Dyad-analysis/Sweeping
Function / known / predicted /AraC (5/122)
DNA related / - / 3
Electrochemical potential driven transporters / 2 / 6
Group Translocators / - / 1
Primary Active Transporters / 1 / 6
RNA related / 1 / 17
Transporters of Unknown Classification / - / 3
adaptation to stress / - / 2
building block biosynthesis / - / 17
carbon utilization / 5 / 9
central intermediary metabolism / - / 9
energy metabolism, carbon / - / 5
energy production/transport / - / 2
function not assigned by Riley / - / 48
genetic unit regulated / 1 / 9
macromolecule degradation / - / 4
macromolecules (cellular constituent) biosynthesis / - / 4
metabolism of other compounds / - / 3
protection / - / 3
protein related / - / 11
type of regulation / 1 / 17
ArcA (10/128)
Channel-type Transporters / - / 1
DNA related / - / 1
Electrochemical potential driven transporters / 2 / 5
Primary Active Transporters / 2 / 5
RNA related / 1 / 15
Transporters of Unknown Classification / - / 5
adaptation to stress / 1 / 3
building block biosynthesis / - / 13
carbon utilization / 2 / 17
central intermediary metabolism / 2 / 14
energy metabolism, carbon / 6 / 8
energy production/transport / 3 / 3
function not assigned by Riley / - / 57
genetic unit regulated / 1 / 8
macromolecule degradation / - / 1
macromolecules (cellular constituent) biosynthesis / 1 / 3
metabolism of other compounds / - / 2
protection / 1 / -
protein related / - / 5
type of regulation / 1 / 19
ArgR (6/28)
Primary Active Transporters / - / 1
RNA related / 1 / -
adaptation to stress / - / 2
building block biosynthesis / 6 / 1
carbon utilization / - / 2
central intermediary metabolism / - / 3
function not assigned by Riley / - / 17
macromolecules (cellular constituent) biosynthesis / - / 1
metabolism of other compounds / - / 1
protein related / - / 3
type of regulation / 1 / 3
FNR (20/1164)
Channel-type Transporters / - / 14
DNA related / - / 25
Electrochemical potential driven transporters / 2 / 60
Group Translocators / - / 19
Primary Active Transporters / 2 / 55
RNA related / 3 / 100
Transporters of Unknown Classification / - / 20
adaptation to stress / - / 35
building block biosynthesis / 1 / 101
carbon utilization / 4 / 105
central intermediary metabolism / 2 / 111
energy metabolism, carbon / 13 / 48
energy production/transport / 9 / 21
function not assigned by Riley / - / 491
genetic unit regulated / 3 / 48
macromolecule degradation / - / 24
macromolecules (cellular constituent) biosynthesis / 1 / 65
metabolism of other compounds / 1 / 19
protection / 1 / 17
protein related / 1 / 72
type of regulation / 3 / 124
LexA (8/55)
DNA related / 7 / 10
Electrochemical potential driven transporters / - / 3
RNA related / 1 / 3
Transporters of Unknown Classification / - / 2
adaptation to stress / - / 1
building block biosynthesis / - / 5
carbon utilization / - / 3
central intermediary metabolism / - / 2
energy production/transport / - / 1
function not assigned by Riley / - / 24
genetic unit regulated / 1 / 2
macromolecule degradation / 1 / -
macromolecules (cellular constituent) biosynthesis / - / 5
protection / 2 / 2
protein related / 2 / 2
type of regulation / 3 / 6
PurR (13/36)
DNA related / - / 3
Electrochemical potential driven transporters / - / 4
RNA related / 2 / 3
Transporters of Unknown Classification / - / 1
adaptation to stress / - / 1
building block biosynthesis / 11 / 6
carbon utilization / 3 / 1
central intermediary metabolism / 5 / 3
energy metabolism, carbon / - / 1
function not assigned by Riley / 1 / 10
genetic unit regulated / 1 / 2
macromolecule degradation / - / 1
macromolecules (cellular constituent) biosynthesis / - / 4
metabolism of other compounds / 1 / 1
protection / - / 1
protein related / - / 4
type of regulation / 2 / 6
TrpR (5/80)
DNA related / - / 3
Electrochemical potential driven transporters / 1 / 3
RNA related / 1 / 9
Transporters of Unknown Classification / - / 2
adaptation to stress / - / 6
building block biosynthesis / 5 / 5
carbon utilization / - / 4
central intermediary metabolism / - / 8
energy metabolism, carbon / - / 4
energy production/transport / - / 2
function not assigned by Riley / - / 36
genetic unit regulated / 1 / 6
macromolecule degradation / - / 1
macromolecules (cellular constituent) biosynthesis / - / 6
protection / - / 4
protein related / - / 7
type of regulation / 1 / 10
TyrR (8/22)
DNA related / - / 1
Electrochemical potential driven transporters / 3 / -
RNA related / 1 / 3
building block biosynthesis / 7 / 4
carbon utilization / - / 3
central intermediary metabolism / - / 2
energy metabolism, carbon / - / 1
function not assigned by Riley / - / 9
genetic unit regulated / 1 / 2
protein related / - / 2
type of regulation / 1 / 5
The table provides comparison between the functional annotations of genes known to be regulated by a given protein and the functional annotations of the predicted set of genes (excluding known genes). The first number between parentheses after the name of the regulator is the number of known genes, the second is the number of predicted genes. Functions were assigned by the group of Monica Riley [16], and were obtained from the GenProtEc web site (http://genprotec.mbl.edu/). More than 30% of the genes in E. coli do not have a functional assignment.
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