Plant primary metabolism (Arabidopsis thaliana)

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Photosystem IILumenElectron transport pathglucose kinaseUTPADPstarchxyluloase-5-phosphateribulose-1,5-bisphosphateglutathione S-transferasehexokinaseglucose 6-phosphatephosphoglycerate mutaseglutamate5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferaseFADH2glycerate 2-phosphateUDP-glucoseS-sdenosylmethioninedihydroxy-acid dehydrataseglyceraldehyde 3-phosphate dehydrogenaseplastoquinonesedoheptulose 1,7-bisphosphatase2-oxoglutarate dehydrogenasefructose 1,6-bisphosphateO2erythrose 4-phosphateoxaloacetate30S ribosomalprotein S5Cystathionineglutamyl-tRNA (Glu)pyruvate dehydrogenase3-phosphoglyceratefructose-1,6-bisphosphatasecystathionine gamma-lyaseglucan endo-1,3-beta-glucosidaseacidic isoformcitrate synthasesucroseheat shock cognate 70 kDa protein 1NAD+glyceraldehyde-3-phosphate dehydrogenasecitrateglutathione disulfide2,6-diaminopimelatesucrose synthaseCysteinephosphoenolpyruvate carboxylasetransketolase1,3-bisphosphoglycerateluminal-binding protein 1DNAPPiSuccinyl-CoAsmall subunitribosomal protein S1FAD+glycerate 1,3-bisphosphateglutathione reductasesuccinateperoxiredoxin-2EH2O2-cys peroxiredoxin-like proteinisocitrateRuBisCO SSUthioredoxin reductase5-amino-levulinateCO2 + H2OH2O2ketol-acid reductoisomeraseribose 5-phosphateaspartatealanineglutamyl-tRNA reductasediaminopimelate decarboxylaseaspartate 4-decarboxylasefumaratealanine dehydrogenase2-aceto-2-hydroxybutanoatefructose 6-phosphateCoAfructosePPi-dependent phosphofructokinasefructose-1,6-bisphosphatebranched-chain-amino-acid transaminasePiserine acetyltransferasediaminopimelate epimeraseglutathione-S-transferaseadenosylhomocysteinasemalic enzymePPiinvertasecopper chaperoneGlycolysisoxaloacetateplastocyanin 2carbonic anhydrase 1glutamate-1-semialdehyde2,1-aminomutase 2glutathione-S-transferaseADP-glucoseS-adenosylmethionine synthaseelongation factorEF-G/SCO1phosphoglycerate kinaseacetolactate synthaseATPhexose phosphate isomeraseIsoleucinecystathionine beta-lyasephosphoglycerate kinasesedoheptulose 1,7-bisphosphatetRNAGluHCO3-phosphoglucomutaseferredoxin-NADP+ reductasephosphoribulokinasemyrosinase 1phosphoenolpyruvateluminal-binding protein 2CO2fructose 6-phosphatePorphyrin and ChlorophyllmetabolismH2CO3ribonucleoproteinNADPHphosphopyruvate hydrataseglycine-rich RNA-binding protein 7H+H+Valinemalateisocitrate dehydrogenasestarch posphorylasefructose 1,6-bisphosphate aldolaseH2O + O22,3-dihydroxy-isovalerateamylaseglutathioneribulose 5-phosphate 3-epimerase activityO2 + H+ribulose 5-phosphate isomeraseglutamate—tRNA ligaseCO2Thylakoid lumenal 19 kDa proteinglucose 1-phosphatethioredoxin2-oxoglutarateRuBisCO LSUH2Oglucose-6-phosphate isomeraseglutaredoxinS-AdenosylhomocysteineNADHDNA 5-methylcytosineSerinecarbonic anhydrase 2pyruvateHomocysteinestarch synthasepyruvate kinaseferredoxinglucose 1-phosphateaconitaseADP-glucose pyrophosphorylaseRuBisCO activaseDNA (cytosine-5-)-methyltransferasecysteine proteinase inhibitor 6serine ammonia-lyaseglucoselipoxygenase 2fumaraseO-acetyl-L-serineCO2fructose-1,6-bisphosphatasesuccinyl-CoA synthetaseNADP+malate dehydrogenasepyruvate dehydrogenasemalic enzymesuccinate dehydrogenasesedoheptulose 7-phosphatePLC1glutamate-1-semialdehydemeso-2,6-diaminopimelatelysinePLC2ribulose 5-phosphateglycerate 3-phosphateAcetyl-CoAglyceraldahyde-3-phosphateDihydroxyacetone phosphatetriose phosphate isomeraseH2OaldolaseH2OPitransketolaseDihydroxyacetone phosphateglyceraldahyde-3-phosphatetriose phosphate isomeraseNADPHNADP+ATPADPmalate dehydrogenaseNAD+NADHATPADPATPADPATP-dependent phosphofructokinasePiATPADPPiH2OPihexokinaseATPADPglucose 6-phosphatePiglucoseATPADPfructose 1,6-bisphosphatealdolasefructose 6-phosphatePiH2OATPPPiphosphoglucomutaseUDP-glucose pyrophosphorylasePPiH2OpyruvateCoACO2NAD+NADHNAD+NADHCoACO2NAD+NADHCoAH2OATPADPmalateH2ONAD+NADHNAD+NADHRuBisCO activasealdolasealdolasealdolasepyruvate2-Acetolactate2,3-dihydroxy-3-methylvalerate2-oxo-3-methylvalerate2-oxo-isovalerateSucrose MetabolismStarch MetabolismCalvin CycleTCA Cycle(Krebs Cycle)Valine and IsoleucineBiosynthesisPhotorespirationisocitrateisocitrate dehydrogenase2-oxoglutarateNADP+NADPHCO2CO2Glutamate Biosynthesis2H+Cytochrome b6fPhotosystem IATPaseH+H+H+H+NAD+NADHATPADPPiPiPiStromaChloroplastMethionineO-phosphoserine sulfhydrylaseCysteine and Methionine BiosynthesisRibosomeMediator ComplexNAD+NADHNucleusATPADPNADHNAD+NADHNAD+MitochondrionApoplastVacuoleGAPC1GAPC2NADP-ME2NAD-ME1NAD-ME2


