Username:
Password:
Register
Reset password

Biochemical Space

Processes

+ Cyanobacterium in its environment
o Environmental processes
+ Cellular processes
o Respiration and photosynthesis
o Carbon concentrating mechanism (CCM)
o Respiration
o Clock mechanism
o Metabolism

Navigation
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.

Annotations
Models
Relations
Rules
Processes
+Fridlyand et al. 1995

Part of:

+photobioreactor

Contains:

+cell
+proton
+carbon dioxide
+water
+hydrogencarbonate
+carbonic acid
+carbonate
+hydroxide
+Bronsted acid
+Bronsted base
+Carbon dioxide hydration
Carbon dioxide hydration
Rule: CO2::liq + H2O::liq <=> HCO3{-}::liq + h{+}::liq
Details
+Water self-dissociation
Water self-dissociation.
Rule: H2O::liq <=> h{+}::liq + OH{-}::liq
Details
+Bicarbonate/carbonate conversion I
Bicarbonate/carbonate conversion at low pH.
Rule: HCO3{-}::liq <=> CO3{2-}::liq + h{+}::liq
Details
+Bicarbonate/carbonate conversion II
Bicarbonate/carbonate conversion at high pH.
Rule: HCO3{-}::liq + OH{-}::liq <=> CO3{2-}::liq + H2O::liq
Details
+Buffer acid-base reaction
Buffer acid-base reaction.
Rule: HA::liq <=> h{+}::liq + A{-}::liq
Details
+Bubble-liquid carbon dioxide transfer
Bubble-liquid carbon dioxide transfer
Rule: CO2::bub <=> CO2::liq
Details
+Carbon dioxide excretion
Carbon dioxide excretion by the cells.
Rule: CO2::cell <=> CO2::liq
Details
+Bicarbonate excretion
Bicarbonate excretion from cells.
Rule: HCO3{-}::cell <=> HCO3{-}::liq
Details
+Diffusion of HCO3_m between med and pps
Diffusion of HCO3_m between the bulk medium and the perisplasmic space through the unstirred layer
Rule: HCO3{-}::liq <=> HCO3{-}::pps
Details
+Diffusion of CO2 between liq and pps
Diffusion of CO2 between the bulk medium and the perisplasmic space through the unstirred layer
Rule: CO2::liq <=> CO2::pps
Details
Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: 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