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Model repository

Models

+ Miyoshi et al. 2007
+ Plyusnina et al. (in prep.)
+ Hertel et al. 2013
+ Jablonsky et al. 2014
+ Clark et al. 2014 (in progress)
+ Fridlyand et al. 1995
o Grimaud et al. 2014
o E-cyano team 2017, clock & C-N metabolism
o Müller et al. 2019

Stoichiometry matrix of Jablonsky et al. 2014

This page displays stoichiometry matrix of selected model

Entities are in rows, rules in columns

You can also download SBRML file clicking on link below.


(LIGHT_1 : ADP + Pi → ATP) (CC_1 : RuBP + CO2 → 2*3PGA) (CC_10 : S7P + GAP ↔ Ri5P + Xu5P) (CC_11 : Ri5P ↔ Ru5P) (CC_12 : Xu5P ↔ Ru5P) (CC_13 : Ru5P + ATP → RuBP + ADP) (CC_2 : 3PGA + ATP → BPGA + ADP) (CC_3 : BPGA + NADPH ↔ GAP + NADPp + Pi) (CC_4 : GAP ↔ DHAP) (CC_5 : GAP + DHAP ↔ FBP) (CC_6 : FBP → F6P + Pi) (CC_7 : F6P + GAP ↔ E4P + Xu5P) (CC_8 : DHAP + E4P ↔ SBP) (CC_9 : SBP → S7P + Pi) (CO2 dif : CO2{external} -> CO2{cytosol}) (GC_1 : GOA -> TSA) (GC_2 : TSA -> GCEA) (GL_1 : F6P → FBP) (GL_2a : GAP + NADPp + Pi ↔ BPGA + NADPH) (GL_2b : GAP + NADPp + Pi ↔ BPGA + NADPH) (GL_3a : 3PGA ↔ 2PGA) (GL_3b : 3PGA ↔ 2PGA) (GL_3c : 3PGA ↔ 2PGA) (GL_4 : 2PGA ↔ PEP) (GSM_1 : GOA -> GLY) (GSM_2 : 3PGA -> SER) (LIGHT_2 : NADPp → NADPH) (OX_1 : GOA -> OXA) (PP_1 : RuBP + O2 → 2PG + 3PGA) (PP_2a : 2PG -> GCA) (PP_2b : 2PG -> GCA) (PP_3 : GCA -> GOA) (PP_4 : GOA + SER <-> HPR + GLY) (PP_5 : 2*GLY -> SER) (PP_6 : HPR -> GCEA) (PP_7 : GCEA + ATP -> 3PGA + ADP) (Sink Glycine : GLY → Sink2) (Sink oxalate : OXA -> Sink4) (Sink PEP : PEP -> 3 * Sink_PEP) (Sink Serine : SER -> Sink2) (Sink Threonine : THR -> Sink2) (Sink1_DHAP : DHAP -> 3 * Sink_DHAP) (Sink1_E4P : E4P -> 4 * Sink_E4P) (Sink1_Ri5P : Ri5P -> 5 * Sink_Ri5P) (SS_1 : F6P ↔ G6P) (PP_8: GCEA + ATP -> ppGA + ADP)
Sink_Ri5P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0
Sink_E4P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0
PGA 0 2 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 1 1 -1 -1 -1 0 0 -1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
Pi -1 0 0 0 0 0 0 1 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Sink_DHAP 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0
Sink_PEP 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0
GOA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 0 -1 0 0 -1 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
GAP 0 0 -1 0 0 0 0 1 -1 -1 0 -1 0 0 0 0 0 0 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
GLY 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 -2 0 0 -1 0 0 0 0 0 0 0 0 0
ATP 1 0 0 0 0 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 -1
ppGA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
F6P 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0
DHAP 0 0 0 0 0 0 0 0 1 -1 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0
GCEA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 -1
Sink2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0
Ru5P 0 0 0 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CO2_cyt 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
NADPp 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 -1 -1 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
GCA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SER 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 -1 1 0 0 0 0 0 -1 0 0 0 0 0 0
OXA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0
Xu5P 0 0 1 0 -1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Ri5P 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0
FBP 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HPR 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0
PGCA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
E4P 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0
BPGA 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RuBP 0 -1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TSA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PEP 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0
G6P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
THR 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0
Sink4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
S7P 0 0 -1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CO2_ext 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SBP 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
NADPH 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
ADP -1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1



Analysis data:     SBRML
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