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Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling and understanding metabolism
Matteo BRILLI
Fondazione Edmund Mach/CRIFunctional genomics
Via Mach 138010 San Michele all’Adige (TN)
Italymatteo.brilli [at] fmach.it
FEM PhD Summer School
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Outline
1 Background: what is metabolism
2 Systems Biology
3 A step back: modeling gene regulation
4 Modeling metabolism
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
What is metabolism
All biochemical reactions that can potentially take place in a cell.
An example metabolicnetwork of small size, fromFlavobacteriumpsychrophilum (taken fromDuchaud et al. [2007] )
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
The most studied metabolic network, Escherichia coli:
a nucleoside3’-phosphate
lytic mureintransglycosylaseE: emtA
glucono-delta-lactone
a CDP-2,3,4-saturated-
diacylglycerol
a phosphatidylcholine
a holo-[acp]
peptidoglycanD-alanyl-
DAP crosslink
KDO2-lipid IVA
disulfideoxidoreductase:dsbG
lipid IVA
a 2,3,4-saturated 2-lysophosphatidate
a peptide
GTP
3-phytase:agp
membrane-boundlytic mureintransglycosylaseB: mltB
a shortglucan
oxaloacetate
tyrosine kinaseinvolved incolanic acidbiosynthesis:wzc
N-acetylmuramoyl-L-alanineamidase 2: amiB
disulfideoxidoreductase:dsbA
KDO2-lipid A
a fatty acid
UDP-2,3-bis(3-hydroxymyristoyl)
glucosamine
membrane-boundlytic mureintransglycosylaseF: mltF
peptidoglycantetrapeptide,
glycan chain 1
DsbG
L-Ala-gamma-D-Glu-DAP-
D-Ala
alpha-amylase:malS
an octanoyl-[acp]
phenylacetaldehyde
UDP-2,3-bis(3-hydroxymyristoyl)
glucosamine
an MDO-O-glucose
di-trans,poly-cis-
undecaprenyldiphosphate
peptidyl-prolylcis-transisomerase(PPIase): surA
a peptidewith a leadersequence
an MDO-O-glucose
hydroperoxidaseI: katG
a peptidoglycan
peptidoglycanpolymer withGlcNAc end
DsbD
alpha-D-glucose-1-
phosphatase:yihX
cytochromeC552: nrfA
L-lactate
N-acetyl-anhydromuramyl-L-alanine-amidase: ampD
Cu2+
aminoacetoneoxidase: tynA
multicopperoxidase withrole in copperhomeostasis:cueO
L-lactate
a carboxylate
hydroperoxidaseI: katG
a peptidoglycan
a phospholipidolefinic
fatty acid
peptidyl-prolylcis-transisomerase:ppiD
peptidylprolylisomerase: fkpB
a palmitoleoyl-[acp]
argininedecarboxylase,degradative: adiA
D-lactate
a single-stranded
RNA
1,4-dihydroxy-2-naphthoate
L-Ala-gamma-D-Glu-DAP-
D-Ala
lytic mureintransglycosylaseE: emtA
beta-D-glucose
an acyl-[acp]
beta-D-glucose-6-phosphate
a glucosylatedglucose
acceptor
NADPH
peptidylprolylisomerase: fkpB
nitrite
holo-EntB
serineproteaseDo: degP
soluble lytic mureintransglycosylase: slt
uridine-5’-phosphate
a shortglucan
phenylethylamineoxidase: tynA
nitrite
a leadersequence
phytate
Cu+
D-alanine
peptidoglycantetrapeptide,
glycan chain 2
superoxide
2,3-dihydroxybenzoate
peptidylproline(omega = 0)
p-aminobenzoylglutamate
a protein-L-tyrosinephosphate
a holo-[acp]
penicillin-bindingprotein1A: mrcA
peptidoglycanpolymer with 1,6-
anhydromuropeptide end
a 1-lyso-2-acyl-sn-glycero-3-
phosphocholine
sugarphosphatase:
ybiV
penicillin-bindingprotein7: pbpG
an L-1-phosphatidyl-
glycerol
an MDO-6-(glycerophospho)
-D-glucose
peptidoglycanpolymer
a nucleoside2’,3’-cyclicphosphate
membrane-boundlytic mureintransglycosylaseC: mltC
formatedehydrogenase-
O: fdoI fdoH fdoG
aldose sugardehydrogenase: yliI
periplasmictrehalase:treA
anhydro-N-acetylmuramoyl-L-alanineamidase: amiD
DsbGoxidized
ribonucleotidemonophosphatase:nagD
(5-L-glutamyl)-L-peptide
sugarphosphatase:
yidA
L-glutamate
gamma-glutamyltranspeptidase: ggt
a dodecanoyl-[acp]
all-trans-farnesyl
diphosphate
a myristoyl-[acp]
phosphoglucoseisomerase: pgi
diphosphoundecaprenyl-[GlcNAc-MurNAc-pentapeptide]n+1
diacylglycerolpyrophosphatephosphatase:pgpB
D-myo-inositol(1,2,4,5,6)-
pentakisphosphate
beta-D-glucose
UQ or MQ UQH2or MQH2
pyruvate di-trans,poly-cis-
undecaprenylphosphate
lipid IVA
a 1-acyl-sn-glycerol-3-phosphate
thiocyanate
L-arginine
L-arginine
an acyl-[acp]
DsbDoxidized
multicopperoxidase withrole in copperhomeostasis:cueO
peptidylproline(omega = 180)
peptidoglycanpolymer withGlcNAc end
DsbD
an MDO-6-(glycerophospho)
-D-glucose
H2O
D-alanine
a 5-L-glutamyl-L-amino acid
peptidyl-prolylcis-transisomeraseC (rotamaseC): ppiC
a standardalpha
amino acid
a substitutedbeta-
amino acid
3’-nucleotidase:cpdB
Cu2+
a long-linear glucan
phenylethylamine
a 2,3,4-saturated L-
phosphatidate
[+ 4 isozymes]
membrane-boundlytic mureintransglycosylaseA: mltA
methylglyoxal
a fatty acid
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenyl-N-acetylglucosamine
a myristoyl-[acp]
L-1-glycero-3-phosphocholine
KDO2-lipid IVA
GlcNAc-1,6-anhMurNAc-L-Ala-gamma-
D-Glu-DAP-D-Ala
N-acetyl-anhydromuramyl-L-alanine-amidase: ampD
thioesteraseII: tesB
an L-1-phosphatidyl-ethanolamine
N-acetylmuramate
pyruvate
diguanylatecyclase: yeaP
UQH2
a tRNAprecursor
a holo-[acp]
trimethylamine
a single-stranded
RNA
EntB
lipid Adisaccharide
a quinol
a holo-[acp]
FKBP-typepeptidylprolylcis-transisomerase:slyD
a ribonucleoside
N-acetylmuramoyl-L-alanyl-D-glutamyl-L-
lysyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine
undecaprenylphosphate-
alpha-L-Ara4N
triggerfactor; amolecularchaperoneinvolvedin celldivision: tig
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenol
a holo-[acp]
Fe3+
a 2,3,4-saturated L-
phosphatidate
peptidoglycanDAP-DAPcrosslink
a holo-[acp]
UDP-sugarhydrolase:ushA
N-acetylmuramoyl-L-alanineamidase 1: amiA
a polypeptide
UQ
a quinone
serineendoprotease,periplasmic: degQ
tetrahydrothiophene
argininedecarboxylase,biosynthetic:speA
a phospholipidcyclopropane
fatty acid
beta-D-glucose-6-phosphate
membrane-boundlytic mureintransglycosylaseC: mltC
di-trans,poly-cis-
undecaprenylphosphate
a CDP-diacylglycerol
an MDO-6-(glycerophospho)
-D-glucose
a dodecanoyl-[acp]
ubiquinol-8
peptidoglycanpolymer with 1,6-
anhydromuropeptide end
a 1,2-diacylglycerol
argininedecarboxylase,degradative: adiA
argininedecarboxylase,degradative: adiA
a polypeptide
a 1,2-diacylglycerol
peptidylproline(omega = 0)
peptidoglycantetrapeptide,
glycan chain 2
a proteinwith
oxidizeddisulfidebonds
superoxidedismutase(Mn): sodA
a CDP-diacylglycerol
sulfite
broadspecificity 5’(3’)-nucleotidase andpolyphosphatase:surE
coenzyme A
uridine-5’-phosphate
acyl-CoAthioesterase:yciA
oxidizedcytochrome
c552
a 1-lyso-2-acyl-sn-glycero-3-
phosphoethanolamine
a holo-[acp]
L-arginine
di-trans,poly-cis-
undecaprenyldiphosphate
beta-D-glucose-6-phosphate
an oxidizedelectronacceptor
a shortglucan
murein DD-endopeptidase,penicillin-insensitive: mepA
a 2,3,4-saturated
fattyacyl-[acp]
formatedehydrogenase-
O: fdoI fdoH fdoG
alpha-D-galactose
thiosulfate
protoheme IX
beta-D-glucosideglucohydrolase,periplasmic: bglX
UQ
penicillin-bindingprotein6: dacC
an L-1-phosphatidyl-ethanolamine
N-acetyl-anhydromuramyl-L-alanine-amidase: ampD
orotate
UDP-2,3-diacylglucosaminehydrolase: lpxH
a proteinL-tyrosine
2,3-bis(3-hydroxymyristoyl)-
beta-D-glucosaminyl1-phosphate
uridine-5’-diphosphate
a ribonucleosidemonophosphate
trehalose
formatedehydrogenase-
O: fdoI fdoH fdoG
nitritereductasecomplex:nrfA nrfBnrfC nrfD
a shortglucan
D-alanyl-D-alanine
a UDP-sugara reducedelectronacceptor
KDO2-lipid IVA
peptidylproline(omega = 180)
a holo-[acp]
asparaginaseII: ansB
diguanylatecyclase: yddV
dihydroorotate
multifunctional acyl-CoA thioesterase Iand protease I andlysophospholipaseL1: tesA
an MDO-O-glucose
demethylmenaquinone-8
an alpha-D-aldose-1-phosphate
phospholipaseA1: pldA
reducedcytochrome
c552
a phosphatidylcholine
multifunctional acyl-CoA thioesterase Iand protease I andlysophospholipaseL1: tesA
NADH
a peptidoglycan
di-trans,poly-cis-
undecaprenyldiphosphate
a holo-[acp]
ubiquinone-8
a 1,2-diacylglycerol-3-phosphate
a D-amino acid
penicillin-bindingprotein1A: mrcA
glucose-1-phosphatase:
agp
a 1-lyso-2-acyl-sn-glycero-3-
phosphocholine
a 2,3,4-saturated
fattyacyl-[acp]
p-aminobenzoate
pyruvate
membrane-boundlytic mureintransglycosylaseB: mltB
L-aspartate
2’,3’-cyclic nucleotide2’-phosphodiesterase:cpdB
a single-stranded
RNA
phosphoglucoseisomerase: pgi
peptidoglycantripeptide,
glycan chain 1
an L-1-phosphatidylglycerol-
phosphate
NAD+
KDO2-lipid A
a nonglucosylated
glucoseacceptor
D-fructose-6-phosphate
a proteinwith
reducedsulfidegroups
5’-nucleotidase:ushA
di-trans,poly-cis-
undecaprenylphosphate
cyclicdi-3’,5’-
guanylate
endo-1,4-D-glucanase:bcsZ
octanoate
pyruvate
a 1,4-alpha-D-glucan
undecaprenylpyrophosphatephosphatase:pgpB
DsbDoxidized
DsbCoxidized
beta-lactamase;penicillinresistance:ampC
amineoxidase (Cucontaining): tynA
argininedecarboxylase,biosynthetic:speA
multicopperoxidase withrole in copperhomeostasis:cueO
a diacylglycerolpyrophosphate
alpha-D-glucose 1-phosphate
an L-1-phosphatidyl-
glycerol
disulfideoxidoreductase:dsbC
GlcNAc-1,6-anhMurNAc
KDO2-lipidA, coldadapted
a tRNA
a nucleoside3’-phosphate
L-glutamate
adenosine 3’,5’-bisphosphate
a holo-[acp]
a ribonucleoside
all-trans-octaprenyl
diphosphate
maltohexaose
heme o
demethylmenaquinone-8
tetrahydrothiophene1-oxide
periplasmicnitratereductase:napGnapH napCnapA napB
a peptide
a carboxylate
N-acetylmuramyl-L-alanineamidase: amiC
argininedecarboxylase,biosynthetic:speA
nitrate
a long-linear glucan
broadspecificity 5’(3’)-nucleotidase andpolyphosphatase:surE
peptidoglycanpolymer
thiosulfatesulfurtransferase:glpE
UDP-N-acetylmuramoyl-
L-alanyl-D-glutamyl-meso-2,6-
diaminopimelyl-D-alanyl-D-alanine
ferritin iron-storagecomplex:ftnA
an aldehyde
DsbC
trimethylamineN-oxide
3-octaprenyl-4-hydroxybenzoate
all transundecaprenyl
phosphate
D-glucose
phosphatidylglycerophosphataseB: pgpB
a peptide
putative p-aminobenzoyl-glutmatehydrolase: abgB
UDP-2,3-diacylglucosaminehydrolase: lpxH
a protein-L-tyrosinephosphate
GlcNAc-1,6-anhMurNAc-L-Ala-gamma-
D-Glu-DAP-D-Ala
malate
2-carboxymuconate
agmatine
an aliphaticamine
p-aminobenzoate
NADP+beta-D-glucose
KDO2-lipid IVA
pyrimidinenucleotidase:yjjG
a 1-lyso-2-acyl-sn-glycero-3-
phosphocholine
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenyl-N-acetylglucosamine
glycerol
UQH2
H2O
thiosulfatesulfurtransferase:pspE
a 1,2-diacylglycerol-3-phosphate
di-trans,poly-cis-
undecaprenyldiphosphate
4-hydroxybenzoate
a proteinL-tyrosine
beta-D-galactose
cardiolipin
2,3-bis(3-hydroxymyristoyl)-
beta-D-glucosaminyl1-phosphate
1,4-dihydroxy-2-naphthoate
a beta-lactam
sugarphosphatase:
yigL
GlcNAc-1,6-anhMurNAc
asparaginaseIII: iaaA
phosphatidylethanolamine-KDO2-lipidA
aldose-1-epimerase:galM
superoxidedismutaseprecursor(Cu-Zn): sodC
CMP
a 2-oxo acid
aminoacetone
diguanylatecyclase: ydeH
Fe2+
D-fructose-6-phosphate
p-aminobenzoylglutamate
a 1,2-diacylglycerol-3-phosphate
uridine-5’-phosphate
succinate
diphosphoundecaprenyl-[GlcNAc-MurNAc-
pentapeptide]n
CTP
L-asparagine
hydrogenperoxide
triggerfactor; amolecularchaperoneinvolvedin celldivision: tig
murein DD-endopeptidase,penicillin-insensitive: mepA
phosphoglyceroltransferase II: mdoB
lipid Adisaccharide
Cu+
agmatine
all-trans-octaprenyl
diphosphate
D-fructose-6-phosphate
hydrogencyanide
agmatine
L-Ara4N-modifiedKDO2-Lipid A
a carboxylate
KDO2-lipid A
fumarate
phosphoglucoseisomerase: pgi
a myristoyl-[acp]
hydrogenperoxide
peptidyl-prolylcis-transisomerase;in proteinfolding:fkpA
CmtABmannitol
PTSpermease
pyruvate
TdcC
malate fumarateL-aspartate
DNApolymeraseIV (Y-family DNApolymerase;translesionDNAsynthesis): dinB
L-lactate
a hydroquinone
H-protein-S-(aminomethyldihydrolipoyl)
lysine
D-serinedeaminase:dsdA
1,6-anhydro-N-acetylmuramate
MinE
L-asparaginyl-tRNAasn
a beta-ketoacyl-[acp]
geranylfarnesyldiphosphate
L-lyxose
YceI
alkalinephosphatase:phoA
xanthosine-5-phosphate
6-phospho-beta-D-
glucosyl-(1,4)-D-glucose
acetylornithinetransaminase:argD
RecFORcomplex:recOrecR recF
a trans-delta3-cis-delta5-dodecenoyl-[acp]
stationaryphasemismatch/uracil DNAglycosylase:mug
a citryl-[acp]
METABOLIC REGULATORSBIOSYNTHESIS
aminoimidazolecarboxamide
ribonucleotide
di-trans,poly-cis-
undecaprenyldiphosphate
MgtA
lipoatebiosynthesis
andincorporation I
deoxyadenosine adenosine
inosine deoxyuridine thymidine deoxyinosine
uridine deoxycytidine
cytidine
H2
tRNApro
1-ethyladenine
ALCOHOLS DEGRADATION
1,3-diphosphateglycerate
chorismate
L-glutaminyl-tRNAgln
a (R)-3-hydroxy-cis-vaccenoyl-
[acp]
AlsR
octaprenyldiphosphatesynthase: ispB
PFL-deactivase:adhE
phosphoglycerate mutase,cofactor independent: gpmM
L-serine
NADPphosphatase
2-phosphoglycerate
gluconokinaseII: idnK
fructoselysine6-kinase: frlD
guaninedeaminase:
guaD
L-valine
salicin-6-phosphatearbutin-6-phosphate
alpha-D-glucose1-phosphate
NtrC
2-dehydro-3-deoxy-D-galactonate-6-phosphate
pyridoxaminetransporter
D-glutamate
glucose-1-phosphateadenylyltransferase:glgC
alanineracemase 1,PLP-binding,biosynthetic: alr
naphthoate-CoAsynthase: menB
a palmitoyl-[acp]
YbjO
o-succinylbenzoate-CoA ligase: menE
L-valyl-tRNAval
tryptophan synthase,alpha subunit: trpA
beta-D-ribopyranose
glycerophosphodiesterphosphodiesterase,cytosolic: ugpQ
DjlA
PRPPbiosynthesis II
6-phospho-D-gluconate
shikimatedehydrogenase: aroE
N-acetylneuraminatelyase: nanA
shikimatedehydrogenase: ydiB
glutathionylspermidine
quinolinatephosphoribosyltransferase:nadC
nucleosidediphosphatekinase: ndk
DNAn
respiration (anaerobic)
ribonucleoside-triphosphatereductase: nrdD
a DNA 6-methylaminopurine
sugarphosphatase:yfbT
D-alanine
tRNA containing 6-Isopentenyladenosine
trans-aconitate
arsenite
L-idonateD-gluconate
7,8-dihydropteroate
2-thiouridine
deoxycytidine
L-threonine
acetyl-CoA:acetoacetyl-CoA transferase,beta subunit: atoA
YjhF
L-aspartate
a 5,10-methylene-tetrahydrofolate
menadione
phosphatidylglycerophosphataseA: pgpA
enoyl-CoAhydratase: fadJ
RodZ
Targlu-Me
glyoxylate
cytosine
NAD salvage pathway I
a lipoyl-[acp]
D-fructose
polyphosphatekinase: ppk
L-cysteinyl-tRNAcys
PhoR-Phis
selenocysteinebiosynthesis
AlkB repairsystem foralkylatedDNA andRNA: alkB
an rRNA
hydrophilicsolute orion < 600 Da
GDPpyrophosphokinase: relA
biotinsulfoxidereductase:bisC
L-xylulosekinase: lyxK
L-histidine
glutamate-5-semialdehydedehydrogenase:proA
NapD
lipoate acetyltransferaseN6-(dihydrolipoyl)lysine
alpha-D-glucose 1-phosphate
beta-hydroxyacyl-ACPdehydratase: fabZ
phosphoribosyl-ATP
a nucleosidediphosphate
an oxidizedferredoxin
phosphoglyceratemutase 2: ytjC
predicted acyl-CoAdehydrogenase: ydiO
rRNAcontaining
pseudouridine
fructose-1,6-bisphosphatase:yggF
fatty acid oxidationcomplex, betacomponent: fadA
6-hydroxymethyl-dihydropterindiphosphate
23S rRNApseudouridine2604synthase: rluF
UhpC-glucose-6-P
ClpAP:clpA clpP
a diacylglycerolprolipoprotein
D-glyceraldehyde-3-phosphate
acetol
phosphatidylserinedecarboxylase: psd
NADHpyrophosphatase:nudC
beta-D-glucose-6-phosphate
a trans hex-2-enoyl-[acp]
octanoate
a (3R)-3-hydroxyacyl-CoA
glutamate-1-semialdehydeaminotransferase:hemL
molybdenumcofactor
K+
exopolyphosphatase: ppx
alpha-ribazole-5’-P
an aliphaticomega-
aminoaldehyde
formate
an aldehydeor ketone
SetB
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
pantothenatesynthetase: panC
a quinone
methylglyoxalreductase: dkgA
methionineand methyl-
donor-molecule
biosynthesis
formyl-CoA
FATTY ACIDS AND LIPIDS BIOSYNTHESIS
L-fucosemutarotase:fucU
pyruvate
H2
succinyl-CoA
di-trans,poly-cis-undecaprenyl
phosphate
a reducedthioredoxin
a nucleosidediphosphate
L-fucose isomerase: fucI
deoxyribose-phosphatealdolase: deoC
fused 4’-phosphopantothenoylcysteinedecarboxylase andphosphopantothenoylcysteinesynthetase: dfp
cholinedehydrogenase:betA
RESPIRATION
superpathway of arginineand polyamine biosynthesis
purine nucleosidephosphorylase:
deoD
purine deoxyribonucleosides degradation
pyruvate
L-methionine
Blc
2-hydroxy-6-oxonona-2,4-diene-1,9-dioate
carbonicanhydrase1: cynT
a nucleosidetriphosphate
trehalose
aminopeptidaseN: pepN
D-mannonate
GltIJKLglutamate
ABCtransporter
a lipopolysaccharide
acetyl-CoA:acetoacetyl-CoA transferase,
alpha subunit: atoD
L-lysine
superpathway oflipopolysaccharide biosynthesis
agmatine
GntT
beta-D-galactose
phosphotyrosine-proteinphosphatase: etp
alanineracemase2, PLP-binding:dadX
ArsB
D-fructose
L-valine
an oxidizedferredoxin
formate
lysinedecarboxylase2: ldcC
formate
MinD
7,8-dihydroneopterin
triphosphate
D-mannitol
O-acetyl-L-serine
formatedehydrogenase:fdhF
uridine-5’-diphosphate
nicotinate
DNAcontaining
a basewith lesion
CTP
3-hydroxyacyl-CoAdehydrogenase: fadJ
ADP
L-cystathionine
poly-beta-1,6-N-acetyl-D-glucosamine
methioninesulfoxidereductaseB: msrB
FxsA
D-glyceraldehyde-3-phosphate
NAD+
HMP-PPhydrolase:nudJ
L-threonine
an oxidizedcytochrome c
riboflavin
an inactiveribonucleosidetriphosphatereductase
adenosyl-cobinamidephosphate
superpathway of phenylalanine,tyrosine, and tryptophan biosynthesis
YaiO
a beta-keto-cis-delta5-dodecenoyl-[acp]
N-substitutedaminoacyl-
tRNA
L-Ala-gamma-D-Glu
diacetylchitobiose-6-phosphatehydrolase: chbF
adenine
dTDP-glucosepyrophosphorylase:rfbA
nicotinate-mononucleotideadenylyltransferase:nadD
lipopolysaccharidecore biosynthesis;phosphorylation ofcore heptose: rfaP
L-aspartateoxidase: nadB
isopentenyldiphosphate
dTDP
adenosinethiamine
triphosphate
5’-phosphoribosyl-N-formylglycineamide
fructoselysine6-phosphatedeglycase: frlB
L-glutamine
indoleL-tryptophan
2-oxopentenoate
lauroylacyltransferase:lpxL
pyruvate
NAD(P)H:quinoneoxidoreductase:ytfG
3-oxoadipyl-CoA
alpha-mannosidase:mngB
peptidyl-tRNAhydrolase:pth
a tRNA
protein phosphatase1 modulatesphosphoproteins,signals proteinmisfolding: pphA
RstACheB
L-glutamate
deoxyguanosinetriphosphatetriphosphohydrolase: dgt
UDP-glucose:(glucosyl)LPS alpha-1,2-glucosyltransferase: rfaJ
(R)-beta-lysine
NADHoxidoreductase: hcr
acyl-CoAthioesterase:yciA
UDP-L-Ara4O C-4" transaminase:arnB
non-specific ion/solute
CELL STRUCTURES BIOSYNTHESIS
phosphogluconatedehydratase: edd
galactitol-1-phosphatedehydrogenase: gatD
phosphoenolpyruvate
D-serine
xylosedegradation I
a hydroquinone
6-phospho-beta-glucosidaseA: bglA
tagatose-1,6-bisphosphatealdolase 1: kbaZ kbaY
3-deoxy-D-manno-
octulosonate
molybdopterinsynthase:moaE moaD
UDP-N-acetylglucosamine-2-epimerase: rffE
geranyl-diphosphate
dITP
a tRNA
C1 COMPOUNDSUTILIZATION AND
ASSIMILATION
glyceratekinase I: garK
glycerol-3-phosphateacyltransferase: plsB
L-aspartate
CaiT
FMNH2
tartronatesemialdehyde
a trans tetradec-2-enoyl-[acp]
CDP
xanthine
phospho-TorR
nitrite
L-isoleucine
UDP-N-acetyl-D-mannosamine
Targlu
AtoS-Phis
L-proline
alpha-D-glucose 1-phosphate
BarA-Pasp
L-ribulose
NorV
formylTHF biosynthesis I
serinehydroxymethyltransferase: glyA
2-deoxy-D-glucose 6-phosphate
aconitate hydratase 1: acnA
UDP-N-acetylmuramate
tetrahydrofolate
dihydrolipoamideacetyltransferase:aceF
nucleosidediphosphatekinase: ndk
fructose-1,6-bisphosphatase I: fbp
N5-carboxyaminoimidazoleribonucleotide mutase: purE
D-glyceraldehyde-3-phosphate
a reducedferredoxin
rRNAcontaining N6-methyladenine
guanylatekinase: gmk
L-Ala-D/L-Gluepimerase:ycjG
indole
L-tryptophan
YgdQ
phosphoribosylglycinamideformyltransferase: purN
a [citrate(pro-3S)-
lyase](citrylform)
YjcG
methanol
ribonucleoside-triphosphatereductase: nrdD
nitric oxide
(2S)-2-isopropyl-3-oxosuccinate
O-succinyl-L-homoserine
adenylatecyclase: cyaA
ADP-ribose
glutathione
fructose bisphosphatealdolase class II: fbaA
proteasespecific forYgjD: yeaZ
UDP-D-glucose
aminoimidazolecarboxamide
ribonucleotide
di-trans,poly-cis-
pentaprenyldiphosphate
phosphoglyceromutase 1: gpmA
2,5-diketo-D-gluconatereductaseB: dkgB
AMINES AND POLYAMINES DEGRADATION
glutamyl-tRNA
synthetase:gltX
pyridoxine
seryl-tRNAsynthetase:
serS
phosphohydroxythreonineaminotransferase: serC
asparaginyl-tRNA
synthetase:asnS
L-lactaldehydedegradation(anaerobic)
KdpD
pyridoxalkinase2: pdxY
BaeS
a 3’-terminalunsaturated
sugar
RNaseD: rnd
EmrKY-TolC
putativemultidrug
effluxtransportsystem
[+ 6 isozymes]
imidazoleglycerol-phosphatedehydratase: hisB
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenol
a quinone
ATPphosphoribosyltransferase: hisG
UidC
UDP-glucose 6-dehydrogenase:ugd
GDP-mannose 4,6-dehydratase: gmd
YraP
2-ketoaldonatereductase: ghrB
N-hydroxyarylamineO-acetyltransferase:nhoA
7-keto-8-aminopelargonate
salvage pathways of adenine,hypoxanthine, and their nucleosides
L-glutamate
23Sribosomal
RNA
a carboxylated-biotinylated-
BCCP
CheB-Pasp: cheB
tRNAser
L-ribulose-5-phosphate
a quinone
oxaloacetate
sulfite
beta-galactosidase:lacZ
nitrate
an acetyl-[acp]
L-methionine
L-Ala-L-Glu
L-carnitine
2-protocatechuoylphloroglucinolcarboxylate
glutamatebiosynthesis III
gamma-glutamyl-gamma-aminobutyratehydrolase: puuD
4-aminobutyratetransaminase: gabT
pyrimidine deoxyribonucleotides de novo biosynthesis
2-phosphoglycerate
PotE
adenosine 3’,5’-bisphosphate
propionyl-CoA
23S rRNA 2’-O-ribose C2498methyltransferase:rlmM
phenylacetaldehyde
menaquinone-8
ADP
molybdate
a ribosomalprotein-
N-acetyl-L-alanine
betaine aldehydedehydrogenase:betB
acetaldehydedehydrogenase:adhE
ribonucleosidehydrolase 3: rihC
a nucleoside3’,5’-cyclicphosphate
YfaV
cytidinedeaminase:cdd
7,8-dihydroneopterin
triphosphate
CheB-Pasp: cheB
CRISPR-associatedcomplexfor antiviraldefense:casEcasD casCcasB casA
D-galacturonateisomerase: uxaC
tagatose-1,6-bisphosphatealdolase 2: gatZ gatY
DNAcontaining arecognition
site
acyl-CoAdehydrogenase: fadE
phospho-RcsB
acetylphosphate
D-allosedegradation
NlpD
coenzyme A
citrate lyasesynthetase:citC
dTDP-L-rhamnosesynthetase:rfbD rfbC
methyleneTHFenzyme: folD
an (R)-3-hydroxydecanoyl-
[acp]
2-oxoglutarate
AMP
dihydrolipoyltranssuccinylaseN6-(lipoyl)lysine
FtsN
fructose-1-phosphate
OuterMembrane
FerricEnterobactinTransportSystem
BarA
ArcB
an alpha-D-aldose-1-phosphate
an oxidizednitroaromatic
compound
phosphopentomutase:deoB
L-aspartate
a 1-acyl-sn-glycerol-3-phosphate
NAD synthetase,NH3-dependent: nadE
Trgglu
trehalosedegradationII (trehalase)
NMN amidohydrolase
50Sribosomalsubunit
protein L7
orotatephosphoribosyltransferase: pyrE
D-alanine
malatedehydrogenase:mdh
aconitatehydratase1: acnA
DegS
(2S)-2-amino-3-oxo-4-phosphonooxybutanoate
L-leucyl-tRNAleu
histidyl-tRNA
synthetase:hisS
(2R,4S)-2-methyl-2,4-dihydroxydihydrofuran-
3-one
tRNAnucleotidyltransferase: cca
CheB-Pasp
N1-methyladenine
acetylornithinetransaminase,catabolic: astC
ferricdicitrate
a trans-delta2-decenoyl-[acp]
spermidine
D-xylose
glyoxylatereductase:ghrA
3-(3-hydroxyphenyl)
propionate
a protein
CTP synthetase: pyrG
5-methyl-tetrahydrofolate
L-aspartate
5,10-methylenetetrahydrofolate
reductase: metF
Ap4Asynthetase:lysU
1-hydroxy-2-methyl-2-(E)-butenyl 4-
diphosphate
serinehydroxymethyltransferase: glyA
EIIAsc
mannosylglycerate
NarQ-Phis
L-threonine
L-methionine
CheB-Pasp: cheB
2-oxobutanoate
H+
an rRNA
YbjYZ
e14 prophage;site-specificDNArecombinase:pinE
Tapglu
lipoyl-proteinligase: lipB
NhaA
freemethionine-(R)-sulfoxidereductase:yebR
TisB
trehalosebiosynthesis I
delta(2)-isopentenylpyrophosphatetRNA-adenosinetransferase: miaA
phosphatidylserinesynthase: pssA
transketolaseI: tktA
acetyl-CoA
6-phosphogluconatedehydrogenase(decarboxylating): gnd
L-threonine
hybrid-cluster
proteinox
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
prephenate
ubiquinol-8
alpha-xylosidase:yicI
a myristoyl-[acp]
KASI: fabB
Tsrglu
dihydroneopterinphosphate
PhoB-Pasp
CreC
spermidine
GTPaseassociatedwith the50S subunitof theribosome:hflX
a C4-dicarboxylatea C4-dicarboxylate
2-dehydropantolactone
phytate
acetoacetyl-CoAtransferase:atoD atoA
pyridoxine5’-phosphateoxidase:pdxH
a biotinylatedBCCP
(monomer)
formate
oxaloacetate
kynurenine
YbhC
a protein
glyoxalaseI: gloA
6,7-dimethyl-8-ribityllumazinesynthase: ribE
methylglyoxalreductase: dkgB
S-adenosyl-L-methionine
a BCCP(monomer)
guanosine-5’-phosphate
DNApolymeraseII: polB
TorS-Pasp723
glutamyl-tRNAreductase: hemA
succinyl-CoA
an N10-formyl-tetrahydrofolate
YkgB
YjjL
chorismate
6-phosphogluconatedehydrogenase(decarboxylating): gnd
2-octaprenyl-6-methoxy-
1,4-benzoquinol
dimethylbenzimidazole
pyruvateformate-lyase: pflB
L-lactatedehydrogenase:
lldD
quinolinate
pyridoxamine5’-phosphate
maltotetraose
laurate
tRNApseudouridine65 synthase: truC
peptidoglycantripeptide-
Lpp crosslink
endonucleaseIV: nfo
RNApyrophosphohydrolase:rppH
isopentenyldiphosphate
xyloseisomerase:xylA
protein phosphatase1 modulatesphosphoproteins,signals proteinmisfolding: pphA
H2
deoxyribodipyrimidinephotolyase(photoreactivation): phr
D-fructose-6-phosphate
UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelateligase: mpl
NADkinase: nadK
tetrahydrodipicolinate
L-aspartyl-4-phosphate
YeiM
a purineribonucleoside
EnvC
putrescine
an oxidizedelectron
acceptor
rhamnosedegradation
a reducedelectronacceptor
ATP
glycerol-3-phosphatedehydrogenase,biosynthetic: gpsA
pyridoxal 5’-phosphate
alkanesulfonatemonooxygenase,FMNH2-dependent: ssuD
beta-D-glucose
BaeR
a 1,2-diacylglycerol
amidophosphoribosyltransferase: purF
UvrABCNucleotideExcisionRepairComplex:uvrB uvrCuvrA uvrD
RecG, DNAhelicase,resolutionof Hollidayjunctions,branchmigration:recG
autoinducer AI-2 biosynthesis
5,10-methenyltetrahydrofolate
AdiC
glutathione S-transferase:gst
EptA
(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran
2-dehydro-3-deoxygalactonatekinase: dgoK
L-Ala-gamma-D-Glu-Dap
diacetylreductase
uridylyltransferase:glnD
D-fructose-6-phosphate
cob(I)alamin
guanylatecyclase
PhoB
dihydrolipoyltranssuccinylase N6-(S-succinyldihydrolipoyl)lysine
S-ribosyl-L-homocysteine
glyoxylate
L-ornithine
trehalose-6-phosphatesynthase:otsA
L-selenocysteine
quinoneoxidoreductase: qor
pyruvate
D-mannitol
2,3-dihydro-2,3-dihydroxybenzoatedehydrogenase: entA
D-glucuronate
D-mannose-6-phosphate
4-hydroxybenzoate
D-lactatedehydrogenase:ldhA
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
all-trans-hexaprenyl
diphosphate
formatehydrogenlyasecomplex: hycDhycC hycF hycGhycB hycE fdhF
LolA
ZntA
L-threoninehomoserine
deoxyribose-1-phosphate
K+
oxaloacetate
10-formyltetrahydrofolate:L-methionyl-tRNA(fMet)N-formyltransferase: fmt
isovaleryl-CoA
ribosepyranase:rbsD
biotin
D-alanyl-D-alanine
L-fucoseisomerase: fucI
3,4-dihydroxyphenylacetyl-CoA
pyruvate formate-lyase: pflB
6-phospho-beta-glucosidase;cryptic: ascB
deoxyribose-phosphatealdolase: deoC
L-glyceraldehyde3-phosphatereductase: yghZ
nicotinate mononucleotide
L-isoleucine
NADHdehydrogenase(quinone)
YccA
DNAligase: ligA
L-alanine
D-ribulose
ThiS-COAMP
chorismate
lipoamidedehydrogenase: lpd
L-aspartate
7,8-dihydroneopterin
triphosphate
a reducedglutaredoxin
beta-D-glucose-6-phosphate
trehalose 6-phosphate
acetyl-CoA
oxaloacetate
acetylornithinedeacetylase: argE
10-formyl-tetrahydrofolate
superpathway of glycolysis, pyruvatedehydrogenase, TCA, and glyoxylate bypass
all-trans-farnesyldiphosphate
a peptide
3-phenylpropionate
tRNAcontaining N1-methylguanine
guanosine-5’-phosphate
a tRNAcontaining
glutamylatedqueuosine
acetyl-CoA
quinolmonooxygenase:ygiN
tRNAcontainingqueuine
dihydrofolatereductase: folA
MLPS
beta-D-glucose
TtdT
L-aspartateL-glutamate
glutathione
a trans dodec-2-enoyl-[acp]
tRNAasp
D-alloseD-fructuronateD-gluconate
D-ribose
methanol
ClpP serineprotease:clpP
D-mannose-6-phosphate
glycinebetaine
poly-beta-1,6-N-acetyl-D-glucosamineN-deacetylase:pgaB
2,3-dihydroxy-3-methylvalerate
thioglycolate
all-trans-octaprenyl
diphosphate
D-fructose
10-formyl-tetrahydrofolate
cobinamide-Pguanylyltransferase: cobU
cysteinesynthase B: cysM
cobinamideadenosyltransferase:btuR
NADH
crotonobetainyl-CoA
hydratase: caiD
isopentenyldiphosphate
oxidizedflavorubredoxin
DNA withlesion
resolvedthroughRec-
mediatedpathway
L-serine
NADbiosynthesis
I (fromaspartate)
gamma-glutamylkinase: proB
amylomaltase:malQ
uroporphyrinogenIII synthase: hemD
a trans-2-enoyl-CoA
4-hydroxy-2-oxo-
valerate
beta-D-glucose-6-phosphate
KASII: fabF
beta-ketoacyl-[acyl-carrier-protein] reductase: fabG
L-serine
a trans-polyisoprenyln-PP
2-oxo-3-hydroxy-4-phosphobutanoate
3-deoxy-D-manno-octulosonate8-phosphatesynthase: kdsA
[GlnK]
glutamyl-tRNAsynthetase: gltX
lipoatesynthase:lipA
glycogensynthase:glgA
predictedAutoinducer-2 kinase: lsrK
PotE
5-ketogluconate
pyridoxal 5’-phosphate
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-
meso-2,6-diaminopimelate
2-phosphoglycerate
a mRNA
an unknownC3 fragment
2-amino-3-ketobutyrate
CoA ligase: kbl
acetohydroxybutanoatesynthase: ilvN ilvB
enolase: eno
propionatekinase: tdcD
lysine 2,3-aminomutase:yjeK
Tsx
CynX
2,3-dihydroxy-3-methylvalerate
deoxyadenosinedeaminase: add
hypoxanthinephosphoribosyltransferase: hpt
formyltetrahydrofolatedeformylase: purU
bifunctional NadRtranscriptionalrepressor and NMNadenylyltransferase:nadR
3-phosphoglycerate
SugE
glyceratekinaseI: garK
a palmitoyl-[acp]
YmgF
L-glycerol 3-phosphate
ribonucleoside-diphosphatereductase:nrdB nrdA
purinenucleotidase:yrfG
pantothenate
dTDP-glucosepyrophosphorylase2: rffH
chorismatelyase: ubiC
acetaldehydedehydrogenase:adhE
D-glyceraldehyde-3-phosphate
3-phosphoglycerate
2-ketobutyrateformate-lyase: tdcE
superpathway ofphenylethylamine
degradation
a 3-oxo-dodecanoyl-[acp]
dihydromonapterin-triphosphate
a dodecanoyl-[acp]
ribonucleosidehydrolase 3: rihC
indole-3-glycerol-phosphate
a deamineatedamine donor
YhjE
a reducedcytochrome c
maltotriose
L-galactonate
chorismate
alanine racemase2, PLP-binding: dadX
ribonucleoside-diphosphatereductase 2:nrdF nrdE
L-alanine
(R)-pantolactone
a 1,4-alpha-D-glucan
thiaminediphosphate
long chainpolyphosphate
an alcohol
CybC
2-oxoglutarate
an L-1-phosphatidylglycerol-
phosphate
branched-chainamino-acidaminotransferase:ilvE
succinate
D-lactate
a tRNAcontaining 7-
aminomethyl-7-deazaguanineat position 34
beta-D-glucose-6-phosphate
RseP
a tRNA
UDP-D-galactose
deoxyribose-1-phosphate
D-malatedehydrogenase(decarboxylating): yeaU
glucono-delta-lactone
YrbG
D-4-hydroxy-2-keto-
glutarate
glutamine synthetaseadenylyltransferase:
glnE
folate polyglutamylation I
aconitate hydratase 1: acnA
fumarase A: fumA
octaprenyldiphosphatesynthase: ispB
YebF
L-fuculose-phosphatealdolase: fucA
L-aspartate
L-serine
L-seryl-tRNAser
formaldehydedehydrogenase,glutathione-dependent: frmA
L-serine
beta-hydroxyacyl-ACPdehydratase: fabZ
SdaC
nicotinamidemononucleotide
3-phosphoserineaminotransferase: serC
lipoamide
KASI: fabB
L-aspartate
D-fructose
a tRNA
malate fumarateL-aspartate
pyruvate kinase II: pykA
L-xylulose
D-alpha,beta-D-heptose-7-phosphate
4-(cytidine 5’-diphospho)
-2-C-methyl-D-erythritol
fusedglutathionylspermidineamidase /glutathionylspermidinesynthetase: gsp
SucB-S-succinyldihydrolipoate
cellobiosechitobiose
tRNA 2-selenouridinesynthase: ybbB
hepta-acylatedKDO2-lipid A
UraA
methyl red
a tRNA
selenocysteinelyase: sufS
a phosphatemonoester
beta-D-glucose
Trgglu-Me
allantoate
pyruvate
adeninephosphoribosyltransferase: apt
D-glyceraldehyde-3-phosphate
GTPcyclohydrolaseII: ribA
D-ribose-5-phosphate
ribonucleosidehydrolase 2(pyrimidine-specific): rihB
L- and D-methionineuptake ABCpermease
FucP
AMP
UDP-N-acetyl-D-mannosaminuronicaciddehydrogenase: rffD
aminopeptidaseN: pepN
YdgR
2-amino-3-oxobutanoate
tRNAMet cytidineacetyltransferase:tmcA
beta-D-glucose-6-phosphate
L-alanyl-tRNAala
nitrite
glutamineABC
transporter
predicted L-xylulose 5-phosphate3-epimerase:sgbU
D-glucosyl-lipopolysaccharide
glutaminase A
D-4’-phosphopantothenate
YjcG
reducedflavorubredoxin:norV
L-isoleucine
glycyl-tRNAsynthetase:glyQ glyS
diaminopimelateepimerase: dapF
pseudouridine
thiamin ABCtransporter
octaprenyldiphosphatesynthase: ispB
beta-ketoadipyl-CoA thiolase: paaJ
ADP-sugarpyrophosphorylase:nudE
oligopeptideABC
transporter
dUMP
cystathionine-beta-lyase: metC
alpha-ribazole
predictedpseudouridine5’-phosphateglycosidase:pscG
D-alloseABC
transporter
YgaZ/YgaHL-valineexportercomplex
tRNA containing 5-methylaminomethyl-
2-thiouridylate
AMINO ACIDS DEGRADATION
UidB
malonyl-CoA-ACPtransacylase: fabD
(R)-methylmalonyl-
CoA
acetoacetatedegradation
(to acetyl CoA)
tRNA m6A37methyltransferase:yfiC
uridylyltransferase:glnD
ethanoldehydrogenase:adhP
uridylyl-removingenzyme: glnD
tRNAasn
biosynthesisof 4-amino-4-deoxy-L-arabinose-
modified lipid A
L-methioninesulfoxide
UDP-D-galactose
a peptideantibiotic
D-fructose-6-phosphate
AtpI
aldehydedehydrogenaseA, NAD-linked: aldA
carnitine-CoAligase: caiC
10-formyl-tetrahydrofolate
N-acetyl-D-glucosamineglucosamineD-fructose
beta-D-glucoseD-mannose
nitrite
hydroxymethylpyrimidinekinase: thiD
thiaminephosphatesynthase:thiE
2-keto-L-gulonate
peptidoglycan biosynthesis I
CleavedDNA
lactose
RecJ: recJ
a polypeptide
acetaldehyde
FMNphosphatase:yigB
xanthine
SstT
a ribosomalprotein-
L-alanine
pyridoxine5’-phosphate
synthase:pdxJ
CO2
iron dicitrateABC
transporter
3-(3-hydroxyphenyl)propionate 2-hydroxylase:mhpA
a 3-oxo-palmitoyl-[acp]
4-hydroxy-2-ketovaleratealdolase: mhpE
a nucleosidediphosphate
