An exploration tool of Arabidopsis metabolism

ChloroKB
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Tenth release, September 20th, 2023




New content


This tenth release contains eight new or revised maps containing 89 new reviewed proteins, representing nitrate transport, ammonium transport and its regulation, as well as other regulatory processes. The Nitrate transport map is the principal part of this 10th update with an exhaustive representation of the molecular actors of nitrate transport at the cellular level (in a generic cell), with 47 proteins involved, among which 32 are well-characterized and 15 still await biochemical/genetic characterizations.





Ninth release, May 10th, 2022


New features


A complete stoichiometry matrix of the reconstructed network can be downloaded (download icon on the welcome page).


The quantitative data document was improved with hyperlinks, chemical identifiers, source biological material and the compartment where the metabolite was quantified. The document can be exported as a csv file.


Cross references: The MASCP Gator link is not anymore active; please use the peptideAtlas link.




New content


This ninth release contains 68 new reviewed proteins, represented in six new maps representing additional processes in lipid metabolism in the endoplasmic reticulum (ER) and the mitochondrion.






Eighth release, June 30th, 2021


New features


A stoichiometric matrix of the reconstructed network can be optained by clicking the downloadable document icon in the welcome page.




New content


This eighth release contains 68 new reviewed proteins, represented in twelve new maps focusing on lipid synthesis in the endoplasmic reticulum (ER) and lipid trafficking between the ER and the plastid.






Seventh release, February 23rd, 2021


New features


In this release, the display in the molecule description pages (proteins, metabolites, chemical inhibitors, complexes) was modified and the screen space use was optimized. Icons of maps containing the molecule queried are represented together with their names. The names of the metabolic maps also appear when sliding the mouse over the map icons.



New content


This seventh release contains 2 new maps: one is dedicated to Sugar transport (sucrose, glucose, maltose etc.) and the other to Polyol transport (Sorbitol, xylitol etc. ), at the cellular level. Please note that sugar transport is cell specific; the sugar transport map represents a generic cell; comments in the map (grey ovals) provide indications of the cell type where the transporters are expressed.



Sixth release, October 2nd, 2020


New features


The different kind of reactions in ChloroKB can now be searched using the following keywords: "transport", "RXN" and "NotInMetacyc". There are 379 transport reactions, 1136 reactions with MetaCYC identifiers and 258 reactions for which identifiers could not be found in MetaCYC.




New content


This sixth release contains 152 new reviewed proteins, represented in 11 new maps. Quantitative data for many metabolites can be downloaded.



Metabolic pathways:




Fifth release, July 10th, 2019


New features


See the second release (below) on March 6th, 2018


New content


This fifth release contains 39 new reviewed proteins, represented in 4 new maps. With this release, we completed the reconstruction of starch metabolism (synthesis and degradation).



Metabolic pathways:




Fourth release, December 20th, 2018


New content


This fourth release contains 56 new reviewed proteins (total 1329), represented in 15 new maps (total 171 maps).



Metabolic pathways:



New detailed regulatory processes:




Third release, June 6th, 2018


New features


See the second release (below) on March 6th, 2018


New content


ChloroKB reconstructed metabolic network now extends far beyond chloroplast metabolism; In this third release, the representation of the synthesis of organic acids by the mitochondrion and the cytosol is completed. 89 new proteins are represented in 8 new maps and some maps have been modified (e.g. L-aspartate metabolism is represented in a single map, L-aspartate, showing the different functions of L-aspartate in the chloroplast-mainly used as a precursor-and in the other compartments, where it is involved for example in the Aspartate-Glutamate shuttle during photorespiration).



Metabolic pathways:



New HUBS:



New detailed regulatory processes:




Second release, March 6th, 2018

New features


Multidomain proteins are now graphically represented


This new feature allows to distinguish two kinds of multifunctional proteins: the ones that catalyze different reactions in the same active site (e.g. Aspartate/Prephenate aminotransferase in L-tyrosine and L-phenylalanine map) from the ones with several domains catalyzing a given reaction (e.g. the protein PHYLLO in Phylloquinone synthesis). This also allows the representation of proteins with regulatory domains (see for example the Aspartate kinases map).



Physiological direction of reversible reactions


The double arrows symbolizing reversible reactions in CellDesigner are now represented with a white and a black end: the black end points towards the presumed physiological direction of the flux in leaf (see for example the aspartate kinase step in the L-lysine and L-threonine map).



New content


87 new reviewed proteins are represented in 22 new maps.



Metabolic pathways:



Some extra-chloroplastic processes are being represented:



New hubs:



New detailed regulatory processes: