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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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

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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82871	view	16:28, 10 November 2015	Jmelius	Correct outdated id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

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Name	Type	Database reference	Comment
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)	Q42306 Q42046 Q0WVH4 F4HRR5 F4KA76 B3H5S2 P10795 P10796 P10797 P10798
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

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