AMINO ACIDS BIOSYNTHESIS
isocitratedehydrogenasekinase: aceK
L-carnitine
a protein L-methionine
L-methionine
6-phosphogluconolactonase: pgl
superpathway of N-acetylglucosamine, N-acetylmannosamine
and N-acetylneuraminate
degradation
ADP
RNase R: rnr
DcuA
ethanoldehydrogenase:adhP
MQH2
ribose ABCtransporter
D-glycerate
TorT
hypoxanthine
lipid Adisaccharidesynthase: lpxB
a ribonucleosidediphosphate
UDP-N-acetylglucosamineacyltransferase: lpxA
a phospholipid
NADH
an isocitratedehydrogenase
L-alanine
L-cysteine
a macrolideantibiotic
6-phospho-beta-glucosidaseB; cryptic:bglB
SucB-lipoate
H+
3-phospho-hydroxypyruvate
diacylglycerolkinase: dgkA
acetaldehyde
KDO2-lipid IVA
3-deoxy-D-manno-octulosonatecytidylyltransferase:kdsB
D-ribose-5-phosphate
vitaminB12 ABC
transporter
UhpC
PspB
adenosine
dipeptideABC
transporter
thiosulfateABC
transporter
NAD+
CheA
aspartateaminotransferase,PLP-dependent: aspC
GDP-alpha-D-glucose
a proteinL-glutamate
alpha-D-ribose-1-phosphate
galactitol-1-phosphate
an apo-[acp]
taurinedegradation IV
AceF-lipoate
L-phenylalanine L-tryptophan
L-tyrosine
4,5-dihydroxy-2,3-pentanedione
HdeA
TorS-Phis850
pseudouridine5’-phosphate
lipoyl-proteinligase A: lplA
5’-deoxyadenosine
L-cysteine
4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate
lipid A-core 1-diphosphate
ClpXP:clpX clpP
TrkA
TehA
L-tartrate
16S rRNAcontaining
C5-methylatedcytosine
O-antigenligase: rfaL
UDP-glucose:(glucosyl)LPS alpha-1,2-glucosyltransferase: rfaJ
PspD
KDO2-lipid A
TdcE
D-tyrosyl-tRNATyr
a sugar
urate
pyruvateoxidationpathway
H-Gcv-protein-
(lipoyl)lysine
pyridoxalkinase: pdxK
protein involvedin KdoIIIattachment duringlipopolysaccharidecore biosynthesis: rfaZ
multidrug
pyridoxamine-oxaloacetatetransaminase
a maltodextrin
fused nitric oxidedioxygenase anddihydropteridinereductase 2: hmp
enterobactinsynthasemultienzymecomplex: entEentF entD entB
leucyl-tRNAsynthetase:
leuS
poly(A)polymeraseI: pcnB
resolvasome:ruvA ruvB ruvC
arginyl-tRNAsynthetase:
argS
tyrosyl-tRNAsynthetase:
tyrS
S-adenosyl-L-methioninamine
ITP
adenosylcobinamide-GDP
cellobiosesalicinarbutin
EriC
L-ribulose-5-phosphate
an alkylphosphate
oxamate
cis-vaccenate
S-methyl-L-methionine
glyoxylatereductaseB: ghrB
chemotaxis proteinmethyltransferase:cheR
succinate semialdehydedehydrogenase, NADP+-dependent: gabD
allothreonine
galactoseABC
transporter
histidinebiosynthesis
UDP-N-acetylenolpyruvoylglucosaminereductase: murB
cyclic-GMP
pyruvate
adenosylcobalamin-5’-phosphate
L-fuculose
3-methyl-2-oxobutanoatehydroxymethyltransferase:panB
a 2,3,4-saturated 2-lysophosphatidate
aspartatekinase: thrA
quinolinatesynthase: nadA
2-acetolactate
holo-[acyl-carrier-protein]synthase:acpS
lysine/arginine/ornithine
ABCTransporter
disulfideisomerase,periplasmic:dsbG
D-glucosamine-6-phosphate
arabinoseABC
transporter
SucB-lipoate
arginineABC
transporter
a carboxylate
RssB
ArcAB Two-Component
SignalTransduction
System
dATP
succinate
pantothenatekinase: coaA
ribonucleosidehydrolase 3: rihC
dCMPphosphohydrolase:yfbR
glucose 6-phosphate-1-dehydrogenase: zwf
RNApolymerase,core enzyme:rpoBrpoC rpoA
ethanoldegradation
beta-ketoacyl-[acyl-carrier-protein]reductase:fabG
N-succinyl-L,L-2,6-
diaminopimelate
7-cyano-7-carbaguanine
glucokinase:glk
gamma-glutamylputrescineoxidase: puuB
beta-D-ribofuranose
tRNAIle-lysidinesynthetase:tilS
NarUYgfU
L-methionine-(R)-S-oxide
glycolate
NhaB
cyanate
di-trans,poly-cis-decaprenyldiphosphate
mannitol-1-phosphate 5-dehydrogenase:mtlD
ITPase: yjjX
arylsulfatase:aslA
BetT
NADP+
YafY
quinatedehydrogenase:ydiB
acetyl-CoAbiosynthesis
(from pyruvate)
uracil
NarP-Pasp
KASIII: fabH
NADPH
ribose 1,5-bisphosphokinase:phnN
beta-hydroxyacyl-ACP dehydratase: fabZ
L-glutamine
phenylalanyl-tRNA
synthetase:pheT pheS
(R)-methylmalonyl-CoA
molybdopteringuaninedinucleotidesynthase: mobA
BarA
coenzyme B12
5’,5’’’-diadenosine
tetraphosphate
deoxyuridine
fused predictedacetyl-
CoA:acetoacetyl-CoA transferase:
alpha subunit/beta subunit: ydiF
superpathway ofacetate utilization
and formation
L-glutamate
YjcD
folylpoly-alpha-glutamatesynthetase
4-aminobutyrate
a trans-2-enoyl-CoA
TorR
a proteinL-cysteine
a reducedthioredoxin
dihydroxyacetonephosphate
Nitrogen RegulationTwo-Component System
glutathionebiosynthesis
YgfO
L-ribulose 5-phosphate 4-epimerase: araD
serinehydroxymethyltransferase: glyA
putrescine
Ag43
fructosebisphosphatealdolaseclass II: fbaA
uracil
NADH pyrophosphatase: nudC
D-fructose-6-phosphate
ClpAXP:clpXclpA clpP
tryptophansynthase:trpB trpA
thymidylatesynthase:
thyA
sulfateadenylyltransferase:cysD cysN
beta-L-fucose
KDO2-lipid A
an alkylhydroperoxide
1-acylglycerol-3-phosphateacyltransferase: plsC
octyl alpha-D-glucopyranoside
L-methionine
an alcohol
L-proline
2,3-dihydroxybenzoylserine
AROMATIC COMPOUNDS DEGRADATION
acetate
ethanoldehydrogenase:adhP
xanthosine
imidazoleglycerolphosphatesynthase:hisF hisH
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
ADP-sugarpyrophosphatase:nudF
allose-6-phosphateisomerase/ ribose-5-phosphateisomeraseB: rpiB
histidinaldehydrogenase:hisD
pyridoxine
a maltodextrin
predictedpseudouridinekinase: pscK
BglH
trans-aconitatemethyltransferase: tam
glutathione S-transferase:yfcG
trans-2-decenoyl-ACPisomerase:fabA
L-1,2-propanedioloxidoreductase:fucO
5-amino-6-ribitylamino-2,4(1H,3H)-
pyrimidinedione5’-phosphate
CheA-Phis
putrescineaminotransferase: ygjG
D-gluconate
ethanolamineammonia-lyase:eutC eutB
cyanate
fructose 1,6-bisphosphatase: ybhA
dGTP
spermidinesynthase:speE
xanthosinetriphosphatepyrophosphatase:rdgB
a DNAcyclobutadipyrimidine
L-2,3-dihydrodipicolinate
putrescine
D-cysteine
L-glutamate
purine nucleosidephosphorylase:deoD
ornithinecarbamoyltransferase:argF
UDP-N-acetylmuramate-alanine ligase: murC
Slp
guanosine-5’-phosphate
beta-1,6-galactofuranosyltransferase: wbbI
phosphoglyceratemutase, cofactorindependent: gpmM
2-oxopent-4-enoatehydratase:mhpD
a phosphorylatedisocitrate
dehydrogenase
a beta-hydroxy cisdelta5-dodecenoyl-[acp]
2-hydroxy-6-ketonona-2,4-dienedioatehydrolase:mhpC
CodB
BasR
phosphopentomutase:deoB
6-phosphofructokinase I: pfkA
D-ribulose-5-phosphate
dCMP
acetyl-CoA
phosphateABC
transporter
As3H3O6
citrate
alcoholdehydrogenase:adhE
YjeM
YhjV
NfrB
phosphoglycerate kinase: pgk
EamA
selenite
pyruvate
fumarase B: fumB
pyridoxamine
a tRNA
L-arabinosedegradation I
nicotinamidemononucleotide
CTP
tRNApseudouridine
CpxR
MscS
inosine
nicotinamide
guanosine-5’-triphosphate,3’-diphosphatepyrophosphatase: gpp
lipoyl-proteinligase: lipB
adenosylmethioninedecarboxylase: speD
5’-deoxyadenosine
5-phospho-beta-D-ribosyl-amine
CDP-diglyceridesynthetase: cdsA
phosphatidylglycerophosphatase C
pyruvate
FhuE
L-tryptophan
biotin-carboxylcarrierprotein
succinate semialdehyde
fructose-1-phosphatase:yqaB
malatedehydrogenase(oxaloacetate-decarboxylating)(NADP+): maeB
beta-D-glucose
2-methylthio-N-6-
isopentyladenosine-37 tRNA
hydroxypyruvateisomerase: hyi
L-serinedeaminaseI: sdaA
4’-phosphopantetheine
enolase: eno
fructosebisphosphatealdolaseclass I: fbaB
fructose 6-phosphatealdolase1: fsaA
uridine-5’-phosphate
N-ethylsuccinimide
GDP-4-dehydro-6-deoxy-
D-mannose
3-alpha,12-alpha-
dihydroxy-7-oxo-5-beta-
cholanate
3-dehydroquinatesynthase: aroB
D-gluconate
3-phosphoshikimate-1-carboxyvinyltransferase:aroA
YtjB
thiaminediphosphate
tRNAArg2
YhgN
AcrAD-TolCmultidrug
effluxtransportsystem
ADP-heptose:LPSheptosyltransferaseI: rfaC
nicotinate-mononucleotideadenylyltransferase: nadD
inositolmonophosphatase:suhB
NMN nucleosidase
4-nitrobenzaldehyde
aspartatesemialdehydedehydrogenase: asd
lipoate
N5-carboxyaminoimidazoleribonucleotide
diacetylchitobiose-6-phosphate
methylglyoxalsynthase: mgsA
bifunctional riboflavinkinase / FMNadenylyltransferase: ribF
urate
a 2’-deoxyribonucleoside
triphosphate
3,4-dihydroxy-2-butanone 4-phosphatesynthase:ribB
OmpR-Pasp
sulphurdioxide
a polypeptide
cobinamide kinase: cobU
acetaldehydedehydrogenase2: mhpF
spermidineputrescine
phosphoribosylanthranilateisomerase: trpC
guanosine
ATP
AMP
L-aspartate
beta-hydroxyacyl-ACPdehydratase:fabZ
lysinedecarboxylase:cadA
a holo-[acp]
a lipopolysaccharide
D-fructose-6-phosphate
L-arginino-succinate
isopentenyldiphosphate
tyrosineaminotransferase: tyrB
7-aminomethyl-7-deazaguanine
indole-3-glycerol-phosphate
MinC
prephenatedehydrogenase: tyrA
folylpoly-alpha-glutamatesynthetase
dihydrouracil
hydrophilicsolute orion < 600 Da
RcsB
GntU
S-lactoylglutathionehydrolase: yeiG
NAD(P)H:quinoneoxidoreductase:wrbA
an L-1-phosphatidylserine
CMP
16S-rRNAs
1-amino-propan-2-ol
galactaratedehydratase: garD
a hexanoyl-[acp]
ZnuA/ZnuB/ZnuC ABCtransporter
UDP-L-Ara4O
L-galactonate
D-fructose-6-phosphate
menadiol
2-oxobutanoate
a ThiSsulfur-carrier
protein
methylglyoxal
allantoindegradation
IV (anaerobic)
an apo-GcvHprotein
2-oxoglutarate
H-Gcv-protein-(dihydrolipoyl)lysine
HdeB
D-glyceraldehyde-3-phosphate
2,3-bis(3-hydroxymyristoyl)-
beta-D-glucosaminyl1-phosphate
L-serineL-threonine
an mRNA with 5’-monophosphate
YgjV
L-rhamnoseL-lyxose
D-sorbitol
cis-aconitate
putrescineABC
transporter
CO2
ferredoxinNAD+reductase:hcaD
KDO2-(lauroyl)-lipid IVA
methioninesulfoxidereductaseB: msrB
coenzyme A
L-ribulokinase:araB
glutathione
adenylyl-glutamine synthase
N-acetyl-D-glucosamine-6-phosphateD-glucosamine-6-phosphate
D-fructose-6-phosphatebeta-D-glucose-6-phosphate
D-mannose-6-phosphate
GltF
pyridoxal
sulfatereduction I
(assimilatory)
formyl-CoAtransferase: frc
Li+
AcrAB-TolCmultidrug
effluxtransportsystem
xanthosine-5-phosphate
L-xylulose-5-phosphate
N-ethylmaleimide
a tRNAArg2containinginosine atthe wobble
position
L-idonate 5-dehydrogenase:idnD
Fe2+
PanF
2-dehydropantoate2-reductase: panE
NADH
4-hydroxy-L-threoninephosphatedehydrogenase,NAD-dependent: pdxA
NarP
erythrose 4-phosphatedehydrogenase:epd
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-
meso-2,6-diaminopimelate
ZraSR Two-Component
SignalTransduction
System
carboxylesterase:bioH
phenylacetate
OTHER BIOSYNTHESIS
ornithine decarboxylase,biosynthetic: speC
ArcB
UDP-GlcA C-4"-decarboxylase:arnA
a 2,3,4-saturated
fattyacyl-[acp]
fatty acidoxidationcomplex,alphacomponent:fadB
fused 4’-phosphopantothenoylcysteinedecarboxylase andphosphopantothenoylcysteinesynthetase: dfp
UDP-[N-acetyl-D-
glucosamine]n
CheB-Pasp: cheB
gamma-glutamylkinase-GP-reductasemultienzymecomplex:proA proB
an isocitratedehydrogenase
4-aminobutyrateaminotransferase: puuE
TorS-Phis443
YnfJ
D-ribulose-1-phosphate
CheB-Pasp: cheB
1,4-alpha-glucanbranchingenzyme:glgB
succinate
aspartate 1-decarboxylase:panD
dihydrodipicolinatereductase: dapB
isochorismate
L-serine
an rRNA
cyclopropanefatty acylphospholipidsynthase: cfa
acetaldehydedehydrogenase2: mhpF
O-succinyl-L-homoserine
malatesynthaseG: glcB
phosphopantetheineadenylyltransferase: coaD
an aldehyde
2-O-alpha-mannosyl-D-glycerate transportingphosphotransferase
system
L-valine L-leucineL-isoleucine
putrescine
selenide
phosphate
5-dehydro-4-deoxy-D-glucarate
6-phospho-D-gluconate
nucleosidediphosphatekinase: ndk
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatereductase: ispH
D-glycerate
HipA
CcmABCDEprotoheme
IX ABCtransporter
D-fructose-6-phosphate
L-fucose
propionyl-CoA
NmpC
UDP-N-acetyl-D-
glucosamine
uracilphosphorylase:deoA
branchedchain aminoacids ABCtransporter
AMP
bicarbonate
a tRNA
ArgO
D-erythrose-4-phosphate
cyclic-AMP
purinenucleotidase:yrfG
NADP(H)-dependent FMNreductase: ssuE
adenosinedeaminase: add
L,D-transpeptidaseYbiS: ybiS
glyoxylate
D-cycloserine beta-alanine
D-serine D-alanine
glycine L-alanine
formaldehydeoxidation II
(glutathione-dependent)
palmitatebiosynthesis
II (bacteriaand plants)
sulfate
L-alanine
isopentenyldiphosphate
isomerase: idi
ethanol
NarX-Phis
N-6-isopentyl
adenosine-37 tRNA
acetohydroxybutanoatesynthase: ilvH ilvI
a cis-vaccen-2-enoyl-[acp]
RhtA
all-trans-heptaprenyldiphosphate
glutamate-pyruvateaminotransferase:alaB
a reducedelectronacceptor
glucosyl-heptosyl3-
KDO2-lipid A-
phosphate
glutathionedisulfide
2,3-bis(3-hydroxymyristoyl)-
beta-D-glucosaminyl1-phosphate
YicJ
uridinephosphorylase:udp
dihydroneopterinaldolase: folB
2-dehydropantoyl-lactone reductase(B-specific)
phosphoenolpyruvatecarboxylase: ppc
QmcA
phosphoenolpyruvatecarboxykinase (ATP): pck
MalM
L-threo-3-phenylserine
propionyl-P
CopA
tRNAlys
phosphoglucoseisomerase: pgi
glyceraldehyde3-phosphatedehydrogenase-A complex: gapA
EIITre
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
23S rRNA 2’-O-ribose G2251methyltransferase:rlmB
UTP
acetyl-CoA
melibiose
HMP-PPhydrolase/ thiaminpyrophosphatehydrolase: nudJ
p-aminobenzoate
a (3R)-3-hydroxyacyl-[acp]
UhpB-Phis
NADP+
fumaraseA: fumA
RplL
ethyl-(2R)-methyl-(3S)-
hydroxybutanoate
phosphoglyceratemutase 2: ytjC
pyruvatekinaseI: pykF
multifunctional 2-keto-3-deoxygluconate
6-phosphatealdolase and 2-keto-4-hydroxyglutarate
aldolase andoxaloacetate
decarboxylase: eda
BarA-Phis
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
fumarate
S-ureidoglycolate
dTDP-4-dehydro-6-deoxy-
D-glucose
fructose bisphosphatealdolase class I: fbaB
a nucleicacid with aterminal 5’-phosphate
fructose 1,6-bisphosphatase II: glpX
YaaJ
L-lysine
MdoG
PspA
an oxidizedferredoxin
NAD+
a damagedDNA
(purine orpyrimidine)
PheP
cytosine
glycogenbiosynthesis I (from
ADP-D-Glucose)
a DNAsegment
a tetrahydrofolatepolyglutamate
XapB
purine nucleosidephosphorylase:deoD
alpha-L-arabinose
gluconokinaseI: gntK
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
rRNAcontaining 2’-O-methylcytosine
D-glyceraldehyde-3-phosphate
a thioredoxin
allantoateamidohydrolase:allC
galactitol-1-phosphate
glycolaldehyde
YbgQ
DNA with G-A mismatch
CheB-Pasp: cheB
4-acetamido-4,6-dideoxy-D-galactosetransferase: rffT
L-arginine
a peptide
a reducedflavodoxin
heme d
an octanoyl-[acp]
guanosine
methyl-1,4-benzoquinone
DcuR
a phosphatidylcholine
inosine
fructose 6-phosphatealdolase2: fsaB
tartronatesemialdehydereductase: garR
Fsr
phosphoglyceratekinase: pgk
dTDP-fucosamineacetyltransferase:rffC
alpha-D-glucose
dTDP-glucose4,6-dehydratase2: rffG
a 2,3,4-saturatedfatty acyl CoA
ferricdihydroxybenzoylserine
toxin ofthe YafQ-DinJ toxin-antitoxinsystem: yafQ
succinatesemialdehyde
6-phosphofructokinaseI: pfkA
K+
CMP
N-succinyl-L-diaminopimelatedesuccinylase:dapE
dAMP
biotin
tRNA containing 5-methylaminomethyl-
2-thiouridylate
homoserinekinase: thrB
anaerobicnucleoside-triphosphatereductaseactivatingsystem: fprnrdG nrdD
beta-N-acetylglucosaminidase:nagZ
anhydro-N-acetylmuramicacid kinase: anmK
orotate
sn-glycerol-3-phosphate
acetohydroxybutanoatesynthase: ilvN ilvB
choline
succinyl-CoA synthetase: sucC sucD
pyridoxal 5’-phosphate
dTTP
3-keto-L-gulonate 6-phosphate
NarK
oleate beta-oxidation
beta-D-glucose
fatty acid beta-oxidation I
ThiS
UTP
serineacetyltransferase:cysE
ferriccoprogen
ATP
H-Gcv-protein-
(lipoyl)lysine
acetaldehyde
lipid kinase:yegS
L-asparagine
a tRNA
phosphoribosyl-ATPpyrophosphatase: hisI
MrdB
6-carboxy-5,6,7,8-tetrahydropterin
BaeR-Pasp
6-phospho-D-gluconate
histidinol-phosphatase:hisB
mannose-6-phosphateisomerase: manA
(deoxynucleotides)(m)
UDP-glucose 4-epimerase: galE
YhjX
1,4-dihydroxy-2-naphthoyl-CoA
guanosine-5’-phosphate
a nucleoside
guanosine-3’,5’-bis(diphosphate) 3’-diphosphatase: spoT
D-alanine-D-alanineligase B: ddlB
7,8-dihydropteroate
crotonobetainyl-CoA
alpha-D-ribose-1-phosphate
tRNAsec
a 3-oxo-hexanoyl-[acp]
a 1,4-alpha-D-glucan
CbdAB
a glycerophosphodiester
UDP-galactose biosynthesis(salvage pathway from
galactose using UDP-glucose)
an ADP-sugar
GTP
GTPpyrophosphokinase: relA
maltose
glutaminase:yneH
OuterMembrane
FerricCitrate
TransportSystem
fosmidomycin
L-idonate
undecaprenyldiphosphatesynthase: ispU
dihydrodipicolinatesynthase: dapA
an N10-formyl-tetrahydrofolate
NAD+
xanthine
methyltransferasefor 50S ribosomalsubunit proteinL11: prmA
putrescine/spermidine
ABCtransporter
selenate
xanthosine
thymidinephosphorylase:deoA
adenosine 3’,5’-bisphosphate
glutamate racemase: murI
glycerol-3-P ABC
transporter
deoxyuridinekinase: tdk
GlnA
FtsE/FtsX ABCtransporter
glycine
3-chloro-D-alaninedehydrochlorinase:dcyD
potassiumion P-typeATPase
transporter
precursor-Z
YijP
homoserinedehydrogenase:metL
pyruvateoxidase:poxB
a phosphorylatedisocitrate
dehydrogenase
diaminopimelatedecarboxylase: lysA
cytidine
folylpoly-gamma-glutamatesynthetase:folC
trehalose 6-phosphate
2-octaprenylphenol
thiaminpyrophosphatehydrolase: nudJ
MipA
low-specificityL-threoninealdolase: ltaE
tetraacyldisaccharide4’-kinase: lpxK
L-ascorbate-6-phosphate
DNA withlesion
catabolicthreoninedehydratase: tdcB
lipoate
a citryl-[acp]succinylglutamatedesuccinylase: astE
pyridoxal
alcoholdehydrogenase:adhE
a tetrahydrofolatepolyglutamate
fumarase A: fumA
gamma-butyrobetaine
AP siteremoved
from DNA
a drug
succinyl-CoA
ammoniumhydroxide
a FeS-protein
lauroylacyltransferase:lpxL
D-erythrose-4-phosphate
D-aminopropanoldehydrogenase:gldA
superpathway of KDO2-lipid A biosynthesis
dihydroxy-aciddehydratase: ilvD
phosphateacetyltransferase: pta
2-methylcitratecycle I
folylpoly-alpha-glutamatesynthetase
L-aspartate
YihN
citratesynthase: gltA
serineactivatingenzyme: entF
cadaverine
pyruvateformate-lyase: tdcE
cobalamin-independent
homocysteinetransmethylase:
metE
2,3-diketo-L-gulonate
pyruvatedehydrogenasemultienzymecomplex: lpdaceF aceE
acetylglutamatekinase: argB
isocitratedehydrogenase: icd
2-hydroxyglutarate
mannose-6-phosphateisomerase:manA
propionate
guanosine-5’-diphosphate
PsiE
vitaminB12 outermembranetransportcomplex
succinate
AlsR-allose
a DNAadenine
DNA withlesion
spermidine
L-tryptophan
S-formylglutathionehydrolase: yeiG
dihydropteridinereductase: nfsB
L-alanine
H2O
ThDPadenylyltransferase
YigG
RNA(n)
tRNA (m1G37)methyltransferase:trmD
prolinedegradation I
L-methionyl-tRNAfmet
a cis-delta3-decenoyl-[acp]
N-acetylglutamylphosphatereductase: argC
sugar phosphatase: ybiV
2’-(5-triphosphoribosyl)-3’-dephospho-CoA
D-alanyl-D-alanine
a nucleosidemonophosphate
histidineABC
transporter
KDOIII-lipopolysaccharide
methanol
a 3-oxo-decanoyl-[acp]
an acyl-CoA
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylatesynthase: menD
taurine ABCtransporter
sugarphosphatase:yigL
glucosamine-6-phosphatedeaminase: nagB
MntH
CheY-Pasp
Tsrglu-Me
branched-chainamino-acidaminotransferase:ilvE
RcsB-phosphate
tyrosineaminotransferase:tyrB
branched-chainamino-acidaminotransferase:ilvE
MsbA
ADP-L-glycero-D-mannoheptose-6-epimerase: rfaD
Ca2+
methylerythritolphosphate pathway
phosphoenolpyruvate
glyceratekinaseII: glxK
aldehydedehydrogenaseA, NAD-linked: aldA
D-gluconate
a reducedferredoxin
7-cyano-7-carbaguanine
acetaldehyde
diadenosinetetraphosphatase:apaH
CPS-53 (KpLE1)prophage;deoxyribonucleoside5’-monophosphatephosphatase: yfdR
aminomethyltransferase: gcvT
Eco
Osmoregulatory Two-ComponentSignal Transduction System
dATP
Lipid A-core
ATP
pryidoxinetranporter
L-methionine
pyridoxalkinase: pdxK
lipoate
proteindisulfideisomerase:dsbC
uroporphyrinogendecarboxylase: hemE
beta-hydroxyacyl-ACP dehydratase: fabZ
GDP-alpha-D-mannose
phosphoribosyl-formamido-carboxamide
deoxyguanosine
NADPH
long chainpolyphosphate
dCMPphosphohydrolase:yfbR
isethionate
6-carboxy-5,6,7,8-tetrahydropterinsynthase: queD
meso-diaminopimelate
GDP-mannosemannosylhydrolase:gmm
cadaverine
purine nucleotides de novo biosynthesis I
spermidinesynthase:
speE
glutaminase B
N-acetyl-L-glutamate 5-
semialdehyde
SbmA
succinylornithinetransaminase: astC
AMP
pyruvatekinaseII: pykA
fumaraseB: fumB
L-tyrosine
a malonyl-[acp]
aconitatehydratase1: acnA
adenylyl-[glutaminesynthetase]
glycerol
1,6-anhydro-N-acetylmuramicacid recycling
acetaldehydedehydrogenase:adhE
phenylacetyl-CoA
EvgA
3,5-tetradecadienoate
RstB-Phis
3-phenylpropionate-2’,3’-dihydrodioldehydrogenase: hcaB
chorismate
aspartateaminotransferase,PLP-dependent: aspC
L-glutamine
D-gluconate
ATP
2-dehydro-3-deoxy-D-gluconate
acetyl-CoA
transaldolaseA: talA
multidrug
beta-hydroxyacyl-ACPdehydratase: fabZ
allose-6-phosphateisomerase/ ribose-5-phosphateisomeraseB: rpiB
modulatorof RNase IIstability: gmr
ZraS-Phis
ethanol
malonyl-CoA
uridylyl-[GlnK]
ADP-L-glycero-
D-manno-heptose
EIIGat
sugarphosphatase:ybiV
L-seryl-AMP
acetaldehyde
L-rhamnulosekinase: rhaB
D-glyceraldehyde-3-phosphate
superpathway of methylglyoxal degradation
L-tryptophan
beta-D-glucose 1-phosphate
dihydrolipoamideL-leucine
molybdopteringuanine
dinucleotide
allantoinase:allB
proteinkinase: yeaG
3-dehydroquinate
L-seryl-AMP
all-trans-geranyl-geranyl
diphosphate
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
NAD-dependentdihydropyrimidinedehydrogenase:yeiA yeiT
pyridine nucleotidetranshydrogenase
enterochelinesterase: fes
UTP
uracilphosphorylase:deoA
FAD
L-arginine
D-glycerate
methylmalonyl-CoAdecarboxylase: scpB
CMP-3-deoxy-D-manno-
octulosonate
glycolate
D-xylulose-5-phosphate
PhoR
L-glutamate
acetyl-CoA
hydroquinone
L-glutamate
UDP-2,3-diacylglucosaminehydrolase: lpxH
L-aspartate
L-1,2-propanediol
cyclopropanefatty acid
(CFA)biosynthesis
BarA-Phis
cAMPphosphodiesterase:cpdA
ribonucleosidehydrolase 3: rihC
malatedehydrogenase:mdh
S-formylglutathione
deoxyribose-5-phosphate
beta-D-glucose-6-phosphate
myristoyl-acylcarrier protein(ACP)-dependentacyltransferase:lpxM
a tRNAprecursor
superpathwayof menaquinone-8 biosynthesis
pimeloyl-CoA
PhnC/PhnD/PhnEalkylphosphonateABC transporter
PhoRB Two-Component
SignalTransduction
System
XylF/XylG/XylH
xylose ABCtransporter
4-carboxyaminoimidazoleribonucleotide
fructose-1-phosphate
beta-D-glucose-6-phosphate
glyoxylate
a tRNA
deoxycytidine
dUMP
beta-D-glucose
acetatekinase B: ackB
lipidhydroperoxideperoxidase: tpx
L-fuculose-phosphatealdolase: fucA
2-C-methyl-D-erythritol-2,4-
cyclodiphosphate
alpha-L-fucose
a citratelyase holo-[acyl-carrier
protein]
GltIJKLglutamate
ABCtransporter
homoserine O-succinyltransferase:metA
aconitatehydratase 1: acnA
D-xylulose-5-phosphate
an acetoacetyl-[acp]
propionyl-CoA
isovaleryl-CoAdehydrogenase/ predictedacyl-CoAdehydrogenase:aidB
phosphorylatedserine/threonine
kinase HipA
UDP-3-O-(3-hydroxymyristoyl)
glucosamine
phosphoglycolatephosphatase: gph
D-xylulose-5-phosphate
ThiI: thiI
seryl-tRNAsynthetase:serS
rRNAcontaining N1-methylguanine
L-valine
L-carnitinyl-CoA
colanic acid
methionineadenosyltransferase:metK
cyanase:cynS
an oxidizedelectronacceptor
5’-deoxyadenosine
L-ornithine
GMP-N-epsilon-(N-alpha-acetyl lysinemethyl ester) 5’-phosphoramidate
methylglyoxal
NarL
methyleneTHFenzyme: folD
3-mercaptopyruvate
beta-D-glucose-6-phosphate
N-acetylneuraminate
glutaminesynthetase:glnA
D-alanine
CirA
pyridoxamine5’-phosphate
YfjS
oxaloacetate
dTDP
L-methionine
glycogenphosphorylase-limit dextrinalpha-1,6-glucohydrolase:glgX
lactose
D-ribose
D-ribose-5-phosphate
EvgS-Phis
L-lactaldehyde
L-glutamate
S-acetyldihydrolipoamide
sulfite reductase-(NADPH): cysI cysJ
cadaverine
DcuB
a beta-D-glucuronoside
3-oxoacyl-CoA
O-succinylhomoserine(thiol)-lyase: metB
protoporphyrinogen IX
D-lactate
L-glutamate
YifK
N-acetylglucosamine-6-phosphatedeacetylase: nagA
acetolactatesynthase: ilvMilvG_2 ilvG_1
adenosine 3’,5’-bisphosphate
superpathwayof hexuronide
and hexuronatedegradation
L-homocysteine
NAD+
phosphoenolpyruvate
1,6-anhydro-N-acetylmuramate
MdoD
pyruvatedehydrogenase:aceE
YdeA
enoyl-ACP reductase(NADPH): fabI
undecaprenyldiphosphatesynthase: ispU
dihydroneopterintriphosphatepyrophosphohydrolase:nudB
a DNA withalkylatedadenine
enoyl-ACP reductase(NAD[P]H): fabI
beta-hydroxydecanoyl-ACP dehydrase: fabA
dihydrofolatereductase: folM
RNasePH: rph
L-ascorbate
alpha-ribazole-5’-P
lipoyl-proteinligase A: lplA
glycine
glyoxylate
3-phenylpropionate and3-(3-hydroxyphenyl)
propionate degradation
L-galactonatedegradation
undecaprenyl N-acetyl-glucosaminyl-N-acetyl-
mannosaminuronatepyrophosphate
a mismatchedDNA base pair
L-serinedeaminaseIII: tdcG
GTP cyclohydrolaseI: folE
pyridine nucleotidetranshydrogenase:pntA pntB
23S rRNApseudouridinesynthase: rluD
aldehydedehydrogenase:astD
aspartatekinase: metL
pyruvate formate-lyase: pflB
7,8-diaminopelargonicacid synthase: bioA
acetaldehydedehydrogenase2: mhpF
H+
AMP
cobalamin-independent
homocysteinetransmethylase:
metE
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
D-ribose
uracil-DNA-glycosylase:ung
a 2’,3’-cyclic-phosphate-terminated
RNA
KDO2-(palmitoleoyl)
-lipid IVA
Mg2+Co2+Ni2+
a DNAcontainingabasic site
cobalamin-dependenthomocysteinetransmethylase:metH
beta-hydroxyacyl-ACPdehydratase: fabZ
pyruvatekinase II: pykA
orotidine-5’-phosphate
alpha-L-arabinose
KASI: fabB
phosphoribosylformylglycinamidesynthetase: purL
carbamate
KdgT
a pyrimidine
N-succinyldiaminopimelate-aminotransferase: argD
threoninesynthase:thrC
a protein
L-citrulline
octaprenyldiphosphatesynthase: ispB
acetatekinase: ackA
EamB
YfbV
trimethylamineN-oxide
asparaginaseI: ansA
an rRNA
dTDP-D-fucosamine
superpathway of glycolysisand Entner-Doudoroff
acetate
malate
sugarphosphatase:yidA
coenzyme A
CadB
palmitoleate
16S rRNA m7G527methyltransferase:rsmG
7-aminomethyl-7-deazaguanine
FtsB
Lpp
ThiS-COAMP
5-phosphoribosyl-N-formylglycineamidine
AMP
uridine-5’-phosphate
GTP
phosphoribulosylformimino-AICAR-P
DcuB
pyridoxamine
glycerol
homoserine O-succinyltransferase:metA
nitrite
D-sedoheptulose-7-phosphate
psicoselysine
L-phenylalanine
dCMP
KdpDE Two-Component
SignalTransduction
System
EIINag
an (R)-3-hydroxymyristoyl-
[acp]
glutathionylspermidine
YihO
NanT
argininosuccinatesynthase: argG
23S rRNAand tRNApseudouridinesynthase: rluA
dethiobiotin
acetyl-CoAcarboxyltransferase:accD accA
chloride
maltodextringlucosidase:malZ
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenyl-N-acetylglucosamine
beta-hydroxydecanoyl-ACP dehydrase: fabA
undecaprenyl-N-acetyl-alpha-
D-glucosaminyl-pyrophosphate
L,D-transpeptidaseYcbB: ycbB
1-deoxy-D-xylulose
a trans-2-enoyl-CoA
a nucleotide
gamma-butyrobetainyl-
CoA
beta-D-glucuronidase:uidA queuine
altronateoxidoreductase:uxaB
a tRNA
a non-methylatedribosomalprotein L11
tRNAcontaininguridine at
position 54
EnvZ
pyridoxaltransporter
YejA/YejB/YejE/YejF ABCtransporter
pyruvate
GDP-L-fucose
chromatereductase:yieF
an (R)-3-hydroxybutanoyl-
[acp]
iron (III)hydroxamate
ABCtransporter
ADP-L-glycero-
D-manno-heptose
a quinone
L-serine
ADP-D-glucose
dihydrofolatereductase: folA
protoheme IX
isochorismate
NRZ
aminodeoxychorismatelyase: pabC
pyridine nucleotidetranshydrogenase,soluble: sthA
formaldehyde
an RNA
rRNAcontaining N2-methylguanine
glutathioneredox
reactions II
L-leucyl-tRNAleu
N-acetyl-D-mannosamine-6-phosphate
Tsrglu
shikimate
L-carnitinyl-CoA
lipoylateddomain
DcuC
2-cis,6-trans,10-trans-geranylgeranyldiphosphate
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
ADP
D-ribose
L-ribulose 5-phosphate4-epimerase:araD
transaldolaseB: talB
maltose ABCtransporter
a reducednitroaromatic
compound
L-methionine
YejM
di-trans,poly-cis-octaprenyldiphosphate
S-lactoyl-glutathione
L-glutamate
phosphatidylglycerol-prolipoproteindiacylglyceryltransferase; amajor membranephospholipid: lgt
glutamate-putrescineligase: puuA
putativenucleoside (IDP)diphosphatase:yibQ
NirC
pyrazinoate
sn-glycerol-3-phosphate
adenosylcobalamin salvagefrom cobinamide and cobalamin
Lipid A-core
guanine
all-trans-octaprenyl
diphosphate
YdeE
Zn2+
nucleosidediphosphatekinase: ndk
bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinonemethylase and S-adenosylmethionine:2-DMKmethyltransferase: ubiE
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
dihydroneopterinmonophosphatedephosphorylase
L,L-diaminopimelate
nitrite
CycA
isopentenyldiphosphate
proline ABCtransporter
salicin-6-phosphate
ureidoglycine
Na+
bifunctionalbiotin-[acetyl-CoA-carboxylase]ligase andtranscriptionalrepressor: birA
alpha-N-acetylneuraminate
CreB
a single-stranded
RNA
aliphaticsulfonate
ABCtransporter
D-carnitinyl-CoA
iron (III)hydroxamate
complex
maltose
2-aminomalonate-semialdehyde
GDPreductase:nrdB nrdA
an O-antigen
adenylosuccinatelyase: purB
KASI: fabB
cardiolipin synthase: cls
IMPdehydrogenase:guaB
cis-aconitate
KASIII: fabH
5’-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazolelyase: purB
a methylatedprotein
1-acylglycerol-3-phosphateacyltransferase: plsC
NRA
endonucleaseIII; specific forapurinic and/or apyrimidinicsites: nth
3-hydroxypropionate
KASII: fabF
adenosine
acetyl-CoA
adenosine
N2-succinyl-L-glutamate 5-semialdehyde
N-acetylneuraminate
mannitol-1-phosphate
allantoateamidohydrolase:allC
D-arabinose5-phosphateisomerase:kdsD
L,D-carboxypeptidaseA: ldcA
phosphoadenosine-5’-phosphosulfate
glycinecleavagesystem:gcvT gcvHgcvP lpd
NH4+
S-methyl-5’-thioadenosine
UDP-galactopyranosemutase: glf
a peptide
fused N-acetylglucosamine-1-phosphateuridyltransferaseand glucosamine-1-phosphateacetyltransferase:glmU
cellobiose-6-phosphatesalicin-6-phosphatearbutin-6-phosphate
a ribonucleosidediphosphate
pyruvateformate-lyaseactivatingenzyme: pflA
a stabilizedRecA
filament-DNA
complex
L-lactaldehyde
L-arginine
S-adenosyl-L-methionine
N-acetylglutamyl-phosphate
methylcitratesynthase: prpC
fatty acid oxidationcomplex, alphacomponent: fadB
3-hydroxybutyryl-CoA epimerase: fadJ
XylE
phenylpyruvate
7-cyano-7-deazaguaninereductase: queF
1-chloro-2,4-dinitrobenzene
Tapglu-Me
a trans-2-enoyl-CoA
tRNAmet
mono-, di-, ortrisaccharide< 600 Da
McrBCrestrictionendonuclease:mcrC mcrB
L-cystathionine
7,8-dihydrofolate
nitrite
TnaB
3-demethylubiquinol-8
allulose-6-phosphate3-epimerase:alsE
EIISga
pyruvate
23S rRNA m2A2503methyltransferase:rlmN
NtrB-P
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
N-succinyl-2-amino-6-ketopimelate
threoninedeaminase: ilvA
undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-
4-acetamido-4,6-dideoxy-D-galactose
pyrophosphate
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
N2-succinyl-L-ornithine
D-lactatedehydrogenase: dld
GDP-fucosesynthase: fcl
dimethylallyldiphosphate
serine/threonineproteinkinase: rdoA
galactokinase: galK
CybB
a phosphoprotein
ShiA
YdhE
D-allose
tRNAcontaining a
thionucleotide
L-methionine
YbfM
low-specificityL-threoninealdolase:ltaE
TorS
superpathway ofD-glucarate and
D-galactaratedegradation
PENTOSE PHOSPHATE PATHWAYS
D-altronate
Hda
EnvZ-Phis
3-(3-hydroxyphenyl)propionate
pyruvate dehydrogenase: aceE
5-phosphoribosyl1-pyrophosphate
L-rhamnonate
tetraacyldisaccharide4’-kinase: lpxK
ThiI: thiI
3-deoxy-D-manno-octulosonatecytidylyltransferase:kdsB
L-histidine
diaminetransaminase:ygjG
chemotaxis proteinmethyltransferase:cheR
acetohydroxybutanoatesynthase: ilvH ilvI
a thioredoxin
tRNAthr
3-phospho-L-serine
D-fructose-6-phosphate
D-arabinose
FMNphosphatase:ybjI
D-tagaturonate
pre-crRNA
molybdopterinsynthase
D-glucosamine1-phosphate
2-oxobutanoate
2-phosphoglycerate
homoserine
pyridoxamine5’-phosphate
6-phosphofructokinaseII: pfkB
thiosulfatesulfate
argininosuccinatelyase: argH
glycine
4-hydroxyphenylpyruvate
L-alanine
tetrahydrofolate
TatABCEproteinexport
complex
Cld
ribonucleaseII: rnb
L-glutamate
geranylfarnesyldiphosphate
phenylethylamine
thymidinephosphorylase:deoA
3-dehydro-shikimate
tRNAleu
Ni2+
acetate kinase: ackA
hydrogenase4: hyfH hyfFhyfE hyfDhyfC hyfBhyfA hyfG hyfI
a DNAcontainingabasic site
glycine
citrate
3-isopropylmalatedehydrogenase:leuB
2,3-diaminopropionateammonia-lyase: ygeX
L-selenocysteinyl-tRNAsec
lysinedecarboxylase2: ldcC
YfcA
D-ribulose-5-phosphate
D-arabinose5-phosphateisomerase:gutQ
argininedegradation
II (ASTpathway)
5-phosphoribosyl1-pyrophosphate
TyrP
an AP(apurinicor apyrimidinic)
site createdby glycosylic
bond cleavage
a tRNA
branched-chainamino-acidaminotransferase:ilvE
(R)-malate
phosphoglucomutase: pgm
OmpR
D-mannonatedehydratase:uxuA
D-tyrosine
purine nucleosidephosphorylase:deoD
lipid Adisaccharidesynthase: lpxB
fucosedegradation
uridine-5’-diphosphate
2-dehydro-3-deoxy-D-gluconate
ammonia
FMN
acetyl-CoA
1-deoxy-D-xylulose 5-phosphate
(2R,3S)-3-isopropylmalate
acetyl-CoA
nicotinate adeninedinucleotide
a [citrate(pro-3S)-
lyase](acetylform)
sn-glycerol-1-phosphate
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenyl-N-acetylglucosamine
XTPase: yjjX
tryptophandegradation
II (viapyruvate)
2-aceto-2-hydroxy-butyrate
putativephenylacetate-CoA oxygenase:paaE paaDpaaC paaB paaA
EIIGut
lipoate acetyltransferaseN6-(lipoyl)lysine
acetaldehydedehydrogenase:aldB
UDP-N-acetylglucosamineacyltransferase: lpxA
acetaldehyde
non-specific ion/solutemaltose
DcuS
L-histidine
dihydroneopterintriphosphatepyrophosphohydrolase:nudB
glutaredoxinreductase
a C4-dicarboxylatea C4-dicarboxylate
hydrophilicsolute orion < 600 Da
L-arginyl-tRNAarg
3-chloro-D-alanine
FadL
S-adenosyl-L-methioninecycle I (prokaryotic)
L-glutamine
5-amino-levulinate
L-cysteineO-acetyl-L-serine
a 2,3,4-saturated
fattyacyl CoA
cardiolipin
ureidoglycolase:allA
pyruvatesynthase
alpha-D-mannose 1-phosphate
