Plant primary metabolism (Arabidopsis thaliana)

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Description

Plant Primary Metabolism Metapathway

Contains:

- Calvin Cycle (chloroplast) - Glycolysis (cytosol) - Krebs Cycle (mitochondria)

The pathway is currently under construction and does not yet contain A. thaliana annotations.

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View approved pathways at the new wikipathways.org. This website will shutdown soon.

Quality Tags

Ontology Terms

Bibliography

Karve A, Rauh BL, Xia X, Kandasamy M, Meagher RB, Sheen J, Moore BD; ''Expression and evolutionary features of the hexokinase gene family in Arabidopsis.''; Planta, 2008 PubMed Europe PMC Scholia

History

View all...

Revision	Action	Time	User	Comment
117248	view	09:59, 19 May 2021	Eweitz	Modified title
111815	view	19:09, 8 September 2020	Egonw	Matched the data source with the given identifier.
105896	view	11:36, 16 August 2019	Mkutmon	HMDB identifier normalization
102643	view	07:49, 16 January 2019	Tokimatsu	Reverted to version '2018年3月5日 (月) 08:39' by Tokimatsu
102642	view	07:47, 16 January 2019	Tokimatsu	Fix interactions
102641	view	07:40, 16 January 2019	Tokimatsu	Fixed connections.
102640	view	07:26, 16 January 2019	Tokimatsu	remove reactions/metabolites undiscovered from Brassicaceae. Add reaction IDs.
102639	view	07:19, 16 January 2019	Tokimatsu	remove reactions/metabolites undiscovered from Brassicaceae. Add reaction IDs.
96282	view	08:39, 5 March 2018	Egonw	Not a chemical conversion.
82871	view	16:28, 10 November 2015	Jmelius	Correct outdated id
78382	view	10:22, 7 January 2015	MaintBot	added missing graphIds
76240	view	08:49, 21 June 2014	Sbohler	Grouped cytosolic malic enzymes 1, 2, and 3.
76235	view	06:19, 20 June 2014	Sbohler	Coorected myrosinase annotations (vacuole)
76234	view	15:37, 19 June 2014	Anwesha	Annotated some nodes
75849	view	09:02, 11 June 2014	Sbohler	Modified description
75847	view	04:59, 11 June 2014	Egonw	Added two more missing metabolite IDs.
75846	view	04:50, 11 June 2014	Egonw	Added missing database names for two protein IDs.
75331	view	14:45, 19 May 2014	Sbohler	Moved apoplastic protein out of the cell border.
75330	view	14:42, 19 May 2014	Sbohler	Parts added to the pathway, including RNA for PLC1,2, NAD-ME1,2, NADP-ME2.
74123	view	20:17, 31 March 2014	Egonw	Removed the list of Uniprot identifiers from the Xref, which can hold only one.
74122	view	20:16, 31 March 2014	Egonw	Copied the multiple identifiers to the comment field.
71812	view	18:17, 18 October 2013	Egonw	Added a bunch of missing metabolite identifiers.
71448	view	19:14, 17 October 2013	MaintBot	Automated update of data sources
65321	view	18:01, 6 June 2013	Sbohler	Periodical save, work in progress
65316	view	17:51, 6 June 2013	Sbohler	work in progress
65312	view	17:40, 6 June 2013	Sbohler	Periodical save, work in progress
65024	view	21:00, 4 June 2013	MaintBot	Ontology Term : 'glycolysis pathway' added !
65023	view	21:00, 4 June 2013	MaintBot	Ontology Term : 'Krebs cycle pathway' added !
65022	view	20:59, 4 June 2013	MaintBot	Modified categories
62875	view	12:56, 3 May 2013	Sbohler	Modified description
62874	view	12:54, 3 May 2013	Sbohler	Modified description
62873	view	12:50, 3 May 2013	Sbohler	New pathway

External references

DataNodes

View all...

