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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

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hydrogencarbonate{-} [HCO3{-}]



Annotations
Models
Relations
Rules
Processes
+External links
chebi:17544

Part of:

+medium
+extracellular space
+cell
+carboxysome
+cytosol
+inner cytoplasm region
+outer cytoplasm region

Is state of:

+hydrogencarbonate
+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 thylakoid membrane 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
Details
+Carbon dioxide hydration
Carbon dioxide hydration
Rule: CO2::liq + H2O::liq <=> HCO3{-}::liq + h{+}::liq
Details
+Carbon dioxide hydroxylation
Carbon dioxide hydroxylation/dehydroxylation
Rule: CO2::?X + OH{-}::?X <=> HCO3{-}::?X ; ?X = {liq, ocy, icy, cax}
modifier: ca
Details
+Bicarbonate/carbonate conversion I
Bicarbonate/carbonate conversion at low pH.
Rule: HCO3{-}::liq <=> CO3{2-}::liq + h{+}::liq
Details
+Bicarbonate/carbonate conversion II
Bicarbonate/carbonate conversion at high pH.
Rule: HCO3{-}::liq + OH{-}::liq <=> CO3{2-}::liq + H2O::liq
Details
+Bicarbonate excretion
Bicarbonate excretion from cells.
Rule: HCO3{-}::cell <=> HCO3{-}::liq
Details
+hydrogen-carbonate:L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating)
Rule: 2 ATP::cyt + C00064::cyt + HCO3{-}::cyt + H2O::cyt + h{+}::cyt => 2 ADP::cyt + orthophosphate::cyt + C00025::cyt + C00169::cyt
modifier: 6-3-5-5
Details
+R148
Rule: HCO3{-}::cax + h{+}::cax <=> H2CO3::cax
Details
+Acetyl-CoA:carbon-dioxide ligase (ADP-forming)
Rule: ATP::cyt + C00024::cyt + HCO3{-}::cyt + h{+}::cyt => ADP::cyt + orthophosphate::cyt + C00083::cyt
modifier: 6-4-1-2
Details
+phosphoenolpyruvate carboxylase (enzyme name)
Rule: C00074::cyt + HCO3{-}::cyt + h{+}::cyt => orthophosphate::cyt + C00036::cyt
modifier: 4-1-1-31
Details
+5-amino-1-(5-phospho-D-ribosyl)imidazole:carbon-dioxide ligase (ADP-forming)
Rule: ATP::cyt + C03373::cyt + HCO3{-}::cyt + h{+}::cyt => ADP::cyt + orthophosphate::cyt + C15667::cyt
modifier: 6-3-4-18
Details
+R673
Rule: HCO3{-}::ext + ATP::cyt + H2O::cyt => HCO3{-}::cyt + ADP::cyt + orthophosphate::cyt
Details
+R674
Rule: HCO3{-}::ext + C01330::ext => HCO3{-}::cyt + C01330::cyt
Details
+R720
Rule: HCO3{-}::cyt => HCO3{-}::cax
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 from icy to cax
Diffusion of HCO3_m into and out of the carboxysomes
Rule: HCO3{-}::icy => HCO3{-}::cax
Details
+Inward diffusion of accumulated HCO3_m
Inward diffusion of accumulated HCO3_m from outer to inner cytoplasmic regions, through the concentric thylakoid membranes
Rule: HCO3{-}::ocy => HCO3{-}::icy
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
+CO2 (de)hydratation
(De)hydratation of CO2 producing HCO3{-}
Rule: CO2::?X + OH{-}::?X <=> HCO3{-}::?X ; ?X = {cyt, cax}
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