serine/threoninekinaseHipA: hipA
EntS-TolCEnterobactin
EffluxTransportSystem
AmpG
HtrE
L-cysteinedesulfhydrase:tnaA
DNAcontaining arecognition
site
H+
galactosyl-glucosyl3-heptosyl3-
KDO2-lipid A-bisphosphate
D-allose-6-phosphate
guanosine
2-deoxy-D-glucose
protoheme IX
hydroxymethylpyrimidine
an AP(apurinicor apyrimidinic)
site createdby glycosylic
bond cleavage
stationaryphasemismatch/uracil DNAglycosylase:mug
pyruvate
tagatose-1,6-bisphosphate
7-alpha-hydroxysteroiddehydrogenase:hdhA
a lipopolysaccharide
a sugarphosphate
SECONDARY METABOLITES DEGRADATION
L-glutamate
FeoB
homocysteinemethyltransferase:mmuM
N-(5’-phospho-L-ribosyl-formimino)-5-amino-1-(5’-phosphoribosyl)-4-imidazolecarboxamideisomerase: hisA
histidinoldehydrogenase:hisD
tyrosinephosphatase:wzb
H2
dihydroxyacetonephosphate
2-methylisocitratelyase: prpB
fused heptose7-phosphatekinase/heptose1-phosphateadenyltransferase:rfaE
ATP
D-glucosamine-6-phosphate
L-lactaldehyde
S-adenosyl-L-methionine
N-acetylmuramicacid 6-phosphateetherase: murQ
NAD+
PhoQ
D-gluconate
3-keto-L-gulonate 6-phosphatedecarboxylase:ulaD
tRNA(m5U54)methyltransferase:trmA
D-glucaratedehydratase:gudD
hydroxymethylpyrimidinephosphate
acetate
2-O-alpha-mannosyl-D-glyceratedegradation
UTP
mannose-1-phosphateguanylyltransferase:cpsB
mureintripeptide
ABCtransporter
superpathway ofalanine biosynthesis
an L-1-phosphatidyl-
glycerol
UDP-glucose-hexose-1-phosphateuridylyltransferase:galT
an alkanesulfonate
AceF
2-oxoglutarate
a deoxynucleotideD-alanine
a 2’-deoxyribonucleoside
monophosphate
aryl carrierprotein/ serine
activatingenzyme
superoxide
glycolate
purine nucleosidephosphorylase:deoD
4-diphosphocytidyl-2C-methyl-D-erythritolsynthase: ispD
dihydroxyacetone phosphate
1-deoxyxylulose-5-phosphatesynthase: dxs
MdoC
N-acetylmuramate6-phosphate
D-galactose
PhoB-Pasp
prephenatedehydratase: pheA
BasS
a drug
a reducedferredoxin
BioP
NtrB
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatereductase: ispH
an aliphaticalpha,omega-
diamine
acetoacetate
beta-D-galactose
formate
a ThiS-ThiI acyl-disulfide
resolution ofrecombinational
junctionformation of twointact strands
acetohydroxybutanoatesynthase: ilvMilvG_2 ilvG_1
fused N-acetylglucosamine-1-phosphateuridyltransferaseand glucosamine-1-phosphateacetyltransferase:glmU
deoxyadenosine
K+
fructoselysine-6-phosphate
TCA CYCLE
dTDP-4-dehydrorhamnose3,5-epimerase: rfbC
LacY
HYD2
YojI
glycine betainebiosynthesis
I (Gram-negativebacteria)
acetohydroxybutanoatesynthase: ilvMilvG_2 ilvG_1
deoxyadenosinedeaminase: add
pyridoxal 5’-phosphate
dTDP-4-dehydro-6-deoxy-
D-glucose
deoxyguanylatekinase: gmk
an AP(apurinicor apyrimidinic)
site createdby glycosylic
bond cleavage
S-adenosylmethionine:tRNAribosyltransferase-isomerase: queA
propionatekinase: ackA
fumarate
L-methionine-(S)-S-oxide
a phosphoprotein
inosine-5’-phosphate
nicotinamidemononucleotide
pyruvate
a 3-oxo-meristoyl-[acp]
thymidinekinase: tdk
urea
D-sedoheptulose7-phosphateisomerase: lpcA
coenzyme A
2-keto-3-deoxy-L-
rhamnonate
uroporphyrinogen-III
mixed acid fermentation
xanthine-guaninephosphoribosyltransferase: gpt
ArcB-Phis717
phosphate acetyltransferase: pta
beta-N-acetylneuraminatea carboxylate
trans-2-enoyl-CoAreductase(NADPH)
a supercoiledduplex DNA
BrnQ
D-fructuronate
dihydrolipoyltranssuccinylase: sucB
uridine
PPPi
D-myo-inositol(1,2,3,4,5)-
pentakisphosphate
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
betainealdehyde
shikimate-3-phosphate
tRNAtrp
a tRNA containingepoxyqueuosineat position 34
cystathionine-beta-lyase: metC
ADP-L-glycero-beta-
D-manno-heptose
biosynthesis
a tRNA
cadaverine
sugarphosphatase:yigL
3-deoxy-D-arabino-heptulosonate-7-phosphate
L-alanine
CheY
fructoselysineand
psicoselysinedegradation
lipoyl-proteinligase: lipB
sugarphosphatase:yidA
FtsL
4-(glutamylamino)butanoate
nitric oxide
cob(I)alamin
alpha-D-glucose1-phosphate
RNA 3’-terminalphosphatecyclase: rtcA
adenineglycosylase;G.C --> T.Atransversions:mutY
GDP-alpha-D-mannose
INORGANIC NUTRIENTS METABOLISM
MdoH
shikimate kinase I: aroK
malate
pentose phosphate pathway
2-dehydro-3-deoxyphosphoheptonatealdolase: aroH
alpha-D-galactose1-phosphate
a quaternary amine L-proline
PitB
CO2
phosphoribosyl-AMP
thymidine
L-proline
2,3-dihydroxybenzoyl-
AMP
MscL
cytosine
NAD+
NADphosphorylation anddephosphorylation
16S rRNA m5C967methyltransferase:rsmB
NAD+
L-cysteinedesulfhydrase
melibiosemelibiose
trans-delta2,cis-delta4-
decadienoyl-CoA
3,4-dihydroxyphenylacetate
pyruvate
lineardimeric GMP
folylpoly-alpha-glutamatesynthetase
UDP-3-O-(3-hydroxymyristoyl)-
N-acetylglucosamine
23S rRNA 2’-O-ribose U2552methyltransferase:rlmE
aminopeptidaseA/I: pepA
AraE
23S rRNA m5U747methyltransferase:rlmC
dCTPdeaminase: dcd
2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinonehydroxylase: ubiF
mannoseisomerase:yihS
2-octaprenylphenolhydroxylase: ubiB
KdpE-Pasp
D-3-phosphoglyceratedehydrogenase: serA
a trans-delta2-enoyl-
acyl-[acp]
pyruvateformate-
lyase
EIIMtl
PhoP-Pasp
ribonucleosidehydrolase 1(pyrimidine-specific): rihA
oxalurate
(KDO)-lipid IVA
MdtM
L-glyceraldehyde3-phosphate
L-fuculokinase:fucK
lipoyl-proteinligase A: lplA
hydrogenase3: hycE hycBhycG hycFhycC hycD
nitrousoxide
D-glycerate
KASI: fabB
glyceroldehydrogenase:gldA
cytidine
D-galacturonateD-glucuronate
MelB
bifunctional riboflavinkinase / FMNadenylyltransferase: ribF
fused diaminohydroxyphosphoribosylaminopyrimidinedeaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase: ribD
thiamin(thiazolemoiety)biosynthesisprotein: thiF
dTTP
dihydroxy-aciddehydratase: ilvD
an alcohol
dihydroxy-aciddehydratase: ilvD
indole-3-glycerolphosphatesynthase: trpC
adenine
a standardalpha
amino acid
tryptophan synthase,beta subunit dimer: trpB
chorismatesynthase: aroC
ATP
nicotinamide
3-dehydroquinatedehydratase: aroD
FocA
N-(5’-phosphoribosyl)-anthranilate
23S rRNAand tRNApseudouridinesynthase: rluA
5-keto-D-gluconate 5-reductase:idnO
pyruvate
2,3-dihydroxybenzoyl-
AMP
D-glucarate
5-keto-D-gluconate 5-reductase:idnO
tyrosineaminotransferase: tyrB
threoninedeaminase: ilvA
aspartatekinaseIII: lysC
malate fumarateL-aspartate
acetylmaltose
16S-rRNAs
dGTP
hydroxymethylbilane
adenine
2,5-diamino-6-(ribosylamino)
-4-(3H)-pyrimidinone5’-phosphate
cyanatedegradation
D-ribose
Tsrglu
D-ribose-5-phosphate
L-cysteinedesulfhydrase
NarU
inorganicpyrophosphatase: ppa
ribosomal-protein-S5-alanine N-acetyltransferase:rimJ
FrlA
ChaA
a glycerolester
acetolactatesynthase: ilvN ilvB
YeeF
2-isopropylmalatesynthase: leuA
ZraP
cobalamin-independenthomocysteinetransmethylase:metE
an (R)-3-hydroxypalmitoyl-
[acp]
L-leucine
an N-acetyl-D-
hexosamine
aminopropylcadaverine
an mRNA
NADPHquinonereductase:mdaB
AaeABHydroxylated,
AromaticCarboxylicAcid EffluxTransport
System
glycolate
CheB-Pasp: cheB
L-asparagine
(2S)-2-isopropylmalate
formaldehyde
FimD
L-tryptophan
bifunctional beta-cystathionase,PLP-dependentand regulatorof maltoseregulon: malY
aspartatekinase: metL
a properlymatched
DNAbase pair
homoserinedehydrogenase:thrA
L-lysine
CPS-53 (KpLE1)prophage;deoxyribonucleoside5’-monophosphatephosphatase: yfdR
2-ketoglutaratedehydrogenase complex
guanosinekinase: gsk
L-serinedeaminaseII: sdaB
2-deoxyglucose-6-phosphatase:yniC
4-diphosphocytidyl-2-C-methylerythritolkinase: ispE
GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-DAP-D-AlaGlcNAc-1,6-anhMurNAc
thiaminediphosphate
1-deoxy-D-xylulose5-phosphatereductoisomerase: dxr
formate-tetrahydrofolateligase
lipid IVA
dCDP
2-ketobutyrateformate-lyase
/ pyruvateformate-lyase
ferricenterobactin
ABCtransporter
a nucleoside-5’-phosphate
carbamoyl phosphatesynthetase: carA carB
a DNAwith uracil
DNAn
a purine base
L-serine
dihydroorotate oxidase: pyrD
tRNA withGU(N)
anticodon
lipoyl-proteinligase: lipB
YgjD
predicted L-galactonateoxidoreductase:yjjN
sulfate ABCtransporter
O-succinyl-L-homoserine
EmrAB-TolC
multidrugefflux
transportsystem
a methylatedribosomalprotein L11
taurinedioxygenase:tauD
hydroxypyruvate
beta-phosphoglucomutase: ycjU
[+ 2 isozymes]
a tRNAcontaining N7-methylguanine
LysP nicotinamideriboside
valine-pyruvateaminotransferase:avtA
palmitoyltransferasefor LipidA: pagP
CreC-Phis
an alcohol
ferricenterobactin
an unstableRecA
filament-DNA
complex
putative enoyl-CoA hydratase/isomerase ofphenylacetatedegradation: paaF
YhhJ
tetrapyrrolebiosynthesis I
L,D-carboxypeptidaseA: ldcA
guanosine-5’-phosphate
lipopolysaccharidecore biosynthesis;heptosyl transferseIV; probably hexosetransferase: waaU
glutathione
7,8-diaminopelargonate
myristoyl-acylcarrier protein(ACP)-dependentacyltransferase:lpxM
undecaprenyldiphosphatesynthase: ispU
lipopolysaccharidecore biosynthesisprotein; heptosyltransferase III: rfaQ
L-phenylalanyl-tRNAphe
a prolipoprotein
CO2
sirohydrochlorin
L-serine
D-alanine
HtpX
guanosine-5’-phosphate
H-Gcv-protein-(lipoyl)lysine
sn-glycerol-3-phosphate
UDP-N-acetyl-D-glucosaminebeta-1,6-N-acetyl-D-glucosaminyltransferase:pgaC
di-trans,poly-cis-hexaprenyldiphosphate
fused nitric oxidedioxygenase anddihydropteridinereductase 2: hmp
farnesyldiphosphatesynthase: ispA
2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
D-tagaturonate
bicarbonate
spermidine
di-trans,poly-cis-
undecaprenyldiphosphate
aminodeoxychorismatesynthase: pabA pabB
acetoacetyl-CoA
hybrid-cluster
proteinred
3-hydroxypropionaldehyde
L-lysine
O-phospho-L-homoserine
ATP
L-aspartate
3-octaprenyl-4-hydroxybenzoatecarboxy-lyase: ubiD
bifunctional 3-demethylubiquinone-83-O-methyltransferaseand 2-octaprenyl-6-hydroxyphenolmethylase: ubiG
N2-succinyl-L-arginine
L-cysteine
a quercetin
putativeselenatereductase:ygfMxdhD ygfK
YidK
an aliphaticalpha,omega-
diamine
uridylyl-glutaminesynthase PII
ADP
asparaginesynthetaseB: asnB
a carboxylate
2,4-dinitrophenyl-S-glutathione
a trans oct-2-enoyl-[acp]
pyruvate
YiaMNOBindingProtein-
dependentSecondary(TRAP)
Transporter
4-hydroxybenzoate
isopentenyl-adenosineA37 tRNAmethylthiolaseMiaB: miaB
mannitol-1-phosphate
a debranchedlimit dextrin
nicotinamidemononucleotide
a trans-delta2-decenoyl-[acp]
enterobactinbiosynthesis
lipoyl-ACP
Chemotactic SignalTransduction System
a palmitoleoyl-[acp]
dUDP
2-oxo-3-deoxygalactonate6-phosphatealdolase: dgoA
pyruvate
2-dehydro-3-deoxy-D-galactonate
precorrin-2dehydrogenase:cysG
Cr6+
acetate
fatty acidoxidationcomplex,alphacomponent:fadB
Cd2+Zn2+
superpathwayof glycol
metabolismand degradation
tagatose-6-phosphate
acyl carrier proteinphosphodiesterase:acpH
6-phospho-D-gluconate
D-galactitol
hydrogen sulfide
ATP
YcfT
NarP-Pasp
tRNAileX
salvage pathwaysof pyrimidine
deoxyribonucleotides
2’-deoxyguanosine-5’-diphosphate
5’-methylthioadenosine/S-adenosylhomocysteinenucleosidase: mtn
L-phenylalanine
a glycogen
acetyl-CoA synthetase(AMP-forming): acs
an oxidizedthioredoxin
formate
16S rRNA m3U1498methyltransferase:rsmE
4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate
4-aminobutyrate
beta-D-ribopyranose
a fatty acid
acetolactatesynthase: ilvH ilvI
L-methionyl-tRNAmet
isopropylmalateisomerase:leuD leuC
an L-1-phosphatidyl-ethanolamine
5-aminoimidazoleribonucleotide
acetate
lipoyl-proteinligase A: lplA
coenzyme A
L-ascorbate-6-phosphate
alaninedegradation I
agmatine
3-phosphoglycerate
dTDP-alpha-L-
rhamnose
GltS
D-galactose
2’-deoxyadenosine-5’-diphosphate
OsmY
GDP-alpha-D-mannose
AtoSC Two-Component
SignalTransduction
System
tartronatesemialdehyde
octyl beta-1,6-D-galactofuranosyl-
alpha-D-glucopyranoside
Cu+
GMPsynthetase:guaA
ribonucleoside-diphosphatereductase:nrdB nrdA
asparaginesynthetaseA: asnA
ribonucleoside-diphosphatereductase 2:nrdF nrdE
SucB
GARtransformylase2: purT
SucB-lipoate
IMPcyclohydrolase:purH
guanine
2-dehydro-3-deoxy-D-gluconate-6-phosphate
2-oxoglutarate dehydrogenasecomplex: lpd sucB sucA
L-rhamnoseisomerase: rhaA
5-enolpyruvyl-shikimate-3-phosphate
ADPreductase:nrdB nrdA
K+
UDP-glucose-hexose-1-phosphateuridylyltransferase:galT
CTP
PPPi
porphobilinogen
pyruvate
aspartateammonia-lyase: aspA
beta-L-rhamnose
pyridoxalphosphatase:ybhA
glyoxylatereductase:ghrA
RseC
dihydroorotase: pyrC
L-tryptophan
Trgglu-Me
phosphoribosyl-AMPcyclohydrolase: hisI
hypoxanthine
nucleosidediphosphatekinase: ndk
cis-aconitate
anaerobiccoproporphyrinogenIII oxidase: hemN
citratelyase: citEcitF citD
histidinol-phosphateaminotransferase:hisC
D-glyceraldehyde-3-phosphate
2-oxoglutarate
succinate semialdehydedehydrogenase,NAD+-dependent: sad
a cis,trans-polyisoprenyln-PP
nucleosidediphosphate kinase: ndk
ribonucleoside-triphosphatereductase: nrdD
N-acetylglucosaminyltransferase: murG
a singlestranded
DNA
L-arginine
thiamine-phosphate
4-methyl-2-oxopentanoate
23S rRNAm3psi1915methyltransferase:rlmH
D-fructose-6-phosphate
D-arabinose5-phosphate
alcoholdehydrogenase:adhE
sugarphosphatase:yigL
ribonucleosidehydrolase 1(pyrimidine-specific): rihA
pyruvate
pyridoxine-5’-phosphate
carbamoylphosphatesynthetase:carA carB
replicativeDNAhelicase:dnaB
DNA combinedwith exogenousDNA to form a
recombinationaljunction
L-methionine
formate
DcuR-Pasp56
(KDO)-lipid IVA
5-amino-6-ribitylamino-2,4(1H,3H)-
pyrimidinedione
dihydroxyacetonephosphate
L-asparagine
L-alanine
3-octaprenyl-4-hydroxybenzoatedecarboxylasetogether withUbiG: ubiX
a (3S)-3-hydroxyacyl-CoA
aspartatekinase: thrA
2-phosphoglycolate
2’-deoxyguanosine-5’-diphosphate
4-coumaroyl-CoA
acetyl-CoA
6-phospho-beta-glucosidaseB; cryptic:bglB
FtsW
adenine
N-acetyl-L-glutamate
riboflavin
beta-D-glucose-6-phosphate
malate
D-allose
2-phospho-4-(cytidine 5’-diphospho)
-2-C-methyl-D-erythritol
a polypeptide
a tRNAcontainingqueuosine
acetaldehyde
PflB
fructose-1,6-bisphosphatase I: fbp
rep helicase,a single-strandedDNAdependentATPase: rep
fructose bisphosphatealdolase class II: fbaA
2-keto-3-deoxy-L-
rhamnonate
alpha-D-glucose6-phosphate
UDP-N-acetylmuramoylalanyl-D-glutamate 2,6-diaminopimelate ligase: murE
maltodextrinphosphorylase:malP
undecaprenyldiphosphatesynthase: ispU
GltP
UDP-N-acetylmuramate
(S)-methylmalonyl-
CoA
CpxAR Two-Component
SignalTransduction
System
malate dehydrogenase: mdh
UDP-2,3-diacylglucosamine
hydrolase: lpxH
KefB
a tRNA
L-cysteinedesulfhydrase:metC
dihydroxyacetonephosphate
beta-ketoacyl-[acyl-carrier-protein] reductase: fabG
KASI: fabB
galactokinase: galK
KASI: fabB
KDO2-lipid A
chitobiosedegradation
GadC
methylglyoxalreductase(NADH-dependent): ydjG
phosphoglyceromutase1: gpmA
colanic acid building blocks biosynthesis
adenylylsulfatekinase: cysC
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
sn-glycerol-3-phosphate
glutathionesynthetase: gshB
lipoamide dehydrogenase: lpd
UDP-N-acetyl-D-
glucosamine
3-deoxy-D-manno-octulosonate8-phosphatephosphatase:kdsC
partially N- deacetylatedpoly-beta-1,6-
N-acetyl-D- glucosamine
DsdX
HcaT
UDP reductase:nrdB nrdA
glucosyl-heptosyl2-
KDO2-lipid A-
phosphate
(S)-1-pyrroline-5-carboxylate fructose-1,6-
bisphosphate
7,8-dihydro-D-neopterin
folylpoly-gamma-glutamatesynthetase:folC
an L-1-phosphatidyl-
glycerol
an RNA
ethyleneglycol
AqpZ
phosphopentomutase:deoB
S-adenosyl-L-methionine
DNAn
trehalose 6-phosphate
a 5,10-methylene-tetrahydrofolate
6-hydroxymethyl-7,8-dihydropterinpyrophosphokinase: folK
H+
IdnT
phosphoribosylglycinamideformyltransferase: purN
glutamyl-QtRNA(Asp)synthetase:yadB
lysinedecarboxylase:cadA
GMPreductase:guaC
a hydroquinone
undecaprenylphosphate-
alpha-L-Ara4FN
acetylphosphate
acetaldehyde
nickel ABCtransporter
beta-D-glucose-6-phosphate
agmatinase:speB
galactosyl-glucosyl2-heptosyl3-
KDO2-lipid A-bisphosphate
3-phenylpropionatedioxygenasesystem: hcaDhcaC hcaF hcaE
2-dehydro-3-deoxy-D-
gluconate-6-phosphate
YhfC
ALDEHYDE DEGRADATION
L-alanine
chemotaxis proteinmethyltransferase:cheR
non-specific ion/solute
nicotinamide mononucleotide
ArcB-Phis292
protoporphyrin IX
S-ribosylhomocysteinelyase: luxS
acetate
succinate
precorrin-2
tRNAnucleotidyltransferase: cca
choline
beta-D-glucose
pyruvate
23Sribosomal
RNA
lactose
geranyldiphosphatesynthase: ispA
D-xylose
glutamate-cysteineligase: gshA
a trans-delta2-enoyl-acyl-[acp]
homoserine lactonehomoserine
5,10-methylene-
THF
trehalose-6-phosphatephosphatase,biosynthetic:otsB
H+
octaprenyldiphosphatesynthase: ispB
S-hydroxymethylglutathione
dIMP
L-ornithine
diacetyl
selenophosphate
pyruvate
tRNAgln
dTMP
RcsC-Phis
a proteinL-tyrosine
16S rRNAm62A1518,m62A1519dimethyltransferase: ksgA
nucleoside triphosphatepyrophosphohydrolase:mazG
tryptophanase:tnaA
ribose-1,5-bisphosphate
DNAn
an (R)-3-hydroxyoctanoyl-
[acp]
an (R)-3-hydroxydecanoyl-[acp]
lactosedegradation III
L-cysteine
fumarate
deoxyribose-5-phosphate
dihydroxyacetonephosphate
DcuS-Phis349
5’,5’’’-diadenosine
tetraphosphate
DNAcytosinemethylase:dcm
beta-galactosidase:lacZ
peptidoglycantetrapeptide,
glycan chain 1
TDP-rhamnose
o-succinylbenzoate
D-xylulose-5-phosphate
KDO2-lipid IVA
L-fuculokinase: fucK
propionyl-CoA
2-keto-isovalerate
superpathwayof asparaginebiosynthesis
thiamin(thiazolemoiety)biosynthesisprotein: thiF
ExuT
2-keto-3-deoxy-L-rhamnonatealdolase: yfaU
5-phosphoribosyl1-pyrophosphate
an oxidizedelectronacceptor
NanC
a protein-L-tyrosinephosphate
deoxyribose-1-phosphate
mannokinase
all-trans-heptaprenyldiphosphate
L-lysine
8-amino-7-oxononanoatesynthase: bioF
L-proline
D-glyceraldehyde-3-phosphate
UvrY
NfrA
2-oxobutanoate
rRNA
L-ribulose-5-phosphate4-epimerase:sgbE
L-aspartate
gamma-aminobutyraldehydedehydrogenase: ydcW
GTP
N-acetylneuraminate
a carbohydrate
myo-inositol
L-glutamyl-tRNAGlu
ribonucleoside-diphosphatereductase 2:nrdF nrdE
D-alanyl-D-alanine-adding enzyme: murF
a nucleosidemonophosphate
iron (III)hydroxamate
complex
CMP
Aer
dephospho-CoA kinase: coaE
23S rRNA m2G1835methyltransferase:rlmG
a 2’-deoxyribonucleoside
diphosphate
propionate
citratelyase: citEcitF citD
adenine
KefC
16S rRNA m5C1407methyltransferase:rsmF
inosine kinase: gsk
HMP-PPhydrolase:cof
protein with lowundecaprenylpyrophosphatephosphataseactivity: lpxT
cysteinesulfinatedesulfinase:csdA csdE
a 3’-phosphate-terminated
RNA
6-phospho-beta-glucosidaseB; cryptic:bglB
trehalose
L-alanine
GDP-L-fucose
FimC
CARBOXYLATES DEGRADATION
oxaloacetate
agmatinase: speB
UDP-2,3-bis(3-hydroxymyristoyl)
glucosamine
4-hydroxybenzoateoctaprenyltransferase:ubiA
D-arabinose5-phosphate
alpha-iminosuccinate
apo-citrate lyasephosphoribosyl-dephospho-CoAtransferase: citX
fused heptose7-phosphatekinase/heptose1-phosphateadenyltransferase:rfaE
cytidinedeaminase: cdd
KDO2-lipidA, coldadapted
asparaginesynthetaseB: asnB
2-octaprenyl-6-methoxyphenolhydroxylase: ubiH
benzaldehyde
colanic acid
2-oxoglutarate
L-cysteine
molybdopterin
succinatesemialdehydereductase: yihU
an oxidizedthioredoxin
dihydroneopterintriphosphate 2’-epimerase: folX
4-aminobutyrate
DcrB
galactitoldegradation
guanosine-5’-diphosphate
L-glutamategamma-
semialdehyde
octaprenyldiphosphatesynthase: ispB
PhoQ-Phis
holo-[acylcarrierprotein]synthase2: acpT
L-aspartate-semialdehyde
UDP-D-glucose
UDP-D-galacto-1,4-
furanose
(E)-3-(methoxycarbonyl)pent-2-enedioate
UvrY-Pasp
a drug
melibiose
undecaprenylphosphate-
alpha-L-Ara4N
dihydroxyacetonephosphate
an apo-GcvHprotein
ferricdicitrate
acetaldehydedehydrogenase2: mhpF
fructose-1,6-bisphosphatase: yggF
CO
NMNH
L-glutamine:D-fructose-6-phosphateaminotransferase:glmS
glycogen
lipoatebiosynthesis
andincorporation II
succinate
dTDP-4-dehydrorhamnosereductase: rfbD
L-homocysteine
thymidylatesynthase: thyA
1,3-diphosphateglycerate
AsmA
ATP
4-methyl-5-(beta-
hydroxyethyl)thiazole
N5-glutaminemethyltransferase:prmB
UDP-D-glucose
MutHLScomplex,methyl-directedmismatchrepair: mutHmutS mutL
peptidoglycanDAP-DAPcrosslink
alpha-D-glucose
acetaldehyde
rRNAcontaining
pseudouridine
chromatereductase:yieF
purine nucleosidephosphorylase:
deoD
a holo-[acp]
glycine
methylglyoxal
DNAadeninemethylase:dam
pseudouridine5’-phosphate
4-aminobutanal
nicotinatemononucleotide
dihydrofolatesynthetase: folC
an (R)-3-hydroxymyristoyl-
[acp]
L-rhamnose
pyrimidine deoxynucleosidetriphosphatepyrophosphohydrolase: nudI
nitrousoxide
2,3-diaminopropionate
di-trans,poly-cis-
undecaprenylphosphate
glucose 6-phosphate-1-dehydrogenase: zwf
methylmalonyl-CoA epimerase
tRNA-specificadenosinedeaminase:tadA
L-asparagine
NupG
L-glutamate
maltodextrinphosphorylase:malP
SohB
a peptide
beta-D-glucose-6-phosphate
3-phosphoglycerate
superpathway ofgluconate degradation
RstB
lipopolysaccharidecore biosynthesisprotein: rfaS
arsenate
CheB-Pasp: cheB
galactosyl-glucosyl-heptosyl3-
KDO2-lipid A-bisphosphate
pyruvate kinase II: pykA
tRNAcontaining N6-methyladenine
uracil
branched-chainamino-acidaminotransferase:ilvE
alpha-D-glucose 6-phosphate
beta-hydroxyacyl-ACP dehydratase: fabZ
L-cystathionine
acetyl-CoA carboxylase:accB accC accA accD
hemebiosynthesis fromuroporphyrinogen II
phosphate
a tRNA containing 5-carboxymethylaminomethyl-
2-thiouridine
D-glyceraldehyde-3-phosphate
phosphoenolpyruvate synthase: pps
phosphopantetheinyltransferase: entD
prolyl-tRNAsynthetase:
proS
carbamoyl-phosphate
L-pantoate
isoleucyl-tRNA
synthetase:ileS
aspartyl-tRNA
synthetase:aspS
Tsrgln
S-adenosyl-L-methionine
putative enoyl-CoA hydratase/isomerase ofphenylacetatedegradation: paaG
Targln
succinate
N-acetyl-glucosamine-1-phosphate
D-galactonatedegradation
lipoyl-proteinligase A: lplA
23Sribosomal
RNA
triose phosphate isomerase: tpiA
enolase: eno
succinate
beta-D-galactose
citrate synthase: gltA
guanosine-5’-diphosphate
oxaloacetate
L-1,2-propanediol
molybdopterinsynthase
NrfE
poly-beta-1,6-N-acetyl-D-glucosamine
a DNAsegment
in reverseorientation
acetoin
a C4-dicarboxylatea C4-dicarboxylate
ribosomal-protein-S18-alanine N-acetyltransferase: rimI
ribonucleosidehydrolase 3: rihC
23S rRNA m5C1962methyltransferase: rlmI
beta-D-glucose
23S rRNA m1G745methyltransferase:rrmA
D-methionineL-methionine
an aldehyde
2-oxoglutarate
D-altronatedehydratase:uxaA
fructose 1,6-bisphosphatase II: glpX
3-octaprenyl-4-hydroxybenzoate
DgoT
riboflavinsynthase:ribC
NADP+
6-pyruvoyltetrahydropterin
1-deoxy-D-xylulose 5-phosphate
malate synthase A: aceB
S-adenosyl-L-homocysteine
o-succinylbenzoyl-CoA
L-glutamyl-tRNAGlu
KDO2-lipid IVA
phosphate
L-glutamine
UDP-D-glucuronate
phosphoglycerate mutase 2: ytjC
phosphopentomutase:deoB
a DNA pairof adjacentpyrimidines
fructose bisphosphatealdolase class I: fbaB
YiaF
bifunctional aconitate hydratase2 and 2-methylisocitrate
dehydratase: acnB
D-mannonateoxidoreductase:uxuB
D-threo-isocitrate
DcuA
isocitrate dehydrogenase: icd
fused diaminohydroxyphosphoribosylaminopyrimidinedeaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase: ribD
a glutaminesynthetase PII
alpha-D-galactose1-phosphate
an N-acetyl-D-hexosaminide
D-ribulose-5-phosphate
fructosedegradation
D-xylose
gamma-glutamyl-gamma-aminobutyraldehydedehydrogenase: puuC
dihydroxyacetonekinase: dhaLdhaK dhaM
superpathway of threonine metabolism
transketolaseI: tktA
D-mannose
pyruvate kinase I: pykF
glyceraldehyde3-phosphatedehydrogenase-A complex: gapA
alanine racemase1, PLP-binding,biosynthetic: alr
1-deoxyxylulose-5-phosphatesynthase: dxs
aminoacetone
phosphohydroxymethylpyrimidinekinase: thiD
malate fumarate succinate orotateL-aspartate
O-succinylhomoserine(thiol)-lyase: metB
an acid
UDP-N-acetylmuramoyl-L-alanyl-D-
glutamyl-meso-2,6-diaminoheptanedioate-
D-alanine
phosphoglucoseisomerase: pgi
YgjDdegradation
products
propionyl-CoA:succinateCoA transferase: scpC
acidphosphatase:appA
7,8-dihydroneopterintriphosphate
a dipeptide
3-(2,3-dihydroxyphenyl)
propionate
DcuC
dihydroxyacetonephosphate
2-dehydro-3-deoxy-D-
gluconate-6-phosphate
putative ring-cleavage enzymeof phenylacetatedegradation: maoC
2-oxoglutarate
5-phospho-ribosyl-
glycineamide
tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:mnmA
phenylacetaldehydedehydrogenase: feaB
1-deoxy-D-xylulose 5-phosphate
D-fructose-6-phosphateL-glutamine
3,5-tetradecadienoyl-
CoA
all-trans-hexaprenyl
diphosphate
3-deoxy-D-manno-octulosonate8-phosphatephosphatase:kdsC
YedZ
L-serine
D-mannose-6-phosphate
D-galactonate
sirohemebiosynthesis
ZinT
AmtB
acetate
D-Tyr-tRNATyrdeacylase:dtd
1-(o-carboxyphenylamino)-1’-deoxyribulose-
5’-phosphate
phosphoglucosaminemutase: glmM
D-xylose
homoserine
L-glutamate
DNApolymeraseI, 3’ --> 5’polymerase,5’ --> 3’and 3’ --> 5’exonuclease:polA
dTDP-glucose 4,6-dehydratase:rfbB
cellobiose-6-phosphatediacetylchitobiose-6-phosphate
FliY
dihydrofolatereductase: folM
D-fructose-6-phosphate
folylpoly-gamma-glutamatesynthetase:folC
S-adenosyl-L-methionine
a 2,3,4-saturatedfatty acyl CoA
D-erythro-imidazole-glycerol-phosphate
protoporphyrinogenoxidase: hemG
KASI: fabB
L-valine
anamineated
amine donor
cobalamin-dependent
homocysteinetransmethylase:
metH
purine nucleosidephosphorylase:
deoD
a 1,4-alpha-D-glucan
YidY
thioredoxinreductase:trxB
glycolateL-lactate
acetate
AMPnucleosidase: amn
acetaldehydedehydrogenase2: mhpF
cis-3-(carboxyethyl)-3,5-
cyclohexadiene-1,2-diol
16S rRNA m2G1207methyltransferase:rsmC
FtsP
alpha-D-galactose 1-phosphate
tetrahydrofolate
6-phospho-beta-glucosidaseA: bglA
rRNAcontaining 2-methyladenine
D-glyceraldehyde-3-phosphate
xanthinedehydrogenase:xdhC xdhB xdhA
nigerose
glucose-1-phosphateuridylyltransferase:galU galF
alpha-amylase:amyA
an alcohol
a butyryl-[acp]
phosphomannomutase:cpsG
an N-acetoxyarylamine
NarL-Pasp
L-glutamate
phosphohistidinephosphatase: sixA
L-asparagine
L-cysteinedegradation II
glycerol-3-phosphate
acyltransferase:plsB
tRNAcontaining 5,6-dihydrouridine
formatehydrogenlyasecomplex: hycDhycC hycF hycGhycB hycE fdhF
glycosidehydrolase:ygjK
N-ethylmaleimidereductase, FMN-linked: nemA
thiocyanate
an oxidizedthioredoxin
cytosine
3-phosphoglycerate
2,3-dihydroxy-isovalerate
3-hydroxypropionaldehyde
cytosinedeaminase:
codA
L-1,2-propanedioloxidoreductase:fucO
glyoxylatecarboligase:gcl
hypoxanthine
chorismate mutase: pheA
tryptophanyl-tRNA
synthetase: trpS
glucokinase: glk
valyl-tRNAsynthetase:
valS
UDP-D-glucose
cysteinyl-tRNA
synthetase:cysS
RhaT
an rRNA
an alkylhydroperoxide
GlcNAc-1,6-anhMurNAc
UDP-3-O-acyl-N-acetylglucosaminedeacetylase: lpxC
uracilphosphoribosyltransferase: upp
Tapglu
multifunctional2-keto-3-deoxygluconate 6-phosphate aldolaseand 2-keto-4-hydroxyglutaratealdolase andoxaloacetatedecarboxylase: eda
siroheme
protein-(glutamine-N5)methyltransferase:prmC
2-octaprenyl-6-hydroxyphenol
dCTP
shikimate kinase II: aroL
non-specific ion/solute
PRPPbiosynthesis I
LamB
hydroxyphenylacetyl-CoA thioesterase: paaI
L-fucose
5’-deoxyadenosine
ATP
alkylhydroperoxidereductase: ahpF ahpC
an L-1-phosphatidylglycerol-
phosphate
ribonucleosidehydrolase 3: rihC
mannitol-1-phosphate
putativeoxidoreductaseFe-S subunit;possiblecomponentof selenatereductase: ygfK
glyoxylatereductaseB: ghrB
oxalate
enterobactin
D-ribulose-5-phosphate
2-dehydro-3-deoxyphosphoheptonatealdolase: aroG
D-galactonatedehydratase: dgoD
pyruvate
anthranilate synthasecomponent II: trpD
superpathway of leucine, valine,and isoleucine biosynthesis
AnsP
PII-UMP
NarQ
CDP
deoxyguanosine
argininesuccinyltransferase:astA
3-deoxy-D-manno-
octulosonate
cytidine
maltose
UDP-N-acetyl-beta-D-mannosaminouronate
UhpA
GabP
L-methionine
glutamatedehydrogenase:gdhA
2-oxobutanoate
asparaginesynthetaseA: asnA
asparaginaseIII: iaaA
sorbitol-6-phosphatedehydrogenase:srlD
ethanolamine
YncD
a nucleosidetriphosphate
COFACTORS, PROSTHETIC GROUPS, ELECTRON CARRIERS BIOSYNTHESIS
cytidinekinase: udk
RseA
cytidylatekinase: cmk
GlpF
phosphoenolpyruvatecarboxylase: ppc
ketogluconate metabolism
tetrahydrofolate
NarK
a DNAsegment
citratesynthase:gltA
lipoate acetyltransferase: aceF
hydroxymethylbilanesynthase: hemC
N5-methyl-L-glutamine
pyruvate
glucose and glucose-1-phosphate degradation
YjhB
tRNA (Gm18) 2’-O-methyltransferase:trmH
shikimatedehydrogenase: ydiB
methionyl-tRNA
synthetase:metG
alpha-D-glucose 1-phosphate
trans-aconitate
a 1,4-alpha-D-glucan
DNAwithoutlesion
HflD
N-acetylneuraminatemutarotase: nanM
xanthosinephosphorylase:xapA
taurine
methylglyoxal
all-trans-geranyl-geranyl
diphosphate
purine nucleosidephosphorylase:deoD
K+
UDP-N-acetyl-D-
glucosamine
dihydroxyacetonephosphate
uroporphyrin III C-methyltransferase:cysG
YceE
D-glyceraldehyde-3-phosphate
NUCLEOSIDES AND NUCLEOTIDES BIOSYNTHESIS
PhoE
asparaginesynthetaseB: asnB
GTP
elongatortRNAmet
D-galactono-1,4-lactone
BglG-P
dGMP
guanosine-5’-diphosphate
3-keto-L-gulonate
pantothenateand coenzyme
A biosynthesis I
lipoylateddomain
YiiP
ribonucleoside-triphosphatereductase: nrdD
L-lysyl-tRNAlys
a [citrate(pro-3S)-
lyase](citrylform)
triose phosphateisomerase: tpiA
L-rhamnulose-1-phosphate
valine-pyruvateaminotransferase:avtA
acetaldehyde
enolase: eno
MQH2
nitric oxide
alpha-L-arabinose
D-galacturonate
phosphoenolpyruvatesynthase: pps
malate
GTP
phosphoserinephosphatase: serB
L-tyrosyl-tRNAtyr
lipid Adisaccharide
a cis-delta5-dodecenoyl-[acp]
4-coumarate
a palmitoleoyl-[acp]
an acetoacetyl-[acp]
superpathway of arginineand ornithine degradation
phenylacetate-CoA ligase: paaK
enterobactin
MQH2
AMP
superpathway of aspartateand asparagine biosynthesis;
interconversion ofaspartate and asparagine
N-acetyl-D-glucosamine
Ni2+Mg2+
Lnt
unknown
Asr
ferricenterobactin
ribonucleosidetriphosphatereductaseactivase: nrdG
3’-phospho-adenylylsulfatereductase: cysH
an rRNA
a cis-vaccenoyl-
[acp]
pyrimidinedeoxyribonucleosides
degradation
crypticadeninedeaminase:ade
pyrazinamide
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
L-Ala-gamma-D-Glu
polyisoprenoidbiosynthesis (E. coli)
L-tyrosine
all-trans-farnesyl
diphosphate
a biotinylatedBCCP (dimer)
alpha-D-glucose 6-phosphate
predicted 3-hydroxy-acyl-CoAdehydrogenaseof phenylacetatedegradation: paaH
xanthine-guaninephosphoribosyltransferase: gpt
Fdh-N
FERMENTATION
CorA
2,4-dienoyl-CoAreductase:fadH
pyruvate
2-methylcitratedehydratase: prpD
ribose-5-phosphateisomeraseA: rpiA
xanthine-guaninephosphoribosyltransferase: gpt
cobinamide
fumaratereductase:frdD frdCfrdB frdA
lipoyl-ACP
GntP
a holo-[acp]
D-mannose-6-phosphate
beta-alanine
5-methyluridine-modified 23S
ribosomal RNA
3-hydroxy-5-cis-tetradecenoyl-
CoA
2,3-dihydroxybenzoate
a proteinL-beta-
isoaspartatealpha-
methyl ester
L-threonyl-tRNAthr
a [citrate(pro-3S)-lyase](thiol
form)
S-ribosyl-L-homocysteine
N-acetyl-D-glucosamine-6-phosphate
D-gluconate
lipoatesalvage andmodification
a phosphatemonoester N-methyltryptophan
demethylmenaquinone-8
catabolicthreoninedehydratase:tdcB
D-alanine-D-alanineligase A: ddlA
ribonucleotidemonophosphatase:nagD
guanosine-5’-diphosphate
anthranilate
LepA
YtfM
beta-D-glucose
5-phosphoribosyl1-pyrophosphate
RstBA Two-Component
SignalTransduction
System
L-proline
a drug
MarC
UDP-3-O-[3-hydroxymyristoyl]glucosamineN-acetyltransferase: lpxD
phosphodiesterase,heme-regulated: dos
L-aspartyl-tRNAasp
a 1,4-alpha-D-glucan
tRNA uridine
cholate
formate
acetohydroxy acidisomeroreductase:ilvC
KDOtransferase:waaA
EvgA-Pasp
glutaminedegradation I
CheB-Pasp: cheB
PnuC
uridylate kinase: pyrH
a ThiIpersulfide
succinylargininedihydrolase: astB
phosphodiesterase /predicted L-ascorbate6-phosphatelactonase: ulaG
alpha-dehydro-beta-deoxy-D-glucaratealdolase: garL
L-glutamate
palmitoleoylacyltransferase:lpxP
2-keto-L-gulonate
N3-methylcytosine
a polypeptide
KASII: fabF
maltopentaose
purine nucleosidephosphorylase:deoD
D-glucono-delta-lactone-6-phosphate
acetaldehydedehydrogenase:adhE
7-aminomethyl-7-deazaguanine
acetate
L-xylulose-5-phosphate
a thioredoxin
agmatine
glycolate
1-phosphofructokinase:fruK
putative diacylglycerolcholinephosphotransferase:ynbA
gamma-glutamyl-L-putrescine
N-carbamoyl-L-aspartate
an RNA
trehalose
H+
P-DPD
acetyl-esterase: aes
inosine-5’-phosphate
L-arginine
deoxyinosine
pyruvate
isochorismatesynthase 1: entC
a [citrate(pro-3S)-
lyase](acetylform)
pirin-likeprotein:yhhW
3-dehydroquinate
inositolmonophosphatase:suhB
2,3-dihydroxybenzoate-AMP ligase: entE
cytoplasmictrehalase: treF
nitrite
4,5-dihydroxy-2,3-pentanedione
2-isopropylmaleate
2,3-dihydro-2,3-dihydroxybenzoate
AMP
3-deoxy-D-manno-
octulosonate8-P
ThiS-COSH
UDP-N-acetyl-D-glucosamine
4’-phosphopantetheine
hydroxylamine
acetyl-CoA
FtsQ
H+
pyruvate
citrate
GTP
chemotaxis proteinmethyltransferase:
cheR
uracil
deoxyuridine
L-rhamnonatedehydratase:yfaW
glucosedehydrogenase: gcd
pyrimidine deoxynucleosidetriphosphatepyrophosphohydrolase: nudI
a DNAcontaining aapyrimidinic
site
CsgB
citratelyase: citEcitF citD
a deoxynucleoside
L-asparagine
cysteinedesulfurase:iscS
putrescine
formate
an oxidizedflavodoxin
Trgglu
aspartatecarbamoyltransferase: pyrI pyrB
alpha-D-ribose-1-phosphate
beta-hydroxyacyl-ACPdehydratase: fabZ
broadspecificity 5’(3’)-nucleotidase andpolyphosphatase:surE
glycolateoxidase:glcFglcE glcD
dimethylallyldiphosphate
1-amino-propan-2-one-3-
phosphate
L-glutamate
glycerol 2-phosphate
alpha-D-glucose1-phosphate
1-deoxyxylulose-5-phosphatesynthase: dxs
a deoxynucleotide