Name	Type	Database reference
1,3-bisphosphoglycerate	Metabolite
2-oxoglutarate dehydrogenase	Protein
2-oxoglutarate	Metabolite	CHEBI:30916 (ChEBI)
3-phosphoglycerate	Metabolite
ADP	Metabolite
ADP-glucose pyrophosphorylase	Protein
ADP-glucose	Metabolite	HMDB06557 (HMDB)
ADP	Metabolite	CHEBI:16761 (ChEBI)
ATP-dependent phosphofructokinase	Protein
ATP	Metabolite	HMDB00538 (HMDB)
Acetyl-CoA	Metabolite	HMDB01206 (HMDB)
CO2	Metabolite	HMDB01967 (HMDB)
CoA	Metabolite
Dihydroxyacetone phosphate	Metabolite	HMDB01473 (HMDB)
FAD+	Metabolite	HMDB01248 (HMDB)
FADH2	Metabolite	HMDB01197 (HMDB)
H+	Metabolite	CHEBI:15378 (ChEBI)
H2O	Metabolite	HMDB02111 (HMDB)
HCO3-	Metabolite	CHEBI:17544 (ChEBI)
NAD+	Metabolite	HMDB00902 (HMDB)
NADH	Metabolite	HMDB01487 (HMDB)
NADP+	Metabolite	HMDB00217 (HMDB)
NADPH	Metabolite	HMDB00221 (HMDB)
PPi	Metabolite
PPi-dependent phosphofructokinase	Protein
Pi	Metabolite
RuBisCO LSU	Protein
RuBisCO SSU	Protein	Q42306 Q42046 Q0WVH4 F4HRR5 F4KA76 B3H5S2 P10795 P10796 P10797 P10798 (Uniprot-TrEMBL)
RuBisCO activase	Protein
Succinyl-CoA	Metabolite	HMDB01022 (HMDB)
UDP-glucose	Metabolite
UDP-glucose pyrophosphorylase	Protein
UTP	Metabolite	CHEBI:15713 (ChEBI)
aconitase	Protein
aldolase	Protein
amylase	Protein	GO:0016160 (GeneOntology)
citrate synthase	Protein
citrate	Metabolite	CHEBI:30769 (ChEBI)
erythrose 4-phosphate	Metabolite	HMDB01321 (HMDB)
fructose 1,6-bisphosphatase	Protein
fructose 1,6-bisphosphate aldolase	Protein	GO:0004332 (GeneOntology)
fructose 1,6-bisphosphate	Metabolite	HMDB01058 (HMDB)
fructose 6-phosphate	Metabolite	HMDB00124 (HMDB)
fructose-1,6-bisphosphatase	Protein
fructose-1,6-bisphosphate	Metabolite	HMDB01058 (HMDB)
fructose	Metabolite	HMDB00660 (HMDB)
fumarase	Protein
fumarate	Metabolite	CHEBI:29806 (ChEBI)
glucose 1-phosphate	Metabolite	HMDB01586 (HMDB)
glucose 6-phosphate	Metabolite	HMDB01401 (HMDB)
glucose kinase	Protein
glucose-6-phosphate isomerase	Protein	GO:0004347 (GeneOntology)
glucose	Metabolite	HMDB00122 (HMDB)
glyceraldahyde-3-phosphate	Metabolite
glyceraldehyde 3-phosphate dehydrogenase	Protein	GO:0004365 (GeneOntology)
glyceraldehyde-3-phosphate dehydrogenase	Protein
glycerate 1,3-bisphosphate	Metabolite
glycerate 2-phosphate	Metabolite
glycerate 3-phosphate	Metabolite
hexokinase	Protein	GO:0004396 (GeneOntology)
hexose phosphate isomerase	Protein
invertase	Protein
isocitrate dehydrogenase	Protein	GO:0004449 (GeneOntology)
isocitrate	Metabolite	CHEBI:30887 (ChEBI)
malate	Metabolite
malate dehydrogenase	Protein	GO:0016615 (GeneOntology)
malate dehydrogenase	Protein	GO:0016619 (GeneOntology)
malic enzyme	Protein	GO:0004470 (GeneOntology)
oxaloacetate	Metabolite	CHEBI:16452 (ChEBI)
phosphoenolpyruvate carboxylase	Protein
phosphoenolpyruvate	Metabolite	CHEBI:18021 (ChEBI)
phosphoglucomutase	Protein	GO:0004614 (GeneOntology)
phosphoglycerate kinase activity	Protein	GO:0004618 (GeneOntology)
phosphoglycerate kinase	Protein	GO:0004618 (GeneOntology)
phosphoglycerate mutase	Protein	GO:0004619 (GeneOntology)
phosphopyruvate hydratase	Protein	GO:0004634 (GeneOntology)
phosphoribulokinase	Protein
pyruvate	Metabolite
pyruvate dehydrogenase	Protein	GO:0004738 (GeneOntology)
pyruvate kinase	Protein	GO:0004743 (GeneOntology)
pyruvate	Metabolite	CHEBI:15361 (ChEBI)
ribose 5-phosphate	Metabolite	HMDB01548 (HMDB)
ribulose 5-phosphate 3-epimerase activity	Protein	GO:0004750 (GeneOntology)
ribulose 5-phosphate isomerase	Protein
ribulose 5-phosphate	Metabolite	HMDB00618 (HMDB)
ribulose-1,5-bisphosphate	Metabolite
sedoheptulose 1,7-bisphosphatase	Protein
sedoheptulose 1,7-bisphosphate	Metabolite	CHEBI:17969 (ChEBI)
sedoheptulose 7-phosphate	Metabolite	HMDB01068 (HMDB)
starch posphorylase	Protein
starch synthase	Protein
starch	Metabolite	CHEBI:28017 (ChEBI)
succinate dehydrogenase	Protein	GO:0000104 (GeneOntology)
succinate	Metabolite	CHEBI:30779 (ChEBI)
succinyl-CoA synthetase	Protein
sucrose synthase	Protein
sucrose	Metabolite	HMDB00258 (HMDB)
transketolase	Protein	GO:0004802 (GeneOntology)
triose phosphate isomerase	Protein
xyluloase-5-phosphate	Metabolite

Annotated Interactions

Source	Target	Type	Database reference	Comment
RuBisCO LSU		mim-catalysis	REACT_1827.5 (Reactome)

Plant primary metabolism (Arabidopsis thaliana)

From WikiPathways

Description

Please use the New WikiPathways

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