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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.

dioxygen [O2]

Dioxygen plays important role in cellular respiration, oxygen is reduced to water, thus closing the biological water-oxygen redox cycle

Annotations
Models
Relations
Rules
Processes
+External links
kegg:C00007
+Plyusnina et al. (in prep.)
+Jablonsky et al. 2014
+Respiration and photosynthesis
Details
+Respiration
Details

Part of:

+extracellular space
+carboxysome
+periplasmic space
+cytosol
+lumen

States:

+dioxygen{-}
+plastoquinole oxidation in the cytoplasmic membrane
oxidation of plastoquinole in the cytoplasmic membrane
Rule: pqh2::cym + O2::cyt + 2 h{+}::cyt => pq::cym + 2 H2O::cyt
modifier: CydBD
Details
+plastoquinole oxidation in the thylakoid membrane
oxidation of plastoquinole in the thylakoid membrane
Rule: pqh2::tlm + O2::lum + 2 h{+}::lum => pq::tlm + 2 H2O::lum
modifier: CydBD
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
+plastocyanin (PC) oxidation in the thylakoid lumen
oxidation of plastocyanin in the thylakoid lumen, proton translocation from cytoplasm (cyt) to thylakoid lumen (lum)
Rule: 4 pc{-}::lum + O2::lum + 8 h{+}::cyt => 4 pc{+}::lum + 2 H2O::lum + 4 h{+}::lum
modifier: Cox
Details
+L-Proline,2-oxoglutarate:oxygen oxidoreductase (4-hydroxylating)
Rule: C00148::cyt + C00026::cyt + O2::cyt => C01157::cyt + succinate::cyt + CO2::cyt
modifier: 1-14-11-2
Details
+R95
Rule: C05430::cyt + NADPH::cyt + h{+}::cyt + O2::cyt => C05431::cyt + 2 H2O::cyt + NADP{+}::cyt
Details
+R96
Rule: C05431::cyt + NADPH::cyt + h{+}::cyt + O2::cyt => C05432::cyt + 2 H2O::cyt + NADP{+}::cyt
Details
+beta-carotene,NADH:oxygen 3-oxidoreductase
Rule: C02094::cyt + NADH::cyt + h{+}::cyt + O2::cyt => C08591::cyt + NAD+::cyt + H2O::cyt
modifier: 1-14-13-x
Details
+beta-cryptoxanthin,NADH:oxygen 3'-oxidoreductase
Rule: C08591::cyt + NADH::cyt + h{+}::cyt + O2::cyt => C06098::cyt + NAD+::cyt + H2O::cyt
modifier: 1-14-13-x
Details
+echinenone,NADH:oxygen 3-oxidoreductase
Rule: C08592::cyt + NADH::cyt + h{+}::cyt + O2::cyt => C15966::cyt + NAD+::cyt + H2O::cyt
modifier: 1-14-13-x
Details
+R102
Rule: C02094::cyt + NADPH::cyt + h{+}::cyt + O2::cyt => C08592::cyt + NADP{+}::cyt + H2O::cyt + h{+}::cyt
Details
+Coproporphyrinogen:oxygen oxidoreductase(decarboxylating)
Rule: C03263::cyt + O2::cyt => C01079::cyt + 2 CO2::cyt + 2 H2O::cyt
modifier: 1-3-3-3
Details
+protoporphyrinogen-IX:oxygen oxidoreductase
Rule: 2 C01079::cyt + 3 O2::cyt => 2 C02191::cyt + 6 H2O::cyt
modifier: 1-3-3-4
Details
+magnesium-protoporphyrin-IX 13-monomethyl ester,NADPH:oxygen oxidoreductase (hydroxylating) R06265
Rule: C04536::cyt + NADPH::cyt + h{+}::cyt + O2::cyt => C11829::cyt + NADP{+}::cyt + H2O::cyt
modifier: 1-14-13-81
Details
+magnesium-protoporphyrin-IX 13-monomethyl ester,NADPH:oxygen oxidoreductase (hydroxylating) R06266
Rule: C11829::cyt + NADPH::cyt + h{+}::cyt + O2::cyt => C11830::cyt + NADP{+}::cyt + 2 H2O::cyt