predictedthiosulfatesulfurtransferase:ynjE
L-Ala-gamma-D-Glu-DAP-
D-Ala
a DNAcontaining
a purinic site
D-mannose
thiosulfatesulfate
6-phospho-D-gluconate
CDP-choline
phosphate
acetohydroxy acidisomeroreductase:ilvC
H2O
YchM
coproporphyrinogenoxidase, aerobic: hemF
NADP+
UDP-D-galactose
SetA
AtoS
SIGNAL TRANSDUCTION PATHWAYS
nicotinate-nucleotidedimethylbenzimidazolephosphoribosyltransferase: cobT
2-deoxygluconate
tRNAcontainingguanine
cobalaminadenosyltransferase:
btuR
pyrimidinephosphatase
trans-2-decenoyl-ACP isomerase: fabA
enoyl-ACP reductase(NADH): fabI
glycolaldehyde
YebS
alpha-D-glucose
DNAligase: ligB
phosphoenolpyruvate
2-aminobutyrate
beta-hydroxyacyl-ACP dehydrase: fabA
dihydroxy-acetone
undecaprenyldiphosphatesynthase: ispU
a holo-[acp]
3-methyladenine
salvage pathways of pyrimidine ribonucleotides
dTDP-4-acetamido-4,6-dideoxy-D-galactose
ZraR-phosphate
2-keto-3-methyl-valerate
formaldehyde
phosphateacetyltransferase: pta
uracil
YhcB
anadenylated
ThiS sulfur-carrierprotein
ubiquinone-8
PhoB
threoninedehydrogenase: tdh
CMP-3-deoxy-D-manno-
octulosonate
fructose 1,6-bisphosphatase: ybhA
crotonobetainyl-CoA reductase: caiA
L-ornithine
thymidine
a 2’-deoxyribonucleoside
diphosphate
a 1-acyl-sn-glycerol-3-phosphate
glyoxylate
phosphoribosylformylglycinamidecyclo-ligase: purM
an (R)-3-hydroxymyristoyl-
[acp]
UDP-D-glucose
2-ketoaldonatereductase: ghrB
acetaldehyde
acetyl-CoAsynthetase (AMP-forming): acs
cobalamin 5’-phosphatesynthase:cobS
MQH2
BaeS-Phis
ribonucleoside-triphosphatereductase: nrdD
GMPsynthetase:guaA
2-oxoglutarate
adenylatekinase: adk
a rhamnosyllipopolysaccharide
degradationof pyrimidine
ribonucleosides
uridinekinase: udk
NADPH
L-gamma-glutamylcysteine
ZitB
UDP-2,3-bis(3-hydroxymyristoyl)
glucosamine
AICARtransformylase:purH
AceF-lipoate
erythronate-4-phosphatedehydrogenase:pdxB
xanthosine
predicted N-acetylmannosamine-6-phosphateepimerase: nanE
acetoin
acetaldehyde
nucleosidediphosphatekinase: ndk
superpathwayof glutamatebiosynthesis
oxaloacetate
10-formyl-tetrahydrofolate
D-galactonate
Cr3+
undecaprenyldiphosphatesynthase: ispU
TrxA
S-adenosyl-dependentmethyltransferase:mraW
a decanoyl-[acp]
3-keto-L-gulonate
XTP
RcsCB Two-ComponentSignal Transduction System
4-hydroxybutyrate
a protein-L-glutamate--O5-methyl-
ester
L-arabinose
5,10-methenyltetrahydrofolate
EIIBgl
adenine
D-glucono-delta-
lactone-6-phosphate
porphobilinogensynthase: hemB
uroporphyrin III C-methyltransferase:cysG
a transhexadecenoyl-[acp]
YjdL
DNAcontaining
a basewith lesion
RhtB
1,6-anhydro-N-acetylmuramate
S-acetyldihydrolipoamide
UDP-3-O-acyl-N-acetylglucosaminedeacetylase: lpxC
chloride
lactose
octaprenyldiphosphatesynthase: ispB
EIIFru
KDOtransferase:waaA
Mtr
isovaleryl-CoAdehydrogenase /predicted acyl-CoAdehydrogenase: aidB
cob(I)alamin
subunit of fatty acidoxidation complex: fadI
5’-methylthioadenosine/S-adenosylhomocysteine
nucleosidase: mtn
CARBOHYDRATES BIOSYNTHESIS
serinehydroxymethyltransferase: glyA
lysyl-tRNAsynthetase,constitutive:
lysS
Pit
D-allosekinase: alsK
glycine cleavagecomplex
AMINOACYL-TRNA CHARGING
xanthine
SucB
an N-hydroxy-
arylamine
adenosine 5’-phosphosulfate
phenylhydantoinase:hyuA
myristoyl-acylcarrier protein(ACP)-dependentacyltransferase:lpxM
an acylphosphate
CreB-Pasp
spermidineacetyltransferase:speG
YedY
D-beta-D-heptose-1,7-bisphosphate
a 1,4-alpha-D-glucan
leucyl,phenylalanyl-tRNA-proteintransferase: aat
pyrimidine deoxynucleosidetriphosphatepyrophosphohydrolase: nudI
NarX Nitrate/Nitrite-DependentTwo-Component Regulatory System
phosphoribosylformiminoAICAR-phosphate
manno(fructo)kinase: mak
QseB
D-beta-D-heptose-1-phosphate
ribose 1-phosphokinase
D-ribose-5-phosphate
an N10-formyl-tetrahydrofolate
aspartatekinase III: lysC
lipoamide dehydrogenase: lpd
L-methionine
d-biotin d-sulfoxide
2-O-(6- phospho-
alpha-mannosyl)-
D-glycerate
UDP-3-O-(3-hydroxymyristoyl)
glucosamine
2-phosphoglycerate
acid phosphatase/phosphotransferase:aphA
UDP-glucose 4-epimerase: galE
LldP
CheB-Pasp: cheB
ATP-dependentDNAhelicase: recQ
N-formyl-L-methionyl-tRNAfmet
N-methyltryptophanoxidase: solA
TrkG
dTMP
an N-D-ribosylpyrimidine
hybrid-clusterprotein: hcp
AMINES AND POLYAMINES BIOSYNTHESIS
L-2-hydroxyglutarateoxidase: lhgO
acetate kinase B: ackB
NrdD
S-formylglutathionehydrolase: frmB
beta-ketoesterreductase:dkgA
allolactose
UhpA-Pasp
UDP-N-acetyl-D-glucosamine
1-deoxy-D-xylulose 5-phosphate
phosphoglucose isomerase: pgi
L-histidyl-tRNAhis
CpxP
peptidedeformylase:def
purine nucleosidephosphorylase:deoD
serinehydroxymethyltransferase: glyA
5-ketogluconate
ribose-phosphatediphosphokinase: prs
nitritereductase:nirB nirD
RsxE
ferricdihydroxybenzoylserine
L-threonine
OmpN
AlkB repairsystem foralkylatedDNA andRNA: alkB
guanosine-5’-diphosphate
octaprenyldiphosphatesynthase: ispB
1,3-propanediol
pyruvate kinase I: pykF
thiamin
glyceraldehyde 3-phosphatedehydrogenase-A complex: gapA
4-(2-aminophenyl)-2,4-
dioxobutanoate
uracil
adenosine-3’(2’),5’-bisphosphatenucleotidase:cysQ
bifunctional aconitate hydratase2 and 2-methylisocitrate
dehydratase: acnB
S-adenosyl-L-homocysteine
phenylhydantoin
RsxG
D-amino aciddehydrogenase:dadA
ATPsynthase
N-acetyl-D-glucosamine
PPPi
RsxD
an alcohol
isochorismatesynthase 2: menF
phosphodiesterase,heme-regulated: dos
’activated’tRNA
xanthosinephosphorylase:xapA
1,4-dihydroxy-2-naphthoateoctaprenyltransferase:menA
a peptide
meso-diaminopimelate
beta-N-acetylglucosaminidase:nagZ
diacetylchitobiose-6-phosphatehydrolase: chbF
RsxA
L-rhamnoseisomerase:rhaA
Lit
a fatty acid
ppGpp biosynthesis
Zn2+
CDP reductase:nrdB nrdA
OmpL
L-aspartate
D-ribose-5-phosphate
CsgA
tRNApseudouridine13 synthase: truD
5-phosphoribosyl1-pyrophosphate
UhpT
2-oxoglutarate
YicE
2-deoxy-D-gluconate 3-dehydrogenase:kduD
pyridoxal
RsxC
YiiP
acetyl-CoA
indole
a proteinwith
incorrectdisulfidebonds
RsxB
D-arabinose5-phosphateisomerase:gutQ
B3496
acetyl-CoAsynthetase(AMP-forming): acs
tRNAdihydrouridinesynthase: dusC
Ap3Asynthetase:lysU
beta-D-glucose-6-phosphate
enterobactin
XDP
MhpT
lipopolysaccharidecore biosynthesisprotein: rfaY
ADP-heptose:LPSheptosyltransferaseI: rfaC
citrate
glutaminesynthetase
deadenylylatingenzyme: glnE
Kch
lipid IVA
L-seryl-tRNAsec
PII
CARBOHYDRATES DEGRADATION
gamma-butyrobetainyl-
CoA:carnitine CoAtransferase: caiB
homoserinedehydrogenase:metL
nicotinate adenine dinucleotide
L-allo-threonine
NUCLEOSIDES AND NUCLEOTIDES DEGRADATION AND RECYCLINGL-histidinol-phosphate
carbamoyl-phosphate
thiaminbiosynthesisproteinThiC: thiC
cysteinedesulfurase:iscS
a DNAcontaining 6-O-methylguanine
purine nucleosidephosphorylase:
deoD
thiaminkinase: thiK
maltoseacetyltransferase:maa
tartronatesemialdehydereductase2: glxR
histidinol
3-keto-L-gulonate 6-phosphate
putativepyruvatesynthase:ydbK
caiEprotein: caiE
L-aspartate-semialdehyde
RhtC
1,3-diphosphateglycerate
L-lysine
polynucleotidephosphorylase:pnp
L-cysteine
(1R,6R)-6-hydroxy-2-succinylcyclohexa-
2,4-diene-1-carboxylate
adenosinedeaminase: add
4-methyl-5-(beta-
hydroxyethyl)thiazole
phosphate
pyridoxamine
salvage pathways of guanine, xanthine, and their nucleosides
nucleotide-sugarhydrolase:nudK
UDP-GlcNAc-enolpyruvate
Tapgln
a crotonyl-[acp]
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
acetoinsynthesis:poxB
a nucleoside-5’-phosphate
trans-delta2-decenoyl-
CoA
L-lysine
protoheme IX
L-fuculose-1-phosphate
tRNAala
a reducedFeS-protein
gluconeogenesis I
uroporphyrinogen-III
phosphodiesterase, c-di-GMP-specific: yahA
acetyl-CoA
a DNAcontainingabasic site
ProY
glycerolkinase: glpK
an oxidizedthioredoxin
NlpA
UDP-D-galactose
UDP-D-glucose
NADPHquinonereductase:mdaB
alpha-galactosidase:melA
phosphopentomutase:deoB
xylulokinase:xylB
sirohydrochlorinferrochelatase: cysG
isocitratedehydrogenasephosphatase: aceK
BarA-UvrY Two-Component
SignalTransduction
System
lysidine-modifiedtRNAileX
S-ribosylhomocysteinelyase: luxS
2-keto-3-methyl-valerate
succinate
a tripeptide
a 1,2-diacylglycerol
dethiobiotinsynthetase: bioD
3-methyl-adenine DNAglycosylase I,constitutive:tag
sugar phosphatase: yigL
ferrochelatase:hemH
selenide,waterdikinase:selD
dephospho-CoA
tRNAgly
ribosedegradation
rRNAcontaining
N3-methylatedpseudouridine
flavin biosynthesis I (bacteria)
YihP
L-methionine
fructose-1,6-bisphosphate
L-leucine
a [citrate(pro-3S)-
lyase](acetylform)
fumaraseC: fumC
malate
UDP-N-acetylglucosamineenolpyruvoyl transferase: murA
L-cysteine
adenylo-succinate
Lipid A-core
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
CitT
N-acetyl-D-glucosamine
salicinarbutin
L-lyxosedegradation
xanthinedehydrogenase:xdhC xdhB xdhA
deoxyadenosine
L-xylulose 5-phosphate3-epimerase:ulaE
dTDP-D-glucose
NupX
PspC
pyruvate
L-idarate
glyceroldegradation V
alpha-D-glucose1-phosphate
4-nitrobenzylalcohol
tRNAarg
NADH
L-lactate
formaldehyde
succinate
L-serine
a proteinL-beta-
isoaspartate
pyridoxamine5’-phosphateoxidase: pdxH
D-galactarate
selenide
a beta-D-galactoside
isopropylmalateisomerase:leuD leuC
acetohydroxy acidisomeroreductase:ilvC
2-keto-isovalerate
3-mercaptopyruvate:cyanidesulfurtransferase: sseA
a thioredoxin
glucose-1-phosphateuridylyltransferase:
galU galF
hydroxypyruvate
glucosyl-heptosyl3-
KDO2-lipid A-bisphosphate
glutathionereductase: gor
a tRNAcontaining 2’-O-methylguanosine
tRNAGlu
NADsynthetase, NH3-dependent: nadE
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatesynthase: ispG
2C-methyl-D-erythritol 2,4-cyclodiphosphatesynthase: ispF
L-isoaspartate proteincarboxylmethyltransferasetype II: pcm
deoxyinosine
bifunctional beta-cystathionase,PLP-dependentand regulatorof maltoseregulon: malY
CreCB Two-ComponentSignal Transduction System
6-hydroxymethyl-7,8-dihydropterin
isopentenyldiphosphateisomerase: idi
a protein
tRNA containing 5-methylaminomethyl-
2-thiouridylate
octaprenyldiphosphatesynthase: ispB
BasR-Pasp
(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylatesynthase: menH
beta-D-glucose-6-phosphate
xylulokinase:xylB
D-myo-inositol (1)-monophosphate
D-glyceraldehyde-3-phosphate
pyrimidineribonucleotides denovo biosynthesis
homoserinedehydrogenase:thrA
23S rRNA m5U1939methyltransferase:rlmD
glycerol-3-phosphate-dehydrogenase,anaerobic:glpC glpB glpA
RstA-Pasp
uridine
phosphogluconatedehydratase: edd
methioninesulfoxidereductaseA: msrA
EIIMan
2,5-didehydro-
D-gluconate
6-phosphofructokinaseII: pfkB
spermidineacetyltransferase:speG
fructose-1,6-bisphosphatase: yggF
two-componentalkanesulfonatemonooxygenase
an octanoylateddomain
coproporphyrinogen III
5,6,7,8-tetrahydropteridine
inosine
GTP
exonucleaseIII: xthA
glycyl-tRNAgly
a 2,3,4-saturated
fattyacyl CoA
D-ribose-5-phosphate
acetol
NtrC-P
YddG
glycerol
coenzyme A
sugar phosphatase: yidA
ribonucleotidemonophosphatase:nagD
folylpoly-gamma-glutamatesynthetase:folC
PhoQP Two-Component
SignalTransduction
System
purine nucleosidephosphorylase:
deoD
TorS
2-oxoglutarate
superpathway ofhexitol degradation
NupC
S-adenosyl-L-methionine
tRNA chargingpathway
7,8-dihydrofolate
alpha-D-glucose 1-phosphate
glutaminesynthetase: glnA
adenosylcobinamide-GDP
L-serine
CpxA-Phis
MQ
YbcL
heptosyl-KDO2-
lipid IVA
methylmalonyl-CoAmutase: scpA
L-Ala-D-Glu-meso-
A2pm
DcuS-Phis349
a 1-acyl-sn-glycerol-3-phosphate
biotincarboxylase:accC
dCTP
L-aspartyl-4-phosphate
dihydroorotate
lipid Adisaccharide
Na+
coenzyme A
KdpD-Phis
EIIGlc
D-lactate
16S rRNA m2G966methyltransferase:rsmD
2-oxoglutarate
D-ribose
dihydroxy-acetone
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase: murD
fructose 1,6-bisphosphataseII: glpX
all-trans-octaprenyl
diphosphate
glycine
an aromaticsulfate
5,10-methylene-
THF
trimethylamine
nitrite
deoxyinosinetriphosphatepyrophosphatase:rdgB
pyrroline-5-carboxylatereductase:proC
alpha-D-glucose1-phosphate
octaprenyldiphosphatesynthase: ispB
2-hydroxyglutarate
a cis-3-enoyl-CoA
pyruvateformate-
lyase
2’-(5’-phosphoribosyl)-3’-dephospho-
CoA biosynthesisI (citrate lyase)
S-adenosyl-L-methionine
YfaZ
RNA(n)
D-alanine
an mRNA
3-deoxy-D-manno-octulosonate8-phosphatesynthase: kdsA
beta-ketoadipyl-CoA thiolase: paaJ
D-mannose
cis-dihydrodiolderivative of
phenylacetyl-CoA
(2S,3S)-2-methylcitrate
pyruvate
an (R)-3-hydroxydodecanoyl-
[acp]
S-allantoin
multidrug
lipoatesynthase: lipA
2-ketoaldonatereductase: ghrB
superpathway of fatty acid biosynthesis
rRNA containing7-methylguanosine
ADP-D-glycero-
D-manno-heptose
selenocysteinesynthase: selA
tRNA-dihydrouridinesynthase A: dusA
dTDP-alpha-L-rhamnose
thiamin
long chainpolyphosphate
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-
meso-2,6-diaminopimelyl-D-alanyl-D-alanine
YaaU
glycogen degradation I
prolinebiosynthesis I
a 2,3,4-saturatedfatty acyl-[acp]
L-ornithine L-lysine L-arginine
glutaminase:ybaS
an octanoyl-[acp]
ribose-5-phosphateisomeraseA: rpiA
glucokinase:glk
Tsrglu-Me
1,4-dihydroxy-2-naphthoate
pyruvate
alpha-D-ribose-1-phosphate
H+
biotinsynthase: bioB
glycogenphosphorylase:glgP
2-keto-3-deoxygluconokinase:kdgK
acetyl-CoA
D-glucuronateisomerase:uxaC
L-3,4-dihydroxybutan-2-one-4-phosphate
SecM
an N-substitutedamino acid
a ribonucleosidetriphosphate
glutamatesynthase:gltD gltB
guanosine
triphosphoribosyl-dephospho-CoAsynthase: citG
biotinbiosynthesis I
MurJ
coenzyme A
YehA
N-alpha-acetyl lysinemethyl ester
KgtP
3-(2,3-dihydroxyphenyl)propionatedioxygenase: mhpB
an aceticester
QseB-Phosphorylatedtranscriptional
activator
thiamine-phosphate
fructose-1,6-bisphosphate
ribosomal-protein-L12-serineacetyltransferase:rimL
4-amino-4-deoxychorismate
cytochromebd-I terminal
oxidase
purine nucleosidephosphoramidase:hinT
PutP
cytochromebo terminal
oxidase
mureinpeptideamidaseA: mpaA
superpathwayof serine
and glycinebiosynthesis I
N-acetyl-D-glucosaminekinase: nagK
D-threo-isocitrate
tetrahydrofolate
an rRNA
erythronate-4-phosphate
L-rhamnulose
ribosomesmall subunit-dependentGTPaseA: rsgA
acyl-ACPsynthetase:aas
methylisocitrate
dUTP
GDPdiphosphokinase: spoT
GLYCOLYSIS
N-acetyl-D-mannosamine
ZipA
L-prolyl-tRNApro
fused PutAtranscriptionalrepressor / prolinedehydrogenase/ 1-pyrroline-5-carboxylatedehydrogenase:putA
guanine
RcsB
pyruvateformate-lyaseactivatingenzyme: pflA
phosphoglyceromutase1: gpmA
xanthosine
an RNA
fructoselysine
phosphoenolpyruvatesynthase: pps
a lipopolysaccharide
fructose 1,6-bisphosphatase:ybhA
degradation of purine ribonucleosides
lipoate
NADP-dependentdehydrogenase:yqhD
FMN
L-glutamate
an octanoylateddomain
xanthosine-5-phosphate
nicotinatephosphoribosyltransferase: pncB
rRNAcontaining 2’-
O-methyluridine
tRNApseudouridine55 synthase: truB
propionyl-CoAcarboxylase
methylmalonylpathway
CMP
cobalaminsynthase: cobS
xanthine
D-arabinose5-phosphateisomerase:kdsD
di-trans,poly-cis-
heptaprenyldiphosphate
a peptide
D-Ala-D-Aladipeptidase:ddpX
undecaprenyldiphosphatesynthase: ispU
pyruvate formate-lyase: tdcE
Cd2+
UDP-D-galacto-1,4-
furanose
FMN
4-(phosphonooxy)-threonine
a deoxyribonucleicacid
aconitatehydratase 1: acnA
acetaldehyde
lipoylated domain
Ivy
putrescine
dTTP
pyrimidine (deoxy)nucleoside triphosphatepyrophosphohydrolase:nudG
nitrate
L-rhamnose
OmpG
3-hydroxy aciddehydrogenase:ydfG
cyclicdi-3’,5’-
guanylate
lipoamidedehydrogenase: lpd
fumarate
L-phenylalanine
UDP-D-galactose
a proteinwith correct
disulfidebonds
D-glucaratedehydratase: gudD
2,3-dihydroxybenzoate
L-cysteineO-acetyl-L-serine
fructose-1,6-bisphosphate
fatty acid oxidationcomplex, alphacomponent: fadB
salicylalcohol
dodecenoyl-CoAD-isomerase: fadJ
a tRNA
glucosyl-heptosyl2-
KDO2-lipid A
phosphoenolpyruvate
D,D-heptose 1,7-bisphosphatephosphatase:gmhB
succinyl-CoA
acetate
D-sorbitol-6-phosphate
ArcB-Pasp
CTP
N-acetyl-D-glucosamine-6-phosphate
YdhC
peptideuptake ABCtransporter
23S rRNA m6A1618methyltransferase:rlmF
pyridoxaminekinase: pdxK
endonucleaseVIII: nei
peptidoglycantetrapeptide,
glycan chain 1
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylatesynthase: menD
AROMATIC COMPOUNDSBIOSYNTHESIS
flavorubredoxinreductase: norW
carbamoyl-phosphate
galactoside O-acetyltransferase:lacA
AceF
a mRNA
6-phosphogluconatephosphatase: yieH
spermidine
a ribonucleosidetriphosphate
YcdU
a 2’-deoxyribonucleoside
triphosphate
NAD(P)H:quinoneoxidoreductase:wrbA
L-lactaldehyde
chromatereductase:yieF
beta-D-glucose
superpathway of lysine, threonineand methionine biosynthesis I
D-sedoheptulose-7-phosphate
lysinedegradation I
P-DPD
threonyl-tRNA
synthetase:thrS
D-fructose-6-phosphate
alanyl-tRNAsynthetase:
alaS
KASI: fabB
serinehydroxymethyltransferase: glyA
isochorismatase:entB
glycine betaine L-proline
glutaminyl-tRNA
synthetase:glnS
beta-D-glucose-6-phosphate
KDO2-(lauroyl)-lipid IVA
PgaA
a semiquinone
predictedgalactose 1-dehydrogenase:yhhX
YidI
N,N’-dimethyl-p-phenylenediamine
FDH-O
acylphosphatase:yccX
3-hydroxyadipyl-CoA
dTDP-4-dehydro-6-
deoxy-D-glucose
isocitrate lyase: aceA
succinate dehydrogenase:sdhA sdhB sdhC sdhD
ppGpp
conversionof succinate
to propionate
fumarase C: fumC
6,7-dihydropteridine
tRNA:Cm32/Um32methyltransferase:trmJ
a 1,2-diacylglycerol-3-phosphate
Mn2+Fe2+
palmitate
N2-succinylglutamate
inosine
6-phosphofructokinase II: pfkB
cofactor
oxidizedthioredoxin
a tRNA
23Sribosomal
RNAmethylatedat position
G2251
D-glucose
tRNApseudouridinesynthase I: truA
guanine
an alcohol
guanosine-5’-diphosphate
melibiosedegradation
3-sulfinoalanine
L-serinedegradation
L-aspartate
L,D-transpeptidaseYnhG: ynhG
an rRNA
IDP
a carboxylicester
ZupT
an oxidizedthioredoxin
a tRNAcontaining 2’-O-methylcytosine
or 2’-O-methyluridine
L-ascorbatedegradation,
anaerobic
enterobactin
molybdateABC
transporter
guanosine-5’-phosphate
Ogt: ogt
2,5-diketo-D-gluconatereductaseA: dkgA
NarL-Pasp
low-specificityL-threoninealdolase:ltaE
tetrahydrofolate biosynthesis
pyridoxal
a protein
2-phosphoglycerate
D-mannosedegradation
gamma-glutamyl-gamma-aminobutyraldehydedehydrogenase: puuC
YiaB
DNA containing5-methylcytosine
AMP
methioninesulfoxidereductaseA: msrA
homocysteinemethyltransferase:mmuM
sugarphosphatase:ybiV
ZraS
L-leucyl-protein
glutathione
O-antigen biosynthesis
L-serine
HemX
galactose-1-phosphateuridylyltransferase:galT
phospho-N-acetylmuramoyl-pentapeptide transferase: mraY
a tRNA
tRNA (m7G46)methyltransferase: trmI
uridine-5’-diphosphate
lysyl-tRNAsynthetase:
lysU
L-ribulose 5-phosphate4-epimerase:ulaF
Fiu
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
phosphoglyceratemutase, cofactorindependent: gpmM
cis-2-methylaconitate
CadB
malatedehydrogenase,NAD-requiring: maeA
cyclic-AMP
tRNAdihydrouridinesynthase: dusB
tRNAcys
NADsynthetase, NH3-dependent: nadE
an activeribonucleosidetriphosphatereductase
Targlu-Me
a protein-L-methionine-(S)-S-oxide
aspartatesemialdehydedehydrogenase: asd
YhaU
2-octaprenyl-6-methoxyphenol
methylmalonyl-CoA mutase: scpA
nicotinamidase: pncA
L-glutamate
Trggln
rhamnulose-1-phosphatealdolase: rhaD
YdhX
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
KdpE
glycerol-3-phosphateacyltransferase: plsB
deoxyuridinetriphosphatase: dut
a 1,2-diacylglycerol-3-phosphate
an alcohol
L-quinate
ribokinase:rbsK
dGTPpyrophosphohydrolase: mutT
CurliSecretion
andAssemblyComplex
tRNAtyr
nucleosidediphosphatekinase: ndk
D-allulose-6-phosphate
L,D-transpeptidaseYcfS: ycfS
allose-6-phosphateisomerase/ ribose-5-phosphateisomeraseB: rpiB
a peptide
AtoC-Pasp
L-isoleucyl-tRNAile
D-glyceraldehyde-3-phosphate
heptosyl-KDO2-lipid A
ribonucleoside-diphosphatereductase 2:nrdF nrdE
BasSR Two-Component
SignalTransduction
System
dTMP kinase: tmk
tartronatesemialdehyde
shikimate
UDP-N-acetyl-D-mannosaminuronicacid transferase: rffM
D-alanine
fatty acyl-CoAsynthetase: fadD
pantothenate
a DNA withunresolved
recombitionalor holidayjunctions,
created by RecA
CO2
phosphoenolpyruvate
dephospho-CoA
formate-tetrahydrofolateligase
BasS-Phis
BaeSR Two-Component
SignalTransduction
System
succinate
2,3-diketo-L-gulonatereductase:yiaK
EvgSA Two-Component
SignalTransduction
System
YhaO
putative ring-cleavage enzymeof phenylacetatedegradation: maoC
phosphatidylglycerophosphatesynthase: pgsA
PflB
transketolaseII: tktB
dTDP-4-oxo-6-deoxy-D-glucosetransaminase: rffA
MQ
2-dehydropantoate
(S)-1-pyrroline-5-carboxylate
oxalyl-CoA
a cis-delta3-decenoyl-
[acp]
D-glucarate
a dipeptide
3-deoxy-D-manno-
octulosonate8-P
L-arabinoseisomerase: araA
cis-aconitate
K+
MelB
D-alanine
GTPase thatinteracts withmethylmalonyl-CoA mutase: argK
formamidopyrimidineDNA glycosylase: mutM
glyoxalase III
acetyl-CoAacetyltransferase:atoB
LolB
pyruvate dehydrogenasemultienzyme complex: lpd aceF aceE
6-phosphogluconolactonase: pgl
RssB-P
protein N6-(lipoyl)lysine
coenzyme A
aminoacetaldehyde
cis-vaccenatebiosynthesis
nitrate
biotinsulfoxidereductase:bisC
BglG
KDOtransferase:waaA
2-O-(6-phospho-alpha-
mannosyl)-D-glycerate
alpha-ketoglutaratereductase: serA
beta-D-galactose
fused PutAtranscriptionalrepressor / prolinedehydrogenase/ 1-pyrroline-5-carboxylatedehydrogenase:putA
uridinephosphorylase:udp
L-tyrosine
5’-phosphoribosyl-4-(N-succinocarboxamide)
-5-aminoimidazole
PuuP
lipopolysaccharideglucosyltransferaseI: rfaG
ProP
CTP
RcsF-P
UDP-D-glucose:(glucosyl)LPS alpha-1,3-glucosyltransferase: rfaI
gluconokinaseII: idnK
a reducedelectronacceptor
alpha-D-glucose-1-phosphatase: yihX
GTP
Tapglu
a limitdextrin
DNApolymeraseV: umuDumuC
formyl-L-methionylpeptide
3-dehydro-2-deoxy-D-gluconate
DcuS
phosphoglyceratekinase: pgk
an aromaticamino acid
lactose
bicarbonate
octanoate
malatedehydrogenase:mdh
KefAfructose-1,6-bisphosphataseI: fbp
guanosine 3’-diphosphate
5’-triphosphate
multifunctional2-keto-3-deoxygluconate 6-phosphate aldolaseand 2-keto-4-hydroxyglutaratealdolase andoxaloacetatedecarboxylase: eda
CDP
an apo-[acp]
UDP-N-acetylmuramoyl-L-alanine
Targlu
RfbX
flavodoxinNADP+reductase: fpr
pyruvate
uridine-5’-diphosphate
isocitratedehydrogenase: icd
purine nucleosidephosphorylase:
deoD
dTTP
anthranilatesynthase: trpD trpE
YegH
2-dehydro-3-deoxyphosphoheptonatealdolase: aroF
histidinal
NlpE
tRNAcontaining
ribothymidineat position 54
pyridoxamine-phosphatetransaminase
L-homocysteine
dihydroxyacetonephosphate
methyl-1,4-benzoquinol
RcsC
a ThiI sulfur-carrierprotein
tetrahydrodipicolinatesuccinylase: dapD
cobalamin-dependenthomocysteinetransmethylase:metH
cysteinebiosynthesis I
cytidinedeaminase:cdd
a nucleoside-5’-phosphate
an oxidizedglutaredoxin
anthranilate
gamma-glutamyl-gamma-aminobutyraldehyde
D-threo-isocitrate
CMP-3-deoxy-D-manno-
octulosonate
NADH-azoreductase,FMN-dependent:azoR
aspartateaminotransferase,PLP-dependent: aspC
ADP-heptose:LPSheptosyltransferaseII: rfaF
ornithinecarbamoyltransferase: argI
a 3-oxo-octanoyl-[acp]
dihydroxy-acetone
rRNA containingN6,N6-
dimethyladenine
6-phospho-beta-glucosidase;cryptic: ascB
trehalosedegradation
I (lowosmolarity)
KDOtransferase:waaA
R-4’-phosphopantothenoyl-
L-cysteine
GfcA
acetaldehydedehydrogenase:adhE
AtoC
heptosyl2-KDO2-lipid A
a phenol
fusedglutathionylspermidineamidase /glutathionylspermidinesynthetase: gsp
beta-hydroxyacyl-ACPdehydratase: fabZ
glycine
methyleneTHFenzyme: folD
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
OmpC
tRNA-guaninetransglycosylase: tgt
UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6-D-galactosyltransferase:rfaB
UDP-3-O-[3-hydroxymyristoyl]glucosamineN-acetyltransferase: lpxD
2-phosphoglycolate
an N10-formyl-tetrahydrofolate
dihydrofolatesynthetase: folC
methionineadenosyltransferase:
metK
peptidoglycantetrapeptide,
glycan chain 2
thioredoxinpathway
NarX
23S rRNApseudouridine2605synthase: rluB
deoxycytidine
NarL
multidrug
L-methionine
sugarphosphatase:yfbT
DNApolymeraseIII, alphasubunit: dnaE
DctA
acidphosphatase:appA
N-acetylmannosaminekinase: nanK
DL-lactaldehyde
phosphatidylglycerophosphataseB: pgpB
a phospholipidolefinic
fatty acid
pyruvate
a single-stranded
RNA
multidrug
S-adenosyl-L-methionine
L-lysine
N-acetyl-L-ornithine
cysteinesynthase A: cysK
D-arabinosedegradation I
deoxyguanosine
protein N6-(dihydrolipoyl)
lysine
aryl carrierprotein: entF
L-lysine
4-nitrobenzaldehydereductase: dkgB
S-carboxymethyl-D-cysteine
NADP-dependentdehydrogenase:yqhD
a protein L-methionine
UDP-N-acetyl-D-
glucosamine
L-arginine
D-glutamate
23S rRNApseudouridinesynthase: rluC
Targlu
2-C-methyl-D-
erythritol-4-phosphate
a protein-L-glutamine
ZraR
hydrogencyanide
L-homocysteine
D-ribose-5-phosphate
glycerol
pyruvate
pyrazinamidase:pncA
2-hydroxyglutaratesynthase
Kup
a polypeptide
glyoxalaseII: gloB
trehalose-6-phosphatehydrolase:treC
YgjI
a tRNAcontaining 7-
aminomethyl-7-deazaguanineat position 34
a 2,3-dehydroacyl-CoA
6,7-dimethyl-8-(1-D-ribityl)lumazine
DNA withremovedadenine
mismatchleaving
an AP site
D-sorbitol-6-phosphate
gluconolactonase
hypoxanthinephosphoribosyltransferase: hpt
thiolperoxidase:bcp
bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinonemethylase and S-adenosylmethionine:2-DMKmethyltransferase: ubiE
glyceroldehydrogenase:gldA
o-succinylbenzoatesynthase: menC
excised base
tRNAhis
H2O
chorismate mutase: tyrA
methylglyoxalreductase: yeaE
5-methylaminomethyl-2-thiouridinemethyltransferase:mnmC
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-
meso-2,6-diaminopimelate
L-tartratedehydratase:ttdB ttdA
a CDP-diacylglycerol
multidrug
Autoinducer2-degradingprotein: lsrG
Trgglu
dGMP
adenosylcobinamide
hydroxyethylthiazolekinase: thiM
D-ribose-5-phosphate
an organicmolecule
S-ureidoglycolate
thiamin(thiazolemoiety)biosynthesisprotein: thiF
S-adenosyl-L-methionine
dihydrolipoyltranssuccinylaseN6-(dihydrolipoyl)lysine
YneN
fatty acid oxidationcomplex, alphacomponent: fadB
FATTY ACID AND LIPIDS DEGRADATION
a ThiS-ThiF acyl-disulfide
oxaloacetate
PhoP
thioesteraseIII: ybaW
2,3-diketo-L-gulonate
HsrA
L-ribulose-5-phosphate
dTDP-D-glucose
a protein-S-methyl-L-cysteine
glycine decarboxylase: gcvP
an L-1-phosphatidyl-glycerol
OmpA
glucokinase:glk
L-glutamate-5-phosphate
a damagedDNA
pyrimidine
EntF
enterobacterial commonantigen biosynthesis
Blr
citrate
glutathione S-transferase:yfcF
a (3S)-3-hydroxyacyl-CoA
selenophosphate
D-cysteinedesulfhydrase,PLP-dependent: dcyD
UhpB
uridine
D-ribose
D-xylulose-5-phosphate
dihydrouracil
beta-hydroxyacyl-ACPdehydratase: fabZ
lipoate acetyltransferase N6-(S-acetyldihydrolipoyl)lysine
GlpT
KASI: fabB
3-methylcrotonyl-CoA
TorT-TMAO
UDP-L-Ara4FN
GlcA
a phospholipidcyclopropane
fatty acid
acetate CoA-transferase
L-glyceraldehyde3-phosphatereductase: yghZ
Co2+Fe2+
a trans-polyisoprenyln-PP
AroP
Tapglu-Me
XTP
orotidine-5’-phosphate-decarboxylase: pyrF
uracil
restrictionof DNA at 5-methylcytosineresidues: mcrA
transketolaseII: tktB
oxaloacetate
DNA adeninemethyltransferase:yhdJ
chemotaxis proteinmethyltransferase:cheR
a 1,4-alpha-D-glucan
nucleosidediphosphate kinase: ndk
GalP
[+ 3 isozymes]
xyloglucanoligosaccharide
thiamin biosynthesis I
an aldehyde
ureidoglycolatedehydrogenase:allD
maltodextringlucosidase:malZ
hydroxymethylpyrimidinephosphate
D-ribulose-5-phosphate
base withlesion
biotin
an aliphaticN-acetyl-diamine
citrate
cytidinedeaminase: cdd
uracil
guanosine-5’-diphosphate
amylomaltase:malQ
superpathway of pyridoxal 5’-phosphate biosynthesis and salvage
uridine
a ribonucleosidediphosphate
L-alanine
UDP-D-glucuronate
5’,5’-diadenosinetriphosphate
a glucoronide
ATP
phosphoenolpyruvate
2-hydroxyglutarate
ADP-sugarpyrophosphatase:nudF
23S rRNA m2G2445methyltransferase:rlmL
dihydropteroatesynthase: folP
probable 6-phospho-beta-glucosidase:glvG
UDP-3-O-(3-hydroxymyristoyl)-
N-acetylglucosamine
acetaldehydedehydrogenase:adhE
NADPHnitroreductase:nfsA
CpxA
fructose-1-phosphate
glycerophosphoryldiesterphosphodiesterase,periplasmic: glpQ
UDP-D-glucuronate
glycerol degradation I
guanosine-5’-phosphate
ubiquinone-8biosynthesis(prokaryotic)
long chainpolyphosphate
an oxidizedthioredoxin
MdtABC-TolC
multidrugefflux
transportsystem
pyruvate
L-Ala-gamma-D-Glu-Dap
L-rhamnosemutarotase:rhaM
ATP
fumarase C: fumC
inosine-5’-phosphate
fumaratereductase: frdDfrdC frdB frdA
tRNAphe
KdpD
YnfA
EvgS
UDP-L-Ara4Nformyltransferase:arnA
alpha-D-mannose1-phosphate
arbutin-6-phosphate
Ca2+ Na+ K+
a tRNA
phosphoglucomutase: pgm
c-di-GMPphosphodiesterase:yhjH
acetate
taurine
L-xylulosekinase: lyxK
2-oxobutanoate
a protein-L-methionine-(R)-S-oxide
GDP-mannosemannosylhydrolase:gmm
beta-D-galactose
correspondingcarbamoylamino acid
carnitine degradation I
a cis,trans-polyisoprenyln-PP
5-aminoimidazoleribonucleotide
uridine-5’-diphosphate
predicted alpha-ribazole-5’-Pphosphatase: cobC
D-erythrose-4-phosphate
phosphoproteinphosphatase: pphB
glutamate-1-semialdehyde
ADP
dGTP
ribulosephosphate3-epimerase:rpe
homoserine
di-trans,poly-cis-nonaprenyl
diphosphate
AlkB repairsystem foralkylatedDNA andRNA: alkB
methionylpeptide
inosine-5’-phosphate
uroporphyrinogen-III
MdtJIspermidine
SMRtransporter
EIIChb
D-xylulose
2-aceto-2-hydroxy-butyrate
fructoselysine 3-epimerase: frlC
L,D-transpeptidaseErfK: erfK
UhpBA Two-Component
SignalTransduction
System
TrkH
precorrin-1
D-ribose
methylglyoxalreductase(NADPH-dependent)
L-cysteine
a fatty acid
predicted acetoindehydrogenase:yohF
sn-glycerol-3-phosphate
O-succinylhomoserinelyase: metB
pre-cofactor
IdnT
bifunctional NadRtranscriptionalrepressor and NMNadenylyltransferase:nadR
CO2
N-acetylmuramicacid PTSpermease
phosphoribosylamine-glycine ligase: purD
thiamin(thiazolemoiety)biosynthesisprotein: thiF
MdtO
thiaminemonophosphatekinase: thiL
thiaminbiosynthesis
ThiGHcomplex:thiH thiG
4,5-dihydroxy-2,3-pentanedione
L-glutamate
adenylosuccinatesynthetase: purA
phospholipid biosynthesis I
palmitoleatebiosynthesis
beta-D-glucose-6-phosphate
N5-carboxyaminoimidazoleribonucleotidesynthetase: purK
phosphoribosylaminoimidazole-succinocarboxamide synthase: purC
nucleosidediphosphatekinase: ndk
multifunctional2-keto-3-deoxygluconate 6-phosphate aldolaseand 2-keto-4-hydroxyglutaratealdolase andoxaloacetatedecarboxylase: eda
L-Ala-D-Glu-meso-A2pm
ribonucleoside-diphosphatereductase 2:nrdF nrdE
a 6-acetyl-beta-D-
galactoside
crRNA
2-keto-isovalerate
phosphoenolpyruvatecarboxylase: ppc
dTMP
ethyl-2-methylacetoacetate
leucine ABCtransporter
pyruvatekinase I: pykF
HlyE
tRNAile
OuterMembrane
FerrichromeTransportSystem
YhhS
2-trans,5-cis-tetradecadienoyl-
CoA
fumarase B: fumB
NarQ Nitrate/Nitrite-DependentTwo-Component Regulatory System
aspartateaminotransferase,PLP-dependent: aspC
imidazoleacetol-
phosphate
an (R)-3-hydroxyhexanoyl-
[acp]
an N-acetylspermidine
HYD1
formate
a drug
pyridoxalphosphatase:cof
N-acetylglutamatesynthase: argA
RcsF
Zn2+
a holo-[acp]
UDP-4-amino-4-deoxy-L-arabinose
ATP
23S rRNAcontaining
C5-methylatedcytosine
ornithinedecarboxylase,biosynthetic:speC
octaprenyldiphosphatesynthase: ispB
partially N-deacetylated
poly-beta-1,6-N-acetyl-D-glucosamine
NarP
a holo-[acp]
5’-deoxyadenosine
tRNA containing 5-methylaminomethyl-
2-selenouridine
aldehydedehydrogenase A,NAD-linked: aldA
L-tryptophanyl-tRNAtrp
16S rRNAcontaining
N3-methylated
uridine
a 3-oxo-cis-vaccenoyl-
[acp]
YagU
N-acetyl-D-glucosamine-6-phosphate
5-amino-6-(5’-phosphoribosylamino)
uracil
fatty acid oxidationcomplex, alphacomponent: fadB
heme dsynthase:katE
short chain acyl-CoAsynthetase: fadK
polynucleotidephosphorylase:pnp
pyruvate
L-glutamategamma-
semialdehyde
an acyl-[acp]
DNA Cleavedat Recognition
Site
L-tartrate
N-acetyl-D-glucosamine-6-phosphate
dihydroxyacetonephosphate
dTDP-4-dehydro-6-deoxy-
L-mannose
sulfate
methanol
tRNAtyr
TorSR Two-Component Signal Transduction System
NarK
arsenatereductase:arsC
DNA (without 6-O-methylguanine)
oxidizedribonucleoside-
triphosphatereductase
tRNAval
YfhM
L-cysteinedesulfhydrase
succinate
protein-tyrosine-phosphatase:pphB
L-valine L-leucineL-isoleucine
bifunctional 3-demethylubiquinone-83-O-methyltransferaseand 2-octaprenyl-6-hydroxyphenolmethylase: ubiG nicotinate
mononucleotide
L-homocysteine
AraJ
tetrahydrofolate
EcoCyc: Escherichia coli K-12 MG1655 Cellular OverviewAuthors: Peter D. Karp
Ingrid KeselerAlexander ShearerAnamika Kothari
Suzanne PaleyMarkus KrummenackerTomer AltmanIan Paulsen
Amanda MackieAaron JohnsonJulio Collado-VidesCesar Bonavides-Martinez
Socorro Gama-CastroMartin PeraltaAlberto Santos-ZavaletaJohn L Ingraham
Robert GunsalusAn online version of this diagram is available through EcoCyc.org and may be used for analysis of omics datasets. Lines in thediagram correspond to reactions; nodes correspond to metabolites. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways in the right, signaling pathways in the bottom-left.Pathways are colored according to their cellular function, such as biosynthesis of cofactors. Reactions not assigned to any pathway are in the far right of the cytoplasm. In the inner and outer membranes are transporters (with arrows) and othermembrane proteins. In the periplasm are periplasmic enzymes and other periplasmic proteins. Connections between pathways are omitted for legibility.
Copyright ' 2009 SRI International. All Rights Reserved. This diagram was automatically generated by SRI International Pathway Tools version 13.0, authors S. Paley and P. Karp.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
The most studied metabolic network, Escherichia coli:
a nucleoside3’-phosphate
lytic mureintransglycosylaseE: emtA
glucono-delta-lactone
a CDP-2,3,4-saturated-
diacylglycerol
a phosphatidylcholine
a holo-[acp]
peptidoglycanD-alanyl-
DAP crosslink
KDO2-lipid IVA
disulfideoxidoreductase:dsbG
lipid IVA
a 2,3,4-saturated 2-lysophosphatidate
a peptide
GTP
3-phytase:agp
membrane-boundlytic mureintransglycosylaseB: mltB
a shortglucan
oxaloacetate
tyrosine kinaseinvolved incolanic acidbiosynthesis:wzc
N-acetylmuramoyl-L-alanineamidase 2: amiB
disulfideoxidoreductase:dsbA
KDO2-lipid A
a fatty acid
UDP-2,3-bis(3-hydroxymyristoyl)
glucosamine
membrane-boundlytic mureintransglycosylaseF: mltF
peptidoglycantetrapeptide,
glycan chain 1
DsbG
L-Ala-gamma-D-Glu-DAP-
D-Ala
alpha-amylase:malS
an octanoyl-[acp]
phenylacetaldehyde
UDP-2,3-bis(3-hydroxymyristoyl)
glucosamine
an MDO-O-glucose
di-trans,poly-cis-
undecaprenyldiphosphate
peptidyl-prolylcis-transisomerase(PPIase): surA
a peptidewith a leadersequence
an MDO-O-glucose
hydroperoxidaseI: katG
a peptidoglycan
peptidoglycanpolymer withGlcNAc end
DsbD
alpha-D-glucose-1-
phosphatase:yihX
cytochromeC552: nrfA
L-lactate
N-acetyl-anhydromuramyl-L-alanine-amidase: ampD
Cu2+
aminoacetoneoxidase: tynA
multicopperoxidase withrole in copperhomeostasis:cueO
L-lactate
a carboxylate
hydroperoxidaseI: katG
a peptidoglycan
a phospholipidolefinic
fatty acid
peptidyl-prolylcis-transisomerase:ppiD
peptidylprolylisomerase: fkpB
a palmitoleoyl-[acp]
argininedecarboxylase,degradative: adiA
D-lactate
a single-stranded
RNA
1,4-dihydroxy-2-naphthoate
L-Ala-gamma-D-Glu-DAP-
D-Ala
lytic mureintransglycosylaseE: emtA
beta-D-glucose
an acyl-[acp]
beta-D-glucose-6-phosphate
a glucosylatedglucose
acceptor
NADPH
peptidylprolylisomerase: fkpB
nitrite
holo-EntB
serineproteaseDo: degP
soluble lytic mureintransglycosylase: slt
uridine-5’-phosphate
a shortglucan
phenylethylamineoxidase: tynA
nitrite
a leadersequence
phytate
Cu+
D-alanine
peptidoglycantetrapeptide,
glycan chain 2
superoxide
2,3-dihydroxybenzoate
peptidylproline(omega = 0)
p-aminobenzoylglutamate
a protein-L-tyrosinephosphate
a holo-[acp]
penicillin-bindingprotein1A: mrcA
peptidoglycanpolymer with 1,6-
anhydromuropeptide end
a 1-lyso-2-acyl-sn-glycero-3-
phosphocholine
sugarphosphatase:
ybiV
penicillin-bindingprotein7: pbpG
an L-1-phosphatidyl-
glycerol
an MDO-6-(glycerophospho)
-D-glucose
peptidoglycanpolymer
a nucleoside2’,3’-cyclicphosphate
membrane-boundlytic mureintransglycosylaseC: mltC
formatedehydrogenase-
O: fdoI fdoH fdoG
aldose sugardehydrogenase: yliI
periplasmictrehalase:treA
anhydro-N-acetylmuramoyl-L-alanineamidase: amiD
DsbGoxidized
ribonucleotidemonophosphatase:nagD
(5-L-glutamyl)-L-peptide
sugarphosphatase:
yidA
L-glutamate
gamma-glutamyltranspeptidase: ggt
a dodecanoyl-[acp]
all-trans-farnesyl
diphosphate
a myristoyl-[acp]
phosphoglucoseisomerase: pgi
diphosphoundecaprenyl-[GlcNAc-MurNAc-pentapeptide]n+1
diacylglycerolpyrophosphatephosphatase:pgpB
D-myo-inositol(1,2,4,5,6)-
pentakisphosphate
beta-D-glucose
UQ or MQ UQH2or MQH2
pyruvate di-trans,poly-cis-
undecaprenylphosphate
lipid IVA
a 1-acyl-sn-glycerol-3-phosphate
thiocyanate
L-arginine
L-arginine
an acyl-[acp]
DsbDoxidized
multicopperoxidase withrole in copperhomeostasis:cueO
peptidylproline(omega = 180)
peptidoglycanpolymer withGlcNAc end
DsbD
an MDO-6-(glycerophospho)
-D-glucose
H2O
D-alanine
a 5-L-glutamyl-L-amino acid
peptidyl-prolylcis-transisomeraseC (rotamaseC): ppiC
a standardalpha
amino acid
a substitutedbeta-
amino acid
3’-nucleotidase:cpdB
Cu2+
a long-linear glucan
phenylethylamine
a 2,3,4-saturated L-
phosphatidate
[+ 4 isozymes]
membrane-boundlytic mureintransglycosylaseA: mltA
methylglyoxal
a fatty acid
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenyl-N-acetylglucosamine
a myristoyl-[acp]
L-1-glycero-3-phosphocholine
KDO2-lipid IVA
GlcNAc-1,6-anhMurNAc-L-Ala-gamma-
D-Glu-DAP-D-Ala
N-acetyl-anhydromuramyl-L-alanine-amidase: ampD
thioesteraseII: tesB
an L-1-phosphatidyl-ethanolamine
N-acetylmuramate
pyruvate
diguanylatecyclase: yeaP
UQH2
a tRNAprecursor
a holo-[acp]
trimethylamine
a single-stranded
RNA
EntB
lipid Adisaccharide
a quinol
a holo-[acp]
FKBP-typepeptidylprolylcis-transisomerase:slyD
a ribonucleoside
N-acetylmuramoyl-L-alanyl-D-glutamyl-L-
lysyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine
undecaprenylphosphate-
alpha-L-Ara4N
triggerfactor; amolecularchaperoneinvolvedin celldivision: tig
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenol
a holo-[acp]
Fe3+
a 2,3,4-saturated L-
phosphatidate
peptidoglycanDAP-DAPcrosslink
a holo-[acp]
UDP-sugarhydrolase:ushA
N-acetylmuramoyl-L-alanineamidase 1: amiA
a polypeptide
UQ
a quinone
serineendoprotease,periplasmic: degQ
tetrahydrothiophene
argininedecarboxylase,biosynthetic:speA
a phospholipidcyclopropane
fatty acid
beta-D-glucose-6-phosphate
membrane-boundlytic mureintransglycosylaseC: mltC
di-trans,poly-cis-
undecaprenylphosphate
a CDP-diacylglycerol
an MDO-6-(glycerophospho)
-D-glucose
a dodecanoyl-[acp]
ubiquinol-8
peptidoglycanpolymer with 1,6-
anhydromuropeptide end
a 1,2-diacylglycerol
argininedecarboxylase,degradative: adiA
argininedecarboxylase,degradative: adiA
a polypeptide
a 1,2-diacylglycerol
peptidylproline(omega = 0)
peptidoglycantetrapeptide,
glycan chain 2
a proteinwith
oxidizeddisulfidebonds
superoxidedismutase(Mn): sodA
a CDP-diacylglycerol
sulfite
broadspecificity 5’(3’)-nucleotidase andpolyphosphatase:surE
coenzyme A
uridine-5’-phosphate
acyl-CoAthioesterase:yciA
oxidizedcytochrome
c552
a 1-lyso-2-acyl-sn-glycero-3-
phosphoethanolamine
a holo-[acp]
L-arginine
di-trans,poly-cis-
undecaprenyldiphosphate
beta-D-glucose-6-phosphate
an oxidizedelectronacceptor
a shortglucan
murein DD-endopeptidase,penicillin-insensitive: mepA
a 2,3,4-saturated
fattyacyl-[acp]
formatedehydrogenase-
O: fdoI fdoH fdoG
alpha-D-galactose
thiosulfate
protoheme IX
beta-D-glucosideglucohydrolase,periplasmic: bglX
UQ
penicillin-bindingprotein6: dacC
an L-1-phosphatidyl-ethanolamine
N-acetyl-anhydromuramyl-L-alanine-amidase: ampD
orotate
UDP-2,3-diacylglucosaminehydrolase: lpxH
a proteinL-tyrosine
2,3-bis(3-hydroxymyristoyl)-
beta-D-glucosaminyl1-phosphate
uridine-5’-diphosphate
a ribonucleosidemonophosphate
trehalose
formatedehydrogenase-
O: fdoI fdoH fdoG
nitritereductasecomplex:nrfA nrfBnrfC nrfD
a shortglucan
D-alanyl-D-alanine
a UDP-sugara reducedelectronacceptor
KDO2-lipid IVA
peptidylproline(omega = 180)
a holo-[acp]
asparaginaseII: ansB
diguanylatecyclase: yddV
dihydroorotate
multifunctional acyl-CoA thioesterase Iand protease I andlysophospholipaseL1: tesA
an MDO-O-glucose
demethylmenaquinone-8
an alpha-D-aldose-1-phosphate
phospholipaseA1: pldA
reducedcytochrome
c552
a phosphatidylcholine
multifunctional acyl-CoA thioesterase Iand protease I andlysophospholipaseL1: tesA
NADH
a peptidoglycan
di-trans,poly-cis-
undecaprenyldiphosphate
a holo-[acp]
ubiquinone-8
a 1,2-diacylglycerol-3-phosphate
a D-amino acid
penicillin-bindingprotein1A: mrcA
glucose-1-phosphatase:
agp
a 1-lyso-2-acyl-sn-glycero-3-
phosphocholine
a 2,3,4-saturated
fattyacyl-[acp]
p-aminobenzoate
pyruvate
membrane-boundlytic mureintransglycosylaseB: mltB
L-aspartate
2’,3’-cyclic nucleotide2’-phosphodiesterase:cpdB
a single-stranded
RNA
phosphoglucoseisomerase: pgi
peptidoglycantripeptide,
glycan chain 1
an L-1-phosphatidylglycerol-
phosphate
NAD+
KDO2-lipid A
a nonglucosylated
glucoseacceptor
D-fructose-6-phosphate
a proteinwith
reducedsulfidegroups
5’-nucleotidase:ushA
di-trans,poly-cis-
undecaprenylphosphate
cyclicdi-3’,5’-
guanylate
endo-1,4-D-glucanase:bcsZ
octanoate
pyruvate
a 1,4-alpha-D-glucan
undecaprenylpyrophosphatephosphatase:pgpB
DsbDoxidized
DsbCoxidized
beta-lactamase;penicillinresistance:ampC
amineoxidase (Cucontaining): tynA
argininedecarboxylase,biosynthetic:speA
multicopperoxidase withrole in copperhomeostasis:cueO
a diacylglycerolpyrophosphate
alpha-D-glucose 1-phosphate
an L-1-phosphatidyl-
glycerol
disulfideoxidoreductase:dsbC
GlcNAc-1,6-anhMurNAc
KDO2-lipidA, coldadapted
a tRNA
a nucleoside3’-phosphate
L-glutamate
adenosine 3’,5’-bisphosphate
a holo-[acp]
a ribonucleoside
all-trans-octaprenyl
diphosphate
maltohexaose
heme o
demethylmenaquinone-8
tetrahydrothiophene1-oxide
periplasmicnitratereductase:napGnapH napCnapA napB
a peptide
a carboxylate
N-acetylmuramyl-L-alanineamidase: amiC
argininedecarboxylase,biosynthetic:speA
nitrate
a long-linear glucan
broadspecificity 5’(3’)-nucleotidase andpolyphosphatase:surE
peptidoglycanpolymer
thiosulfatesulfurtransferase:glpE
UDP-N-acetylmuramoyl-
L-alanyl-D-glutamyl-meso-2,6-
diaminopimelyl-D-alanyl-D-alanine
ferritin iron-storagecomplex:ftnA
an aldehyde
DsbC
trimethylamineN-oxide
3-octaprenyl-4-hydroxybenzoate
all transundecaprenyl
phosphate
D-glucose
phosphatidylglycerophosphataseB: pgpB
a peptide
putative p-aminobenzoyl-glutmatehydrolase: abgB
UDP-2,3-diacylglucosaminehydrolase: lpxH
a protein-L-tyrosinephosphate
GlcNAc-1,6-anhMurNAc-L-Ala-gamma-
D-Glu-DAP-D-Ala
malate
2-carboxymuconate
agmatine
an aliphaticamine
p-aminobenzoate
NADP+beta-D-glucose
KDO2-lipid IVA
pyrimidinenucleotidase:yjjG
a 1-lyso-2-acyl-sn-glycero-3-
phosphocholine
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenyl-N-acetylglucosamine
glycerol
UQH2
H2O
thiosulfatesulfurtransferase:pspE
a 1,2-diacylglycerol-3-phosphate
di-trans,poly-cis-
undecaprenyldiphosphate
4-hydroxybenzoate
a proteinL-tyrosine
beta-D-galactose
cardiolipin
2,3-bis(3-hydroxymyristoyl)-
beta-D-glucosaminyl1-phosphate
1,4-dihydroxy-2-naphthoate
a beta-lactam
sugarphosphatase:
yigL
GlcNAc-1,6-anhMurNAc
asparaginaseIII: iaaA
phosphatidylethanolamine-KDO2-lipidA
aldose-1-epimerase:galM
superoxidedismutaseprecursor(Cu-Zn): sodC
CMP
a 2-oxo acid
aminoacetone
diguanylatecyclase: ydeH
Fe2+
D-fructose-6-phosphate
p-aminobenzoylglutamate
a 1,2-diacylglycerol-3-phosphate
uridine-5’-phosphate
succinate
diphosphoundecaprenyl-[GlcNAc-MurNAc-
pentapeptide]n
CTP
L-asparagine
hydrogenperoxide
triggerfactor; amolecularchaperoneinvolvedin celldivision: tig
murein DD-endopeptidase,penicillin-insensitive: mepA
phosphoglyceroltransferase II: mdoB
lipid Adisaccharide
Cu+
agmatine
all-trans-octaprenyl
diphosphate
D-fructose-6-phosphate
hydrogencyanide
agmatine
L-Ara4N-modifiedKDO2-Lipid A
a carboxylate
KDO2-lipid A
fumarate
phosphoglucoseisomerase: pgi
a myristoyl-[acp]
hydrogenperoxide
peptidyl-prolylcis-transisomerase;in proteinfolding:fkpA
CmtABmannitol
PTSpermease
pyruvate
TdcC
malate fumarateL-aspartate
DNApolymeraseIV (Y-family DNApolymerase;translesionDNAsynthesis): dinB
L-lactate
a hydroquinone
H-protein-S-(aminomethyldihydrolipoyl)
lysine
D-serinedeaminase:dsdA
1,6-anhydro-N-acetylmuramate
MinE
L-asparaginyl-tRNAasn
a beta-ketoacyl-[acp]
geranylfarnesyldiphosphate
L-lyxose
YceI
alkalinephosphatase:phoA
xanthosine-5-phosphate
6-phospho-beta-D-
glucosyl-(1,4)-D-glucose
acetylornithinetransaminase:argD
RecFORcomplex:recOrecR recF
a trans-delta3-cis-delta5-dodecenoyl-[acp]
stationaryphasemismatch/uracil DNAglycosylase:mug
a citryl-[acp]
METABOLIC REGULATORSBIOSYNTHESIS
aminoimidazolecarboxamide
ribonucleotide
di-trans,poly-cis-
undecaprenyldiphosphate
MgtA
lipoatebiosynthesis
andincorporation I
deoxyadenosine adenosine
inosine deoxyuridine thymidine deoxyinosine
uridine deoxycytidine
cytidine
H2
tRNApro
1-ethyladenine
ALCOHOLS DEGRADATION
1,3-diphosphateglycerate
chorismate
L-glutaminyl-tRNAgln
a (R)-3-hydroxy-cis-vaccenoyl-
[acp]
AlsR
octaprenyldiphosphatesynthase: ispB
PFL-deactivase:adhE
phosphoglycerate mutase,cofactor independent: gpmM
L-serine
NADPphosphatase
2-phosphoglycerate
gluconokinaseII: idnK
fructoselysine6-kinase: frlD
guaninedeaminase:
guaD
L-valine
salicin-6-phosphatearbutin-6-phosphate
alpha-D-glucose1-phosphate
NtrC
2-dehydro-3-deoxy-D-galactonate-6-phosphate
pyridoxaminetransporter
D-glutamate
glucose-1-phosphateadenylyltransferase:glgC
alanineracemase 1,PLP-binding,biosynthetic: alr
naphthoate-CoAsynthase: menB
a palmitoyl-[acp]
YbjO
o-succinylbenzoate-CoA ligase: menE
L-valyl-tRNAval
tryptophan synthase,alpha subunit: trpA
beta-D-ribopyranose
glycerophosphodiesterphosphodiesterase,cytosolic: ugpQ
DjlA
PRPPbiosynthesis II
6-phospho-D-gluconate
shikimatedehydrogenase: aroE
N-acetylneuraminatelyase: nanA
shikimatedehydrogenase: ydiB
glutathionylspermidine
quinolinatephosphoribosyltransferase:nadC
nucleosidediphosphatekinase: ndk
DNAn
respiration (anaerobic)
ribonucleoside-triphosphatereductase: nrdD
a DNA 6-methylaminopurine
sugarphosphatase:yfbT
D-alanine
tRNA containing 6-Isopentenyladenosine
trans-aconitate
arsenite
L-idonateD-gluconate
7,8-dihydropteroate
2-thiouridine
deoxycytidine
L-threonine
acetyl-CoA:acetoacetyl-CoA transferase,beta subunit: atoA
YjhF
L-aspartate
a 5,10-methylene-tetrahydrofolate
menadione
phosphatidylglycerophosphataseA: pgpA
enoyl-CoAhydratase: fadJ
RodZ
Targlu-Me
glyoxylate
cytosine
NAD salvage pathway I
a lipoyl-[acp]
D-fructose
polyphosphatekinase: ppk
L-cysteinyl-tRNAcys
PhoR-Phis
selenocysteinebiosynthesis
AlkB repairsystem foralkylatedDNA andRNA: alkB
an rRNA
hydrophilicsolute orion < 600 Da
GDPpyrophosphokinase: relA
biotinsulfoxidereductase:bisC
L-xylulosekinase: lyxK
L-histidine
glutamate-5-semialdehydedehydrogenase:proA
NapD
lipoate acetyltransferaseN6-(dihydrolipoyl)lysine
alpha-D-glucose 1-phosphate
beta-hydroxyacyl-ACPdehydratase: fabZ
phosphoribosyl-ATP
a nucleosidediphosphate
an oxidizedferredoxin
phosphoglyceratemutase 2: ytjC
predicted acyl-CoAdehydrogenase: ydiO
rRNAcontaining
pseudouridine
fructose-1,6-bisphosphatase:yggF
fatty acid oxidationcomplex, betacomponent: fadA
6-hydroxymethyl-dihydropterindiphosphate
23S rRNApseudouridine2604synthase: rluF
UhpC-glucose-6-P
ClpAP:clpA clpP
a diacylglycerolprolipoprotein
D-glyceraldehyde-3-phosphate
acetol
phosphatidylserinedecarboxylase: psd
NADHpyrophosphatase:nudC
beta-D-glucose-6-phosphate
a trans hex-2-enoyl-[acp]
octanoate
a (3R)-3-hydroxyacyl-CoA
glutamate-1-semialdehydeaminotransferase:hemL
molybdenumcofactor
K+
exopolyphosphatase: ppx
alpha-ribazole-5’-P
an aliphaticomega-
aminoaldehyde
formate
an aldehydeor ketone
SetB
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
pantothenatesynthetase: panC
a quinone
methylglyoxalreductase: dkgA
methionineand methyl-
donor-molecule
biosynthesis
formyl-CoA
FATTY ACIDS AND LIPIDS BIOSYNTHESIS
L-fucosemutarotase:fucU
pyruvate
H2
succinyl-CoA
di-trans,poly-cis-undecaprenyl
phosphate
a reducedthioredoxin
a nucleosidediphosphate
L-fucose isomerase: fucI
deoxyribose-phosphatealdolase: deoC
fused 4’-phosphopantothenoylcysteinedecarboxylase andphosphopantothenoylcysteinesynthetase: dfp
cholinedehydrogenase:betA
RESPIRATION
superpathway of arginineand polyamine biosynthesis
purine nucleosidephosphorylase:
deoD
purine deoxyribonucleosides degradation
pyruvate
L-methionine
Blc
2-hydroxy-6-oxonona-2,4-diene-1,9-dioate
carbonicanhydrase1: cynT
a nucleosidetriphosphate
trehalose
aminopeptidaseN: pepN
D-mannonate
GltIJKLglutamate
ABCtransporter
a lipopolysaccharide
acetyl-CoA:acetoacetyl-CoA transferase,
alpha subunit: atoD
L-lysine
superpathway oflipopolysaccharide biosynthesis
agmatine
GntT
beta-D-galactose
phosphotyrosine-proteinphosphatase: etp
alanineracemase2, PLP-binding:dadX
ArsB
D-fructose
L-valine
an oxidizedferredoxin
formate
lysinedecarboxylase2: ldcC
formate
MinD
7,8-dihydroneopterin
triphosphate
D-mannitol
O-acetyl-L-serine
formatedehydrogenase:fdhF
uridine-5’-diphosphate
nicotinate
DNAcontaining
a basewith lesion
CTP
3-hydroxyacyl-CoAdehydrogenase: fadJ
ADP
L-cystathionine
poly-beta-1,6-N-acetyl-D-glucosamine
methioninesulfoxidereductaseB: msrB
FxsA
D-glyceraldehyde-3-phosphate
NAD+
HMP-PPhydrolase:nudJ
L-threonine
an oxidizedcytochrome c
riboflavin
an inactiveribonucleosidetriphosphatereductase
adenosyl-cobinamidephosphate
superpathway of phenylalanine,tyrosine, and tryptophan biosynthesis
YaiO
a beta-keto-cis-delta5-dodecenoyl-[acp]
N-substitutedaminoacyl-
tRNA
L-Ala-gamma-D-Glu
diacetylchitobiose-6-phosphatehydrolase: chbF
adenine
dTDP-glucosepyrophosphorylase:rfbA
nicotinate-mononucleotideadenylyltransferase:nadD
lipopolysaccharidecore biosynthesis;phosphorylation ofcore heptose: rfaP
L-aspartateoxidase: nadB
isopentenyldiphosphate
dTDP
adenosinethiamine
triphosphate
5’-phosphoribosyl-N-formylglycineamide
fructoselysine6-phosphatedeglycase: frlB
L-glutamine
indoleL-tryptophan
2-oxopentenoate
lauroylacyltransferase:lpxL
pyruvate
NAD(P)H:quinoneoxidoreductase:ytfG
3-oxoadipyl-CoA
alpha-mannosidase:mngB
peptidyl-tRNAhydrolase:pth
a tRNA
protein phosphatase1 modulatesphosphoproteins,signals proteinmisfolding: pphA
RstACheB
L-glutamate
deoxyguanosinetriphosphatetriphosphohydrolase: dgt
UDP-glucose:(glucosyl)LPS alpha-1,2-glucosyltransferase: rfaJ
(R)-beta-lysine
NADHoxidoreductase: hcr
acyl-CoAthioesterase:yciA
UDP-L-Ara4O C-4" transaminase:arnB
non-specific ion/solute
CELL STRUCTURES BIOSYNTHESIS
phosphogluconatedehydratase: edd
galactitol-1-phosphatedehydrogenase: gatD
phosphoenolpyruvate
D-serine
xylosedegradation I
a hydroquinone
6-phospho-beta-glucosidaseA: bglA
tagatose-1,6-bisphosphatealdolase 1: kbaZ kbaY
3-deoxy-D-manno-
octulosonate
molybdopterinsynthase:moaE moaD
UDP-N-acetylglucosamine-2-epimerase: rffE
geranyl-diphosphate
dITP
a tRNA
C1 COMPOUNDSUTILIZATION AND
ASSIMILATION
glyceratekinase I: garK
glycerol-3-phosphateacyltransferase: plsB
L-aspartate
CaiT
FMNH2
tartronatesemialdehyde
a trans tetradec-2-enoyl-[acp]
CDP
xanthine
phospho-TorR
nitrite
L-isoleucine
UDP-N-acetyl-D-mannosamine
Targlu
AtoS-Phis
L-proline
alpha-D-glucose 1-phosphate
BarA-Pasp
L-ribulose
NorV
formylTHF biosynthesis I
serinehydroxymethyltransferase: glyA
2-deoxy-D-glucose 6-phosphate
aconitate hydratase 1: acnA
UDP-N-acetylmuramate
tetrahydrofolate
dihydrolipoamideacetyltransferase:aceF
nucleosidediphosphatekinase: ndk
fructose-1,6-bisphosphatase I: fbp
N5-carboxyaminoimidazoleribonucleotide mutase: purE
D-glyceraldehyde-3-phosphate
a reducedferredoxin
rRNAcontaining N6-methyladenine
guanylatekinase: gmk
L-Ala-D/L-Gluepimerase:ycjG
indole
L-tryptophan
YgdQ
phosphoribosylglycinamideformyltransferase: purN
a [citrate(pro-3S)-
lyase](citrylform)
YjcG
methanol
ribonucleoside-triphosphatereductase: nrdD
nitric oxide
(2S)-2-isopropyl-3-oxosuccinate
O-succinyl-L-homoserine
adenylatecyclase: cyaA
ADP-ribose
glutathione
fructose bisphosphatealdolase class II: fbaA
proteasespecific forYgjD: yeaZ
UDP-D-glucose
aminoimidazolecarboxamide
ribonucleotide
di-trans,poly-cis-
pentaprenyldiphosphate
phosphoglyceromutase 1: gpmA
2,5-diketo-D-gluconatereductaseB: dkgB
AMINES AND POLYAMINES DEGRADATION
glutamyl-tRNA
synthetase:gltX
pyridoxine
seryl-tRNAsynthetase:
serS
phosphohydroxythreonineaminotransferase: serC
asparaginyl-tRNA
synthetase:asnS
L-lactaldehydedegradation(anaerobic)
KdpD
pyridoxalkinase2: pdxY
BaeS
a 3’-terminalunsaturated
sugar
RNaseD: rnd
EmrKY-TolC
putativemultidrug
effluxtransportsystem
[+ 6 isozymes]
imidazoleglycerol-phosphatedehydratase: hisB
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenol
a quinone
ATPphosphoribosyltransferase: hisG
UidC
UDP-glucose 6-dehydrogenase:ugd
GDP-mannose 4,6-dehydratase: gmd
YraP
2-ketoaldonatereductase: ghrB
N-hydroxyarylamineO-acetyltransferase:nhoA
7-keto-8-aminopelargonate
salvage pathways of adenine,hypoxanthine, and their nucleosides
L-glutamate
23Sribosomal
RNA
a carboxylated-biotinylated-
BCCP
CheB-Pasp: cheB
tRNAser
L-ribulose-5-phosphate
a quinone
oxaloacetate
sulfite
beta-galactosidase:lacZ
nitrate
an acetyl-[acp]
L-methionine
L-Ala-L-Glu
L-carnitine
2-protocatechuoylphloroglucinolcarboxylate
glutamatebiosynthesis III
gamma-glutamyl-gamma-aminobutyratehydrolase: puuD
4-aminobutyratetransaminase: gabT
pyrimidine deoxyribonucleotides de novo biosynthesis
2-phosphoglycerate
PotE
adenosine 3’,5’-bisphosphate
propionyl-CoA
23S rRNA 2’-O-ribose C2498methyltransferase:rlmM
phenylacetaldehyde
menaquinone-8
ADP
molybdate
a ribosomalprotein-
N-acetyl-L-alanine
betaine aldehydedehydrogenase:betB
acetaldehydedehydrogenase:adhE
ribonucleosidehydrolase 3: rihC
a nucleoside3’,5’-cyclicphosphate
YfaV
cytidinedeaminase:cdd
7,8-dihydroneopterin
triphosphate
CheB-Pasp: cheB
CRISPR-associatedcomplexfor antiviraldefense:casEcasD casCcasB casA
D-galacturonateisomerase: uxaC
tagatose-1,6-bisphosphatealdolase 2: gatZ gatY
DNAcontaining arecognition
site
acyl-CoAdehydrogenase: fadE
phospho-RcsB
acetylphosphate
D-allosedegradation
NlpD
coenzyme A
citrate lyasesynthetase:citC
dTDP-L-rhamnosesynthetase:rfbD rfbC
methyleneTHFenzyme: folD
an (R)-3-hydroxydecanoyl-
[acp]
2-oxoglutarate
AMP
dihydrolipoyltranssuccinylaseN6-(lipoyl)lysine
FtsN
fructose-1-phosphate
OuterMembrane
FerricEnterobactinTransportSystem
BarA
ArcB
an alpha-D-aldose-1-phosphate
an oxidizednitroaromatic
compound
phosphopentomutase:deoB
L-aspartate
a 1-acyl-sn-glycerol-3-phosphate
NAD synthetase,NH3-dependent: nadE
Trgglu
trehalosedegradationII (trehalase)
NMN amidohydrolase
50Sribosomalsubunit
protein L7
orotatephosphoribosyltransferase: pyrE
D-alanine
malatedehydrogenase:mdh
aconitatehydratase1: acnA
DegS
(2S)-2-amino-3-oxo-4-phosphonooxybutanoate
L-leucyl-tRNAleu
histidyl-tRNA
synthetase:hisS
(2R,4S)-2-methyl-2,4-dihydroxydihydrofuran-
3-one
tRNAnucleotidyltransferase: cca
CheB-Pasp
N1-methyladenine
acetylornithinetransaminase,catabolic: astC
ferricdicitrate
a trans-delta2-decenoyl-[acp]
spermidine
D-xylose
glyoxylatereductase:ghrA
3-(3-hydroxyphenyl)
propionate
a protein
CTP synthetase: pyrG
5-methyl-tetrahydrofolate
L-aspartate
5,10-methylenetetrahydrofolate
reductase: metF
Ap4Asynthetase:lysU
1-hydroxy-2-methyl-2-(E)-butenyl 4-
diphosphate
serinehydroxymethyltransferase: glyA
EIIAsc
mannosylglycerate
NarQ-Phis
L-threonine
L-methionine
CheB-Pasp: cheB
2-oxobutanoate
H+
an rRNA
YbjYZ
e14 prophage;site-specificDNArecombinase:pinE
Tapglu
lipoyl-proteinligase: lipB
NhaA
freemethionine-(R)-sulfoxidereductase:yebR
TisB
trehalosebiosynthesis I
delta(2)-isopentenylpyrophosphatetRNA-adenosinetransferase: miaA
phosphatidylserinesynthase: pssA
transketolaseI: tktA
acetyl-CoA
6-phosphogluconatedehydrogenase(decarboxylating): gnd
L-threonine
hybrid-cluster
proteinox
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
prephenate
ubiquinol-8
alpha-xylosidase:yicI
a myristoyl-[acp]
KASI: fabB
Tsrglu
dihydroneopterinphosphate
PhoB-Pasp
CreC
spermidine
GTPaseassociatedwith the50S subunitof theribosome:hflX
a C4-dicarboxylatea C4-dicarboxylate
2-dehydropantolactone
phytate
acetoacetyl-CoAtransferase:atoD atoA
pyridoxine5’-phosphateoxidase:pdxH
a biotinylatedBCCP
(monomer)
formate
oxaloacetate
kynurenine
YbhC
a protein
glyoxalaseI: gloA
6,7-dimethyl-8-ribityllumazinesynthase: ribE
methylglyoxalreductase: dkgB
S-adenosyl-L-methionine
a BCCP(monomer)
guanosine-5’-phosphate
DNApolymeraseII: polB
TorS-Pasp723
glutamyl-tRNAreductase: hemA
succinyl-CoA
an N10-formyl-tetrahydrofolate
YkgB
YjjL
chorismate
6-phosphogluconatedehydrogenase(decarboxylating): gnd
2-octaprenyl-6-methoxy-
1,4-benzoquinol
dimethylbenzimidazole
pyruvateformate-lyase: pflB
L-lactatedehydrogenase:
lldD
quinolinate
pyridoxamine5’-phosphate
maltotetraose
laurate
tRNApseudouridine65 synthase: truC
peptidoglycantripeptide-
Lpp crosslink
endonucleaseIV: nfo
RNApyrophosphohydrolase:rppH
isopentenyldiphosphate
xyloseisomerase:xylA
protein phosphatase1 modulatesphosphoproteins,signals proteinmisfolding: pphA
H2
deoxyribodipyrimidinephotolyase(photoreactivation): phr
D-fructose-6-phosphate
UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelateligase: mpl
NADkinase: nadK
tetrahydrodipicolinate
L-aspartyl-4-phosphate
YeiM
a purineribonucleoside
EnvC
putrescine
an oxidizedelectron
acceptor
rhamnosedegradation
a reducedelectronacceptor
ATP
glycerol-3-phosphatedehydrogenase,biosynthetic: gpsA
pyridoxal 5’-phosphate
alkanesulfonatemonooxygenase,FMNH2-dependent: ssuD
beta-D-glucose
BaeR
a 1,2-diacylglycerol
amidophosphoribosyltransferase: purF
UvrABCNucleotideExcisionRepairComplex:uvrB uvrCuvrA uvrD
RecG, DNAhelicase,resolutionof Hollidayjunctions,branchmigration:recG
autoinducer AI-2 biosynthesis
5,10-methenyltetrahydrofolate
AdiC
glutathione S-transferase:gst
EptA
(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran
2-dehydro-3-deoxygalactonatekinase: dgoK
L-Ala-gamma-D-Glu-Dap
diacetylreductase
uridylyltransferase:glnD
D-fructose-6-phosphate
cob(I)alamin
guanylatecyclase
PhoB
dihydrolipoyltranssuccinylase N6-(S-succinyldihydrolipoyl)lysine
S-ribosyl-L-homocysteine
glyoxylate
L-ornithine
trehalose-6-phosphatesynthase:otsA
L-selenocysteine
quinoneoxidoreductase: qor
pyruvate
D-mannitol
2,3-dihydro-2,3-dihydroxybenzoatedehydrogenase: entA
D-glucuronate
D-mannose-6-phosphate
4-hydroxybenzoate
D-lactatedehydrogenase:ldhA
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
all-trans-hexaprenyl
diphosphate
formatehydrogenlyasecomplex: hycDhycC hycF hycGhycB hycE fdhF
LolA
ZntA
L-threoninehomoserine
deoxyribose-1-phosphate
K+
oxaloacetate
10-formyltetrahydrofolate:L-methionyl-tRNA(fMet)N-formyltransferase: fmt
isovaleryl-CoA
ribosepyranase:rbsD
biotin
D-alanyl-D-alanine
L-fucoseisomerase: fucI
3,4-dihydroxyphenylacetyl-CoA
pyruvate formate-lyase: pflB
6-phospho-beta-glucosidase;cryptic: ascB
deoxyribose-phosphatealdolase: deoC
L-glyceraldehyde3-phosphatereductase: yghZ
nicotinate mononucleotide
L-isoleucine
NADHdehydrogenase(quinone)
YccA
DNAligase: ligA
L-alanine
D-ribulose
ThiS-COAMP
chorismate
lipoamidedehydrogenase: lpd
L-aspartate
7,8-dihydroneopterin
triphosphate
a reducedglutaredoxin
beta-D-glucose-6-phosphate
trehalose 6-phosphate
acetyl-CoA
oxaloacetate
acetylornithinedeacetylase: argE
10-formyl-tetrahydrofolate
superpathway of glycolysis, pyruvatedehydrogenase, TCA, and glyoxylate bypass
all-trans-farnesyldiphosphate
a peptide
3-phenylpropionate
tRNAcontaining N1-methylguanine
guanosine-5’-phosphate
a tRNAcontaining
glutamylatedqueuosine
acetyl-CoA
quinolmonooxygenase:ygiN
tRNAcontainingqueuine
dihydrofolatereductase: folA
MLPS
beta-D-glucose
TtdT
L-aspartateL-glutamate
glutathione
a trans dodec-2-enoyl-[acp]
tRNAasp
D-alloseD-fructuronateD-gluconate
D-ribose
methanol
ClpP serineprotease:clpP
D-mannose-6-phosphate
glycinebetaine
poly-beta-1,6-N-acetyl-D-glucosamineN-deacetylase:pgaB
2,3-dihydroxy-3-methylvalerate
thioglycolate
all-trans-octaprenyl
diphosphate
D-fructose
10-formyl-tetrahydrofolate
cobinamide-Pguanylyltransferase: cobU
cysteinesynthase B: cysM
cobinamideadenosyltransferase:btuR
NADH
crotonobetainyl-CoA
hydratase: caiD
isopentenyldiphosphate
oxidizedflavorubredoxin
DNA withlesion
resolvedthroughRec-
mediatedpathway
L-serine
NADbiosynthesis
I (fromaspartate)
gamma-glutamylkinase: proB
amylomaltase:malQ
uroporphyrinogenIII synthase: hemD
a trans-2-enoyl-CoA
4-hydroxy-2-oxo-
valerate
beta-D-glucose-6-phosphate
KASII: fabF
beta-ketoacyl-[acyl-carrier-protein] reductase: fabG
L-serine
a trans-polyisoprenyln-PP
2-oxo-3-hydroxy-4-phosphobutanoate
3-deoxy-D-manno-octulosonate8-phosphatesynthase: kdsA
[GlnK]
glutamyl-tRNAsynthetase: gltX
lipoatesynthase:lipA
glycogensynthase:glgA
predictedAutoinducer-2 kinase: lsrK
PotE
5-ketogluconate
pyridoxal 5’-phosphate
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-
meso-2,6-diaminopimelate
2-phosphoglycerate
a mRNA
an unknownC3 fragment
2-amino-3-ketobutyrate
CoA ligase: kbl
acetohydroxybutanoatesynthase: ilvN ilvB
enolase: eno
propionatekinase: tdcD
lysine 2,3-aminomutase:yjeK
Tsx
CynX
2,3-dihydroxy-3-methylvalerate
deoxyadenosinedeaminase: add
hypoxanthinephosphoribosyltransferase: hpt
formyltetrahydrofolatedeformylase: purU
bifunctional NadRtranscriptionalrepressor and NMNadenylyltransferase:nadR
3-phosphoglycerate
SugE
glyceratekinaseI: garK
a palmitoyl-[acp]
YmgF
L-glycerol 3-phosphate
ribonucleoside-diphosphatereductase:nrdB nrdA
purinenucleotidase:yrfG
pantothenate
dTDP-glucosepyrophosphorylase2: rffH
chorismatelyase: ubiC
acetaldehydedehydrogenase:adhE
D-glyceraldehyde-3-phosphate
3-phosphoglycerate
2-ketobutyrateformate-lyase: tdcE
superpathway ofphenylethylamine
degradation
a 3-oxo-dodecanoyl-[acp]
dihydromonapterin-triphosphate
a dodecanoyl-[acp]
ribonucleosidehydrolase 3: rihC
indole-3-glycerol-phosphate
a deamineatedamine donor
YhjE
a reducedcytochrome c
maltotriose
L-galactonate
chorismate
alanine racemase2, PLP-binding: dadX
ribonucleoside-diphosphatereductase 2:nrdF nrdE
L-alanine
(R)-pantolactone
a 1,4-alpha-D-glucan
thiaminediphosphate
long chainpolyphosphate
an alcohol
CybC
2-oxoglutarate
an L-1-phosphatidylglycerol-
phosphate
branched-chainamino-acidaminotransferase:ilvE
succinate
D-lactate
a tRNAcontaining 7-
aminomethyl-7-deazaguanineat position 34
beta-D-glucose-6-phosphate
RseP
a tRNA
UDP-D-galactose
deoxyribose-1-phosphate
D-malatedehydrogenase(decarboxylating): yeaU
glucono-delta-lactone
YrbG
D-4-hydroxy-2-keto-
glutarate
glutamine synthetaseadenylyltransferase:
glnE
folate polyglutamylation I
aconitate hydratase 1: acnA
fumarase A: fumA
octaprenyldiphosphatesynthase: ispB
YebF
L-fuculose-phosphatealdolase: fucA
L-aspartate
L-serine
L-seryl-tRNAser
formaldehydedehydrogenase,glutathione-dependent: frmA
L-serine
beta-hydroxyacyl-ACPdehydratase: fabZ
SdaC
nicotinamidemononucleotide
3-phosphoserineaminotransferase: serC
lipoamide
KASI: fabB
L-aspartate
D-fructose
a tRNA
malate fumarateL-aspartate
pyruvate kinase II: pykA
L-xylulose
D-alpha,beta-D-heptose-7-phosphate
4-(cytidine 5’-diphospho)
-2-C-methyl-D-erythritol
fusedglutathionylspermidineamidase /glutathionylspermidinesynthetase: gsp
SucB-S-succinyldihydrolipoate
cellobiosechitobiose
tRNA 2-selenouridinesynthase: ybbB
hepta-acylatedKDO2-lipid A
UraA
methyl red
a tRNA
selenocysteinelyase: sufS
a phosphatemonoester
beta-D-glucose
Trgglu-Me
allantoate
pyruvate
adeninephosphoribosyltransferase: apt
D-glyceraldehyde-3-phosphate
GTPcyclohydrolaseII: ribA
D-ribose-5-phosphate
ribonucleosidehydrolase 2(pyrimidine-specific): rihB
L- and D-methionineuptake ABCpermease
FucP
AMP
UDP-N-acetyl-D-mannosaminuronicaciddehydrogenase: rffD
aminopeptidaseN: pepN
YdgR
2-amino-3-oxobutanoate
tRNAMet cytidineacetyltransferase:tmcA
beta-D-glucose-6-phosphate
L-alanyl-tRNAala
nitrite
glutamineABC
transporter
predicted L-xylulose 5-phosphate3-epimerase:sgbU
D-glucosyl-lipopolysaccharide
glutaminase A
D-4’-phosphopantothenate
YjcG
reducedflavorubredoxin:norV
L-isoleucine
glycyl-tRNAsynthetase:glyQ glyS
diaminopimelateepimerase: dapF
pseudouridine
thiamin ABCtransporter
octaprenyldiphosphatesynthase: ispB
beta-ketoadipyl-CoA thiolase: paaJ
ADP-sugarpyrophosphorylase:nudE
oligopeptideABC
transporter
dUMP
cystathionine-beta-lyase: metC
alpha-ribazole
predictedpseudouridine5’-phosphateglycosidase:pscG
D-alloseABC
transporter
YgaZ/YgaHL-valineexportercomplex
tRNA containing 5-methylaminomethyl-
2-thiouridylate
AMINO ACIDS DEGRADATION
UidB
malonyl-CoA-ACPtransacylase: fabD
(R)-methylmalonyl-
CoA
acetoacetatedegradation
(to acetyl CoA)
tRNA m6A37methyltransferase:yfiC
uridylyltransferase:glnD
ethanoldehydrogenase:adhP
uridylyl-removingenzyme: glnD
tRNAasn
biosynthesisof 4-amino-4-deoxy-L-arabinose-
modified lipid A
L-methioninesulfoxide
UDP-D-galactose
a peptideantibiotic
D-fructose-6-phosphate
AtpI
aldehydedehydrogenaseA, NAD-linked: aldA
carnitine-CoAligase: caiC
10-formyl-tetrahydrofolate
N-acetyl-D-glucosamineglucosamineD-fructose
beta-D-glucoseD-mannose
nitrite
hydroxymethylpyrimidinekinase: thiD
thiaminephosphatesynthase:thiE
2-keto-L-gulonate
peptidoglycan biosynthesis I
CleavedDNA
lactose
RecJ: recJ
a polypeptide
acetaldehyde
FMNphosphatase:yigB
xanthine
SstT
a ribosomalprotein-
L-alanine
pyridoxine5’-phosphate
synthase:pdxJ
CO2
iron dicitrateABC
transporter
3-(3-hydroxyphenyl)propionate 2-hydroxylase:mhpA
a 3-oxo-palmitoyl-[acp]
4-hydroxy-2-ketovaleratealdolase: mhpE
a nucleosidediphosphate
AMINO ACIDS BIOSYNTHESIS
isocitratedehydrogenasekinase: aceK
L-carnitine
a protein L-methionine
L-methionine
6-phosphogluconolactonase: pgl
superpathway of N-acetylglucosamine, N-acetylmannosamine
and N-acetylneuraminate
degradation
ADP
RNase R: rnr
DcuA
ethanoldehydrogenase:adhP
MQH2
ribose ABCtransporter
D-glycerate
TorT
hypoxanthine
lipid Adisaccharidesynthase: lpxB
a ribonucleosidediphosphate
UDP-N-acetylglucosamineacyltransferase: lpxA
a phospholipid
NADH
an isocitratedehydrogenase
L-alanine
L-cysteine
a macrolideantibiotic
6-phospho-beta-glucosidaseB; cryptic:bglB
SucB-lipoate
H+
3-phospho-hydroxypyruvate
diacylglycerolkinase: dgkA
acetaldehyde
KDO2-lipid IVA
3-deoxy-D-manno-octulosonatecytidylyltransferase:kdsB
D-ribose-5-phosphate
vitaminB12 ABC
transporter
UhpC
PspB
adenosine
dipeptideABC
transporter
thiosulfateABC
transporter
NAD+
CheA
aspartateaminotransferase,PLP-dependent: aspC
GDP-alpha-D-glucose
a proteinL-glutamate
alpha-D-ribose-1-phosphate
galactitol-1-phosphate
an apo-[acp]
taurinedegradation IV
AceF-lipoate
L-phenylalanine L-tryptophan
L-tyrosine
4,5-dihydroxy-2,3-pentanedione
HdeA
TorS-Phis850
pseudouridine5’-phosphate
lipoyl-proteinligase A: lplA
5’-deoxyadenosine
L-cysteine
4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate
lipid A-core 1-diphosphate
ClpXP:clpX clpP
TrkA
TehA
L-tartrate
16S rRNAcontaining
C5-methylatedcytosine
O-antigenligase: rfaL
UDP-glucose:(glucosyl)LPS alpha-1,2-glucosyltransferase: rfaJ
PspD
KDO2-lipid A
TdcE
D-tyrosyl-tRNATyr
a sugar
urate
pyruvateoxidationpathway
H-Gcv-protein-
(lipoyl)lysine
pyridoxalkinase: pdxK
protein involvedin KdoIIIattachment duringlipopolysaccharidecore biosynthesis: rfaZ
multidrug
pyridoxamine-oxaloacetatetransaminase
a maltodextrin
fused nitric oxidedioxygenase anddihydropteridinereductase 2: hmp
enterobactinsynthasemultienzymecomplex: entEentF entD entB
leucyl-tRNAsynthetase:
leuS
poly(A)polymeraseI: pcnB
resolvasome:ruvA ruvB ruvC
arginyl-tRNAsynthetase:
argS
tyrosyl-tRNAsynthetase:
tyrS
S-adenosyl-L-methioninamine
ITP
adenosylcobinamide-GDP
cellobiosesalicinarbutin
EriC
L-ribulose-5-phosphate
an alkylphosphate
oxamate
cis-vaccenate
S-methyl-L-methionine
glyoxylatereductaseB: ghrB
chemotaxis proteinmethyltransferase:cheR
succinate semialdehydedehydrogenase, NADP+-dependent: gabD
allothreonine
galactoseABC
transporter
histidinebiosynthesis
UDP-N-acetylenolpyruvoylglucosaminereductase: murB
cyclic-GMP
pyruvate
adenosylcobalamin-5’-phosphate
L-fuculose
3-methyl-2-oxobutanoatehydroxymethyltransferase:panB
a 2,3,4-saturated 2-lysophosphatidate
aspartatekinase: thrA
quinolinatesynthase: nadA
2-acetolactate
holo-[acyl-carrier-protein]synthase:acpS
lysine/arginine/ornithine
ABCTransporter
disulfideisomerase,periplasmic:dsbG
D-glucosamine-6-phosphate
arabinoseABC
transporter
SucB-lipoate
arginineABC
transporter
a carboxylate
RssB
ArcAB Two-Component
SignalTransduction
System
dATP
succinate
pantothenatekinase: coaA
ribonucleosidehydrolase 3: rihC
dCMPphosphohydrolase:yfbR
glucose 6-phosphate-1-dehydrogenase: zwf
RNApolymerase,core enzyme:rpoBrpoC rpoA
ethanoldegradation
beta-ketoacyl-[acyl-carrier-protein]reductase:fabG
N-succinyl-L,L-2,6-
diaminopimelate
7-cyano-7-carbaguanine
glucokinase:glk
gamma-glutamylputrescineoxidase: puuB
beta-D-ribofuranose
tRNAIle-lysidinesynthetase:tilS
NarUYgfU
L-methionine-(R)-S-oxide
glycolate
NhaB
cyanate
di-trans,poly-cis-decaprenyldiphosphate
mannitol-1-phosphate 5-dehydrogenase:mtlD
ITPase: yjjX
arylsulfatase:aslA
BetT
NADP+
YafY
quinatedehydrogenase:ydiB
acetyl-CoAbiosynthesis
(from pyruvate)
uracil
NarP-Pasp
KASIII: fabH
NADPH
ribose 1,5-bisphosphokinase:phnN
beta-hydroxyacyl-ACP dehydratase: fabZ
L-glutamine
phenylalanyl-tRNA
synthetase:pheT pheS
(R)-methylmalonyl-CoA
molybdopteringuaninedinucleotidesynthase: mobA
BarA
coenzyme B12
5’,5’’’-diadenosine
tetraphosphate
deoxyuridine
fused predictedacetyl-
CoA:acetoacetyl-CoA transferase:
alpha subunit/beta subunit: ydiF
superpathway ofacetate utilization
and formation
L-glutamate
YjcD
folylpoly-alpha-glutamatesynthetase
4-aminobutyrate
a trans-2-enoyl-CoA
TorR
a proteinL-cysteine
a reducedthioredoxin
dihydroxyacetonephosphate
Nitrogen RegulationTwo-Component System
glutathionebiosynthesis
YgfO
L-ribulose 5-phosphate 4-epimerase: araD
serinehydroxymethyltransferase: glyA
putrescine
Ag43
fructosebisphosphatealdolaseclass II: fbaA
uracil
NADH pyrophosphatase: nudC
D-fructose-6-phosphate
ClpAXP:clpXclpA clpP
tryptophansynthase:trpB trpA
thymidylatesynthase:
thyA
sulfateadenylyltransferase:cysD cysN
beta-L-fucose
KDO2-lipid A
an alkylhydroperoxide
1-acylglycerol-3-phosphateacyltransferase: plsC
octyl alpha-D-glucopyranoside
L-methionine
an alcohol
L-proline
2,3-dihydroxybenzoylserine
AROMATIC COMPOUNDS DEGRADATION
acetate
ethanoldehydrogenase:adhP
xanthosine
imidazoleglycerolphosphatesynthase:hisF hisH
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
ADP-sugarpyrophosphatase:nudF
allose-6-phosphateisomerase/ ribose-5-phosphateisomeraseB: rpiB
histidinaldehydrogenase:hisD
pyridoxine
a maltodextrin
predictedpseudouridinekinase: pscK
BglH
trans-aconitatemethyltransferase: tam
glutathione S-transferase:yfcG
trans-2-decenoyl-ACPisomerase:fabA
L-1,2-propanedioloxidoreductase:fucO
5-amino-6-ribitylamino-2,4(1H,3H)-
pyrimidinedione5’-phosphate
CheA-Phis
putrescineaminotransferase: ygjG
D-gluconate
ethanolamineammonia-lyase:eutC eutB
cyanate
fructose 1,6-bisphosphatase: ybhA
dGTP
spermidinesynthase:speE
xanthosinetriphosphatepyrophosphatase:rdgB
a DNAcyclobutadipyrimidine
L-2,3-dihydrodipicolinate
putrescine
D-cysteine
L-glutamate
purine nucleosidephosphorylase:deoD
ornithinecarbamoyltransferase:argF
UDP-N-acetylmuramate-alanine ligase: murC
Slp
guanosine-5’-phosphate
beta-1,6-galactofuranosyltransferase: wbbI
phosphoglyceratemutase, cofactorindependent: gpmM
2-oxopent-4-enoatehydratase:mhpD
a phosphorylatedisocitrate
dehydrogenase
a beta-hydroxy cisdelta5-dodecenoyl-[acp]
2-hydroxy-6-ketonona-2,4-dienedioatehydrolase:mhpC
CodB
BasR
phosphopentomutase:deoB
6-phosphofructokinase I: pfkA
D-ribulose-5-phosphate
dCMP
acetyl-CoA
phosphateABC
transporter
As3H3O6
citrate
alcoholdehydrogenase:adhE
YjeM
YhjV
NfrB
phosphoglycerate kinase: pgk
EamA
selenite
pyruvate
fumarase B: fumB
pyridoxamine
a tRNA
L-arabinosedegradation I
nicotinamidemononucleotide
CTP
tRNApseudouridine
CpxR
MscS
inosine
nicotinamide
guanosine-5’-triphosphate,3’-diphosphatepyrophosphatase: gpp
lipoyl-proteinligase: lipB
adenosylmethioninedecarboxylase: speD
5’-deoxyadenosine
5-phospho-beta-D-ribosyl-amine
CDP-diglyceridesynthetase: cdsA
phosphatidylglycerophosphatase C
pyruvate
FhuE
L-tryptophan
biotin-carboxylcarrierprotein
succinate semialdehyde
fructose-1-phosphatase:yqaB
malatedehydrogenase(oxaloacetate-decarboxylating)(NADP+): maeB
beta-D-glucose
2-methylthio-N-6-
isopentyladenosine-37 tRNA
hydroxypyruvateisomerase: hyi
L-serinedeaminaseI: sdaA
4’-phosphopantetheine
enolase: eno
fructosebisphosphatealdolaseclass I: fbaB
fructose 6-phosphatealdolase1: fsaA
uridine-5’-phosphate
N-ethylsuccinimide
GDP-4-dehydro-6-deoxy-
D-mannose
3-alpha,12-alpha-
dihydroxy-7-oxo-5-beta-
cholanate
3-dehydroquinatesynthase: aroB
D-gluconate
3-phosphoshikimate-1-carboxyvinyltransferase:aroA
YtjB
thiaminediphosphate
tRNAArg2
YhgN
AcrAD-TolCmultidrug
effluxtransportsystem
ADP-heptose:LPSheptosyltransferaseI: rfaC
nicotinate-mononucleotideadenylyltransferase: nadD
inositolmonophosphatase:suhB
NMN nucleosidase
4-nitrobenzaldehyde
aspartatesemialdehydedehydrogenase: asd
lipoate
N5-carboxyaminoimidazoleribonucleotide
diacetylchitobiose-6-phosphate
methylglyoxalsynthase: mgsA
bifunctional riboflavinkinase / FMNadenylyltransferase: ribF
urate
a 2’-deoxyribonucleoside
triphosphate
3,4-dihydroxy-2-butanone 4-phosphatesynthase:ribB
OmpR-Pasp
sulphurdioxide
a polypeptide
cobinamide kinase: cobU
acetaldehydedehydrogenase2: mhpF
spermidineputrescine
phosphoribosylanthranilateisomerase: trpC
guanosine
ATP
AMP
L-aspartate
beta-hydroxyacyl-ACPdehydratase:fabZ
lysinedecarboxylase:cadA
a holo-[acp]
a lipopolysaccharide
D-fructose-6-phosphate
L-arginino-succinate
isopentenyldiphosphate
tyrosineaminotransferase: tyrB
7-aminomethyl-7-deazaguanine
indole-3-glycerol-phosphate
MinC
prephenatedehydrogenase: tyrA
folylpoly-alpha-glutamatesynthetase
dihydrouracil
hydrophilicsolute orion < 600 Da
RcsB
GntU
S-lactoylglutathionehydrolase: yeiG
NAD(P)H:quinoneoxidoreductase:wrbA
an L-1-phosphatidylserine
CMP
16S-rRNAs
1-amino-propan-2-ol
galactaratedehydratase: garD
a hexanoyl-[acp]
ZnuA/ZnuB/ZnuC ABCtransporter
UDP-L-Ara4O
L-galactonate
D-fructose-6-phosphate
menadiol
2-oxobutanoate
a ThiSsulfur-carrier
protein
methylglyoxal
allantoindegradation
IV (anaerobic)
an apo-GcvHprotein
2-oxoglutarate
H-Gcv-protein-(dihydrolipoyl)lysine
HdeB
D-glyceraldehyde-3-phosphate
2,3-bis(3-hydroxymyristoyl)-
beta-D-glucosaminyl1-phosphate
L-serineL-threonine
an mRNA with 5’-monophosphate
YgjV
L-rhamnoseL-lyxose
D-sorbitol
cis-aconitate
putrescineABC
transporter
CO2
ferredoxinNAD+reductase:hcaD
KDO2-(lauroyl)-lipid IVA
methioninesulfoxidereductaseB: msrB
coenzyme A
L-ribulokinase:araB
glutathione
adenylyl-glutamine synthase
N-acetyl-D-glucosamine-6-phosphateD-glucosamine-6-phosphate
D-fructose-6-phosphatebeta-D-glucose-6-phosphate
D-mannose-6-phosphate
GltF
pyridoxal
sulfatereduction I
(assimilatory)
formyl-CoAtransferase: frc
Li+
AcrAB-TolCmultidrug
effluxtransportsystem
xanthosine-5-phosphate
L-xylulose-5-phosphate
N-ethylmaleimide
a tRNAArg2containinginosine atthe wobble
position
L-idonate 5-dehydrogenase:idnD
Fe2+
PanF
2-dehydropantoate2-reductase: panE
NADH
4-hydroxy-L-threoninephosphatedehydrogenase,NAD-dependent: pdxA
NarP
erythrose 4-phosphatedehydrogenase:epd
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-
meso-2,6-diaminopimelate
ZraSR Two-Component
SignalTransduction
System
carboxylesterase:bioH
phenylacetate
OTHER BIOSYNTHESIS
ornithine decarboxylase,biosynthetic: speC
ArcB
UDP-GlcA C-4"-decarboxylase:arnA
a 2,3,4-saturated
fattyacyl-[acp]
fatty acidoxidationcomplex,alphacomponent:fadB
fused 4’-phosphopantothenoylcysteinedecarboxylase andphosphopantothenoylcysteinesynthetase: dfp
UDP-[N-acetyl-D-
glucosamine]n
CheB-Pasp: cheB
gamma-glutamylkinase-GP-reductasemultienzymecomplex:proA proB
an isocitratedehydrogenase
4-aminobutyrateaminotransferase: puuE
TorS-Phis443
YnfJ
D-ribulose-1-phosphate
CheB-Pasp: cheB
1,4-alpha-glucanbranchingenzyme:glgB
succinate
aspartate 1-decarboxylase:panD
dihydrodipicolinatereductase: dapB
isochorismate
L-serine
an rRNA
cyclopropanefatty acylphospholipidsynthase: cfa
acetaldehydedehydrogenase2: mhpF
O-succinyl-L-homoserine
malatesynthaseG: glcB
phosphopantetheineadenylyltransferase: coaD
an aldehyde
2-O-alpha-mannosyl-D-glycerate transportingphosphotransferase
system
L-valine L-leucineL-isoleucine
putrescine
selenide
phosphate
5-dehydro-4-deoxy-D-glucarate
6-phospho-D-gluconate
nucleosidediphosphatekinase: ndk
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatereductase: ispH
D-glycerate
HipA
CcmABCDEprotoheme
IX ABCtransporter
D-fructose-6-phosphate
L-fucose
propionyl-CoA
NmpC
UDP-N-acetyl-D-
glucosamine
uracilphosphorylase:deoA
branchedchain aminoacids ABCtransporter
AMP
bicarbonate
a tRNA
ArgO
D-erythrose-4-phosphate
cyclic-AMP
purinenucleotidase:yrfG
NADP(H)-dependent FMNreductase: ssuE
adenosinedeaminase: add
L,D-transpeptidaseYbiS: ybiS
glyoxylate
D-cycloserine beta-alanine
D-serine D-alanine
glycine L-alanine
formaldehydeoxidation II
(glutathione-dependent)
palmitatebiosynthesis
II (bacteriaand plants)
sulfate
L-alanine
isopentenyldiphosphate
isomerase: idi
ethanol
NarX-Phis
N-6-isopentyl
adenosine-37 tRNA
acetohydroxybutanoatesynthase: ilvH ilvI
a cis-vaccen-2-enoyl-[acp]
RhtA
all-trans-heptaprenyldiphosphate
glutamate-pyruvateaminotransferase:alaB
a reducedelectronacceptor
glucosyl-heptosyl3-
KDO2-lipid A-
phosphate
glutathionedisulfide
2,3-bis(3-hydroxymyristoyl)-
beta-D-glucosaminyl1-phosphate
YicJ
uridinephosphorylase:udp
dihydroneopterinaldolase: folB
2-dehydropantoyl-lactone reductase(B-specific)
phosphoenolpyruvatecarboxylase: ppc
QmcA
phosphoenolpyruvatecarboxykinase (ATP): pck
MalM
L-threo-3-phenylserine
propionyl-P
CopA
tRNAlys
phosphoglucoseisomerase: pgi
glyceraldehyde3-phosphatedehydrogenase-A complex: gapA
EIITre
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
23S rRNA 2’-O-ribose G2251methyltransferase:rlmB
UTP
acetyl-CoA
melibiose
HMP-PPhydrolase/ thiaminpyrophosphatehydrolase: nudJ
p-aminobenzoate
a (3R)-3-hydroxyacyl-[acp]
UhpB-Phis
NADP+
fumaraseA: fumA
RplL
ethyl-(2R)-methyl-(3S)-
hydroxybutanoate
phosphoglyceratemutase 2: ytjC
pyruvatekinaseI: pykF
multifunctional 2-keto-3-deoxygluconate
6-phosphatealdolase and 2-keto-4-hydroxyglutarate
aldolase andoxaloacetate
decarboxylase: eda
BarA-Phis
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
fumarate
S-ureidoglycolate
dTDP-4-dehydro-6-deoxy-
D-glucose
fructose bisphosphatealdolase class I: fbaB
a nucleicacid with aterminal 5’-phosphate
fructose 1,6-bisphosphatase II: glpX
YaaJ
L-lysine
MdoG
PspA
an oxidizedferredoxin
NAD+
a damagedDNA
(purine orpyrimidine)
PheP
cytosine
glycogenbiosynthesis I (from
ADP-D-Glucose)
a DNAsegment
a tetrahydrofolatepolyglutamate
XapB
purine nucleosidephosphorylase:deoD
alpha-L-arabinose
gluconokinaseI: gntK
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
rRNAcontaining 2’-O-methylcytosine
D-glyceraldehyde-3-phosphate
a thioredoxin
allantoateamidohydrolase:allC
galactitol-1-phosphate
glycolaldehyde
YbgQ
DNA with G-A mismatch
CheB-Pasp: cheB
4-acetamido-4,6-dideoxy-D-galactosetransferase: rffT
L-arginine
a peptide
a reducedflavodoxin
heme d
an octanoyl-[acp]
guanosine
methyl-1,4-benzoquinone
DcuR
a phosphatidylcholine
inosine
fructose 6-phosphatealdolase2: fsaB
tartronatesemialdehydereductase: garR
Fsr
phosphoglyceratekinase: pgk
dTDP-fucosamineacetyltransferase:rffC
alpha-D-glucose
dTDP-glucose4,6-dehydratase2: rffG
a 2,3,4-saturatedfatty acyl CoA
ferricdihydroxybenzoylserine
toxin ofthe YafQ-DinJ toxin-antitoxinsystem: yafQ
succinatesemialdehyde
6-phosphofructokinaseI: pfkA
K+
CMP
N-succinyl-L-diaminopimelatedesuccinylase:dapE
dAMP
biotin
tRNA containing 5-methylaminomethyl-
2-thiouridylate
homoserinekinase: thrB
anaerobicnucleoside-triphosphatereductaseactivatingsystem: fprnrdG nrdD
beta-N-acetylglucosaminidase:nagZ
anhydro-N-acetylmuramicacid kinase: anmK
orotate
sn-glycerol-3-phosphate
acetohydroxybutanoatesynthase: ilvN ilvB
choline
succinyl-CoA synthetase: sucC sucD
pyridoxal 5’-phosphate
dTTP
3-keto-L-gulonate 6-phosphate
NarK
oleate beta-oxidation
beta-D-glucose
fatty acid beta-oxidation I
ThiS
UTP
serineacetyltransferase:cysE
ferriccoprogen
ATP
H-Gcv-protein-
(lipoyl)lysine
acetaldehyde
lipid kinase:yegS
L-asparagine
a tRNA
phosphoribosyl-ATPpyrophosphatase: hisI
MrdB
6-carboxy-5,6,7,8-tetrahydropterin
BaeR-Pasp
6-phospho-D-gluconate
histidinol-phosphatase:hisB
mannose-6-phosphateisomerase: manA
(deoxynucleotides)(m)
UDP-glucose 4-epimerase: galE
YhjX
1,4-dihydroxy-2-naphthoyl-CoA
guanosine-5’-phosphate
a nucleoside
guanosine-3’,5’-bis(diphosphate) 3’-diphosphatase: spoT
D-alanine-D-alanineligase B: ddlB
7,8-dihydropteroate
crotonobetainyl-CoA
alpha-D-ribose-1-phosphate
tRNAsec
a 3-oxo-hexanoyl-[acp]
a 1,4-alpha-D-glucan
CbdAB
a glycerophosphodiester
UDP-galactose biosynthesis(salvage pathway from
galactose using UDP-glucose)
an ADP-sugar
GTP
GTPpyrophosphokinase: relA
maltose
glutaminase:yneH
OuterMembrane
FerricCitrate
TransportSystem
fosmidomycin
L-idonate
undecaprenyldiphosphatesynthase: ispU
dihydrodipicolinatesynthase: dapA
an N10-formyl-tetrahydrofolate
NAD+
xanthine
methyltransferasefor 50S ribosomalsubunit proteinL11: prmA
putrescine/spermidine
ABCtransporter
selenate
xanthosine
thymidinephosphorylase:deoA
adenosine 3’,5’-bisphosphate
glutamate racemase: murI
glycerol-3-P ABC
transporter
deoxyuridinekinase: tdk
GlnA
FtsE/FtsX ABCtransporter
glycine
3-chloro-D-alaninedehydrochlorinase:dcyD
potassiumion P-typeATPase
transporter
precursor-Z
YijP
homoserinedehydrogenase:metL
pyruvateoxidase:poxB
a phosphorylatedisocitrate
dehydrogenase
diaminopimelatedecarboxylase: lysA
cytidine
folylpoly-gamma-glutamatesynthetase:folC
trehalose 6-phosphate
2-octaprenylphenol
thiaminpyrophosphatehydrolase: nudJ
MipA
low-specificityL-threoninealdolase: ltaE
tetraacyldisaccharide4’-kinase: lpxK
L-ascorbate-6-phosphate
DNA withlesion
catabolicthreoninedehydratase: tdcB
lipoate
a citryl-[acp]succinylglutamatedesuccinylase: astE
pyridoxal
alcoholdehydrogenase:adhE
a tetrahydrofolatepolyglutamate
fumarase A: fumA
gamma-butyrobetaine
AP siteremoved
from DNA
a drug
succinyl-CoA
ammoniumhydroxide
a FeS-protein
lauroylacyltransferase:lpxL
D-erythrose-4-phosphate
D-aminopropanoldehydrogenase:gldA
superpathway of KDO2-lipid A biosynthesis
dihydroxy-aciddehydratase: ilvD
phosphateacetyltransferase: pta
2-methylcitratecycle I
folylpoly-alpha-glutamatesynthetase
L-aspartate
YihN
citratesynthase: gltA
serineactivatingenzyme: entF
cadaverine
pyruvateformate-lyase: tdcE
cobalamin-independent
homocysteinetransmethylase:
metE
2,3-diketo-L-gulonate
pyruvatedehydrogenasemultienzymecomplex: lpdaceF aceE
acetylglutamatekinase: argB
isocitratedehydrogenase: icd
2-hydroxyglutarate
mannose-6-phosphateisomerase:manA
propionate
guanosine-5’-diphosphate
PsiE
vitaminB12 outermembranetransportcomplex
succinate
AlsR-allose
a DNAadenine
DNA withlesion
spermidine
L-tryptophan
S-formylglutathionehydrolase: yeiG
dihydropteridinereductase: nfsB
L-alanine
H2O
ThDPadenylyltransferase
YigG
RNA(n)
tRNA (m1G37)methyltransferase:trmD
prolinedegradation I
L-methionyl-tRNAfmet
a cis-delta3-decenoyl-[acp]
N-acetylglutamylphosphatereductase: argC
sugar phosphatase: ybiV
2’-(5-triphosphoribosyl)-3’-dephospho-CoA
D-alanyl-D-alanine
a nucleosidemonophosphate
histidineABC
transporter
KDOIII-lipopolysaccharide
methanol
a 3-oxo-decanoyl-[acp]
an acyl-CoA
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylatesynthase: menD
taurine ABCtransporter
sugarphosphatase:yigL
glucosamine-6-phosphatedeaminase: nagB
MntH
CheY-Pasp
Tsrglu-Me
branched-chainamino-acidaminotransferase:ilvE
RcsB-phosphate
tyrosineaminotransferase:tyrB
branched-chainamino-acidaminotransferase:ilvE
MsbA
ADP-L-glycero-D-mannoheptose-6-epimerase: rfaD
Ca2+
methylerythritolphosphate pathway
phosphoenolpyruvate
glyceratekinaseII: glxK
aldehydedehydrogenaseA, NAD-linked: aldA
D-gluconate
a reducedferredoxin
7-cyano-7-carbaguanine
acetaldehyde
diadenosinetetraphosphatase:apaH
CPS-53 (KpLE1)prophage;deoxyribonucleoside5’-monophosphatephosphatase: yfdR
aminomethyltransferase: gcvT
Eco
Osmoregulatory Two-ComponentSignal Transduction System
dATP
Lipid A-core
ATP
pryidoxinetranporter
L-methionine
pyridoxalkinase: pdxK
lipoate
proteindisulfideisomerase:dsbC
uroporphyrinogendecarboxylase: hemE
beta-hydroxyacyl-ACP dehydratase: fabZ
GDP-alpha-D-mannose
phosphoribosyl-formamido-carboxamide
deoxyguanosine
NADPH
long chainpolyphosphate
dCMPphosphohydrolase:yfbR
isethionate
6-carboxy-5,6,7,8-tetrahydropterinsynthase: queD
meso-diaminopimelate
GDP-mannosemannosylhydrolase:gmm
cadaverine
purine nucleotides de novo biosynthesis I
spermidinesynthase:
speE
glutaminase B
N-acetyl-L-glutamate 5-
semialdehyde
SbmA
succinylornithinetransaminase: astC
AMP
pyruvatekinaseII: pykA
fumaraseB: fumB
L-tyrosine
a malonyl-[acp]
aconitatehydratase1: acnA
adenylyl-[glutaminesynthetase]
glycerol
1,6-anhydro-N-acetylmuramicacid recycling
acetaldehydedehydrogenase:adhE
phenylacetyl-CoA
EvgA
3,5-tetradecadienoate
RstB-Phis
3-phenylpropionate-2’,3’-dihydrodioldehydrogenase: hcaB
chorismate
aspartateaminotransferase,PLP-dependent: aspC
L-glutamine
D-gluconate
ATP
2-dehydro-3-deoxy-D-gluconate
acetyl-CoA
transaldolaseA: talA
multidrug
beta-hydroxyacyl-ACPdehydratase: fabZ
allose-6-phosphateisomerase/ ribose-5-phosphateisomeraseB: rpiB
modulatorof RNase IIstability: gmr
ZraS-Phis
ethanol
malonyl-CoA
uridylyl-[GlnK]
ADP-L-glycero-
D-manno-heptose
EIIGat
sugarphosphatase:ybiV
L-seryl-AMP
acetaldehyde
L-rhamnulosekinase: rhaB
D-glyceraldehyde-3-phosphate
superpathway of methylglyoxal degradation
L-tryptophan
beta-D-glucose 1-phosphate
dihydrolipoamideL-leucine
molybdopteringuanine
dinucleotide
allantoinase:allB
proteinkinase: yeaG
3-dehydroquinate
L-seryl-AMP
all-trans-geranyl-geranyl
diphosphate
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
NAD-dependentdihydropyrimidinedehydrogenase:yeiA yeiT
pyridine nucleotidetranshydrogenase
enterochelinesterase: fes
UTP
uracilphosphorylase:deoA
FAD
L-arginine
D-glycerate
methylmalonyl-CoAdecarboxylase: scpB
CMP-3-deoxy-D-manno-
octulosonate
glycolate
D-xylulose-5-phosphate
PhoR
L-glutamate
acetyl-CoA
hydroquinone
L-glutamate
UDP-2,3-diacylglucosaminehydrolase: lpxH
L-aspartate
L-1,2-propanediol
cyclopropanefatty acid
(CFA)biosynthesis
BarA-Phis
cAMPphosphodiesterase:cpdA
ribonucleosidehydrolase 3: rihC
malatedehydrogenase:mdh
S-formylglutathione
deoxyribose-5-phosphate
beta-D-glucose-6-phosphate
myristoyl-acylcarrier protein(ACP)-dependentacyltransferase:lpxM
a tRNAprecursor
superpathwayof menaquinone-8 biosynthesis
pimeloyl-CoA
PhnC/PhnD/PhnEalkylphosphonateABC transporter
PhoRB Two-Component
SignalTransduction
System
XylF/XylG/XylH
xylose ABCtransporter
4-carboxyaminoimidazoleribonucleotide
fructose-1-phosphate
beta-D-glucose-6-phosphate
glyoxylate
a tRNA
deoxycytidine
dUMP
beta-D-glucose
acetatekinase B: ackB
lipidhydroperoxideperoxidase: tpx
L-fuculose-phosphatealdolase: fucA
2-C-methyl-D-erythritol-2,4-
cyclodiphosphate
alpha-L-fucose
a citratelyase holo-[acyl-carrier
protein]
GltIJKLglutamate
ABCtransporter
homoserine O-succinyltransferase:metA
aconitatehydratase 1: acnA
D-xylulose-5-phosphate
an acetoacetyl-[acp]
propionyl-CoA
isovaleryl-CoAdehydrogenase/ predictedacyl-CoAdehydrogenase:aidB
phosphorylatedserine/threonine
kinase HipA
UDP-3-O-(3-hydroxymyristoyl)
glucosamine
phosphoglycolatephosphatase: gph
D-xylulose-5-phosphate
ThiI: thiI
seryl-tRNAsynthetase:serS
rRNAcontaining N1-methylguanine
L-valine
L-carnitinyl-CoA
colanic acid
methionineadenosyltransferase:metK
cyanase:cynS
an oxidizedelectronacceptor
5’-deoxyadenosine
L-ornithine
GMP-N-epsilon-(N-alpha-acetyl lysinemethyl ester) 5’-phosphoramidate
methylglyoxal
NarL
methyleneTHFenzyme: folD
3-mercaptopyruvate
beta-D-glucose-6-phosphate
N-acetylneuraminate
glutaminesynthetase:glnA
D-alanine
CirA
pyridoxamine5’-phosphate
YfjS
oxaloacetate
dTDP
L-methionine
glycogenphosphorylase-limit dextrinalpha-1,6-glucohydrolase:glgX
lactose
D-ribose
D-ribose-5-phosphate
EvgS-Phis
L-lactaldehyde
L-glutamate
S-acetyldihydrolipoamide
sulfite reductase-(NADPH): cysI cysJ
cadaverine
DcuB
a beta-D-glucuronoside
3-oxoacyl-CoA
O-succinylhomoserine(thiol)-lyase: metB
protoporphyrinogen IX
D-lactate
L-glutamate
YifK
N-acetylglucosamine-6-phosphatedeacetylase: nagA
acetolactatesynthase: ilvMilvG_2 ilvG_1
adenosine 3’,5’-bisphosphate
superpathwayof hexuronide
and hexuronatedegradation
L-homocysteine
NAD+
phosphoenolpyruvate
1,6-anhydro-N-acetylmuramate
MdoD
pyruvatedehydrogenase:aceE
YdeA
enoyl-ACP reductase(NADPH): fabI
undecaprenyldiphosphatesynthase: ispU
dihydroneopterintriphosphatepyrophosphohydrolase:nudB
a DNA withalkylatedadenine
enoyl-ACP reductase(NAD[P]H): fabI
beta-hydroxydecanoyl-ACP dehydrase: fabA
dihydrofolatereductase: folM
RNasePH: rph
L-ascorbate
alpha-ribazole-5’-P
lipoyl-proteinligase A: lplA
glycine
glyoxylate
3-phenylpropionate and3-(3-hydroxyphenyl)
propionate degradation
L-galactonatedegradation
undecaprenyl N-acetyl-glucosaminyl-N-acetyl-
mannosaminuronatepyrophosphate
a mismatchedDNA base pair
L-serinedeaminaseIII: tdcG
GTP cyclohydrolaseI: folE
pyridine nucleotidetranshydrogenase:pntA pntB
23S rRNApseudouridinesynthase: rluD
aldehydedehydrogenase:astD
aspartatekinase: metL
pyruvate formate-lyase: pflB
7,8-diaminopelargonicacid synthase: bioA
acetaldehydedehydrogenase2: mhpF
H+
AMP
cobalamin-independent
homocysteinetransmethylase:
metE
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
D-ribose
uracil-DNA-glycosylase:ung
a 2’,3’-cyclic-phosphate-terminated
RNA
KDO2-(palmitoleoyl)
-lipid IVA
Mg2+Co2+Ni2+
a DNAcontainingabasic site
cobalamin-dependenthomocysteinetransmethylase:metH
beta-hydroxyacyl-ACPdehydratase: fabZ
pyruvatekinase II: pykA
orotidine-5’-phosphate
alpha-L-arabinose
KASI: fabB
phosphoribosylformylglycinamidesynthetase: purL
carbamate
KdgT
a pyrimidine
N-succinyldiaminopimelate-aminotransferase: argD
threoninesynthase:thrC
a protein
L-citrulline
octaprenyldiphosphatesynthase: ispB
acetatekinase: ackA
EamB
YfbV
trimethylamineN-oxide
asparaginaseI: ansA
an rRNA
dTDP-D-fucosamine
superpathway of glycolysisand Entner-Doudoroff
acetate
malate
sugarphosphatase:yidA
coenzyme A
CadB
palmitoleate
16S rRNA m7G527methyltransferase:rsmG
7-aminomethyl-7-deazaguanine
FtsB
Lpp
ThiS-COAMP
5-phosphoribosyl-N-formylglycineamidine
AMP
uridine-5’-phosphate
GTP
phosphoribulosylformimino-AICAR-P
DcuB
pyridoxamine
glycerol
homoserine O-succinyltransferase:metA
nitrite
D-sedoheptulose-7-phosphate
psicoselysine
L-phenylalanine
dCMP
KdpDE Two-Component
SignalTransduction
System
EIINag
an (R)-3-hydroxymyristoyl-
[acp]
glutathionylspermidine
YihO
NanT
argininosuccinatesynthase: argG
23S rRNAand tRNApseudouridinesynthase: rluA
dethiobiotin
acetyl-CoAcarboxyltransferase:accD accA
chloride
maltodextringlucosidase:malZ
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenyl-N-acetylglucosamine
beta-hydroxydecanoyl-ACP dehydrase: fabA
undecaprenyl-N-acetyl-alpha-
D-glucosaminyl-pyrophosphate
L,D-transpeptidaseYcbB: ycbB
1-deoxy-D-xylulose
a trans-2-enoyl-CoA
a nucleotide
gamma-butyrobetainyl-
CoA
beta-D-glucuronidase:uidA queuine
altronateoxidoreductase:uxaB
a tRNA
a non-methylatedribosomalprotein L11
tRNAcontaininguridine at
position 54
EnvZ
pyridoxaltransporter
YejA/YejB/YejE/YejF ABCtransporter
pyruvate
GDP-L-fucose
chromatereductase:yieF
an (R)-3-hydroxybutanoyl-
[acp]
iron (III)hydroxamate
ABCtransporter
ADP-L-glycero-
D-manno-heptose
a quinone
L-serine
ADP-D-glucose
dihydrofolatereductase: folA
protoheme IX
isochorismate
NRZ
aminodeoxychorismatelyase: pabC
pyridine nucleotidetranshydrogenase,soluble: sthA
formaldehyde
an RNA
rRNAcontaining N2-methylguanine
glutathioneredox
reactions II
L-leucyl-tRNAleu
N-acetyl-D-mannosamine-6-phosphate
Tsrglu
shikimate
L-carnitinyl-CoA
lipoylateddomain
DcuC
2-cis,6-trans,10-trans-geranylgeranyldiphosphate
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
ADP
D-ribose
L-ribulose 5-phosphate4-epimerase:araD
transaldolaseB: talB
maltose ABCtransporter
a reducednitroaromatic
compound
L-methionine
YejM
di-trans,poly-cis-octaprenyldiphosphate
S-lactoyl-glutathione
L-glutamate
phosphatidylglycerol-prolipoproteindiacylglyceryltransferase; amajor membranephospholipid: lgt
glutamate-putrescineligase: puuA
putativenucleoside (IDP)diphosphatase:yibQ
NirC
pyrazinoate
sn-glycerol-3-phosphate
adenosylcobalamin salvagefrom cobinamide and cobalamin
Lipid A-core
guanine
all-trans-octaprenyl
diphosphate
YdeE
Zn2+
nucleosidediphosphatekinase: ndk
bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinonemethylase and S-adenosylmethionine:2-DMKmethyltransferase: ubiE
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
dihydroneopterinmonophosphatedephosphorylase
L,L-diaminopimelate
nitrite
CycA
isopentenyldiphosphate
proline ABCtransporter
salicin-6-phosphate
ureidoglycine
Na+
bifunctionalbiotin-[acetyl-CoA-carboxylase]ligase andtranscriptionalrepressor: birA
alpha-N-acetylneuraminate
CreB
a single-stranded
RNA
aliphaticsulfonate
ABCtransporter
D-carnitinyl-CoA
iron (III)hydroxamate
complex
maltose
2-aminomalonate-semialdehyde
GDPreductase:nrdB nrdA
an O-antigen
adenylosuccinatelyase: purB
KASI: fabB
cardiolipin synthase: cls
IMPdehydrogenase:guaB
cis-aconitate
KASIII: fabH
5’-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazolelyase: purB
a methylatedprotein
1-acylglycerol-3-phosphateacyltransferase: plsC
NRA
endonucleaseIII; specific forapurinic and/or apyrimidinicsites: nth
3-hydroxypropionate
KASII: fabF
adenosine
acetyl-CoA
adenosine
N2-succinyl-L-glutamate 5-semialdehyde
N-acetylneuraminate
mannitol-1-phosphate
allantoateamidohydrolase:allC
D-arabinose5-phosphateisomerase:kdsD
L,D-carboxypeptidaseA: ldcA
phosphoadenosine-5’-phosphosulfate
glycinecleavagesystem:gcvT gcvHgcvP lpd
NH4+
S-methyl-5’-thioadenosine
UDP-galactopyranosemutase: glf
a peptide
fused N-acetylglucosamine-1-phosphateuridyltransferaseand glucosamine-1-phosphateacetyltransferase:glmU
cellobiose-6-phosphatesalicin-6-phosphatearbutin-6-phosphate
a ribonucleosidediphosphate
pyruvateformate-lyaseactivatingenzyme: pflA
a stabilizedRecA
filament-DNA
complex
L-lactaldehyde
L-arginine
S-adenosyl-L-methionine
N-acetylglutamyl-phosphate
methylcitratesynthase: prpC
fatty acid oxidationcomplex, alphacomponent: fadB
3-hydroxybutyryl-CoA epimerase: fadJ
XylE
phenylpyruvate
7-cyano-7-deazaguaninereductase: queF
1-chloro-2,4-dinitrobenzene
Tapglu-Me
a trans-2-enoyl-CoA
tRNAmet
mono-, di-, ortrisaccharide< 600 Da
McrBCrestrictionendonuclease:mcrC mcrB
L-cystathionine
7,8-dihydrofolate
nitrite
TnaB
3-demethylubiquinol-8
allulose-6-phosphate3-epimerase:alsE
EIISga
pyruvate
23S rRNA m2A2503methyltransferase:rlmN
NtrB-P
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
N-succinyl-2-amino-6-ketopimelate
threoninedeaminase: ilvA
undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-
4-acetamido-4,6-dideoxy-D-galactose
pyrophosphate
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
N2-succinyl-L-ornithine
D-lactatedehydrogenase: dld
GDP-fucosesynthase: fcl
dimethylallyldiphosphate
serine/threonineproteinkinase: rdoA
galactokinase: galK
CybB
a phosphoprotein
ShiA
YdhE
D-allose
tRNAcontaining a
thionucleotide
L-methionine
YbfM
low-specificityL-threoninealdolase:ltaE
TorS
superpathway ofD-glucarate and
D-galactaratedegradation
PENTOSE PHOSPHATE PATHWAYS
D-altronate
Hda
EnvZ-Phis
3-(3-hydroxyphenyl)propionate
pyruvate dehydrogenase: aceE
5-phosphoribosyl1-pyrophosphate
L-rhamnonate
tetraacyldisaccharide4’-kinase: lpxK
ThiI: thiI
3-deoxy-D-manno-octulosonatecytidylyltransferase:kdsB
L-histidine
diaminetransaminase:ygjG
chemotaxis proteinmethyltransferase:cheR
acetohydroxybutanoatesynthase: ilvH ilvI
a thioredoxin
tRNAthr
3-phospho-L-serine
D-fructose-6-phosphate
D-arabinose
FMNphosphatase:ybjI
D-tagaturonate
pre-crRNA
molybdopterinsynthase
D-glucosamine1-phosphate
2-oxobutanoate
2-phosphoglycerate
homoserine
pyridoxamine5’-phosphate
6-phosphofructokinaseII: pfkB
