginine biosynthesis via acetylated ornithineMetabolic Pathwayarginine_biosynthesis
L-arginine biosynthetic processGO:0006526

Molecular functions are attached only to leaf annotons. The module-level concept is the biological process, and no generic cytoplasmic location is asserted. Exact PSEPK UniProt accessions ground each family selector without making the reusable reaction architecture species-specific. PAINT nodes are attached only where a local IBD row names a reviewed molecular-function exemplar; they do not establish species-specific pathway usage. Shared carbamoyl-phosphate production and unrelated arginine catabolism are outside this module.

Connections

The cyclic ArgJ release reaction regenerates N-acetyl-L-glutamate for the kinase step; this feedback does not replace the forward eight-step chain or make ArgJ mandatory for the linear ArgA/ArgE route.
Part 1: pathway-initiating glutamate acetylation
L-glutamate to N-acetyl-L-glutamateReactionglutamate_acetylation_step

The initial acetylation can be supplied by a dedicated ArgA enzyme or by the bifunctional ArgJ enzyme used in cyclic acetyl transfer.

Variant set: Glutamate acetylation enzyme variants by enzyme family (One Or More)
Dedicated ArgA implementationReactionargA_initiation_variant

Annotons

ArgA N-acetylglutamate synthase
argA_activity
Participant: Family: ArgA N-acetylglutamate synthase family
Family:
ArgA N-acetylglutamate synthase familyNCBIfam:TIGR01890
Representative Members: PSEPK ArgAUniProtKB:P0A0Z9 Escherichia coli ArgAUniProtKB:P0A6C5
Required Function:
L-glutamate N-acetyltransferase activity, acting on acetyl-CoA as donorGO:0004042

Function

L-glutamate N-acetyltransferase activity, acting on acetyl-CoA as donorGO:0004042
Substrates: L-glutamate acetyl-CoA
Products: N-acetyl-L-glutamate CoA

Dedicated enzyme for the first reaction of the linear route.

Bifunctional ArgJ initiation implementationReactionargJ_initiation_variant

Annotons

ArgJ acetyl-CoA-dependent initiating activity
argJ_initiating_activity
Participant: Family: bifunctional ArgJ family
Family:
bifunctional ArgJ familyNCBIfam:TIGR00120
Representative Members: PSEPK ArgJUniProtKB:P59612 Bacillus subtilis ArgJUniProtKB:P36843
Required Function:
L-glutamate N-acetyltransferase activity, acting on acetyl-CoA as donorGO:0004042

Function

L-glutamate N-acetyltransferase activity, acting on acetyl-CoA as donorGO:0004042
Substrates: L-glutamate acetyl-CoA
Products: N-acetyl-L-glutamate CoA

Initiating activity of bifunctional ArgJ; the same protein can recycle the acetyl group at the ornithine-release step.

Part 2: acetylglutamate kinase
N-acetyl-L-glutamate to N-acetyl-L-glutamyl 5-phosphateReactionacetylglutamate_kinase_step

Annotons

ArgB acetylglutamate kinase
argB_activity
Participant: Family: ArgB acetylglutamate kinase family
Family:
ArgB acetylglutamate kinase familyNCBIfam:TIGR00761
Representative Members: PSEPK ArgBUniProtKB:P59300 Escherichia coli ArgBUniProtKB:P0A6C8
Required Function:
acetylglutamate kinase activityGO:0003991

Function

acetylglutamate kinase activityGO:0003991
Substrates: N-acetyl-L-glutamate ATP
Products: N-acetyl-L-glutamyl 5-phosphate ADP

Activates the acetylated glutamate carboxyl group for reduction.

Part 3: acetylglutamyl-phosphate reductase
N-acetyl-L-glutamyl 5-phosphate to N-acetyl-L-glutamate 5-semialdehydeReactionacetylglutamyl_phosphate_reductase_step

Type 1 and type 2 ArgC proteins are structurally distinct family implementations of the same NADPH-dependent reaction. PANTHER places both PSEPK proteins in PTHR32338:SF10, so the independently verified TIGR01850 and TIGR01851 selectors retain the type distinction.

Variant set: ArgC reductase family variants by enzyme family (One Or More)
Type 1 ArgC implementationReactionargC_type1_variant

Annotons

Type 1 ArgC reductase
argC1_activity
Participant: Family: type 1 ArgC family
Family:
type 1 ArgC familyNCBIfam:TIGR01850
Representative Members: PSEPK ArgC1UniProtKB:Q88QQ6 Escherichia coli ArgCUniProtKB:P11446
Required Function:
N-acetyl-gamma-glutamyl-phosphate reductase activityGO:0003942

Function

N-acetyl-gamma-glutamyl-phosphate reductase activityGO:0003942
Substrates: N-acetyl-L-glutamyl 5-phosphate NADPH proton
Products: N-acetyl-L-glutamate 5-semialdehyde phosphate NADP+

Type 1 family implementation of the ArgC reaction.

Type 2 ArgC implementationReactionargC_type2_variant

Annotons

Type 2 ArgC reductase
argC2_activity
Participant: Family: type 2 ArgC family
Family:
type 2 ArgC familyNCBIfam:TIGR01851
Representative Members: PSEPK ArgC2UniProtKB:P59308 Nostoc ArgC2UniProtKB:P54894
Required Function:
N-acetyl-gamma-glutamyl-phosphate reductase activityGO:0003942

Function

N-acetyl-gamma-glutamyl-phosphate reductase activityGO:0003942
Substrates: N-acetyl-L-glutamyl 5-phosphate NADPH proton
Products: N-acetyl-L-glutamate 5-semialdehyde phosphate NADP+

Type 2 family implementation of the ArgC reaction.

