Phenotype prediction in regulated metabolic networks

Kaleta, Christoph; Centler, Florian; di Fenizio, Pietro Speroni; Dittrich, Peter

doi:10.1186/1752-0509-2-37

BMC Systems Biology

Table 3 Comparison of knockout predictions.

From: Phenotype prediction in regulated metabolic networks

	glc	gl	suc	ac	rib	glc (-O₂)	Dual Substr.	Reference
aceA	+/+/+/+		+/+/+/+	-/-/-/-		+/+/+/+		[30]
aceB				-/-/-/-				[31]
aceEF	-/+/-/-		-/+/-/-	+/+/+/+		+/+/+/+	+/+/+/+ (glc-ac)	[32]
ackA				+/+/+/-				[33]
ackA + pta + acs				-/-/-/-				[33]
acnA	+/+/+/+	+/+/+/+	+/+/+/+	+/+/+/+		+/+/+/+		[31,34]
acnB	+/+/+/+	+/+/+/+	+/+/+/+	-/+/+/+		+/+/+/+		[34]
acnA + acnB	-/-/-/-	-/-/-/-	-/-/-/-	-/-/-/-		-/-/-/-		[34]
acs				+/+/+/+				[33]
adh	+/+/+/+					-/+/+/+		[35]
cyd	+/+/+/+							[36]
cyo	+/+/+/+							[36]
eno	-/-/-/-	-/-/-/-	-/-/-/-				+/+/+/+ (gl-suc)	[37]
fbaA	-/+/+/+							[38]
fbp	+/+/+/+	-/-/-/-	-/-/-/-	-/-/-/-				[39]
frdA	+/+/+/+		+/+/+/+	+/+/+/+		+/+/+/+		[30]
fumA				-/+/-/-		+/+/+/+		[31]
gap	-/-/-/-	-/-/-/-	-/-/-/-				+/+/+/+ (gl-suc)	[37]
glk	+/+/+/+							[38]
glk + pfkA	+/+/+/+							[38]
glk + pts	-/-/-/-							[38]
gltA	-/-/-/-			-/-/-/-				[34]
gnd	+/+/+/+							[38]
icd	-/-/-/-			-/-/-/-				[34]
mdh	+/+/+/+	+/+/+/+	+/+/+/+			+/+/+/+		[40]
ndh	+/+/+/+	+/+/+/+						[41]
nuo	+/+/+/+	+/+/+/+						[41]
pfl						+/+/+/+		[42]
pgi	+/+/+/+	+/-/-/-	+/-/-/-					[38]
pgi + gnd	-/-/-/-							[38]
pgi + zwf	-/-/-/-							[38]
pgk	-/-/-/-	-/-/-/-	-/-/-/-				+/+/+/+ (gl-suc)	[37]
pgl	+/+/+/+							[38]
ppc	-/+/-/-	-/+/-/+	+/+/+/+				+/+/+/+ (gl-suc) +/+/+/+ (glc-suc)	[38,40]
pta				+/+/+/-				[33]
pts	+/+/+/+							[38]
pykA	+/+/+/+							[38]
pykA + pykF	+/+/+/+							[38]
pykF	+/+/+/+							[38]
rpiA	-/+/-/+				+/+/+/+		+/+/+/+ (glc-rib)	[43]
rpiA + rpiB	-/-/-/+				-/+/+/+		+/+/+/+ (glc-rib)	[43]
rpiB	+/+/+/+				+/+/+/+		+/+/+/+ (glc-rib)	[43]
rpiR + rpiA	+/N/+/+				+/N/+/+		+/N/+/+ (glc-rib)	[43]
sdhABCD	+/+/+/+		-/-/-/-	-/-/-/-		+/+/+/+		[30]
sucAB- lpd	-/+/+/+		-/+/+/+	-/+/+/+		+/+/+/+	+/+/+/+ (glc-suc)	[30,32]
tpi	-/+/+/+	-/-/-/-	-/-/-/-	-/-/-/-			+/+/+/+ (glc-suc) +/+/+/+ (glc-gl)	[37,44]
zwf	+/+/+/+							[38]

Comparing in vivo knockout experiment results with predictions made by FBA, rFBA, OT and by aOT. A '+' indicates growth, a '-' no growth of the mutants on the indicated substrate(s). For cases denoted as 'N', data was not available. Results and predictions are derived from in vivo/FBA/rFBA/(a)OT. In vivo data and references, FBA and rFBA predictions are taken from Ref. [19]. In five instances, predictions made by OT deviate from rFBA predictions (bold cases). See text for discussion. The growth medium contained glucose (glc), glycerol (gl), succinate (suc), acetate (ac), or ribose (rib). Anaerobic condition is denoted by '-O₂'.

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