thiosulfatesulfate
argininosuccinatelyase: argH
glycine
4-hydroxyphenylpyruvate
L-alanine
tetrahydrofolate
TatABCEproteinexport
complex
Cld
ribonucleaseII: rnb
L-glutamate
geranylfarnesyldiphosphate
phenylethylamine
thymidinephosphorylase:deoA
3-dehydro-shikimate
tRNAleu
Ni2+
acetate kinase: ackA
hydrogenase4: hyfH hyfFhyfE hyfDhyfC hyfBhyfA hyfG hyfI
a DNAcontainingabasic site
glycine
citrate
3-isopropylmalatedehydrogenase:leuB
2,3-diaminopropionateammonia-lyase: ygeX
L-selenocysteinyl-tRNAsec
lysinedecarboxylase2: ldcC
YfcA
D-ribulose-5-phosphate
D-arabinose5-phosphateisomerase:gutQ
argininedegradation
II (ASTpathway)
5-phosphoribosyl1-pyrophosphate
TyrP
an AP(apurinicor apyrimidinic)
site createdby glycosylic
bond cleavage
a tRNA
branched-chainamino-acidaminotransferase:ilvE
(R)-malate
phosphoglucomutase: pgm
OmpR
D-mannonatedehydratase:uxuA
D-tyrosine
purine nucleosidephosphorylase:deoD
lipid Adisaccharidesynthase: lpxB
fucosedegradation
uridine-5’-diphosphate
2-dehydro-3-deoxy-D-gluconate
ammonia
FMN
acetyl-CoA
1-deoxy-D-xylulose 5-phosphate
(2R,3S)-3-isopropylmalate
acetyl-CoA
nicotinate adeninedinucleotide
a [citrate(pro-3S)-
lyase](acetylform)
sn-glycerol-1-phosphate
N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-
2,6-diaminopimelyl-D-alanyl-D-alanine-
diphosphoundecaprenyl-N-acetylglucosamine
XTPase: yjjX
tryptophandegradation
II (viapyruvate)
2-aceto-2-hydroxy-butyrate
putativephenylacetate-CoA oxygenase:paaE paaDpaaC paaB paaA
EIIGut
lipoate acetyltransferaseN6-(lipoyl)lysine
acetaldehydedehydrogenase:aldB
UDP-N-acetylglucosamineacyltransferase: lpxA
acetaldehyde
non-specific ion/solutemaltose
DcuS
L-histidine
dihydroneopterintriphosphatepyrophosphohydrolase:nudB
glutaredoxinreductase
a C4-dicarboxylatea C4-dicarboxylate
hydrophilicsolute orion < 600 Da
L-arginyl-tRNAarg
3-chloro-D-alanine
FadL
S-adenosyl-L-methioninecycle I (prokaryotic)
L-glutamine
5-amino-levulinate
L-cysteineO-acetyl-L-serine
a 2,3,4-saturated
fattyacyl CoA
cardiolipin
ureidoglycolase:allA
pyruvatesynthase
alpha-D-mannose 1-phosphate
serine/threoninekinaseHipA: hipA
EntS-TolCEnterobactin
EffluxTransportSystem
AmpG
HtrE
L-cysteinedesulfhydrase:tnaA
DNAcontaining arecognition
site
H+
galactosyl-glucosyl3-heptosyl3-
KDO2-lipid A-bisphosphate
D-allose-6-phosphate
guanosine
2-deoxy-D-glucose
protoheme IX
hydroxymethylpyrimidine
an AP(apurinicor apyrimidinic)
site createdby glycosylic
bond cleavage
stationaryphasemismatch/uracil DNAglycosylase:mug
pyruvate
tagatose-1,6-bisphosphate
7-alpha-hydroxysteroiddehydrogenase:hdhA
a lipopolysaccharide
a sugarphosphate
SECONDARY METABOLITES DEGRADATION
L-glutamate
FeoB
homocysteinemethyltransferase:mmuM
N-(5’-phospho-L-ribosyl-formimino)-5-amino-1-(5’-phosphoribosyl)-4-imidazolecarboxamideisomerase: hisA
histidinoldehydrogenase:hisD
tyrosinephosphatase:wzb
H2
dihydroxyacetonephosphate
2-methylisocitratelyase: prpB
fused heptose7-phosphatekinase/heptose1-phosphateadenyltransferase:rfaE
ATP
D-glucosamine-6-phosphate
L-lactaldehyde
S-adenosyl-L-methionine
N-acetylmuramicacid 6-phosphateetherase: murQ
NAD+
PhoQ
D-gluconate
3-keto-L-gulonate 6-phosphatedecarboxylase:ulaD
tRNA(m5U54)methyltransferase:trmA
D-glucaratedehydratase:gudD
hydroxymethylpyrimidinephosphate
acetate
2-O-alpha-mannosyl-D-glyceratedegradation
UTP
mannose-1-phosphateguanylyltransferase:cpsB
mureintripeptide
ABCtransporter
superpathway ofalanine biosynthesis
an L-1-phosphatidyl-
glycerol
UDP-glucose-hexose-1-phosphateuridylyltransferase:galT
an alkanesulfonate
AceF
2-oxoglutarate
a deoxynucleotideD-alanine
a 2’-deoxyribonucleoside
monophosphate
aryl carrierprotein/ serine
activatingenzyme
superoxide
glycolate
purine nucleosidephosphorylase:deoD
4-diphosphocytidyl-2C-methyl-D-erythritolsynthase: ispD
dihydroxyacetone phosphate
1-deoxyxylulose-5-phosphatesynthase: dxs
MdoC
N-acetylmuramate6-phosphate
D-galactose
PhoB-Pasp
prephenatedehydratase: pheA
BasS
a drug
a reducedferredoxin
BioP
NtrB
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatereductase: ispH
an aliphaticalpha,omega-
diamine
acetoacetate
beta-D-galactose
formate
a ThiS-ThiI acyl-disulfide
resolution ofrecombinational
junctionformation of twointact strands
acetohydroxybutanoatesynthase: ilvMilvG_2 ilvG_1
fused N-acetylglucosamine-1-phosphateuridyltransferaseand glucosamine-1-phosphateacetyltransferase:glmU
deoxyadenosine
K+
fructoselysine-6-phosphate
TCA CYCLE
dTDP-4-dehydrorhamnose3,5-epimerase: rfbC
LacY
HYD2
YojI
glycine betainebiosynthesis
I (Gram-negativebacteria)
acetohydroxybutanoatesynthase: ilvMilvG_2 ilvG_1
deoxyadenosinedeaminase: add
pyridoxal 5’-phosphate
dTDP-4-dehydro-6-deoxy-
D-glucose
deoxyguanylatekinase: gmk
an AP(apurinicor apyrimidinic)
site createdby glycosylic
bond cleavage
S-adenosylmethionine:tRNAribosyltransferase-isomerase: queA
propionatekinase: ackA
fumarate
L-methionine-(S)-S-oxide
a phosphoprotein
inosine-5’-phosphate
nicotinamidemononucleotide
pyruvate
a 3-oxo-meristoyl-[acp]
thymidinekinase: tdk
urea
D-sedoheptulose7-phosphateisomerase: lpcA
coenzyme A
2-keto-3-deoxy-L-
rhamnonate
uroporphyrinogen-III
mixed acid fermentation
xanthine-guaninephosphoribosyltransferase: gpt
ArcB-Phis717
phosphate acetyltransferase: pta
beta-N-acetylneuraminatea carboxylate
trans-2-enoyl-CoAreductase(NADPH)
a supercoiledduplex DNA
BrnQ
D-fructuronate
dihydrolipoyltranssuccinylase: sucB
uridine
PPPi
D-myo-inositol(1,2,3,4,5)-
pentakisphosphate
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
betainealdehyde
shikimate-3-phosphate
tRNAtrp
a tRNA containingepoxyqueuosineat position 34
cystathionine-beta-lyase: metC
ADP-L-glycero-beta-
D-manno-heptose
biosynthesis
a tRNA
cadaverine
sugarphosphatase:yigL
3-deoxy-D-arabino-heptulosonate-7-phosphate
L-alanine
CheY
fructoselysineand
psicoselysinedegradation
lipoyl-proteinligase: lipB
sugarphosphatase:yidA
FtsL
4-(glutamylamino)butanoate
nitric oxide
cob(I)alamin
alpha-D-glucose1-phosphate
RNA 3’-terminalphosphatecyclase: rtcA
adenineglycosylase;G.C --> T.Atransversions:mutY
GDP-alpha-D-mannose
INORGANIC NUTRIENTS METABOLISM
MdoH
shikimate kinase I: aroK
malate
pentose phosphate pathway
2-dehydro-3-deoxyphosphoheptonatealdolase: aroH
alpha-D-galactose1-phosphate
a quaternary amine L-proline
PitB
CO2
phosphoribosyl-AMP
thymidine
L-proline
2,3-dihydroxybenzoyl-
AMP
MscL
cytosine
NAD+
NADphosphorylation anddephosphorylation
16S rRNA m5C967methyltransferase:rsmB
NAD+
L-cysteinedesulfhydrase
melibiosemelibiose
trans-delta2,cis-delta4-
decadienoyl-CoA
3,4-dihydroxyphenylacetate
pyruvate
lineardimeric GMP
folylpoly-alpha-glutamatesynthetase
UDP-3-O-(3-hydroxymyristoyl)-
N-acetylglucosamine
23S rRNA 2’-O-ribose U2552methyltransferase:rlmE
aminopeptidaseA/I: pepA
AraE
23S rRNA m5U747methyltransferase:rlmC
dCTPdeaminase: dcd
2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinonehydroxylase: ubiF
mannoseisomerase:yihS
2-octaprenylphenolhydroxylase: ubiB
KdpE-Pasp
D-3-phosphoglyceratedehydrogenase: serA
a trans-delta2-enoyl-
acyl-[acp]
pyruvateformate-
lyase
EIIMtl
PhoP-Pasp
ribonucleosidehydrolase 1(pyrimidine-specific): rihA
oxalurate
(KDO)-lipid IVA
MdtM
L-glyceraldehyde3-phosphate
L-fuculokinase:fucK
lipoyl-proteinligase A: lplA
hydrogenase3: hycE hycBhycG hycFhycC hycD
nitrousoxide
D-glycerate
KASI: fabB
glyceroldehydrogenase:gldA
cytidine
D-galacturonateD-glucuronate
MelB
bifunctional riboflavinkinase / FMNadenylyltransferase: ribF
fused diaminohydroxyphosphoribosylaminopyrimidinedeaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase: ribD
thiamin(thiazolemoiety)biosynthesisprotein: thiF
dTTP
dihydroxy-aciddehydratase: ilvD
an alcohol
dihydroxy-aciddehydratase: ilvD
indole-3-glycerolphosphatesynthase: trpC
adenine
a standardalpha
amino acid
tryptophan synthase,beta subunit dimer: trpB
chorismatesynthase: aroC
ATP
nicotinamide
3-dehydroquinatedehydratase: aroD
FocA
N-(5’-phosphoribosyl)-anthranilate
23S rRNAand tRNApseudouridinesynthase: rluA
5-keto-D-gluconate 5-reductase:idnO
pyruvate
2,3-dihydroxybenzoyl-
AMP
D-glucarate
5-keto-D-gluconate 5-reductase:idnO
tyrosineaminotransferase: tyrB
threoninedeaminase: ilvA
aspartatekinaseIII: lysC
malate fumarateL-aspartate
acetylmaltose
16S-rRNAs
dGTP
hydroxymethylbilane
adenine
2,5-diamino-6-(ribosylamino)
-4-(3H)-pyrimidinone5’-phosphate
cyanatedegradation
D-ribose
Tsrglu
D-ribose-5-phosphate
L-cysteinedesulfhydrase
NarU
inorganicpyrophosphatase: ppa
ribosomal-protein-S5-alanine N-acetyltransferase:rimJ
FrlA
ChaA
a glycerolester
acetolactatesynthase: ilvN ilvB
YeeF
2-isopropylmalatesynthase: leuA
ZraP
cobalamin-independenthomocysteinetransmethylase:metE
an (R)-3-hydroxypalmitoyl-
[acp]
L-leucine
an N-acetyl-D-
hexosamine
aminopropylcadaverine
an mRNA
NADPHquinonereductase:mdaB
AaeABHydroxylated,
AromaticCarboxylicAcid EffluxTransport
System
glycolate
CheB-Pasp: cheB
L-asparagine
(2S)-2-isopropylmalate
formaldehyde
FimD
L-tryptophan
bifunctional beta-cystathionase,PLP-dependentand regulatorof maltoseregulon: malY
aspartatekinase: metL
a properlymatched
DNAbase pair
homoserinedehydrogenase:thrA
L-lysine
CPS-53 (KpLE1)prophage;deoxyribonucleoside5’-monophosphatephosphatase: yfdR
2-ketoglutaratedehydrogenase complex
guanosinekinase: gsk
L-serinedeaminaseII: sdaB
2-deoxyglucose-6-phosphatase:yniC
4-diphosphocytidyl-2-C-methylerythritolkinase: ispE
GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-DAP-D-AlaGlcNAc-1,6-anhMurNAc
thiaminediphosphate
1-deoxy-D-xylulose5-phosphatereductoisomerase: dxr
formate-tetrahydrofolateligase
lipid IVA
dCDP
2-ketobutyrateformate-lyase
/ pyruvateformate-lyase
ferricenterobactin
ABCtransporter
a nucleoside-5’-phosphate
carbamoyl phosphatesynthetase: carA carB
a DNAwith uracil
DNAn
a purine base
L-serine
dihydroorotate oxidase: pyrD
tRNA withGU(N)
anticodon
lipoyl-proteinligase: lipB
YgjD
predicted L-galactonateoxidoreductase:yjjN
sulfate ABCtransporter
O-succinyl-L-homoserine
EmrAB-TolC
multidrugefflux
transportsystem
a methylatedribosomalprotein L11
taurinedioxygenase:tauD
hydroxypyruvate
beta-phosphoglucomutase: ycjU
[+ 2 isozymes]
a tRNAcontaining N7-methylguanine
LysP nicotinamideriboside
valine-pyruvateaminotransferase:avtA
palmitoyltransferasefor LipidA: pagP
CreC-Phis
an alcohol
ferricenterobactin
an unstableRecA
filament-DNA
complex
putative enoyl-CoA hydratase/isomerase ofphenylacetatedegradation: paaF
YhhJ
tetrapyrrolebiosynthesis I
L,D-carboxypeptidaseA: ldcA
guanosine-5’-phosphate
lipopolysaccharidecore biosynthesis;heptosyl transferseIV; probably hexosetransferase: waaU
glutathione
7,8-diaminopelargonate
myristoyl-acylcarrier protein(ACP)-dependentacyltransferase:lpxM
undecaprenyldiphosphatesynthase: ispU
lipopolysaccharidecore biosynthesisprotein; heptosyltransferase III: rfaQ
L-phenylalanyl-tRNAphe
a prolipoprotein
CO2
sirohydrochlorin
L-serine
D-alanine
HtpX
guanosine-5’-phosphate
H-Gcv-protein-(lipoyl)lysine
sn-glycerol-3-phosphate
UDP-N-acetyl-D-glucosaminebeta-1,6-N-acetyl-D-glucosaminyltransferase:pgaC
di-trans,poly-cis-hexaprenyldiphosphate
fused nitric oxidedioxygenase anddihydropteridinereductase 2: hmp
farnesyldiphosphatesynthase: ispA
2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
D-tagaturonate
bicarbonate
spermidine
di-trans,poly-cis-
undecaprenyldiphosphate
aminodeoxychorismatesynthase: pabA pabB
acetoacetyl-CoA
hybrid-cluster
proteinred
3-hydroxypropionaldehyde
L-lysine
O-phospho-L-homoserine
ATP
L-aspartate
3-octaprenyl-4-hydroxybenzoatecarboxy-lyase: ubiD
bifunctional 3-demethylubiquinone-83-O-methyltransferaseand 2-octaprenyl-6-hydroxyphenolmethylase: ubiG
N2-succinyl-L-arginine
L-cysteine
a quercetin
putativeselenatereductase:ygfMxdhD ygfK
YidK
an aliphaticalpha,omega-
diamine
uridylyl-glutaminesynthase PII
ADP
asparaginesynthetaseB: asnB
a carboxylate
2,4-dinitrophenyl-S-glutathione
a trans oct-2-enoyl-[acp]
pyruvate
YiaMNOBindingProtein-
dependentSecondary(TRAP)
Transporter
4-hydroxybenzoate
isopentenyl-adenosineA37 tRNAmethylthiolaseMiaB: miaB
mannitol-1-phosphate
a debranchedlimit dextrin
nicotinamidemononucleotide
a trans-delta2-decenoyl-[acp]
enterobactinbiosynthesis
lipoyl-ACP
Chemotactic SignalTransduction System
a palmitoleoyl-[acp]
dUDP
2-oxo-3-deoxygalactonate6-phosphatealdolase: dgoA
pyruvate
2-dehydro-3-deoxy-D-galactonate
precorrin-2dehydrogenase:cysG
Cr6+
acetate
fatty acidoxidationcomplex,alphacomponent:fadB
Cd2+Zn2+
superpathwayof glycol
metabolismand degradation
tagatose-6-phosphate
acyl carrier proteinphosphodiesterase:acpH
6-phospho-D-gluconate
D-galactitol
hydrogen sulfide
ATP
YcfT
NarP-Pasp
tRNAileX
salvage pathwaysof pyrimidine
deoxyribonucleotides
2’-deoxyguanosine-5’-diphosphate
5’-methylthioadenosine/S-adenosylhomocysteinenucleosidase: mtn
L-phenylalanine
a glycogen
acetyl-CoA synthetase(AMP-forming): acs
an oxidizedthioredoxin
formate
16S rRNA m3U1498methyltransferase:rsmE
4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate
4-aminobutyrate
beta-D-ribopyranose
a fatty acid
acetolactatesynthase: ilvH ilvI
L-methionyl-tRNAmet
isopropylmalateisomerase:leuD leuC
an L-1-phosphatidyl-ethanolamine
5-aminoimidazoleribonucleotide
acetate
lipoyl-proteinligase A: lplA
coenzyme A
L-ascorbate-6-phosphate
alaninedegradation I
agmatine
3-phosphoglycerate
dTDP-alpha-L-
rhamnose
GltS
D-galactose
2’-deoxyadenosine-5’-diphosphate
OsmY
GDP-alpha-D-mannose
AtoSC Two-Component
SignalTransduction
System
tartronatesemialdehyde
octyl beta-1,6-D-galactofuranosyl-
alpha-D-glucopyranoside
Cu+
GMPsynthetase:guaA
ribonucleoside-diphosphatereductase:nrdB nrdA
asparaginesynthetaseA: asnA
ribonucleoside-diphosphatereductase 2:nrdF nrdE
SucB
GARtransformylase2: purT
SucB-lipoate
IMPcyclohydrolase:purH
guanine
2-dehydro-3-deoxy-D-gluconate-6-phosphate
2-oxoglutarate dehydrogenasecomplex: lpd sucB sucA
L-rhamnoseisomerase: rhaA
5-enolpyruvyl-shikimate-3-phosphate
ADPreductase:nrdB nrdA
K+
UDP-glucose-hexose-1-phosphateuridylyltransferase:galT
CTP
PPPi
porphobilinogen
pyruvate
aspartateammonia-lyase: aspA
beta-L-rhamnose
pyridoxalphosphatase:ybhA
glyoxylatereductase:ghrA
RseC
dihydroorotase: pyrC
L-tryptophan
Trgglu-Me
phosphoribosyl-AMPcyclohydrolase: hisI
hypoxanthine
nucleosidediphosphatekinase: ndk
cis-aconitate
anaerobiccoproporphyrinogenIII oxidase: hemN
citratelyase: citEcitF citD
histidinol-phosphateaminotransferase:hisC
D-glyceraldehyde-3-phosphate
2-oxoglutarate
succinate semialdehydedehydrogenase,NAD+-dependent: sad
a cis,trans-polyisoprenyln-PP
nucleosidediphosphate kinase: ndk
ribonucleoside-triphosphatereductase: nrdD
N-acetylglucosaminyltransferase: murG
a singlestranded
DNA
L-arginine
thiamine-phosphate
4-methyl-2-oxopentanoate
23S rRNAm3psi1915methyltransferase:rlmH
D-fructose-6-phosphate
D-arabinose5-phosphate
alcoholdehydrogenase:adhE
sugarphosphatase:yigL
ribonucleosidehydrolase 1(pyrimidine-specific): rihA
pyruvate
pyridoxine-5’-phosphate
carbamoylphosphatesynthetase:carA carB
replicativeDNAhelicase:dnaB
DNA combinedwith exogenousDNA to form a
recombinationaljunction
L-methionine
formate
DcuR-Pasp56
(KDO)-lipid IVA
5-amino-6-ribitylamino-2,4(1H,3H)-
pyrimidinedione
dihydroxyacetonephosphate
L-asparagine
L-alanine
3-octaprenyl-4-hydroxybenzoatedecarboxylasetogether withUbiG: ubiX
a (3S)-3-hydroxyacyl-CoA
aspartatekinase: thrA
2-phosphoglycolate
2’-deoxyguanosine-5’-diphosphate
4-coumaroyl-CoA
acetyl-CoA
6-phospho-beta-glucosidaseB; cryptic:bglB
FtsW
adenine
N-acetyl-L-glutamate
riboflavin
beta-D-glucose-6-phosphate
malate
D-allose
2-phospho-4-(cytidine 5’-diphospho)
-2-C-methyl-D-erythritol
a polypeptide
a tRNAcontainingqueuosine
acetaldehyde
PflB
fructose-1,6-bisphosphatase I: fbp
rep helicase,a single-strandedDNAdependentATPase: rep
fructose bisphosphatealdolase class II: fbaA
2-keto-3-deoxy-L-
rhamnonate
alpha-D-glucose6-phosphate
UDP-N-acetylmuramoylalanyl-D-glutamate 2,6-diaminopimelate ligase: murE
maltodextrinphosphorylase:malP
undecaprenyldiphosphatesynthase: ispU
GltP
UDP-N-acetylmuramate
(S)-methylmalonyl-
CoA
CpxAR Two-Component
SignalTransduction
System
malate dehydrogenase: mdh
UDP-2,3-diacylglucosamine
hydrolase: lpxH
KefB
a tRNA
L-cysteinedesulfhydrase:metC
dihydroxyacetonephosphate
beta-ketoacyl-[acyl-carrier-protein] reductase: fabG
KASI: fabB
galactokinase: galK
KASI: fabB
KDO2-lipid A
chitobiosedegradation
GadC
methylglyoxalreductase(NADH-dependent): ydjG
phosphoglyceromutase1: gpmA
colanic acid building blocks biosynthesis
adenylylsulfatekinase: cysC
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
sn-glycerol-3-phosphate
glutathionesynthetase: gshB
lipoamide dehydrogenase: lpd
UDP-N-acetyl-D-
glucosamine
3-deoxy-D-manno-octulosonate8-phosphatephosphatase:kdsC
partially N- deacetylatedpoly-beta-1,6-
N-acetyl-D- glucosamine
DsdX
HcaT
UDP reductase:nrdB nrdA
glucosyl-heptosyl2-
KDO2-lipid A-
phosphate
(S)-1-pyrroline-5-carboxylate fructose-1,6-
bisphosphate
7,8-dihydro-D-neopterin
folylpoly-gamma-glutamatesynthetase:folC
an L-1-phosphatidyl-
glycerol
an RNA
ethyleneglycol
AqpZ
phosphopentomutase:deoB
S-adenosyl-L-methionine
DNAn
trehalose 6-phosphate
a 5,10-methylene-tetrahydrofolate
6-hydroxymethyl-7,8-dihydropterinpyrophosphokinase: folK
H+
IdnT
phosphoribosylglycinamideformyltransferase: purN
glutamyl-QtRNA(Asp)synthetase:yadB
lysinedecarboxylase:cadA
GMPreductase:guaC
a hydroquinone
undecaprenylphosphate-
alpha-L-Ara4FN
acetylphosphate
acetaldehyde
nickel ABCtransporter
beta-D-glucose-6-phosphate
agmatinase:speB
galactosyl-glucosyl2-heptosyl3-
KDO2-lipid A-bisphosphate
3-phenylpropionatedioxygenasesystem: hcaDhcaC hcaF hcaE
2-dehydro-3-deoxy-D-
gluconate-6-phosphate
YhfC
ALDEHYDE DEGRADATION
L-alanine
chemotaxis proteinmethyltransferase:cheR
non-specific ion/solute
nicotinamide mononucleotide
ArcB-Phis292
protoporphyrin IX
S-ribosylhomocysteinelyase: luxS
acetate
succinate
precorrin-2
tRNAnucleotidyltransferase: cca
choline
beta-D-glucose
pyruvate
23Sribosomal
RNA
lactose
geranyldiphosphatesynthase: ispA
D-xylose
glutamate-cysteineligase: gshA
a trans-delta2-enoyl-acyl-[acp]
homoserine lactonehomoserine
5,10-methylene-
THF
trehalose-6-phosphatephosphatase,biosynthetic:otsB
H+
octaprenyldiphosphatesynthase: ispB
S-hydroxymethylglutathione
dIMP
L-ornithine
diacetyl
selenophosphate
pyruvate
tRNAgln
dTMP
RcsC-Phis
a proteinL-tyrosine
16S rRNAm62A1518,m62A1519dimethyltransferase: ksgA
nucleoside triphosphatepyrophosphohydrolase:mazG
tryptophanase:tnaA
ribose-1,5-bisphosphate
DNAn
an (R)-3-hydroxyoctanoyl-
[acp]
an (R)-3-hydroxydecanoyl-[acp]
lactosedegradation III
L-cysteine
fumarate
deoxyribose-5-phosphate
dihydroxyacetonephosphate
DcuS-Phis349
5’,5’’’-diadenosine
tetraphosphate
DNAcytosinemethylase:dcm
beta-galactosidase:lacZ
peptidoglycantetrapeptide,
glycan chain 1
TDP-rhamnose
o-succinylbenzoate
D-xylulose-5-phosphate
KDO2-lipid IVA
L-fuculokinase: fucK
propionyl-CoA
2-keto-isovalerate
superpathwayof asparaginebiosynthesis
thiamin(thiazolemoiety)biosynthesisprotein: thiF
ExuT
2-keto-3-deoxy-L-rhamnonatealdolase: yfaU
5-phosphoribosyl1-pyrophosphate
an oxidizedelectronacceptor
NanC
a protein-L-tyrosinephosphate
deoxyribose-1-phosphate
mannokinase
all-trans-heptaprenyldiphosphate
L-lysine
8-amino-7-oxononanoatesynthase: bioF
L-proline
D-glyceraldehyde-3-phosphate
UvrY
NfrA
2-oxobutanoate
rRNA
L-ribulose-5-phosphate4-epimerase:sgbE
L-aspartate
gamma-aminobutyraldehydedehydrogenase: ydcW
GTP
N-acetylneuraminate
a carbohydrate
myo-inositol
L-glutamyl-tRNAGlu
ribonucleoside-diphosphatereductase 2:nrdF nrdE
D-alanyl-D-alanine-adding enzyme: murF
a nucleosidemonophosphate
iron (III)hydroxamate
complex
CMP
Aer
dephospho-CoA kinase: coaE
23S rRNA m2G1835methyltransferase:rlmG
a 2’-deoxyribonucleoside
diphosphate
propionate
citratelyase: citEcitF citD
adenine
KefC
16S rRNA m5C1407methyltransferase:rsmF
inosine kinase: gsk
HMP-PPhydrolase:cof
protein with lowundecaprenylpyrophosphatephosphataseactivity: lpxT
cysteinesulfinatedesulfinase:csdA csdE
a 3’-phosphate-terminated
RNA
6-phospho-beta-glucosidaseB; cryptic:bglB
trehalose
L-alanine
GDP-L-fucose
FimC
CARBOXYLATES DEGRADATION
oxaloacetate
agmatinase: speB
UDP-2,3-bis(3-hydroxymyristoyl)
glucosamine
4-hydroxybenzoateoctaprenyltransferase:ubiA
D-arabinose5-phosphate
alpha-iminosuccinate
apo-citrate lyasephosphoribosyl-dephospho-CoAtransferase: citX
fused heptose7-phosphatekinase/heptose1-phosphateadenyltransferase:rfaE
cytidinedeaminase: cdd
KDO2-lipidA, coldadapted
asparaginesynthetaseB: asnB
2-octaprenyl-6-methoxyphenolhydroxylase: ubiH
benzaldehyde
colanic acid
2-oxoglutarate
L-cysteine
molybdopterin
succinatesemialdehydereductase: yihU
an oxidizedthioredoxin
dihydroneopterintriphosphate 2’-epimerase: folX
4-aminobutyrate
DcrB
galactitoldegradation
guanosine-5’-diphosphate
L-glutamategamma-
semialdehyde
octaprenyldiphosphatesynthase: ispB
PhoQ-Phis
holo-[acylcarrierprotein]synthase2: acpT
L-aspartate-semialdehyde
UDP-D-glucose
UDP-D-galacto-1,4-
furanose
(E)-3-(methoxycarbonyl)pent-2-enedioate
UvrY-Pasp
a drug
melibiose
undecaprenylphosphate-
alpha-L-Ara4N
dihydroxyacetonephosphate
an apo-GcvHprotein
ferricdicitrate
acetaldehydedehydrogenase2: mhpF
fructose-1,6-bisphosphatase: yggF
CO
NMNH
L-glutamine:D-fructose-6-phosphateaminotransferase:glmS
glycogen
lipoatebiosynthesis
andincorporation II
succinate
dTDP-4-dehydrorhamnosereductase: rfbD
L-homocysteine
thymidylatesynthase: thyA
1,3-diphosphateglycerate
AsmA
ATP
4-methyl-5-(beta-
hydroxyethyl)thiazole
N5-glutaminemethyltransferase:prmB
UDP-D-glucose
MutHLScomplex,methyl-directedmismatchrepair: mutHmutS mutL
peptidoglycanDAP-DAPcrosslink
alpha-D-glucose
acetaldehyde
rRNAcontaining
pseudouridine
chromatereductase:yieF
purine nucleosidephosphorylase:
deoD
a holo-[acp]
glycine
methylglyoxal
DNAadeninemethylase:dam
pseudouridine5’-phosphate
4-aminobutanal
nicotinatemononucleotide
dihydrofolatesynthetase: folC
an (R)-3-hydroxymyristoyl-
[acp]
L-rhamnose
pyrimidine deoxynucleosidetriphosphatepyrophosphohydrolase: nudI
nitrousoxide
2,3-diaminopropionate
di-trans,poly-cis-
undecaprenylphosphate
glucose 6-phosphate-1-dehydrogenase: zwf
methylmalonyl-CoA epimerase
tRNA-specificadenosinedeaminase:tadA
L-asparagine
NupG
L-glutamate
maltodextrinphosphorylase:malP
SohB
a peptide
beta-D-glucose-6-phosphate
3-phosphoglycerate
superpathway ofgluconate degradation
RstB
lipopolysaccharidecore biosynthesisprotein: rfaS
arsenate
CheB-Pasp: cheB
galactosyl-glucosyl-heptosyl3-
KDO2-lipid A-bisphosphate
pyruvate kinase II: pykA
tRNAcontaining N6-methyladenine
uracil
branched-chainamino-acidaminotransferase:ilvE
alpha-D-glucose 6-phosphate
beta-hydroxyacyl-ACP dehydratase: fabZ
L-cystathionine
acetyl-CoA carboxylase:accB accC accA accD
hemebiosynthesis fromuroporphyrinogen II
phosphate
a tRNA containing 5-carboxymethylaminomethyl-
2-thiouridine
D-glyceraldehyde-3-phosphate
phosphoenolpyruvate synthase: pps
phosphopantetheinyltransferase: entD
prolyl-tRNAsynthetase:
proS
carbamoyl-phosphate
L-pantoate
isoleucyl-tRNA
synthetase:ileS
aspartyl-tRNA
synthetase:aspS
Tsrgln
S-adenosyl-L-methionine
putative enoyl-CoA hydratase/isomerase ofphenylacetatedegradation: paaG
Targln
succinate
N-acetyl-glucosamine-1-phosphate
D-galactonatedegradation
lipoyl-proteinligase A: lplA
23Sribosomal
RNA
triose phosphate isomerase: tpiA
enolase: eno
succinate
beta-D-galactose
citrate synthase: gltA
guanosine-5’-diphosphate
oxaloacetate
L-1,2-propanediol
molybdopterinsynthase
NrfE
poly-beta-1,6-N-acetyl-D-glucosamine
a DNAsegment
in reverseorientation
acetoin
a C4-dicarboxylatea C4-dicarboxylate
ribosomal-protein-S18-alanine N-acetyltransferase: rimI
ribonucleosidehydrolase 3: rihC
23S rRNA m5C1962methyltransferase: rlmI
beta-D-glucose
23S rRNA m1G745methyltransferase:rrmA
D-methionineL-methionine
an aldehyde
2-oxoglutarate
D-altronatedehydratase:uxaA
fructose 1,6-bisphosphatase II: glpX
3-octaprenyl-4-hydroxybenzoate
DgoT
riboflavinsynthase:ribC
NADP+
6-pyruvoyltetrahydropterin
1-deoxy-D-xylulose 5-phosphate
malate synthase A: aceB
S-adenosyl-L-homocysteine
o-succinylbenzoyl-CoA
L-glutamyl-tRNAGlu
KDO2-lipid IVA
phosphate
L-glutamine
UDP-D-glucuronate
phosphoglycerate mutase 2: ytjC
phosphopentomutase:deoB
a DNA pairof adjacentpyrimidines
fructose bisphosphatealdolase class I: fbaB
YiaF
bifunctional aconitate hydratase2 and 2-methylisocitrate
dehydratase: acnB
D-mannonateoxidoreductase:uxuB
D-threo-isocitrate
DcuA
isocitrate dehydrogenase: icd
fused diaminohydroxyphosphoribosylaminopyrimidinedeaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase: ribD
a glutaminesynthetase PII
alpha-D-galactose1-phosphate
an N-acetyl-D-hexosaminide
D-ribulose-5-phosphate
fructosedegradation
D-xylose
gamma-glutamyl-gamma-aminobutyraldehydedehydrogenase: puuC
dihydroxyacetonekinase: dhaLdhaK dhaM
superpathway of threonine metabolism
transketolaseI: tktA
D-mannose
pyruvate kinase I: pykF
glyceraldehyde3-phosphatedehydrogenase-A complex: gapA
alanine racemase1, PLP-binding,biosynthetic: alr
1-deoxyxylulose-5-phosphatesynthase: dxs
aminoacetone
phosphohydroxymethylpyrimidinekinase: thiD
malate fumarate succinate orotateL-aspartate
O-succinylhomoserine(thiol)-lyase: metB
an acid
UDP-N-acetylmuramoyl-L-alanyl-D-
glutamyl-meso-2,6-diaminoheptanedioate-
D-alanine
phosphoglucoseisomerase: pgi
YgjDdegradation
products
propionyl-CoA:succinateCoA transferase: scpC
acidphosphatase:appA
7,8-dihydroneopterintriphosphate
a dipeptide
3-(2,3-dihydroxyphenyl)
propionate
DcuC
dihydroxyacetonephosphate
2-dehydro-3-deoxy-D-
gluconate-6-phosphate
putative ring-cleavage enzymeof phenylacetatedegradation: maoC
2-oxoglutarate
5-phospho-ribosyl-
glycineamide
tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:mnmA
phenylacetaldehydedehydrogenase: feaB
1-deoxy-D-xylulose 5-phosphate
D-fructose-6-phosphateL-glutamine
3,5-tetradecadienoyl-
CoA
all-trans-hexaprenyl
diphosphate
3-deoxy-D-manno-octulosonate8-phosphatephosphatase:kdsC
YedZ
L-serine
D-mannose-6-phosphate
D-galactonate
sirohemebiosynthesis
ZinT
AmtB
acetate
D-Tyr-tRNATyrdeacylase:dtd
1-(o-carboxyphenylamino)-1’-deoxyribulose-
5’-phosphate
phosphoglucosaminemutase: glmM
D-xylose
homoserine
L-glutamate
DNApolymeraseI, 3’ --> 5’polymerase,5’ --> 3’and 3’ --> 5’exonuclease:polA
dTDP-glucose 4,6-dehydratase:rfbB
cellobiose-6-phosphatediacetylchitobiose-6-phosphate
FliY
dihydrofolatereductase: folM
D-fructose-6-phosphate
folylpoly-gamma-glutamatesynthetase:folC
S-adenosyl-L-methionine
a 2,3,4-saturatedfatty acyl CoA
D-erythro-imidazole-glycerol-phosphate
protoporphyrinogenoxidase: hemG
KASI: fabB
L-valine
anamineated
amine donor
cobalamin-dependent
homocysteinetransmethylase:
metH
purine nucleosidephosphorylase:
deoD
a 1,4-alpha-D-glucan
YidY
thioredoxinreductase:trxB
glycolateL-lactate
acetate
AMPnucleosidase: amn
acetaldehydedehydrogenase2: mhpF
cis-3-(carboxyethyl)-3,5-
cyclohexadiene-1,2-diol
16S rRNA m2G1207methyltransferase:rsmC
FtsP
alpha-D-galactose 1-phosphate
tetrahydrofolate
6-phospho-beta-glucosidaseA: bglA
rRNAcontaining 2-methyladenine
D-glyceraldehyde-3-phosphate
xanthinedehydrogenase:xdhC xdhB xdhA
nigerose
glucose-1-phosphateuridylyltransferase:galU galF
alpha-amylase:amyA
an alcohol
a butyryl-[acp]
phosphomannomutase:cpsG
an N-acetoxyarylamine
NarL-Pasp
L-glutamate
phosphohistidinephosphatase: sixA
L-asparagine
L-cysteinedegradation II
glycerol-3-phosphate
acyltransferase:plsB
tRNAcontaining 5,6-dihydrouridine
formatehydrogenlyasecomplex: hycDhycC hycF hycGhycB hycE fdhF
glycosidehydrolase:ygjK
N-ethylmaleimidereductase, FMN-linked: nemA
thiocyanate
an oxidizedthioredoxin
cytosine
3-phosphoglycerate
2,3-dihydroxy-isovalerate
3-hydroxypropionaldehyde
cytosinedeaminase:
codA
L-1,2-propanedioloxidoreductase:fucO
glyoxylatecarboligase:gcl
hypoxanthine
chorismate mutase: pheA
tryptophanyl-tRNA
synthetase: trpS
glucokinase: glk
valyl-tRNAsynthetase:
valS
UDP-D-glucose
cysteinyl-tRNA
synthetase:cysS
RhaT
an rRNA
an alkylhydroperoxide
GlcNAc-1,6-anhMurNAc
UDP-3-O-acyl-N-acetylglucosaminedeacetylase: lpxC
uracilphosphoribosyltransferase: upp
Tapglu
multifunctional2-keto-3-deoxygluconate 6-phosphate aldolaseand 2-keto-4-hydroxyglutaratealdolase andoxaloacetatedecarboxylase: eda
siroheme
protein-(glutamine-N5)methyltransferase:prmC
2-octaprenyl-6-hydroxyphenol
dCTP
shikimate kinase II: aroL
non-specific ion/solute
PRPPbiosynthesis I
LamB
hydroxyphenylacetyl-CoA thioesterase: paaI
L-fucose
5’-deoxyadenosine
ATP
alkylhydroperoxidereductase: ahpF ahpC
an L-1-phosphatidylglycerol-
phosphate
ribonucleosidehydrolase 3: rihC
mannitol-1-phosphate
putativeoxidoreductaseFe-S subunit;possiblecomponentof selenatereductase: ygfK
glyoxylatereductaseB: ghrB
oxalate
enterobactin
D-ribulose-5-phosphate
2-dehydro-3-deoxyphosphoheptonatealdolase: aroG
D-galactonatedehydratase: dgoD
pyruvate
anthranilate synthasecomponent II: trpD
superpathway of leucine, valine,and isoleucine biosynthesis
AnsP
PII-UMP
NarQ
CDP
deoxyguanosine
argininesuccinyltransferase:astA
3-deoxy-D-manno-
octulosonate
cytidine
maltose
UDP-N-acetyl-beta-D-mannosaminouronate
UhpA
GabP
L-methionine
glutamatedehydrogenase:gdhA
2-oxobutanoate
asparaginesynthetaseA: asnA
asparaginaseIII: iaaA
sorbitol-6-phosphatedehydrogenase:srlD
ethanolamine
YncD
a nucleosidetriphosphate
COFACTORS, PROSTHETIC GROUPS, ELECTRON CARRIERS BIOSYNTHESIS
cytidinekinase: udk
RseA
cytidylatekinase: cmk
GlpF
phosphoenolpyruvatecarboxylase: ppc
ketogluconate metabolism
tetrahydrofolate
NarK
a DNAsegment
citratesynthase:gltA
lipoate acetyltransferase: aceF
hydroxymethylbilanesynthase: hemC
N5-methyl-L-glutamine
pyruvate
glucose and glucose-1-phosphate degradation
YjhB
tRNA (Gm18) 2’-O-methyltransferase:trmH
shikimatedehydrogenase: ydiB
methionyl-tRNA
synthetase:metG
alpha-D-glucose 1-phosphate
trans-aconitate
a 1,4-alpha-D-glucan
DNAwithoutlesion
HflD
N-acetylneuraminatemutarotase: nanM
xanthosinephosphorylase:xapA
taurine
methylglyoxal
all-trans-geranyl-geranyl
diphosphate
purine nucleosidephosphorylase:deoD
K+
UDP-N-acetyl-D-
glucosamine
dihydroxyacetonephosphate
uroporphyrin III C-methyltransferase:cysG
YceE
D-glyceraldehyde-3-phosphate
NUCLEOSIDES AND NUCLEOTIDES BIOSYNTHESIS
PhoE
asparaginesynthetaseB: asnB
GTP
elongatortRNAmet
D-galactono-1,4-lactone
BglG-P
dGMP
guanosine-5’-diphosphate
3-keto-L-gulonate
pantothenateand coenzyme
A biosynthesis I
lipoylateddomain
YiiP
ribonucleoside-triphosphatereductase: nrdD
L-lysyl-tRNAlys
a [citrate(pro-3S)-
lyase](citrylform)
triose phosphateisomerase: tpiA
L-rhamnulose-1-phosphate
valine-pyruvateaminotransferase:avtA
acetaldehyde
enolase: eno
MQH2
nitric oxide
alpha-L-arabinose
D-galacturonate
phosphoenolpyruvatesynthase: pps
malate
GTP
phosphoserinephosphatase: serB
L-tyrosyl-tRNAtyr
lipid Adisaccharide
a cis-delta5-dodecenoyl-[acp]
4-coumarate
a palmitoleoyl-[acp]
an acetoacetyl-[acp]
superpathway of arginineand ornithine degradation
phenylacetate-CoA ligase: paaK
enterobactin
MQH2
AMP
superpathway of aspartateand asparagine biosynthesis;
interconversion ofaspartate and asparagine
N-acetyl-D-glucosamine
Ni2+Mg2+
Lnt
unknown
Asr
ferricenterobactin
ribonucleosidetriphosphatereductaseactivase: nrdG
3’-phospho-adenylylsulfatereductase: cysH
an rRNA
a cis-vaccenoyl-
[acp]
pyrimidinedeoxyribonucleosides
degradation
crypticadeninedeaminase:ade
pyrazinamide
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
L-Ala-gamma-D-Glu
