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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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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.

Annotations
Models
Relations
Rules
Processes
+External links
chebi:16526
pubchem:280
+Jablonsky et al. 2014
+Clark et al. 2014 (in progress)
+Fridlyand et al. 1995
+Environmental processes
Details
+Respiration and photosynthesis
Details

Part of:

+bubbles
+headspace
+medium
+extracellular space
+cell
+carboxysome
+periplasmic space
+cytosol
+lumen
+inner cytoplasm region
+outer cytoplasm region
+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
+Bubble-liquid carbon dioxide transfer
Bubble-liquid carbon dioxide transfer
Rule: CO2::bub <=> CO2::liq
Details
+Carbon dioxide excretion
Carbon dioxide excretion by the cells.
Rule: CO2::cell <=> CO2::liq
Details
+1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose-5-phosphate carboxy-lyase(cyclizing)
Rule: C01302::cyt => C03506::cyt + CO2::cyt + H2O::cyt
modifier: 4-1-1-48
Details
+prephenate hydro-lyase (decarboxylating; phenylpyruvate-forming)
Rule: C00254::cyt => C00166::cyt + H2O::cyt + CO2::cyt
modifier: 4-2-1-51
Details
+Prephenate:NAD+ oxidoreductase(decarboxylating)
Rule: C00254::cyt + NAD+::cyt => C01179::cyt + CO2::cyt + NADH::cyt + h{+}::cyt
modifier: 1-3-1-12
Details
+ATP:carbamate phosphotransferase
Rule: ATP::cyt + C00014::cyt + CO2::cyt <=> ADP::cyt + C00169::cyt
modifier: 2-7-2-2
Details
+R56
Rule: C03771::cyt + C00027::cyt => C01035::cyt + CO2::cyt + H2O::cyt
Details
+Urea amidohydrolase
Rule: C00086::cyt + H2O::cyt => CO2::cyt + 2 C00014::cyt
modifier: 3-5-1-5
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
+L-arginine carboxy-lyase (agmatine-forming)
Rule: C00062::cyt => C00179::cyt + CO2::cyt
modifier: 4-1-1-19
Details
+meso-2,6-diaminoheptanedioate carboxy-lyase (L-lysine-forming)
Rule: C00680::cyt => C00047::cyt + CO2::cyt
modifier: 4-1-1-20
Details
+L-threonine-O-3-phosphate carboxy-lyase
Rule: C12147::cyt => C04122::cyt + CO2::cyt
modifier: 4-1-1-81
Details
+Uroporphyrinogen-III carboxy-lyase
Rule: C01051::cyt => C03263::cyt + 4 CO2::cyt
modifier: 4-1-1-37
Details
+Coproporphyrinogen:oxygen oxidoreductase(decarboxylating)
Rule: C03263::cyt + O2::cyt => C01079::cyt + 2 CO2::cyt + 2 H2O::cyt
modifier: 1-3-3-3
Details
+coproporphyrinogen-III:S-adenosyl-L-methionine oxidoreductase(decarboxylating)
Rule: C03263::cyt + 2 C00019::cyt => C01079::cyt + 2 CO2::cyt + 2 C00073::cyt + 2 C05198::cyt
modifier: 1-3-99-22
Details
+carbonate hydro-lyase (carbon-dioxide-forming)
Rule: H2CO3::cax <=> CO2::cax + H2O::cax
modifier: 4-2-1-1
Details
+glycine synthase
Rule: C00037::cyt + C00101::cyt + NAD+::cyt => C00143::cyt + C00014::cyt + CO2::cyt + NADH::cyt + h{+}::cyt
modifier: 2-1-2-10
Details
+glyoxylate carboxy-lyase (dimerizing; tartronate-semialdehyde-forming)
Rule: 2 C00048::cyt => C01146::cyt + CO2::cyt
modifier: 4-1-1-47
Details
+S-adenosyl-L-methionine carboxy-lyase [(5-deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium-forming]
Rule: C00019::cyt + h{+}::cyt => C01137::cyt + CO2::cyt
