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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.

periplasmic space [pps]

The region between cytoplasmic membrane and cell wall.

Annotations
Models
Relations
Rules
Processes
+External links
go:0042597
+Fridlyand et al. 1995

Part of:

+cell

Contains:

+proton
+carbon dioxide
+water
+dioxygen
+plastocyanin
+ATP synthesis in periplasmic space
ATP synthesis, proton translocation from periplasm to cytoplasm
Rule: 3 ADP::cyt + 3 orthophosphate::cyt + 14 h{+}::pps => 3 ATP::cyt + 14 h{+}::cyt + 3 H2O::cyt
modifier: ATPase
Details
+plastocyanin (PC) oxidation in the periplasmatic space
oxidation of plastocyanin in the periplasmatic space, proton translocation from cytoplasm (cyt) to periplasmatic space (pps)
Rule: 4 pc{-}::pps + O2::pps + 8 h{+}::cyt => 4 pc{+}::pps + 2 H2O::pps + 4 h{+}::pps
modifier: Cox
Details
+plastoquinone reduction in the cytoplasmic membrane 3
oxidation of NADPH and reduction of plastoquinone in the thylakoid membrane
Rule: NADPH::cyt + 4 h{+}::cyt + pq::cym + H2O::cyt + CO2::pps => NADP{+}::cyt + 4 h{+}::pps + pqh2::cym + HCO3{-}::cyt
modifier: NDH1_4
Details
+plastoquinone reduction in the cytoplasmic membrane 4
oxidation of NADPH and reduction of plastoquinone in the cytoplasmic membrane
Rule: NADPH::cyt + 5 h{+}::cyt + pq::cym => NADP{+}::cyt + 4 h{+}::pps + pqh2::cym
modifier: NDH1
Details
+R727
Rule: H2O::pps <=> H2O::cyt
Details
+R728
Rule: O2::pps <=> O2::cyt
Details
+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
+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
+Passive diffusion of CO2 between pps and ocy
Passive diffusion of CO2 between periplasmic space and cytoplasm
Rule: CO2::pps <=> CO2::ocy
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