Bacterial carboxyspermidine route to spermidine

A reusable bacterial route in which carboxyspermidine dehydrogenase condenses putrescine with aspartate semialdehyde using NADPH to form carboxyspermidine, followed by decarboxylation of carboxyspermidine to spermidine. Diamine and aspartate-semialdehyde supply are pathway inputs rather than parts of this two-reaction module.

MODULE:bacterial_carboxyspermidine_biosynthesisDRAFTCONCRETEMetabolic Pathwaymodules/bacterial_carboxyspermidine_biosynthesis.yaml
spermidine biosynthetic processGO:0008295
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial-carboxyspermidine-biosynthesis__ppu00330-deep-research-openscientist.md
OpenScientist PSEPK carboxyspermidine pathway review
The species-aware review strongly infers adjacent PP_2928 and PP_2929 as the CASDH-CASDC pair from comparative, family, and synteny evidence; it reports no direct KT2440 biochemical or genetic confirmation.
file:modules/bacterial_carboxyspermidine_biosynthesis-deep-research-openscientist.md
OpenScientist bacterial carboxyspermidine module review
The species-neutral review identifies CASDH and NspC as the obligatory, defining two-reaction core and treats diamine-supply reactions as an interchangeable front end.
RHEA:34095
carboxyspermidine decarboxylase reaction
Defines NspC conversion of carboxyspermidine to spermidine.
file:projects/NCBIFam/ncbifam2go.candidates.tsv
NCBIFam-to-GO candidate mappings
Records NCBIFAM:NF043000 carboxynorspermidine synthase (EC 1.5.1.43) as an exact match to GO:0102143, supporting use of the current GO term for the putrescine-to-carboxyspermidine direction.

The reusable boundary is species-neutral, while this CONCRETE review uses exact Pseudomonas putida KT2440 UniProt exemplars on both leaves. PP_2928 is currently named saccharopine dehydrogenase in UniProt, but its PTHR43796 family assignment, domain architecture, adjacency to nspC, and the species-aware sequence analysis strongly support CASDH. The exact GO label for GO:0102143 is "carboxynorspermidine dehydrogenase activity"; the NCBIFAM:NF043000 exact-match mapping to this term covers EC 1.5.1.43, and use of putrescine yields carboxyspermidine, hence CASDH in this route. Putrescine and aspartate-semialdehyde production are substrate supply outside the core.

3Nodes
2Parts
0Variant Sets
0Variants
2Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_carboxyspermidine_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.

Gene-review completeness (2/2 grounded genes reviewed)

2 complete review(s) · 1 with deep research · 0 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
nspC Q88IS0 ✓ ✓ ✗
PP_2928 Q88IS1 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
Bacterial carboxyspermidine route to spermidineMetabolic Pathwaybacterial_carboxyspermidine_biosynthesis
spermidine biosynthetic processGO:0008295
Context
bacteriaNCBITaxon:2

Connections

CASDH-produced carboxyspermidine is decarboxylated by NspC.
Part 1: carboxyspermidine formation
CASDH-dependent carboxyspermidine formationReactioncasdh_carboxyspermidine_formation

Annotons

Carboxyspermidine dehydrogenase
casdh_dehydrogenase
Participant: Family: carboxyspermidine/carboxynorspermidine dehydrogenase family
Family:
carboxyspermidine/carboxynorspermidine dehydrogenase familyPANTHER:PTHR43796:SF2
Representative Members: PP_2928 CASDH candidate (Pseudomonas putida KT2440)UniProtKB:Q88IS1

Function

carboxynorspermidine dehydrogenase activityGO:0102143
Substrates: putrescine L-aspartate 4-semialdehyde NADPH
Products: carboxyspermidine NADP+

Processes

spermidine biosynthetic processGO:0008295
Part 2: spermidine formation by decarboxylation
NspC-dependent spermidine formationReactionnspc_spermidine_formation

Annotons

NspC carboxyspermidine decarboxylase
nspc_carboxyspermidine_decarboxylase
Participant: Family: carboxyspermidine/carboxynorspermidine decarboxylase family
Family:
carboxyspermidine/carboxynorspermidine decarboxylase familyPANTHER:PTHR43727:SF1
Representative Members: NspC (Pseudomonas putida KT2440)UniProtKB:Q88IS0

Function

carboxy-lyase activityGO:0016831
Substrates: carboxyspermidine
Products: spermidine carbon dioxide

Processes

spermidine biosynthetic processGO:0008295