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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.

outer cytoplasm region [ocy]

The region between plasmalemma and thylakoids

Annotations
Models
Relations
Rules
Processes
+External links
go:0005737
+Fridlyand et al. 1995

Part of:

+cell

Contains:

+carbon dioxide
+hydrogencarbonate
+HCO3_m transport from pps to ocy
Plasmalemma HCO3_m transport from periplasmis space to outer cytoplasm region.
Rule: HCO3{-}::pps => HCO3{-}::ocy
Details
+HCO3_m transport from ocy to pps
HCO3_m transport from outer cytoplasm region toperiplasmis space.
Rule: HCO3{-}::ocy => HCO3{-}::pps
Details
+Inward diffusion of accumulated HCO3_m
Inward diffusion of accumulated HCO3_m from outer to inner cytoplasmic regions, through the concentric thylakoid membranes
Rule: HCO3{-}::ocy => HCO3{-}::icy
Details
+Outward diffusion of CO2 from icy to ocy
Outward diffusion of CO2 from inner to outer cytoplasmic region, through the concentric thylakoid membrane
Rule: CO2::icy => CO2::ocy
Details
+Passive diffusion of CO2 between pps and ocy
Passive diffusion of CO2 between periplasmic space and cytoplasm
Rule: CO2::pps <=> CO2::ocy
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