Part 4: acetylornithine aminotransferase
N-acetyl-L-glutamate 5-semialdehyde to N-acetyl-L-ornithineReactionacetylornithine_aminotransferase_step

The reusable step is grounded by a reviewed anabolic ArgD-like SF79 exemplar; catabolic AstC-like transaminases are outside this module.

Annotons

ArgD acetylornithine aminotransferase
argD_activity
Participant: Family: anabolic ArgD-like acetylornithine aminotransferase family
Family:
anabolic ArgD-like acetylornithine aminotransferase familyPANTHER:PTHR11986:SF79
Representative Members: PSEPK AruC/ArgD2UniProtKB:Q88QW2 Synechocystis ArgDUniProtKB:P73133
Required Function:
N2-acetyl-L-ornithine:2-oxoglutarate 5-transaminase activityGO:0003992

Function

N2-acetyl-L-ornithine:2-oxoglutarate 5-transaminase activityGO:0003992
Substrates: N-acetyl-L-glutamate 5-semialdehyde L-glutamate
Products: N-acetyl-L-ornithine 2-oxoglutarate
Cofactors: pyridoxal 5'-phosphate

Forms the activated ornithine intermediate by PLP-dependent transamination. AstC-like succinylornithine transaminases can show overlapping ACOAT activity, but catabolic-operon membership alone does not make them the preferred biosynthetic implementation.

Part 5: ornithine release
N-acetyl-L-ornithine to L-ornithineReactionornithine_release_step

Ornithine is released either by ArgJ-mediated transfer of the acetyl group back to glutamate or by ArgE-mediated hydrolysis.

Variant set: Ornithine-release enzyme variants by reaction mechanism (One Or More)
Cyclic ArgJ transacetylationReactionargJ_transacetylation_variant

Annotons

ArgJ ornithine acetyltransferase
argJ_recycling_activity
Participant: Family: bifunctional ArgJ family
Family:
bifunctional ArgJ familyNCBIfam:TIGR00120
Representative Members: PSEPK ArgJUniProtKB:P59612 Bacillus subtilis ArgJUniProtKB:P36843
Required Function:
L-glutamate N-acetyltransferase activity, acting on acetyl-L-ornithine as donorGO:0004358

Function

L-glutamate N-acetyltransferase activity, acting on acetyl-L-ornithine as donorGO:0004358
Substrates: N-acetyl-L-ornithine L-glutamate
Products: L-ornithine N-acetyl-L-glutamate

Releases ornithine while regenerating N-acetyl-L-glutamate for the cyclic route.

Hydrolytic ArgE deacetylationReactionargE_deacetylation_variant

Annotons

ArgE acetylornithine deacetylase
argE_activity
Participant: Family: ArgE acetylornithine deacetylase family
Family:
ArgE acetylornithine deacetylase familyNCBIfam:TIGR01892
Representative Members: PSEPK ArgEUniProtKB:Q88CJ5 Escherichia coli ArgEUniProtKB:P23908
Required Function:
acetylornithine deacetylase activityGO:0008777

Function

acetylornithine deacetylase activityGO:0008777
Substrates: N-acetyl-L-ornithine water
Products: L-ornithine acetate

Releases ornithine by hydrolysis in the linear route.

Part 6: ornithine carbamoyltransferase
L-ornithine to L-citrullineReactionornithine_carbamoyltransferase_step

Annotons

Biosynthetic ornithine carbamoyltransferase
argF_activity
Participant: Family: anabolic-type ornithine carbamoyltransferase subfamily
Family:
anabolic-type ornithine carbamoyltransferase subfamilyPANTHER:PTHR45753:SF3
Representative Members: PSEPK ArgFUniProtKB:Q88NX4 Mycobacterium tuberculosis ArgFUniProtKB:P9WIT9
Required Function:
ornithine carbamoyltransferase activityGO:0004585

Function

ornithine carbamoyltransferase activityGO:0004585
Substrates: L-ornithine carbamoyl phosphate
Products: L-citrulline phosphate

First reaction after ornithine formation; family selection distinguishes biosynthetic ArgF/ArgI enzymes from catabolic ArcB.

Part 7: argininosuccinate synthase
L-citrulline to argininosuccinateReactionargininosuccinate_synthase_step

Annotons

ArgG argininosuccinate synthase
argG_activity
Participant: Family: type 1 ArgG argininosuccinate synthase family
Family:
type 1 ArgG argininosuccinate synthase familyNCBIfam:TIGR00032
Representative Members: PSEPK ArgGUniProtKB:P59604 Synechocystis ArgGUniProtKB:P77973
Required Function:
argininosuccinate synthase activityGO:0004055

Function

argininosuccinate synthase activityGO:0004055
Substrates: L-citrulline L-aspartate ATP
Products: argininosuccinate AMP diphosphate

Incorporates aspartate nitrogen into the arginine precursor.

Part 8: terminal argininosuccinate lyase
Argininosuccinate to L-arginineReactionargininosuccinate_lyase_step

Annotons

ArgH argininosuccinate lyase
argH_activity
Participant: Family: ArgH argininosuccinate lyase family
Family:
ArgH argininosuccinate lyase familyNCBIfam:TIGR00838
Representative Members: PSEPK ArgHUniProtKB:P59618 Escherichia coli ArgHUniProtKB:P11447
Required Function:
argininosuccinate lyase activityGO:0004056

Function

argininosuccinate lyase activityGO:0004056
Substrates: argininosuccinate
Products: L-arginine fumarate

Produces L-arginine in the terminal pathway reaction.