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.

Please use the New WikiPathways

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

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://oldclassic.wikipathways.org/index.php/Pathway:WP2499"
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