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.

Quality Tags

Ontology Terms

 

Bibliography

  1. 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...
CompareRevisionActionTimeUserComment
117248view09:59, 19 May 2021EweitzModified title
111815view19:09, 8 September 2020EgonwMatched the data source with the given identifier.
105896view11:36, 16 August 2019MkutmonHMDB identifier normalization
102643view07:49, 16 January 2019TokimatsuReverted to version '2018年3月5日 (月) 08:39' by Tokimatsu
102642view07:47, 16 January 2019TokimatsuFix interactions
102641view07:40, 16 January 2019TokimatsuFixed connections.
102640view07:26, 16 January 2019Tokimatsuremove reactions/metabolites undiscovered from Brassicaceae. Add reaction IDs.
102639view07:19, 16 January 2019Tokimatsuremove reactions/metabolites undiscovered from Brassicaceae. Add reaction IDs.
96282view08:39, 5 March 2018EgonwNot a chemical conversion.
82871view16:28, 10 November 2015JmeliusCorrect outdated id
78382view10:22, 7 January 2015MaintBotadded missing graphIds
76240view08:49, 21 June 2014SbohlerGrouped cytosolic malic enzymes 1, 2, and 3.
76235view06:19, 20 June 2014SbohlerCoorected myrosinase annotations (vacuole)
76234view15:37, 19 June 2014AnweshaAnnotated some nodes
75849view09:02, 11 June 2014SbohlerModified description
75847view04:59, 11 June 2014EgonwAdded two more missing metabolite IDs.
75846view04:50, 11 June 2014EgonwAdded missing database names for two protein IDs.
75331view14:45, 19 May 2014SbohlerMoved apoplastic protein out of the cell border.
75330view14:42, 19 May 2014SbohlerParts added to the pathway, including RNA for PLC1,2, NAD-ME1,2, NADP-ME2.
74123view20:17, 31 March 2014EgonwRemoved the list of Uniprot identifiers from the Xref, which can hold only one.
74122view20:16, 31 March 2014EgonwCopied the multiple identifiers to the comment field.
71812view18:17, 18 October 2013EgonwAdded a bunch of missing metabolite identifiers.
71448view19:14, 17 October 2013MaintBotAutomated update of data sources
65321view18:01, 6 June 2013SbohlerPeriodical save, work in progress
65316view17:51, 6 June 2013Sbohlerwork in progress
65312view17:40, 6 June 2013SbohlerPeriodical save, work in progress
65024view21:00, 4 June 2013MaintBotOntology Term : 'glycolysis pathway' added !
65023view21:00, 4 June 2013MaintBotOntology Term : 'Krebs cycle pathway' added !
65022view20:59, 4 June 2013MaintBotModified categories
62875view12:56, 3 May 2013SbohlerModified description
62874view12:54, 3 May 2013SbohlerModified description
62873view12:50, 3 May 2013SbohlerNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
1,3-bisphosphoglycerateMetabolite
2,3-dihydroxy-3-methylvalerateMetaboliteHMDB12140 (HMDB)
2,3-dihydroxy-isovalerateMetaboliteHMDB12141 (HMDB)
2,6-diaminopimelateMetabolite
