Table 2

List of the reactions with weights other than the default value of one.

Reactions

Weight

Source and/or comment


Basal transcription/translation of condition or transcription factor dependent genes

0.01

Should be significantly lower than regulated expression


Active Degradation

5

Should be significantly higher than the production


Aft1/2p::nucleus = [Glt1/Aco1p-FeS::c, Grx3p::nucleus] ⇒ Aft1/2p::c

10

[73]


Low affinity Fet4p metal transport

0.1

[74]


Glutathione/Cysteine mitochondrial import

0.1

Balance of flux between compartments in wt


Neoglucogenesis enzymatic reactions

0.001

[75]


Reaction catalysed by Zwf1p

10

Major source of NADPH. [76]


TCA cycle (reverse)

0.1

[77]


Atp production by Atp-synthase

5

[78]


O2m::c = [Sod1p-Cu-Zn::c] ⇒ H2O2::c

100

[79]


O2m::m = [Sod2p::m] ⇒ H2O2::m

100

[79]


O2m::(m or c) + H2O2::(m or c) ⇒ Ot::(m or c)

0.2

[79]


O2m::(m or c) + H::(m or c) ⇒ H2O2::(m or c)

0.1

[79]


Ot::(m or c) + Aco1p-FeS::(m or c) ⇒ Aco1p::(m or c)

0.1

Less probable than aconitase reaction but more probable than spontaneous degradation.


O2m::(m or c) + Aco1p-FeS::(m or c ⇒ Aco1p::(m or c)

0.1

Same as "Ot::(m or c) + Aco1p-FeS::(m or c)".


Ot::(m or c) + any iron-sulphur cluster containing protein ⇒ protein without the iron-sulphur cluster

0.05

Less probable than the same reaction involving Aco1p-FeS


O2m::(m or c) + any iron-sulphur cluster containing protein ⇒ protein without the iron-sulphur cluster

0.05

Less probable than the same reaction involving Aco1p-FeS


Ot::c + Met5p-siroheme-FeS::c ⇒ Met5p-siroheme::c

0.01

Less probable than other FeS proteinsdue to presence of siroheme


O2m::c + Met5p-siroheme-FeS::c ⇒ Met5p-siroheme::c

0.01

Less probable than other FeS proteins due to presence of siroheme


H2O2::c = [Ctt1p-Heme::c] ⇒ O2

10

Higher turnover number than most enzymes but less than SODs [80]


H2O2::m = [Cta1p-Heme::m] ⇒ O2

10

Higher turnover number than most enzymes but less than SODs [80]


#O2::ext ⇒ #O2::ext + O2

10

Provides saturating oxygen.


#glucose::ext ⇒ #glucose::ext + glucose::c

0.1

Limited glucose uptake as described in [36]


Degradation of protein or peptide elements

0.01

Must be significantly less than the default.


Degradation of other elements

0.001

Less than proteins degradation.


m or c = mitochondria or cytoplasm.

Achcar et al. BMC Systems Biology 2011 5:51   doi:10.1186/1752-0509-5-51

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