modifier: 4-1-1-50
Details
+pyruvate:thiamin diphosphate acetaldehydetransferase (decarboxylating)
Rule: C00022::cyt + C00068::cyt => C05125::cyt + CO2::cyt
modifier: 2-2-1-6
Details
+4-Methyl-2-oxopentanoate + CO2 <=> (2S)-2-Isopropyl-3-oxosuccinate
Rule: C04236::cyt => C00233::cyt + CO2::cyt
Details
+(2R,3S)-3-methylmalate:NAD+ oxidoreductase
Rule: C06032::cyt + NAD+::cyt => C00109::cyt + CO2::cyt + NADH::cyt + h{+}::cyt
modifier: 1-1-1-85
Details
+Acyl-[acyl-carrier-protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylating)
Rule: C03939::cyt + C01209::cyt => C05744::cyt + CO2::cyt + C00229::cyt
modifier: 2-3-1-179, 2-3-1-180
Details
+butyryl-[acyl-carrier protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylating)
Rule: C05745::cyt + C01209::cyt => C05746::cyt + CO2::cyt + C00229::cyt
modifier: 2-3-1-179
Details
+hexanoyl-[acyl-carrier protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylating)
Rule: C05749::cyt + C01209::cyt => C05750::cyt + CO2::cyt + C00229::cyt
modifier: 2-3-1-179
Details
+Octanoyl-[acyl-carrier protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylating)
Rule: C05752::cyt + C01209::cyt => C05753::cyt + CO2::cyt + C00229::cyt
modifier: 2-3-1-179
Details
+Decanoyl-[acyl-carrier protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylating)
Rule: C05755::cyt + C01209::cyt => C05756::cyt + CO2::cyt + C00229::cyt
modifier: 2-3-1-179
Details
+dodecanoyl-[acyl-carrier-protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylating)
Rule: C05223::cyt + C01209::cyt => C05759::cyt + CO2::cyt + C00229::cyt
modifier: 2-3-1-179
Details
+Tetradecanoyl-[acyl-carrier protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylati
Rule: C05761::cyt + C01209::cyt => C05762::cyt + CO2::cyt + C00229::cyt
modifier: 2-3-1-179
Details
+Hexadecanoyl-[acp] + Malonyl-[acyl-carrier protein] <=> 3-Oxostearoyl-[acp] + Acyl-carrier protein +
Rule: C05764::cyt + C01209::cyt => C16219::cyt + C00229::cyt + CO2::cyt
modifier: 2-3-1-179
Details
+Nicotinate-nucleotide:pyrophosphate phosphoribosyltransferase (carboxylating)
Rule: C03722::cyt + C00119::cyt + h{+}::cyt => C01185::cyt + C00013::cyt + CO2::cyt
modifier: 2-4-2-19
Details
+L-aspartate 1-carboxy-lyase (beta-alanine-forming)
Rule: C00049::cyt => C00099::cyt + CO2::cyt
modifier: 4-1-1-11, 4-1-1-15
Details
+N-[(R)-4'-Phosphopantothenoyl]-L-cysteine carboxy-lyase
Rule: C04352::cyt => C01134::cyt + CO2::cyt
modifier: 4-1-1-36
Details
+6-phospho-D-gluconate:NADP+ 2-oxidoreductase (decarboxylating)
Rule: C00345::cyt + NADP{+}::cyt => C00199::cyt + CO2::cyt + NADPH::cyt + h{+}::cyt
modifier: 1-1-1-44
Details
+pyruvate:NAD+ 2-oxidoreductase (CoA-acetylating)
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
Details
+Isocitrate:NADP+ oxidoreductase (decarboxylating)
Rule: C00311::cyt + NADP{+}::cyt => C00026::cyt + CO2::cyt + NADPH::cyt + h{+}::cyt
modifier: 1-1-1-42
Details
+(S)-Malate:NADP+ oxidoreductase(oxaloacetate-decarboxylating)
Rule: C00149::cyt + NADP{+}::cyt => C00022::cyt + CO2::cyt + NADPH::cyt + h{+}::cyt
modifier: 1-1-1-38
Details
+pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
