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Biochemical Space

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.

carbon dioxide [CO2]

Carbon dioxide (chemical formula CO2) is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom. It is a gas at standard temperature and pressure and exists in Earth's atmosphere in this state, as a trace gas at a concentration of 0.039 per cent by volume.

Part of:

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
oxidation of NADPH and reduction of plastoquinone in the thylakoid membrane
Rule: NADPH::cyt + 4 h{+}::cyt + pq::tlm + H2O::cyt + CO2::lum => NADP{+}::cyt + 4 h{+}::lum + pqh2::tlm + HCO3{-}::cyt
modifier: NDH1_3
Carbon dioxide hydration
Rule: CO2::liq + H2O::liq <=> HCO3{-}::liq + h{+}::liq
Carbon dioxide hydroxylation/dehydroxylation
Rule: CO2::?X + OH{-}::?X <=> HCO3{-}::?X ; ?X = {liq, ocy, icy, cax}
modifier: ca
Bubble-liquid carbon dioxide transfer
Rule: CO2::bub <=> CO2::liq
Carbon dioxide excretion by the cells.
Rule: CO2::cell <=> CO2::liq
Rule: ATP::cyt + C00014::cyt + CO2::cyt <=> ADP::cyt + C00169::cyt
modifier: 2-7-2-2
Rule: C03771::cyt + C00027::cyt => C01035::cyt + CO2::cyt + H2O::cyt
Rule: C00086::cyt + H2O::cyt => CO2::cyt + 2 C00014::cyt
modifier: 3-5-1-5
Rule: C01051::cyt => C03263::cyt + 4 CO2::cyt
modifier: 4-1-1-37
Rule: C00037::cyt + C00101::cyt + NAD+::cyt => C00143::cyt + C00014::cyt + CO2::cyt + NADH::cyt + h{+}::cyt
modifier: 2-1-2-10
Rule: C00022::cyt + C00010::cyt + NAD+::cyt => C00024::cyt + CO2::cyt + NADH::cyt + h{+}::cyt
modifier: 1-8-1-4, 1-2-4-1, 2-3-1-12
Rule: C00209::cyt => C00058::cyt + CO2::cyt
modifier: 4-1-1-2
Rule: C00026::cyt => C00232::cyt + CO2::cyt
modifier: 4-1-1-71
Rule: CO2::cyt <=> CO2::ext
Outward diffusion of CO2 from the carboxysomes of such CO2 as is not fixed there
Rule: CO2::cax => CO2::icy
Outward diffusion of CO2 from inner to outer cytoplasmic region, through the concentric thylakoid membrane
Rule: CO2::icy => CO2::ocy
Passive diffusion of CO2 between periplasmic space and cytoplasm
Rule: CO2::pps <=> CO2::ocy
Diffusion of CO2 between the bulk medium and the perisplasmic space through the unstirred layer
Rule: CO2::liq <=> CO2::pps
Fixation of CO2 generated within the carboxysomes
Rule: CO2::cax => C00182::cax
(De)hydratation of CO2 producing HCO3{-}
Rule: CO2::?X + OH{-}::?X <=> HCO3{-}::?X ; ?X = {cyt, cax}
Fixation of CO2 and formation of PGA in carboxysome
Rule: C01182::cax + CO2::cax + H2O::cax <=> 2 PGA::cax
modifier: 4-1-1-39

Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: 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