2-AcetolactateMetaboliteHMDB06855 (HMDB)
2-aceto-2-hydroxybutanoateMetabolite
2-cys peroxiredoxin-like proteinProteinQ9C5R8 (Uniprot-TrEMBL)
2-oxo-3-methylvalerateMetabolite
2-oxo-isovalerateMetabolite
2-oxoglutarateMetabolite
2-oxoglutarate dehydrogenaseProtein
2H+Metabolite
3-phosphoglycerateMetabolite
30S ribosomal protein S5ProteinP93014
5-amino-levulinateMetabolite
5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferaseProteinO50008 (Uniprot-TrEMBL)
ADPMetabolite
ADP-glucose pyrophosphorylaseProtein
ADP-glucoseMetaboliteHMDB06557 (HMDB)
ATP-dependent phosphofructokinaseProtein
ATPMetaboliteHMDB00538 (HMDB)
Acetyl-CoAMetaboliteHMDB01206 (HMDB)
CO2Metabolite
CO2 + H2OMetabolite
CO2MetaboliteHMDB01967 (HMDB)
Calvin CyclePathway
CoAMetabolite
CystathionineMetaboliteHMDB00099 (HMDB)
Cysteine and Methionine BiosynthesisPathway
CysteineMetaboliteHMDB00574 (HMDB)
DNAMetabolite
DNA (cytosine-5-)-methyltransferaseProtein2.1.1.37 (Enzyme Nomenclature)
DNA 5-methylcytosineMetabolite
Dihydroxyacetone phosphateMetaboliteHMDB01473 (HMDB)
FAD+MetaboliteHMDB01248 (HMDB)
FADH2MetaboliteHMDB01197 (HMDB)
GAPC1RnaAT3G04120 (TAIR)
GAPC2RnaAT1G13440 (TAIR)
Glutamate BiosynthesisPathway
GlycolysisPathway
H+Metabolite
H2CO3Metabolite
H2OMetabolite
H2O + O2Metabolite
H2O2Metabolite
H2OMetaboliteHMDB02111 (HMDB)
HCO3-Metabolite
HomocysteineMetaboliteHMDB00742 (HMDB)
IsoleucineMetaboliteHMDB00172 (HMDB)
MethionineMetaboliteHMDB00696 (HMDB)
NAD+MetaboliteHMDB00902 (HMDB)
NAD-ME1RnaAT2G13560 (TAIR)
NAD-ME2RnaAT4G00570 (TAIR)
NADHMetaboliteHMDB01487 (HMDB)
NADP+MetaboliteHMDB00217 (HMDB)
NADP+MetaboliteHMDB00902 (HMDB)
NADP-ME2RnaAT5G11670 (TAIR)
NADPHMetaboliteHMDB00221 (HMDB)
NADPHMetaboliteHMDB01487 (HMDB)
O-acetyl-L-serineMetabolite
O-phosphoserine sulfhydrylaseProtein2.5.1.65 (Enzyme Nomenclature)
O2Metabolite
O2 + H+Metabolite
PLC1RnaAT1G76100 (TAIR)
PLC2RnaAt1g20340 (TAIR)
PPiMetabolite
PPi-dependent phosphofructokinaseProtein
PhotorespirationPathway
PiMetabolite
Porphyrin and Chlorophyll metabolismPathway
RuBisCO LSUProteinO03042 (Uniprot-TrEMBL)
RuBisCO SSUProtein4.1.1.39 (Enzyme Nomenclature)
RuBisCO activaseProteinP10896 (Uniprot-TrEMBL)
RuBisCO activaseProteinQ941B7 (Uniprot-TrEMBL)
S-AdenosylhomocysteineMetaboliteHMDB00939 (HMDB)
S-adenosylmethionine synthaseProteinQ9SJL8 (Uniprot-TrEMBL)
S-sdenosylmethionineMetaboliteHMDB01185 (HMDB)
SerineMetaboliteHMDB00187 (HMDB)
Starch Metabolism Pathway
Succinyl-CoAMetaboliteHMDB01022 (HMDB)
Sucrose Metabolism Pathway
TCA Cycle (Krebs Cycle)Pathway
Thylakoid lumenal 19 kDa proteinProteinP82658 (Uniprot-TrEMBL)
UDP-glucoseMetabolite
UDP-glucose pyrophosphorylaseProtein
UTPMetabolite
Valine and Isoleucine BiosynthesisPathway
ValineMetaboliteHMDB00883 (HMDB)
acetolactate synthaseProtein
aconitaseProtein
