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Biochemical Space

To browse the processes in cyanobacterium use either the graphical scheme below or the navigation panel on the left. The root level is displayed after clicking on the Biochemical Space tab in the main menu at the top of the screen.

The central feature of the ontology view is the graphical scheme representing the projection of cyanobacterium to respective biological processes. The graphical scheme is active, the individual processes implemented in the project are highlighted yellow when moving the mouse over them. After clicking on any implemented part, corresponding scheme of selected process is viewed.

Models Tab
The Models Tab displays all models containing selected process. More information can be obtained by clicking on specific model. After clicking on Details, you will be redirected to selected model.

Entities Tab
The Entities Tab displays all entities contained in selected process. More information can be obtained by unfolding specific entity and clicking on Details.

Rules Tab
Rules Tab contains information regarding the modeled rules in selected process. Individual rules are categorized into rule types and can be unfolded by clicking on desired one. After clicking on selected rule, more details are viewed.

Carbon concentrating mechanism (CCM)

Fixation of CO2 and formation of PGA in carboxysome
Rule: C01182::cax + CO2::cax + H2O::cax <=> 2 PGA::cax
modifier: 4-1-1-39
Formation of PGA and 2-Phosphoglycolate
Rule: C01182::cax + O2::cax <=> PGA::cax + C00988::cax
modifier: 4-1-1-39
oxidation of NADPH and reduction of plastoquinone in the thylakoid membrane
Rule: NADPH::cyt + 4 h{+}::cyt + pq::tlm + H2O::cyt + CO2::lum => NADP{+}::cyt + 4 h{+}::lum + pqh2::tlm + HCO3{-}::cyt
modifier: NDH1_3
Rule: CO2::cyt <=> CO2::ext

Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI