Revision as of 15:01, 20 September 2018

Model

Achievement Purpose CO₂ uptake CO₂ metabolism Analysis Reference

CO₂ uptake		Kf	Kr
R1	$${[CO_2]_{air} \rightarrow [CO_2]_uptake}$$	9.23E-04	4.78E-04
R2	$${[CO_2]_{uptake} + [H_2O] \rightarrow [H_2CO_3]}$$	0.062	23.7
R3	$${[H_2CO_3] \rightarrow [H^+] + [HCO_3^-]}$$	8000000	4.7E10
R4	$${[HCO_3^-] \rightarrow [H^+] + [CO_3^{2-}]}$$	3	5E10
R5	$${[H^+] + [HCO_3^-] \longleftrightarrow [H_2O] + [CO_2]_{uptake}}$$	Vmax	Km
R5		0.47333	0.0062

E4P	erythrose-4-phosphate
F6P	fructose-6-phosphate
FBP	fructose-1,6-bisphosphate
G6P	glucose-6-phosphate
GAP	glyceraldehyde-3-phosphate
PEP	phosphoenol pyruvate
PYR	pyruvate
R5P	ribose-5-phosphate
Ru5P	ribulose-5-phosphate
S7P	sedoheptulose-7-phosphate
X5P	xylulose-5-phosphate
6PG	6-phosphogluconate
DHAP	Dihydroxyacetone phosphate
3PG	3-Phosphoglyceric acid
RuBP	ribulose-1,5-bisphosphate
PRK	Phosphoribulokinase
Rubisco	Ribulose-1,5-bisphosphate carboxylase/ oxygenase
AcCoA	Acetyl-CoA
CIT	Citrate
ICIT	Isocitrate
AKG	Alpha-ketoglutarate
SUCCoA	Succinyl-CoA
SUCC	Succinate
FUM	Fumarate
MAL	Malate
OAA	Oxaloacetic acid
GOX	Glyoxylate

CO₂ bypass pathway		Vmax (1/S)		KM (mM)
A1	$${Xylose \rightarrow Xylulose}$$ $${Xylulose + ATP \rightarrow X5P}$$	0.02456		124.55879
A2	$${X5P \rightarrow Ru5P}$$	0.08		12.5
A3	$${Ru5P \xrightarrow{PRK} RuBP}$$	225.81858		0.27
A4	$${RuBP + CO_2 \xrightarrow{RuBisCO} 3PG}$$	Vmax	Krubp		KCO₂
A4	$${RuBP + CO_2 \xrightarrow{RuBisCO} 3PG}$$	333.33	53		2.7

Pentose Phosphate Pathway		Vmax (1/S)			KM (mM)
B1	$${Ru5P \rightarrow R5P}$$	0.13672			12.5
B2	$${X5P + R5P \rightarrow S7P + GAP}$$
	$${X5P \rightarrow S7P}$$	58.27			4.96E-09
	$${X5P \rightarrow GAP}$$	58.27			48
	$${R5P \rightarrow S7P}$$	58.27			0.008
	$${R5P \rightarrow GAP}$$	58.27			3.05E-07
B3	$${S7P + GAP \rightarrow F6P + E4P}$$
	$${S7P \rightarrow E4P}$$	58.27			2.524
	$${S7P \rightarrow F6P}$$	58.27			6.10E-09
	$${GAP \rightarrow E4P}$$	58.27			1.73E-07
	$${GAP \rightarrow F6P}$$	58.27			8.23E-09
B4	$${E4P + X5P \rightarrow F6P + GAP}$$
	$${E4P \rightarrow F6P}$$	1			1
	$${E4P \rightarrow GAP}$$	5.827E-4			1.733E-7
	$${X5P \rightarrow F6P}$$	0.05827			1.733E-7
	$${X5P \rightarrow GAP}$$	0.005827			48.8
B5	$${FBP \rightarrow GAP}$$	135.425			4
B6	$${DHAP \longleftrightarrow GAP}$$	Vmf	Vmr		Km_DHAP		Km_GAP
B6	$${DHAP \longleftrightarrow GAP}$$	0.2394	0.24		0.812		0.245
B7	$${FBP \rightarrow DHAP}$$	0.0001247			0.04
B8	$${F6P + ATP \rightarrow FBP + ADP}$$	88.2533			0.017
B9	$${F6P \rightarrow G6P}$$	88.2353			0.017
B10	$${G6P + NADP^+ \rightarrow 6PG + NADPH}$$	Vmax		Km_G6P		Km_NADP
B10	$${G6P + NADP^+ \rightarrow 6PG + NADPH}$$	11.736		0.12		0.0123
B11	$${6PG + NADP^+ \rightarrow Ru5P + NADPH}$$	1.0			0.044
B12	$${GAP + NADP^+ + ADP \rightarrow 3PGA + NADPH + ATP}$$	0.4			0.013
B13	$${3PGA \rightarrow PEP}$$	0.43478			0.23
B14	$${PEP \rightarrow PYR}$$	0.23148			0.45

TCA cycle		Vmf (mM/min)	Vmr (mM/min)	Ks (mM)		Kp (mM)
C1	$${PEP + HCO_3^- + NAD^+ \rightarrow OAA + NADH}$$	1	1	1		1
C2	$${AcCoA \rightarrow CIT}$$	64.8	0.648	0.05		0.12
C3	$${CIT \rightarrow ICIT}$$	31.2	0.312	1.7		0.7
C4	$${ICIT + NADP^+ \rightarrow AKG + NADPH + CO_2}$$	10.2	0.102	0.03		0.3
C5	$${AKG + NAD^+ \rightarrow AKG + NADPH + CO_2}$$	57.344	0.57344	0.1		1.0
C6	$${SUCCoA + ADP \rightarrow SUCC + ATP}$$	6.54	0.0651	0.015		0.15
C7	$${SUCC + FAD \rightarrow FUM + FADH_2}$$	1.02	1.02	0.12		0.15
C8	$${FUM \rightarrow MAL}$$	887.7	87.7	0.25		2.38
C9	$${MAL + NAD^+ \rightarrow OAA + NADH}$$	184	184	0.833		0.0443
C10	$${OAA \rightarrow CIT}$$	64.8	0.648	0.012		0.12
C11	$${PYR \rightarrow NADH + AcCoA + CO_2}$$	Vmax (1/s)		KM (mM)
C11	$${PYR \rightarrow NADH + AcCoA + CO_2}$$	0.00518		1.5
C12	$${ICIT \rightarrow GOX}$$	1.172	0.01172	0.145		0.13
C13	$${GOX \rightarrow MAL}$$	20	0.2	0.057		1.0
C14	$${ICIT \rightarrow SUCC + GOX}$$	Vmf (mM/min)	Vmr (mM/min)	Kicit (mM)	Ksucc (mM)		Kgox (mM)
C14	$${ICIT \rightarrow SUCC + GOX}$$	1.172	0.012	0.145	0.59		0.13

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                                      <h3>Pathway</h3>
                                      <div>
-                                         <img class="col-md-6 smallimg contentimg" src="easy_pathway.png">
+                                         <img class="col-md-6 smallimg contentimg" src="https://static.igem.org/mediawiki/2018/f/f8/T--NCKU_Tainan--model_easypathway.png">
-                                         <img class="col-md-6 contentimg" src="model_pathway.png">
+                                         <img class="col-md-6 contentimg" src="https://static.igem.org/mediawiki/2018/3/3e/T--NCKU_Tainan--model_pathway.png">
                                      </div>
                                      <div class="table">