Rule: 2 fd{+}::cyt + C00022::cyt + C00010::cyt => 2 fd{-}::cyt + C00024::cyt + CO2::cyt + 2 h{+}::cyt
modifier: 1-2-7-1
Details
+Oxalate carboxy-lyase
Rule: C00209::cyt => C00058::cyt + CO2::cyt
modifier: 4-1-1-2
Details
+Formate:ferricytochrome-b1 oxidoreductase
Rule: C00058::cyt + 2 C00995::cyt => CO2::cyt + 2 C00998::cyt + 2 h{+}::cyt
modifier: 1-2-2-1
Details
+L-glutamate 1-carboxy-lyase (4-aminobutanoate-forming)
Rule: C00025::cyt => C00334::cyt + CO2::cyt
modifier: 4-1-1-15
Details
+2-Oxoglutarate carboxy-lyase
Rule: C00026::cyt => C00232::cyt + CO2::cyt
modifier: 4-1-1-71
Details
+orotidine-5'-phosphate carboxy-lyase (UMP-forming)
Rule: C01103::cyt => C00105::cyt + CO2::cyt
modifier: 4-1-1-23
Details
+phytyl-diphosphate:homogentisate phytyltransferase (decarboxylating)
Rule: C05427::cyt + C00544::cyt => C15882::cyt + C00013::cyt + CO2::cyt
modifier: 2-5-1-x
Details
+2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Rule: C00885::cyt + C00026::cyt => C16519::cyt + CO2::cyt
modifier: 2-2-1-9
Details
+1,4-Dihydroxy-2-naphthoate + Phytyl diphosphate <=> 2-Phytyl-1,4-naphthoquinone + CO2 + Diphosphate
Rule: C03657::cyt + C05427::cyt => C13309::cyt + CO2::cyt + C00013::cyt + 2 h{+}::cyt
modifier: 2-5-1-x
Details
+4-Hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating,decarboxylating)
Rule: C01179::cyt + O2::cyt => C00544::cyt + CO2::cyt
modifier: 1-13-11-27
Details
+L-lysine carboxy-lyase (cadaverine-forming)
Rule: C00047::cyt => C01672::cyt + CO2::cyt
modifier: 4-1-1-18
Details
+1-Deoxy-D-xylulose-5-phosphate pyruvate-lyase (carboxylating)
Rule: C00022::cyt + C00118::cyt => C11437::cyt + CO2::cyt
modifier: 2-2-1-7
Details
+R666
Rule: C00097::cyt + ATP::cyt + C11437::cyt + C00082::cyt + C00019::cyt + NADPH::cyt + 3 h{+}::cyt => C04327::cyt + C00013::cyt + C00073::cyt + C00041::cyt + C01468::cyt + C05198::cyt + CO2::cyt + 2 H2O::cyt + C00020::cyt + NADP{+}::cyt
Details
+R671
Rule: CO2::cyt <=> CO2::ext
Details
+2-Amino-3-oxo-4-phosphonooxybutyrate <=> 3-Amino-2-oxopropyl phosphate + CO2
Rule: C07335::cyt => C11638::cyt + CO2::cyt
Details
+S-Adenosyl-L-methionine:1-precorrin-6Y C5,15-methyltransferase (C-12-decarboxylating)
Rule: 2 C00019::cyt + C06319::cyt => 2 C00021::cyt + C06408::cyt + CO2::cyt
modifier: 2-1-1-132
Details
+Outward diffusion of CO2 from cax to icy
Outward diffusion of CO2 from the carboxysomes of such CO2 as is not fixed there
Rule: CO2::cax => CO2::icy
Details
+Outward diffusion of CO2 from icy to ocy
Outward diffusion of CO2 from inner to outer cytoplasmic region, through the concentric thylakoid membrane
Rule: CO2::icy => CO2::ocy
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
+Fixation of CO2
Fixation of CO2 generated within the carboxysomes
Rule: CO2::cax => C00182::cax
Details
+CO2 (de)hydratation
(De)hydratation of CO2 producing HCO3{-}
Rule: CO2::?X + OH{-}::?X <=> HCO3{-}::?X ; ?X = {cyt, cax}
Details
+ 3-phospho-D-glycerate carboxy-lyase
Fixation of CO2 and formation of PGA in carboxysome
Rule: C01182::cax + CO2::cax + H2O::cax <=> 2 PGA::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