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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.

cell [cell]

The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Annotations
Models
Relations
Rules
Processes
+External links
go:0005623
+Plyusnina et al. (in prep.)

Part of:

+medium

Contains:

+carboxysome
+periplasmic space
+cytosol
+cytoplasmic membrane
+thylakoid membrane
+ferredoxin
+carbon dioxide
+water
+hydrogencarbonate
+plastocyanin
+photon
+inner cytoplasm region
+outer cytoplasm region
+fluorescence emission from the chlorophyll of the internal PSI antenna
chlorophyll a (chl, pigment ligand) emits near infra-red {nir} fluorescence
Rule: chl{*}::ps1::tlm => chl{n}::ps1::tlm + photon{nir}::cell
Details
+fluorescence emission from the chlorophyll of the internal PSII antenna
chlorophyll a (chl, pigment ligand) emits near infra-red {nir} fluorescence
Rule: chl{*}::ps2::tlm => chl{n}::ps2::tlm + photon{nir}::cell
Details
+light absorption in the chlorophyll of the internal PSII antenna
chlorophyll a (chl, pigment ligand) is excited by absorption of a photon in the internal antenna of PSII (PSII, pigment-protein complex)
Rule: photon{blue_red}::cell + chl{n}::ps2::tlm => chl{*}::ps2::tlm
Details
+charge recombination between oxidized P700 and reduced Fa
Rule: ps1(p700{+} | fa{-})::tlm => ps1(p700{n} | fa{n})::tlm + photon{red}::cell
modifier: As the recombination is considred as subsequent backward electron transport from Fa- to P700+ through Fx, A1, A0 and aChl, these enities must be in neutral state to accept the electron and hence they are modifiers of the recombination-
Details
+charge recombination between oxidized P700 and reduced Fx
Rule: ps1(p700{+} | fx{-})::tlm => ps1(p700{n} | fx{n})::tlm + photon{red}::cell
modifier: As the recombination is considred as subsequent backward electron transport from Fx- to P700+ through A1, A0 and aChl, these enities must be in neutral state to accept the electron and hence they are modifiers of the recombination-
Details
+reduction of oxidized P700
Rule: pc{n}::cell + p700{+}::ps1::tlm <=> pc{+}::cell + p700{n}::ps1::tlm
Details
+electron transport from Fb to Ferredoxin
Rule: fb{-}::ps1::tlm + fd{n}::cell <=> fb{n}::ps1::tlm + fd{-}::cell
Details
+radiative deactivation of excited states in chlorophyll-containing light-harvesting antenna of photo
Rule: chl{*}::ps1::tlm => chl{n}::ps1::tlm + photon{red}::cell
Details
+absorption of blue/red photon by chlorophyll-containing light-harvesting antenna of photosystem I
Rule: chl{n}::ps1::tlm + photon{blue_red}::cell => chl{*}::ps1::tlm
Details
+radiative deactivation of excited states in phycobilin-containing phycobilisome by fluorescence emis
Rule: pcb{*}::pbs::tlm => pcb{n}::pbs::tlm + photon{red}::cell
Details
+absorption of orange photon by phycobilin-containing phycobilisome
Rule: pcb{n}::pbs::tlm + photon{orange}::cell => pcb{*}::pbs::tlm
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
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