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Biochemical Space

Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure of the model. Manipulation with the navigation panel is realized by unfolding the items in the navigation tree and clicking on a requested system level.

Annotations Tab
All the annotation links to relevant databases for the currently selected entity are displayed on the Annotation Tab below the scheme.

Models Tab
The Models Tab displays all models containing selected entity.

Relations Tab
Relations Tab contains information about relations in which selected entity figures. There are several types of relations: part of, contains, partial composition items and full composition items. This tab also contains organism info which is optional.

Rules Tab
Rules tab contains list of rules which contains selected entity.

Processes Tab
This tab contains set of processes in which selected entity is present.

medium [liq]

Liquid medium, where cells are situated.

Part of:


Carbon dioxide hydration
Rule: CO2::liq + H2O::liq <=> HCO3{-}::liq + h{+}::liq
Water self-dissociation.
Rule: H2O::liq <=> h{+}::liq + OH{-}::liq
Bicarbonate/carbonate conversion at low pH.
Rule: HCO3{-}::liq <=> CO3{2-}::liq + h{+}::liq
Bicarbonate/carbonate conversion at high pH.
Rule: HCO3{-}::liq + OH{-}::liq <=> CO3{2-}::liq + H2O::liq
Buffer acid-base reaction.
Rule: HA::liq <=> h{+}::liq + A{-}::liq
Bubble-liquid carbon dioxide transfer
Rule: CO2::bub <=> CO2::liq
Carbon dioxide excretion by the cells.
Rule: CO2::cell <=> CO2::liq
Bicarbonate excretion from cells.
Rule: HCO3{-}::cell <=> HCO3{-}::liq
Diffusion of HCO3_m between the bulk medium and the perisplasmic space through the unstirred layer
Rule: HCO3{-}::liq <=> HCO3{-}::pps
Diffusion of CO2 between the bulk medium and the perisplasmic space through the unstirred layer
Rule: CO2::liq <=> CO2::pps

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