adenosylhomocysteinaseProteinQ9LK36 (Uniprot-TrEMBL)
alanine dehydrogenaseProtein1.4.1.1 (Enzyme Nomenclature)
alanineMetaboliteHMDB00161 (HMDB)
aldolaseProtein
aldolaseProteinO65581 (Uniprot-TrEMBL)
aldolaseProteinO65581 (Uniprot-SwissProt)
aldolaseProteinQ944G9 (Uniprot-SwissProt)
aldolaseProteinQ944G9 (Uniprot-TrEMBL)
amylaseProteinGO:0016160 (GeneOntology)
aspartateMetabolite
aspartate 4-decarboxylaseProtein4.1.1.12 (Enzyme Nomenclature)
branched-chain-amino-acid transaminaseProtein
carbonic anhydrase 1ProteinP27140 (Uniprot-SwissProt)
carbonic anhydrase 2ProteinP42737 (Uniprot-SwissProt)
citrateMetabolite
citrate synthaseProtein
copper chaperoneProteinO82089 (Uniprot-TrEMBL)
cystathionine beta-lyaseProtein4.4.1.8 (Enzyme Nomenclature)
cystathionine gamma-lyaseProtein4.4.1.1 (Enzyme Nomenclature)
cysteine proteinase inhibitor 6ProteinQ8H0X6 (Uniprot-TrEMBL)
diaminopimelate decarboxylaseProtein4.1.1.20 (Enzyme Nomenclature)
diaminopimelate epimeraseProteinQ9LFG2 (Uniprot-TrEMBL)
dihydroxy-acid dehydrataseProtein
elongation factor EF-G/SCO1ProteinQ94BR7 (Uniprot-TrEMBL)
erythrose 4-phosphateMetaboliteHMDB01321 (HMDB)
ferredoxinProtein
ferredoxin-NADP+ reductaseProteinQ8W493 (Uniprot-TrEMBL)
fructose 1,6-bisphosphate aldolaseProteinGO:0004332 (GeneOntology)
fructose 1,6-bisphosphateMetaboliteHMDB01058 (HMDB)
fructose 6-phosphateMetaboliteHMDB00124 (HMDB)
fructose-1,6-bisphosphataseProtein
fructose-1,6-bisphosphataseProtein3.1.3.11 (Enzyme Nomenclature)
fructose-1,6-bisphosphateMetaboliteHMDB01058 (HMDB)
fructoseMetaboliteHMDB00660 (HMDB)
fumaraseProtein
fumarateMetabolite
glucan endo-1,3-beta-glucosidase acidic isoformProteinP33157 (Uniprot-TrEMBL)
glucose 1-phosphateMetaboliteHMDB01586 (HMDB)
glucose 6-phosphateMetaboliteHMDB01401 (HMDB)
glucose kinaseProtein
glucose-6-phosphate isomeraseProteinGO:0004347 (GeneOntology)
glucoseMetaboliteHMDB00122 (HMDB)
glutamateMetabolite
glutamate-1-semialdehydeMetabolite
glutamate-1-semialdehyde 2,1-aminomutase 2ProteinQ42522 (Uniprot-TrEMBL)
glutamate—tRNA ligaseProtein6.1.1.17 (Enzyme Nomenclature)
glutamyl-tRNA (Glu)Metabolite
glutamyl-tRNA reductaseProtein1.2.1.70 (Enzyme Nomenclature)
glutaredoxinProteinPF00462 (Pfam)
glutathione S-transferaseProteinP46422 (Uniprot-TrEMBL)
glutathione disulfideMetabolite
glutathione reductaseProtein
glutathione-S-transferaseProteinP42760 (Uniprot-TrEMBL)
glutathione-S-transferaseProteinQ9SRY5 (Uniprot-TrEMBL)
glutathioneMetaboliteHMDB00125 (HMDB)
glyceraldahyde-3-phosphateMetabolite
glyceraldehyde 3-phosphate dehydrogenaseProteinGO:0004365 (GeneOntology)
glyceraldehyde-3-phosphate dehydrogenaseProteinP25856 (Uniprot-TrEMBL)
glycerate 1,3-bisphosphateMetabolite
glycerate 2-phosphateMetabolite
glycerate 3-phosphateMetabolite
