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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.

carboxysome [cax]

Microcompartiment surrounded by a protein shell. Plays major role in Carbon Concentrating Mechanism (CCM).

Annotations
Models
Relations
Rules
Processes
+External links
doi:10.1128/MMBR.00061-12.
+Clark et al. 2014 (in progress)
+Fridlyand et al. 1995

Part of:

+cell

Contains:

+proton
+carbon dioxide
+water
+hydrogencarbonate
+dioxygen
+carbonic acid
+hydroxide
+Glycogen
+3-Phospho-D-glycerate
+2-Phosphoglycolate
+D-Ribulose 1,5-bisphosphate
+phosphoglycerate
+carbonic anhydrase
+R148
Rule: HCO3{-}::cax + h{+}::cax <=> H2CO3::cax
Details
+carbonate hydro-lyase (carbon-dioxide-forming)
Rule: H2CO3::cax <=> CO2::cax + H2O::cax
modifier: 4-2-1-1
Details
+R718
Rule: h{+}::cyt <=> h{+}::cax
Details
+R719
Rule: O2::cyt => O2::cax
Details
+R720
Rule: HCO3{-}::cyt => HCO3{-}::cax
Details
+R721
Rule: C01182::cyt => C01182::cax
Details
+R722
Rule: C00197::cax => C00197::cyt
Details
+R723
Rule: C00988::cax => C00988::cyt
Details
+Diffusion of HCO3_m from icy to cax
Diffusion of HCO3_m into and out of the carboxysomes
Rule: HCO3{-}::icy => HCO3{-}::cax
Details
+Outward diffusion of CO2 from cax to icy
Outward diffusion of CO2 from the carboxysomes of such CO2 as is not fixed there
Rule: CO2::cax => CO2::icy
Details
+Fixation of CO2
Fixation of CO2 generated within the carboxysomes
Rule: CO2::cax => C00182::cax
Details
+D-Ribulose 1,5-bisphosphate oxygenase
Formation of PGA and 2-Phosphoglycolate
Rule: C01182::cax + O2::cax <=> PGA::cax + C00988::cax
modifier: 4-1-1-39
Details
+ 3-phospho-D-glycerate carboxy-lyase
Fixation of CO2 and formation of PGA in carboxysome
Rule: C01182::cax + CO2::cax + H2O::cax <=> 2 PGA::cax
modifier: 4-1-1-39
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