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Biochemical Space

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.

Part of:

Contains:

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
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
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
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
Rule: H2O::pps <=> H2O::cyt
Details
Rule: O2::pps <=> O2::cyt
Details
Plasmalemma HCO3_m transport from periplasmis space to outer cytoplasm region.
Rule: HCO3{-}::pps => HCO3{-}::ocy
Details
HCO3_m transport from outer cytoplasm region toperiplasmis space.
Rule: HCO3{-}::ocy => HCO3{-}::pps
Details
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 periplasmic space and cytoplasm
Rule: CO2::pps <=> CO2::ocy
Details
Diffusion of CO2 between the bulk medium and the perisplasmic space through the unstirred layer
Rule: CO2::liq <=> CO2::pps
Details