glycine-rich RNA-binding protein 7ProteinQ03250 (Uniprot-TrEMBL)
heat shock cognate 70 kDa protein 1ProteinP22953 (Uniprot-TrEMBL)
hexokinaseProteinGO:0004396 (GeneOntology)
hexose phosphate isomeraseProtein
invertaseProtein
isocitrateMetabolite
isocitrate dehydrogenaseProteinGO:0004449 (GeneOntology)
isocitrate dehydrogenaseProteinQ9SRZ6 (Uniprot-TrEMBL)
ketol-acid reductoisomeraseProteinQ05758 (Uniprot-TrEMBL)
lipoxygenase 2ProteinP38418
luminal-binding protein 1ProteinQ9LKR3 (Uniprot-TrEMBL)
luminal-binding protein 2ProteinQ39043 (Uniprot-TrEMBL)
lysineMetaboliteHMDB00182 (HMDB)
malateMetabolite
malate dehydrogenaseProteinGO:0016615 (GeneOntology)
malate dehydrogenaseProteinGO:0016619 (GeneOntology)
malic enzymeProteinGO:0004470 (GeneOntology)
malic enzymeProteinQ9LYG3 (Uniprot-TrEMBL)
meso-2,6-diaminopimelateMetabolite
myrosinase 1ProteinP37702 (Uniprot-TrEMBL)
oxaloacetateMetabolite
peroxiredoxin-2EProteinQ949U7 (Uniprot-TrEMBL)
phosphoenolpyruvateMetabolite
phosphoenolpyruvate carboxylaseProtein
phosphoglucomutaseProteinGO:0004614 (GeneOntology)
phosphoglycerate kinaseProtein2.7.2.3 (Enzyme Nomenclature)
phosphoglycerate kinaseProteinGO:0004618 (GeneOntology)
phosphoglycerate mutaseProteinGO:0004619 (GeneOntology)
phosphopyruvate hydrataseProteinGO:0004634 (GeneOntology)
phosphoribulokinaseProtein
plastocyanin 2ProteinP42699 (Uniprot-TrEMBL)
plastoquinoneMetabolite
pyruvateMetabolite
pyruvate dehydrogenaseProteinGO:0004738 (GeneOntology)
pyruvate dehydrogenaseProteinO24457 (Uniprot-TrEMBL)
pyruvate kinaseProteinGO:0004743 (GeneOntology)
ribonucleoproteinProteinQ9ZUU4 (Uniprot-TrEMBL)
ribose 5-phosphateMetaboliteHMDB01548 (HMDB)
ribulose 5-phosphate 3-epimerase activityProteinGO:0004750 (GeneOntology)
ribulose 5-phosphate isomeraseProtein
ribulose 5-phosphateMetaboliteHMDB00618 (HMDB)
ribulose-1,5-bisphosphateMetabolite
sedoheptulose 1,7-bisphosphataseProtein
sedoheptulose 1,7-bisphosphateMetabolite
sedoheptulose 7-phosphateMetaboliteHMDB01068 (HMDB)
serine acetyltransferaseProtein2.3.1.30 (Enzyme Nomenclature)
serine ammonia-lyaseProtein4.3.1.17 (Enzyme Nomenclature)
small subunit ribosomal protein S1ProteinQ93VC7 (Uniprot-TrEMBL)
starchMetabolite
starch posphorylaseProtein
starch synthaseProtein
succinateMetabolite
succinate dehydrogenaseProteinGO:0000104 (GeneOntology)
succinyl-CoA synthetaseProtein
sucrose synthaseProtein
sucroseMetaboliteHMDB00258 (HMDB)
tRNAGluMetabolite
thioredoxin reductaseProtein1.8.1.9 (Enzyme Nomenclature)
thioredoxinProteinIPR013766 (InterPro)
transketolaseProteinGO:0004802 (GeneOntology)
triose phosphate isomeraseProtein
xyluloase-5-phosphateMetabolite

Annotated Interactions

No annotated interactions

Retrieved from "https://classic.wikipathways.org/index.php/Pathway:WP2499"
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