modifier: 1-14-13-81
Details
+magnesium-protoporphyrin-IX 13-monomethyl ester,NADPH:oxygen oxidoreductase (hydroxylating) R06267
Rule: C11830::cyt + NADPH::cyt + h{+}::cyt + O2::cyt => C11831::cyt + NADP{+}::cyt + 2 H2O::cyt
modifier: 1-14-13-81
Details
+superoxide:superoxide oxidoreductase
Rule: 2 O2{-}::cyt + 2 h{+}::cyt => C00027::cyt + O2::cyt
modifier: 1-15-1-1
Details
+hydrogen-peroxide:hydrogen-peroxide oxidoreductase
Rule: 2 C00027::cyt => O2::cyt + 2 H2O::cyt
modifier: 1-11-1-6
Details
+Glyoxylate:oxygen oxidoreductase
Rule: C00048::cyt + O2::cyt + H2O::cyt => C00209::cyt + C00027::cyt
modifier: 1-2-3-5
Details
+glycine:oxygen oxidoreductase (deaminating)
Rule: C00037::cyt + H2O::cyt + O2::cyt => C00048::cyt + C00014::cyt + C00027::cyt
modifier: 1-4-3-19
Details
+stearoyl-CoA 9-desaturase (enzyme name) R370
Rule: C05764::cyt + NADPH::cyt + h{+}::cyt + O2::cyt <=> C16520::cyt + NADP{+}::cyt + 2 H2O::cyt
modifier: 1-14-19-1
Details
+stearoyl-CoA 9-desaturase (enzyme name) R371
Rule: C04088::cyt + NADPH::cyt + h{+}::cyt + O2::cyt <=> C01203::cyt + NADP{+}::cyt + 2 H2O::cyt
modifier: 1-14-19-1
Details
+R372
Rule: C01203::cyt + NADPH::cyt + h{+}::cyt + O2::cyt <=> C16160::cyt + NADP{+}::cyt + 2 H2O::cyt
modifier: 1-14-19-x
Details
+linoleoyl-CoA desaturase (enzyme name) R373
Rule: C16160::cyt + NADPH::cyt + h{+}::cyt + O2::cyt <=> E17::cyt + NADP{+}::cyt + 2 H2O::cyt
modifier: 1-14-19-3
Details
+R374
Rule: C16160::cyt + NADPH::cyt + h{+}::cyt + O2::cyt <=> C16161::cyt + NADP{+}::cyt + 2 H2O::cyt
modifier: 1-14-19-x
Details
+linoleoyl-CoA desaturase (enzyme name) R375
Rule: C16161::cyt + NADPH::cyt + h{+}::cyt + O2::cyt <=> E36::cyt + NADP{+}::cyt + 2 H2O::cyt
modifier: 1-14-19-3
Details
+L-aspartate:oxygen oxidoreductase
Rule: C00049::cyt + O2::cyt => C05840::cyt + C00027::cyt
modifier: 1-4-3-16
Details
+L-Aspartic acid:oxygen oxidoreductase (deaminating)
Rule: C00049::cyt + H2O::cyt + O2::cyt => C00036::cyt + C00014::cyt + C00027::cyt
modifier: 1-4-3-16
Details
+4-Hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating,decarboxylating)
Rule: C01179::cyt + O2::cyt => C00544::cyt + CO2::cyt
modifier: 1-13-11-27
Details
+5,6-dimethylbenzimidazole synthase (enzyme name)
Rule: C01847::cyt + O2::cyt + NADH::cyt + h{+}::cyt => C03114::cyt + C00279::cyt + H2O::cyt + NAD+::cyt
modifier: 1-13-11-79
Details
+R670
Rule: O2::ext <=> O2::cyt
Details
+R719
Rule: O2::cyt => O2::cax
Details
+R725
Rule: O2::lum <=> O2::cyt
Details
+R728
Rule: O2::pps <=> O2::cyt
Details
+Pyridoxine 5-phosphate:oxygen oxidoreductase
Rule: C00627::cyt + O2::cyt <=> C00027::cyt + C00018::cyt
modifier: 1-4-3-5
Details
+precorrin-3A,NADH:oxygen oxidoreductase (20-hydroxylating)
Rule: C05772::cyt + O2::cyt + NADH::cyt + h{+}::cyt => C06406::cyt + NAD+::cyt + H2O::cyt
modifier: 1-14-13-83
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
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