polyisoprenoidbiosynthesis (E. coli)
L-tyrosine
all-trans-farnesyl
diphosphate
a biotinylatedBCCP (dimer)
alpha-D-glucose 6-phosphate
predicted 3-hydroxy-acyl-CoAdehydrogenaseof phenylacetatedegradation: paaH
xanthine-guaninephosphoribosyltransferase: gpt
Fdh-N
FERMENTATION
CorA
2,4-dienoyl-CoAreductase:fadH
pyruvate
2-methylcitratedehydratase: prpD
ribose-5-phosphateisomeraseA: rpiA
xanthine-guaninephosphoribosyltransferase: gpt
cobinamide
fumaratereductase:frdD frdCfrdB frdA
lipoyl-ACP
GntP
a holo-[acp]
D-mannose-6-phosphate
beta-alanine
5-methyluridine-modified 23S
ribosomal RNA
3-hydroxy-5-cis-tetradecenoyl-
CoA
2,3-dihydroxybenzoate
a proteinL-beta-
isoaspartatealpha-
methyl ester
L-threonyl-tRNAthr
a [citrate(pro-3S)-lyase](thiol
form)
S-ribosyl-L-homocysteine
N-acetyl-D-glucosamine-6-phosphate
D-gluconate
lipoatesalvage andmodification
a phosphatemonoester N-methyltryptophan
demethylmenaquinone-8
catabolicthreoninedehydratase:tdcB
D-alanine-D-alanineligase A: ddlA
ribonucleotidemonophosphatase:nagD
guanosine-5’-diphosphate
anthranilate
LepA
YtfM
beta-D-glucose
5-phosphoribosyl1-pyrophosphate
RstBA Two-Component
SignalTransduction
System
L-proline
a drug
MarC
UDP-3-O-[3-hydroxymyristoyl]glucosamineN-acetyltransferase: lpxD
phosphodiesterase,heme-regulated: dos
L-aspartyl-tRNAasp
a 1,4-alpha-D-glucan
tRNA uridine
cholate
formate
acetohydroxy acidisomeroreductase:ilvC
KDOtransferase:waaA
EvgA-Pasp
glutaminedegradation I
CheB-Pasp: cheB
PnuC
uridylate kinase: pyrH
a ThiIpersulfide
succinylargininedihydrolase: astB
phosphodiesterase /predicted L-ascorbate6-phosphatelactonase: ulaG
alpha-dehydro-beta-deoxy-D-glucaratealdolase: garL
L-glutamate
palmitoleoylacyltransferase:lpxP
2-keto-L-gulonate
N3-methylcytosine
a polypeptide
KASII: fabF
maltopentaose
purine nucleosidephosphorylase:deoD
D-glucono-delta-lactone-6-phosphate
acetaldehydedehydrogenase:adhE
7-aminomethyl-7-deazaguanine
acetate
L-xylulose-5-phosphate
a thioredoxin
agmatine
glycolate
1-phosphofructokinase:fruK
putative diacylglycerolcholinephosphotransferase:ynbA
gamma-glutamyl-L-putrescine
N-carbamoyl-L-aspartate
an RNA
trehalose
H+
P-DPD
acetyl-esterase: aes
inosine-5’-phosphate
L-arginine
deoxyinosine
pyruvate
isochorismatesynthase 1: entC
a [citrate(pro-3S)-
lyase](acetylform)
pirin-likeprotein:yhhW
3-dehydroquinate
inositolmonophosphatase:suhB
2,3-dihydroxybenzoate-AMP ligase: entE
cytoplasmictrehalase: treF
nitrite
4,5-dihydroxy-2,3-pentanedione
2-isopropylmaleate
2,3-dihydro-2,3-dihydroxybenzoate
AMP
3-deoxy-D-manno-
octulosonate8-P
ThiS-COSH
UDP-N-acetyl-D-glucosamine
4’-phosphopantetheine
hydroxylamine
acetyl-CoA
FtsQ
H+
pyruvate
citrate
GTP
chemotaxis proteinmethyltransferase:
cheR
uracil
deoxyuridine
L-rhamnonatedehydratase:yfaW
glucosedehydrogenase: gcd
pyrimidine deoxynucleosidetriphosphatepyrophosphohydrolase: nudI
a DNAcontaining aapyrimidinic
site
CsgB
citratelyase: citEcitF citD
a deoxynucleoside
L-asparagine
cysteinedesulfurase:iscS
putrescine
formate
an oxidizedflavodoxin
Trgglu
aspartatecarbamoyltransferase: pyrI pyrB
alpha-D-ribose-1-phosphate
beta-hydroxyacyl-ACPdehydratase: fabZ
broadspecificity 5’(3’)-nucleotidase andpolyphosphatase:surE
glycolateoxidase:glcFglcE glcD
dimethylallyldiphosphate
1-amino-propan-2-one-3-
phosphate
L-glutamate
glycerol 2-phosphate
alpha-D-glucose1-phosphate
1-deoxyxylulose-5-phosphatesynthase: dxs
a deoxynucleotide
predictedthiosulfatesulfurtransferase:ynjE
L-Ala-gamma-D-Glu-DAP-
D-Ala
a DNAcontaining
a purinic site
D-mannose
thiosulfatesulfate
6-phospho-D-gluconate
CDP-choline
phosphate
acetohydroxy acidisomeroreductase:ilvC
H2O
YchM
coproporphyrinogenoxidase, aerobic: hemF
NADP+
UDP-D-galactose
SetA
AtoS
SIGNAL TRANSDUCTION PATHWAYS
nicotinate-nucleotidedimethylbenzimidazolephosphoribosyltransferase: cobT
2-deoxygluconate
tRNAcontainingguanine
cobalaminadenosyltransferase:
btuR
pyrimidinephosphatase
trans-2-decenoyl-ACP isomerase: fabA
enoyl-ACP reductase(NADH): fabI
glycolaldehyde
YebS
alpha-D-glucose
DNAligase: ligB
phosphoenolpyruvate
2-aminobutyrate
beta-hydroxyacyl-ACP dehydrase: fabA
dihydroxy-acetone
undecaprenyldiphosphatesynthase: ispU
a holo-[acp]
3-methyladenine
salvage pathways of pyrimidine ribonucleotides
dTDP-4-acetamido-4,6-dideoxy-D-galactose
ZraR-phosphate
2-keto-3-methyl-valerate
formaldehyde
phosphateacetyltransferase: pta
uracil
YhcB
anadenylated
ThiS sulfur-carrierprotein
ubiquinone-8
PhoB
threoninedehydrogenase: tdh
CMP-3-deoxy-D-manno-
octulosonate
fructose 1,6-bisphosphatase: ybhA
crotonobetainyl-CoA reductase: caiA
L-ornithine
thymidine
a 2’-deoxyribonucleoside
diphosphate
a 1-acyl-sn-glycerol-3-phosphate
glyoxylate
phosphoribosylformylglycinamidecyclo-ligase: purM
an (R)-3-hydroxymyristoyl-
[acp]
UDP-D-glucose
2-ketoaldonatereductase: ghrB
acetaldehyde
acetyl-CoAsynthetase (AMP-forming): acs
cobalamin 5’-phosphatesynthase:cobS
MQH2
BaeS-Phis
ribonucleoside-triphosphatereductase: nrdD
GMPsynthetase:guaA
2-oxoglutarate
adenylatekinase: adk
a rhamnosyllipopolysaccharide
degradationof pyrimidine
ribonucleosides
uridinekinase: udk
NADPH
L-gamma-glutamylcysteine
ZitB
UDP-2,3-bis(3-hydroxymyristoyl)
glucosamine
AICARtransformylase:purH
AceF-lipoate
erythronate-4-phosphatedehydrogenase:pdxB
xanthosine
predicted N-acetylmannosamine-6-phosphateepimerase: nanE
acetoin
acetaldehyde
nucleosidediphosphatekinase: ndk
superpathwayof glutamatebiosynthesis
oxaloacetate
10-formyl-tetrahydrofolate
D-galactonate
Cr3+
undecaprenyldiphosphatesynthase: ispU
TrxA
S-adenosyl-dependentmethyltransferase:mraW
a decanoyl-[acp]
3-keto-L-gulonate
XTP
RcsCB Two-ComponentSignal Transduction System
4-hydroxybutyrate
a protein-L-glutamate--O5-methyl-
ester
L-arabinose
5,10-methenyltetrahydrofolate
EIIBgl
adenine
D-glucono-delta-
lactone-6-phosphate
porphobilinogensynthase: hemB
uroporphyrin III C-methyltransferase:cysG
a transhexadecenoyl-[acp]
YjdL
DNAcontaining
a basewith lesion
RhtB
1,6-anhydro-N-acetylmuramate
S-acetyldihydrolipoamide
UDP-3-O-acyl-N-acetylglucosaminedeacetylase: lpxC
chloride
lactose
octaprenyldiphosphatesynthase: ispB
EIIFru
KDOtransferase:waaA
Mtr
isovaleryl-CoAdehydrogenase /predicted acyl-CoAdehydrogenase: aidB
cob(I)alamin
subunit of fatty acidoxidation complex: fadI
5’-methylthioadenosine/S-adenosylhomocysteine
nucleosidase: mtn
CARBOHYDRATES BIOSYNTHESIS
serinehydroxymethyltransferase: glyA
lysyl-tRNAsynthetase,constitutive:
lysS
Pit
D-allosekinase: alsK
glycine cleavagecomplex
AMINOACYL-TRNA CHARGING
xanthine
SucB
an N-hydroxy-
arylamine
adenosine 5’-phosphosulfate
phenylhydantoinase:hyuA
myristoyl-acylcarrier protein(ACP)-dependentacyltransferase:lpxM
an acylphosphate
CreB-Pasp
spermidineacetyltransferase:speG
YedY
D-beta-D-heptose-1,7-bisphosphate
a 1,4-alpha-D-glucan
leucyl,phenylalanyl-tRNA-proteintransferase: aat
pyrimidine deoxynucleosidetriphosphatepyrophosphohydrolase: nudI
NarX Nitrate/Nitrite-DependentTwo-Component Regulatory System
phosphoribosylformiminoAICAR-phosphate
manno(fructo)kinase: mak
QseB
D-beta-D-heptose-1-phosphate
ribose 1-phosphokinase
D-ribose-5-phosphate
an N10-formyl-tetrahydrofolate
aspartatekinase III: lysC
lipoamide dehydrogenase: lpd
L-methionine
d-biotin d-sulfoxide
2-O-(6- phospho-
alpha-mannosyl)-
D-glycerate
UDP-3-O-(3-hydroxymyristoyl)
glucosamine
2-phosphoglycerate
acid phosphatase/phosphotransferase:aphA
UDP-glucose 4-epimerase: galE
LldP
CheB-Pasp: cheB
ATP-dependentDNAhelicase: recQ
N-formyl-L-methionyl-tRNAfmet
N-methyltryptophanoxidase: solA
TrkG
dTMP
an N-D-ribosylpyrimidine
hybrid-clusterprotein: hcp
AMINES AND POLYAMINES BIOSYNTHESIS
L-2-hydroxyglutarateoxidase: lhgO
acetate kinase B: ackB
NrdD
S-formylglutathionehydrolase: frmB
beta-ketoesterreductase:dkgA
allolactose
UhpA-Pasp
UDP-N-acetyl-D-glucosamine
1-deoxy-D-xylulose 5-phosphate
phosphoglucose isomerase: pgi
L-histidyl-tRNAhis
CpxP
peptidedeformylase:def
purine nucleosidephosphorylase:deoD
serinehydroxymethyltransferase: glyA
5-ketogluconate
ribose-phosphatediphosphokinase: prs
nitritereductase:nirB nirD
RsxE
ferricdihydroxybenzoylserine
L-threonine
OmpN
AlkB repairsystem foralkylatedDNA andRNA: alkB
guanosine-5’-diphosphate
octaprenyldiphosphatesynthase: ispB
1,3-propanediol
pyruvate kinase I: pykF
thiamin
glyceraldehyde 3-phosphatedehydrogenase-A complex: gapA
4-(2-aminophenyl)-2,4-
dioxobutanoate
uracil
adenosine-3’(2’),5’-bisphosphatenucleotidase:cysQ
bifunctional aconitate hydratase2 and 2-methylisocitrate
dehydratase: acnB
S-adenosyl-L-homocysteine
phenylhydantoin
RsxG
D-amino aciddehydrogenase:dadA
ATPsynthase
N-acetyl-D-glucosamine
PPPi
RsxD
an alcohol
isochorismatesynthase 2: menF
phosphodiesterase,heme-regulated: dos
’activated’tRNA
xanthosinephosphorylase:xapA
1,4-dihydroxy-2-naphthoateoctaprenyltransferase:menA
a peptide
meso-diaminopimelate
beta-N-acetylglucosaminidase:nagZ
diacetylchitobiose-6-phosphatehydrolase: chbF
RsxA
L-rhamnoseisomerase:rhaA
Lit
a fatty acid
ppGpp biosynthesis
Zn2+
CDP reductase:nrdB nrdA
OmpL
L-aspartate
D-ribose-5-phosphate
CsgA
tRNApseudouridine13 synthase: truD
5-phosphoribosyl1-pyrophosphate
UhpT
2-oxoglutarate
YicE
2-deoxy-D-gluconate 3-dehydrogenase:kduD
pyridoxal
RsxC
YiiP
acetyl-CoA
indole
a proteinwith
incorrectdisulfidebonds
RsxB
D-arabinose5-phosphateisomerase:gutQ
B3496
acetyl-CoAsynthetase(AMP-forming): acs
tRNAdihydrouridinesynthase: dusC
Ap3Asynthetase:lysU
beta-D-glucose-6-phosphate
enterobactin
XDP
MhpT
lipopolysaccharidecore biosynthesisprotein: rfaY
ADP-heptose:LPSheptosyltransferaseI: rfaC
citrate
glutaminesynthetase
deadenylylatingenzyme: glnE
Kch
lipid IVA
L-seryl-tRNAsec
PII
CARBOHYDRATES DEGRADATION
gamma-butyrobetainyl-
CoA:carnitine CoAtransferase: caiB
homoserinedehydrogenase:metL
nicotinate adenine dinucleotide
L-allo-threonine
NUCLEOSIDES AND NUCLEOTIDES DEGRADATION AND RECYCLINGL-histidinol-phosphate
carbamoyl-phosphate
thiaminbiosynthesisproteinThiC: thiC
cysteinedesulfurase:iscS
a DNAcontaining 6-O-methylguanine
purine nucleosidephosphorylase:
deoD
thiaminkinase: thiK
maltoseacetyltransferase:maa
tartronatesemialdehydereductase2: glxR
histidinol
3-keto-L-gulonate 6-phosphate
putativepyruvatesynthase:ydbK
caiEprotein: caiE
L-aspartate-semialdehyde
RhtC
1,3-diphosphateglycerate
L-lysine
polynucleotidephosphorylase:pnp
L-cysteine
(1R,6R)-6-hydroxy-2-succinylcyclohexa-
2,4-diene-1-carboxylate
adenosinedeaminase: add
4-methyl-5-(beta-
hydroxyethyl)thiazole
phosphate
pyridoxamine
salvage pathways of guanine, xanthine, and their nucleosides
nucleotide-sugarhydrolase:nudK
UDP-GlcNAc-enolpyruvate
Tapgln
a crotonyl-[acp]
bifunctionalaconitatehydratase 2 and2-methylisocitratedehydratase: acnB
acetoinsynthesis:poxB
a nucleoside-5’-phosphate
trans-delta2-decenoyl-
CoA
L-lysine
protoheme IX
L-fuculose-1-phosphate
tRNAala
a reducedFeS-protein
gluconeogenesis I
uroporphyrinogen-III
phosphodiesterase, c-di-GMP-specific: yahA
acetyl-CoA
a DNAcontainingabasic site
ProY
glycerolkinase: glpK
an oxidizedthioredoxin
NlpA
UDP-D-galactose
UDP-D-glucose
NADPHquinonereductase:mdaB
alpha-galactosidase:melA
phosphopentomutase:deoB
xylulokinase:xylB
sirohydrochlorinferrochelatase: cysG
isocitratedehydrogenasephosphatase: aceK
BarA-UvrY Two-Component
SignalTransduction
System
lysidine-modifiedtRNAileX
S-ribosylhomocysteinelyase: luxS
2-keto-3-methyl-valerate
succinate
a tripeptide
a 1,2-diacylglycerol
dethiobiotinsynthetase: bioD
3-methyl-adenine DNAglycosylase I,constitutive:tag
sugar phosphatase: yigL
ferrochelatase:hemH
selenide,waterdikinase:selD
dephospho-CoA
tRNAgly
ribosedegradation
rRNAcontaining
N3-methylatedpseudouridine
flavin biosynthesis I (bacteria)
YihP
L-methionine
fructose-1,6-bisphosphate
L-leucine
a [citrate(pro-3S)-
lyase](acetylform)
fumaraseC: fumC
malate
UDP-N-acetylglucosamineenolpyruvoyl transferase: murA
L-cysteine
adenylo-succinate
Lipid A-core
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
CitT
N-acetyl-D-glucosamine
salicinarbutin
L-lyxosedegradation
xanthinedehydrogenase:xdhC xdhB xdhA
deoxyadenosine
L-xylulose 5-phosphate3-epimerase:ulaE
dTDP-D-glucose
NupX
PspC
pyruvate
L-idarate
glyceroldegradation V
alpha-D-glucose1-phosphate
4-nitrobenzylalcohol
tRNAarg
NADH
L-lactate
formaldehyde
succinate
L-serine
a proteinL-beta-
isoaspartate
pyridoxamine5’-phosphateoxidase: pdxH
D-galactarate
selenide
a beta-D-galactoside
isopropylmalateisomerase:leuD leuC
acetohydroxy acidisomeroreductase:ilvC
2-keto-isovalerate
3-mercaptopyruvate:cyanidesulfurtransferase: sseA
a thioredoxin
glucose-1-phosphateuridylyltransferase:
galU galF
hydroxypyruvate
glucosyl-heptosyl3-
KDO2-lipid A-bisphosphate
glutathionereductase: gor
a tRNAcontaining 2’-O-methylguanosine
tRNAGlu
NADsynthetase, NH3-dependent: nadE
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatesynthase: ispG
2C-methyl-D-erythritol 2,4-cyclodiphosphatesynthase: ispF
L-isoaspartate proteincarboxylmethyltransferasetype II: pcm
deoxyinosine
bifunctional beta-cystathionase,PLP-dependentand regulatorof maltoseregulon: malY
CreCB Two-ComponentSignal Transduction System
6-hydroxymethyl-7,8-dihydropterin
isopentenyldiphosphateisomerase: idi
a protein
tRNA containing 5-methylaminomethyl-
2-thiouridylate
octaprenyldiphosphatesynthase: ispB
BasR-Pasp
(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylatesynthase: menH
beta-D-glucose-6-phosphate
xylulokinase:xylB
D-myo-inositol (1)-monophosphate
D-glyceraldehyde-3-phosphate
pyrimidineribonucleotides denovo biosynthesis
homoserinedehydrogenase:thrA
23S rRNA m5U1939methyltransferase:rlmD
glycerol-3-phosphate-dehydrogenase,anaerobic:glpC glpB glpA
RstA-Pasp
uridine
phosphogluconatedehydratase: edd
methioninesulfoxidereductaseA: msrA
EIIMan
2,5-didehydro-
D-gluconate
6-phosphofructokinaseII: pfkB
spermidineacetyltransferase:speG
fructose-1,6-bisphosphatase: yggF
two-componentalkanesulfonatemonooxygenase
an octanoylateddomain
coproporphyrinogen III
5,6,7,8-tetrahydropteridine
inosine
GTP
exonucleaseIII: xthA
glycyl-tRNAgly
a 2,3,4-saturated
fattyacyl CoA
D-ribose-5-phosphate
acetol
NtrC-P
YddG
glycerol
coenzyme A
sugar phosphatase: yidA
ribonucleotidemonophosphatase:nagD
folylpoly-gamma-glutamatesynthetase:folC
PhoQP Two-Component
SignalTransduction
System
purine nucleosidephosphorylase:
deoD
TorS
2-oxoglutarate
superpathway ofhexitol degradation
NupC
S-adenosyl-L-methionine
tRNA chargingpathway
7,8-dihydrofolate
alpha-D-glucose 1-phosphate
glutaminesynthetase: glnA
adenosylcobinamide-GDP
L-serine
CpxA-Phis
MQ
YbcL
heptosyl-KDO2-
lipid IVA
methylmalonyl-CoAmutase: scpA
L-Ala-D-Glu-meso-
A2pm
DcuS-Phis349
a 1-acyl-sn-glycerol-3-phosphate
biotincarboxylase:accC
dCTP
L-aspartyl-4-phosphate
dihydroorotate
lipid Adisaccharide
Na+
coenzyme A
KdpD-Phis
EIIGlc
D-lactate
16S rRNA m2G966methyltransferase:rsmD
2-oxoglutarate
D-ribose
dihydroxy-acetone
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase: murD
fructose 1,6-bisphosphataseII: glpX
all-trans-octaprenyl
diphosphate
glycine
an aromaticsulfate
5,10-methylene-
THF
trimethylamine
nitrite
deoxyinosinetriphosphatepyrophosphatase:rdgB
pyrroline-5-carboxylatereductase:proC
alpha-D-glucose1-phosphate
octaprenyldiphosphatesynthase: ispB
2-hydroxyglutarate
a cis-3-enoyl-CoA
pyruvateformate-
lyase
2’-(5’-phosphoribosyl)-3’-dephospho-
CoA biosynthesisI (citrate lyase)
S-adenosyl-L-methionine
YfaZ
RNA(n)
D-alanine
an mRNA
3-deoxy-D-manno-octulosonate8-phosphatesynthase: kdsA
beta-ketoadipyl-CoA thiolase: paaJ
D-mannose
cis-dihydrodiolderivative of
phenylacetyl-CoA
(2S,3S)-2-methylcitrate
pyruvate
an (R)-3-hydroxydodecanoyl-
[acp]
S-allantoin
multidrug
lipoatesynthase: lipA
2-ketoaldonatereductase: ghrB
superpathway of fatty acid biosynthesis
rRNA containing7-methylguanosine
ADP-D-glycero-
D-manno-heptose
selenocysteinesynthase: selA
tRNA-dihydrouridinesynthase A: dusA
dTDP-alpha-L-rhamnose
thiamin
long chainpolyphosphate
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-
meso-2,6-diaminopimelyl-D-alanyl-D-alanine
YaaU
glycogen degradation I
prolinebiosynthesis I
a 2,3,4-saturatedfatty acyl-[acp]
L-ornithine L-lysine L-arginine
glutaminase:ybaS
an octanoyl-[acp]
ribose-5-phosphateisomeraseA: rpiA
glucokinase:glk
Tsrglu-Me
1,4-dihydroxy-2-naphthoate
pyruvate
alpha-D-ribose-1-phosphate
H+
biotinsynthase: bioB
glycogenphosphorylase:glgP
2-keto-3-deoxygluconokinase:kdgK
acetyl-CoA
D-glucuronateisomerase:uxaC
L-3,4-dihydroxybutan-2-one-4-phosphate
SecM
an N-substitutedamino acid
a ribonucleosidetriphosphate
glutamatesynthase:gltD gltB
guanosine
triphosphoribosyl-dephospho-CoAsynthase: citG
biotinbiosynthesis I
MurJ
coenzyme A
YehA
N-alpha-acetyl lysinemethyl ester
KgtP
3-(2,3-dihydroxyphenyl)propionatedioxygenase: mhpB
an aceticester
QseB-Phosphorylatedtranscriptional
activator
thiamine-phosphate
fructose-1,6-bisphosphate
ribosomal-protein-L12-serineacetyltransferase:rimL
4-amino-4-deoxychorismate
cytochromebd-I terminal
oxidase
purine nucleosidephosphoramidase:hinT
PutP
cytochromebo terminal
oxidase
mureinpeptideamidaseA: mpaA
superpathwayof serine
and glycinebiosynthesis I
N-acetyl-D-glucosaminekinase: nagK
D-threo-isocitrate
tetrahydrofolate
an rRNA
erythronate-4-phosphate
L-rhamnulose
ribosomesmall subunit-dependentGTPaseA: rsgA
acyl-ACPsynthetase:aas
methylisocitrate
dUTP
GDPdiphosphokinase: spoT
GLYCOLYSIS
N-acetyl-D-mannosamine
ZipA
L-prolyl-tRNApro
fused PutAtranscriptionalrepressor / prolinedehydrogenase/ 1-pyrroline-5-carboxylatedehydrogenase:putA
guanine
RcsB
pyruvateformate-lyaseactivatingenzyme: pflA
phosphoglyceromutase1: gpmA
xanthosine
an RNA
fructoselysine
phosphoenolpyruvatesynthase: pps
a lipopolysaccharide
fructose 1,6-bisphosphatase:ybhA
degradation of purine ribonucleosides
lipoate
NADP-dependentdehydrogenase:yqhD
FMN
L-glutamate
an octanoylateddomain
xanthosine-5-phosphate
nicotinatephosphoribosyltransferase: pncB
rRNAcontaining 2’-
O-methyluridine
tRNApseudouridine55 synthase: truB
propionyl-CoAcarboxylase
methylmalonylpathway
CMP
cobalaminsynthase: cobS
xanthine
D-arabinose5-phosphateisomerase:kdsD
di-trans,poly-cis-
heptaprenyldiphosphate
a peptide
D-Ala-D-Aladipeptidase:ddpX
undecaprenyldiphosphatesynthase: ispU
pyruvate formate-lyase: tdcE
Cd2+
UDP-D-galacto-1,4-
furanose
FMN
4-(phosphonooxy)-threonine
a deoxyribonucleicacid
aconitatehydratase 1: acnA
acetaldehyde
lipoylated domain
Ivy
putrescine
dTTP
pyrimidine (deoxy)nucleoside triphosphatepyrophosphohydrolase:nudG
nitrate
L-rhamnose
OmpG
3-hydroxy aciddehydrogenase:ydfG
cyclicdi-3’,5’-
guanylate
lipoamidedehydrogenase: lpd
fumarate
L-phenylalanine
UDP-D-galactose
a proteinwith correct
disulfidebonds
D-glucaratedehydratase: gudD
2,3-dihydroxybenzoate
L-cysteineO-acetyl-L-serine
fructose-1,6-bisphosphate
fatty acid oxidationcomplex, alphacomponent: fadB
salicylalcohol
dodecenoyl-CoAD-isomerase: fadJ
a tRNA
glucosyl-heptosyl2-
KDO2-lipid A
phosphoenolpyruvate
D,D-heptose 1,7-bisphosphatephosphatase:gmhB
succinyl-CoA
acetate
D-sorbitol-6-phosphate
ArcB-Pasp
CTP
N-acetyl-D-glucosamine-6-phosphate
YdhC
peptideuptake ABCtransporter
23S rRNA m6A1618methyltransferase:rlmF
pyridoxaminekinase: pdxK
endonucleaseVIII: nei
peptidoglycantetrapeptide,
glycan chain 1
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylatesynthase: menD
AROMATIC COMPOUNDSBIOSYNTHESIS
flavorubredoxinreductase: norW
carbamoyl-phosphate
galactoside O-acetyltransferase:lacA
AceF
a mRNA
6-phosphogluconatephosphatase: yieH
spermidine
a ribonucleosidetriphosphate
YcdU
a 2’-deoxyribonucleoside
triphosphate
NAD(P)H:quinoneoxidoreductase:wrbA
L-lactaldehyde
chromatereductase:yieF
beta-D-glucose
superpathway of lysine, threonineand methionine biosynthesis I
D-sedoheptulose-7-phosphate
lysinedegradation I
P-DPD
threonyl-tRNA
synthetase:thrS
D-fructose-6-phosphate
alanyl-tRNAsynthetase:
alaS
KASI: fabB
serinehydroxymethyltransferase: glyA
isochorismatase:entB
glycine betaine L-proline
glutaminyl-tRNA
synthetase:glnS
beta-D-glucose-6-phosphate
KDO2-(lauroyl)-lipid IVA
PgaA
a semiquinone
predictedgalactose 1-dehydrogenase:yhhX
YidI
N,N’-dimethyl-p-phenylenediamine
FDH-O
acylphosphatase:yccX
3-hydroxyadipyl-CoA
dTDP-4-dehydro-6-
deoxy-D-glucose
isocitrate lyase: aceA
succinate dehydrogenase:sdhA sdhB sdhC sdhD
ppGpp
conversionof succinate
to propionate
fumarase C: fumC
6,7-dihydropteridine
tRNA:Cm32/Um32methyltransferase:trmJ
a 1,2-diacylglycerol-3-phosphate
Mn2+Fe2+
palmitate
N2-succinylglutamate
inosine
6-phosphofructokinase II: pfkB
cofactor
oxidizedthioredoxin
a tRNA
23Sribosomal
RNAmethylatedat position
G2251
D-glucose
tRNApseudouridinesynthase I: truA
guanine
an alcohol
guanosine-5’-diphosphate
melibiosedegradation
3-sulfinoalanine
L-serinedegradation
L-aspartate
L,D-transpeptidaseYnhG: ynhG
an rRNA
IDP
a carboxylicester
ZupT
an oxidizedthioredoxin
a tRNAcontaining 2’-O-methylcytosine
or 2’-O-methyluridine
L-ascorbatedegradation,
anaerobic
enterobactin
molybdateABC
transporter
guanosine-5’-phosphate
Ogt: ogt
2,5-diketo-D-gluconatereductaseA: dkgA
NarL-Pasp
low-specificityL-threoninealdolase:ltaE
tetrahydrofolate biosynthesis
pyridoxal
a protein
2-phosphoglycerate
D-mannosedegradation
gamma-glutamyl-gamma-aminobutyraldehydedehydrogenase: puuC
YiaB
DNA containing5-methylcytosine
AMP
methioninesulfoxidereductaseA: msrA
homocysteinemethyltransferase:mmuM
sugarphosphatase:ybiV
ZraS
L-leucyl-protein
glutathione
O-antigen biosynthesis
L-serine
HemX
galactose-1-phosphateuridylyltransferase:galT
phospho-N-acetylmuramoyl-pentapeptide transferase: mraY
a tRNA
tRNA (m7G46)methyltransferase: trmI
uridine-5’-diphosphate
lysyl-tRNAsynthetase:
lysU
L-ribulose 5-phosphate4-epimerase:ulaF
Fiu
beta-ketoacyl-[acyl-carrier-protein]reductase: fabG
phosphoglyceratemutase, cofactorindependent: gpmM
cis-2-methylaconitate
CadB
malatedehydrogenase,NAD-requiring: maeA
cyclic-AMP
tRNAdihydrouridinesynthase: dusB
tRNAcys
NADsynthetase, NH3-dependent: nadE
an activeribonucleosidetriphosphatereductase
Targlu-Me
a protein-L-methionine-(S)-S-oxide
aspartatesemialdehydedehydrogenase: asd
YhaU
2-octaprenyl-6-methoxyphenol
methylmalonyl-CoA mutase: scpA
nicotinamidase: pncA
L-glutamate
Trggln
rhamnulose-1-phosphatealdolase: rhaD
YdhX
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
KdpE
glycerol-3-phosphateacyltransferase: plsB
deoxyuridinetriphosphatase: dut
a 1,2-diacylglycerol-3-phosphate
an alcohol
L-quinate
ribokinase:rbsK
dGTPpyrophosphohydrolase: mutT
CurliSecretion
andAssemblyComplex
tRNAtyr
nucleosidediphosphatekinase: ndk
D-allulose-6-phosphate
L,D-transpeptidaseYcfS: ycfS
allose-6-phosphateisomerase/ ribose-5-phosphateisomeraseB: rpiB
a peptide
AtoC-Pasp
L-isoleucyl-tRNAile
D-glyceraldehyde-3-phosphate
heptosyl-KDO2-lipid A
ribonucleoside-diphosphatereductase 2:nrdF nrdE
BasSR Two-Component
SignalTransduction
System
dTMP kinase: tmk
tartronatesemialdehyde
shikimate
UDP-N-acetyl-D-mannosaminuronicacid transferase: rffM
D-alanine
fatty acyl-CoAsynthetase: fadD
pantothenate
a DNA withunresolved
recombitionalor holidayjunctions,
created by RecA
CO2
phosphoenolpyruvate
dephospho-CoA
formate-tetrahydrofolateligase
BasS-Phis
BaeSR Two-Component
SignalTransduction
System
succinate
2,3-diketo-L-gulonatereductase:yiaK
EvgSA Two-Component
SignalTransduction
System
YhaO
putative ring-cleavage enzymeof phenylacetatedegradation: maoC
phosphatidylglycerophosphatesynthase: pgsA
PflB
transketolaseII: tktB
dTDP-4-oxo-6-deoxy-D-glucosetransaminase: rffA
MQ
2-dehydropantoate
(S)-1-pyrroline-5-carboxylate
oxalyl-CoA
a cis-delta3-decenoyl-
[acp]
D-glucarate
a dipeptide
3-deoxy-D-manno-
octulosonate8-P
L-arabinoseisomerase: araA
cis-aconitate
K+
MelB
D-alanine
GTPase thatinteracts withmethylmalonyl-CoA mutase: argK
formamidopyrimidineDNA glycosylase: mutM
glyoxalase III
acetyl-CoAacetyltransferase:atoB
LolB
pyruvate dehydrogenasemultienzyme complex: lpd aceF aceE
6-phosphogluconolactonase: pgl
RssB-P
protein N6-(lipoyl)lysine
coenzyme A
aminoacetaldehyde
cis-vaccenatebiosynthesis
nitrate
biotinsulfoxidereductase:bisC
BglG
KDOtransferase:waaA
2-O-(6-phospho-alpha-
mannosyl)-D-glycerate
alpha-ketoglutaratereductase: serA
beta-D-galactose
fused PutAtranscriptionalrepressor / prolinedehydrogenase/ 1-pyrroline-5-carboxylatedehydrogenase:putA
uridinephosphorylase:udp
L-tyrosine
5’-phosphoribosyl-4-(N-succinocarboxamide)
-5-aminoimidazole
PuuP
lipopolysaccharideglucosyltransferaseI: rfaG
ProP
CTP
RcsF-P
UDP-D-glucose:(glucosyl)LPS alpha-1,3-glucosyltransferase: rfaI
gluconokinaseII: idnK
a reducedelectronacceptor
alpha-D-glucose-1-phosphatase: yihX
GTP
Tapglu
a limitdextrin
DNApolymeraseV: umuDumuC
formyl-L-methionylpeptide
3-dehydro-2-deoxy-D-gluconate
DcuS
phosphoglyceratekinase: pgk
an aromaticamino acid
lactose
bicarbonate
octanoate
malatedehydrogenase:mdh
KefAfructose-1,6-bisphosphataseI: fbp
guanosine 3’-diphosphate
5’-triphosphate
multifunctional2-keto-3-deoxygluconate 6-phosphate aldolaseand 2-keto-4-hydroxyglutaratealdolase andoxaloacetatedecarboxylase: eda
CDP
an apo-[acp]
UDP-N-acetylmuramoyl-L-alanine
Targlu
RfbX
flavodoxinNADP+reductase: fpr
pyruvate
uridine-5’-diphosphate
isocitratedehydrogenase: icd
purine nucleosidephosphorylase:
deoD
dTTP
anthranilatesynthase: trpD trpE
YegH
2-dehydro-3-deoxyphosphoheptonatealdolase: aroF
histidinal
NlpE
tRNAcontaining
ribothymidineat position 54
pyridoxamine-phosphatetransaminase
L-homocysteine
dihydroxyacetonephosphate
methyl-1,4-benzoquinol
RcsC
a ThiI sulfur-carrierprotein
tetrahydrodipicolinatesuccinylase: dapD
cobalamin-dependenthomocysteinetransmethylase:metH
cysteinebiosynthesis I
cytidinedeaminase:cdd
a nucleoside-5’-phosphate
an oxidizedglutaredoxin
anthranilate
gamma-glutamyl-gamma-aminobutyraldehyde
D-threo-isocitrate
CMP-3-deoxy-D-manno-
octulosonate
NADH-azoreductase,FMN-dependent:azoR
aspartateaminotransferase,PLP-dependent: aspC
ADP-heptose:LPSheptosyltransferaseII: rfaF
ornithinecarbamoyltransferase: argI
a 3-oxo-octanoyl-[acp]
dihydroxy-acetone
rRNA containingN6,N6-
dimethyladenine
6-phospho-beta-glucosidase;cryptic: ascB
trehalosedegradation
I (lowosmolarity)
KDOtransferase:waaA
R-4’-phosphopantothenoyl-
L-cysteine
GfcA
acetaldehydedehydrogenase:adhE
AtoC
heptosyl2-KDO2-lipid A
a phenol
fusedglutathionylspermidineamidase /glutathionylspermidinesynthetase: gsp
beta-hydroxyacyl-ACPdehydratase: fabZ
glycine
methyleneTHFenzyme: folD
beta-hydroxyacyl-ACP dehydrase[multifunctional]:fabA
OmpC
tRNA-guaninetransglycosylase: tgt
UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6-D-galactosyltransferase:rfaB
UDP-3-O-[3-hydroxymyristoyl]glucosamineN-acetyltransferase: lpxD
2-phosphoglycolate
an N10-formyl-tetrahydrofolate
dihydrofolatesynthetase: folC
methionineadenosyltransferase:
metK
peptidoglycantetrapeptide,
glycan chain 2
thioredoxinpathway
NarX
23S rRNApseudouridine2605synthase: rluB
deoxycytidine
NarL
multidrug
L-methionine
sugarphosphatase:yfbT
DNApolymeraseIII, alphasubunit: dnaE
DctA
acidphosphatase:appA
N-acetylmannosaminekinase: nanK
DL-lactaldehyde
phosphatidylglycerophosphataseB: pgpB
a phospholipidolefinic
fatty acid
pyruvate
a single-stranded
RNA
multidrug
S-adenosyl-L-methionine
L-lysine
N-acetyl-L-ornithine
cysteinesynthase A: cysK
D-arabinosedegradation I
deoxyguanosine
protein N6-(dihydrolipoyl)
lysine
aryl carrierprotein: entF
L-lysine
4-nitrobenzaldehydereductase: dkgB
S-carboxymethyl-D-cysteine
NADP-dependentdehydrogenase:yqhD
a protein L-methionine
UDP-N-acetyl-D-
glucosamine
L-arginine
D-glutamate
23S rRNApseudouridinesynthase: rluC
Targlu
2-C-methyl-D-
erythritol-4-phosphate
a protein-L-glutamine
ZraR
hydrogencyanide
L-homocysteine
D-ribose-5-phosphate
glycerol
pyruvate
pyrazinamidase:pncA
2-hydroxyglutaratesynthase
Kup
a polypeptide
glyoxalaseII: gloB
trehalose-6-phosphatehydrolase:treC
YgjI
a tRNAcontaining 7-
aminomethyl-7-deazaguanineat position 34
a 2,3-dehydroacyl-CoA
6,7-dimethyl-8-(1-D-ribityl)lumazine
DNA withremovedadenine
mismatchleaving
an AP site
D-sorbitol-6-phosphate
gluconolactonase
hypoxanthinephosphoribosyltransferase: hpt
thiolperoxidase:bcp
bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinonemethylase and S-adenosylmethionine:2-DMKmethyltransferase: ubiE
glyceroldehydrogenase:gldA
o-succinylbenzoatesynthase: menC
excised base
tRNAhis
H2O
chorismate mutase: tyrA
methylglyoxalreductase: yeaE
5-methylaminomethyl-2-thiouridinemethyltransferase:mnmC
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-
meso-2,6-diaminopimelate
L-tartratedehydratase:ttdB ttdA
a CDP-diacylglycerol
multidrug
Autoinducer2-degradingprotein: lsrG
Trgglu
dGMP
adenosylcobinamide
hydroxyethylthiazolekinase: thiM
D-ribose-5-phosphate
an organicmolecule
S-ureidoglycolate
thiamin(thiazolemoiety)biosynthesisprotein: thiF
S-adenosyl-L-methionine
dihydrolipoyltranssuccinylaseN6-(dihydrolipoyl)lysine
YneN
fatty acid oxidationcomplex, alphacomponent: fadB
FATTY ACID AND LIPIDS DEGRADATION
a ThiS-ThiF acyl-disulfide
oxaloacetate
PhoP
thioesteraseIII: ybaW
2,3-diketo-L-gulonate
HsrA
L-ribulose-5-phosphate
dTDP-D-glucose
a protein-S-methyl-L-cysteine
glycine decarboxylase: gcvP
an L-1-phosphatidyl-glycerol
OmpA
glucokinase:glk
L-glutamate-5-phosphate
a damagedDNA
pyrimidine
EntF
enterobacterial commonantigen biosynthesis
Blr
citrate
glutathione S-transferase:yfcF
a (3S)-3-hydroxyacyl-CoA
selenophosphate
D-cysteinedesulfhydrase,PLP-dependent: dcyD
UhpB
uridine
D-ribose
D-xylulose-5-phosphate
dihydrouracil
beta-hydroxyacyl-ACPdehydratase: fabZ
lipoate acetyltransferase N6-(S-acetyldihydrolipoyl)lysine
GlpT
KASI: fabB
3-methylcrotonyl-CoA
TorT-TMAO
UDP-L-Ara4FN
GlcA
a phospholipidcyclopropane
fatty acid
acetate CoA-transferase
L-glyceraldehyde3-phosphatereductase: yghZ
Co2+Fe2+
a trans-polyisoprenyln-PP
AroP
Tapglu-Me
XTP
orotidine-5’-phosphate-decarboxylase: pyrF
uracil
restrictionof DNA at 5-methylcytosineresidues: mcrA
transketolaseII: tktB
oxaloacetate
DNA adeninemethyltransferase:yhdJ
chemotaxis proteinmethyltransferase:cheR
a 1,4-alpha-D-glucan
nucleosidediphosphate kinase: ndk
GalP
[+ 3 isozymes]
xyloglucanoligosaccharide
thiamin biosynthesis I
an aldehyde
ureidoglycolatedehydrogenase:allD
maltodextringlucosidase:malZ
hydroxymethylpyrimidinephosphate
D-ribulose-5-phosphate
base withlesion
biotin
an aliphaticN-acetyl-diamine
citrate
cytidinedeaminase: cdd
uracil
guanosine-5’-diphosphate
amylomaltase:malQ
superpathway of pyridoxal 5’-phosphate biosynthesis and salvage
uridine
a ribonucleosidediphosphate
L-alanine
UDP-D-glucuronate
5’,5’-diadenosinetriphosphate
a glucoronide
ATP
phosphoenolpyruvate
2-hydroxyglutarate
ADP-sugarpyrophosphatase:nudF
23S rRNA m2G2445methyltransferase:rlmL
dihydropteroatesynthase: folP
probable 6-phospho-beta-glucosidase:glvG
UDP-3-O-(3-hydroxymyristoyl)-
N-acetylglucosamine
acetaldehydedehydrogenase:adhE
NADPHnitroreductase:nfsA
CpxA
fructose-1-phosphate
glycerophosphoryldiesterphosphodiesterase,periplasmic: glpQ
UDP-D-glucuronate
glycerol degradation I
guanosine-5’-phosphate
ubiquinone-8biosynthesis(prokaryotic)
long chainpolyphosphate
an oxidizedthioredoxin
MdtABC-TolC
multidrugefflux
transportsystem
pyruvate
L-Ala-gamma-D-Glu-Dap
L-rhamnosemutarotase:rhaM
ATP
fumarase C: fumC
inosine-5’-phosphate
fumaratereductase: frdDfrdC frdB frdA
tRNAphe
KdpD
YnfA
EvgS
UDP-L-Ara4Nformyltransferase:arnA
alpha-D-mannose1-phosphate
arbutin-6-phosphate
Ca2+ Na+ K+
a tRNA
phosphoglucomutase: pgm
c-di-GMPphosphodiesterase:yhjH
acetate
taurine
L-xylulosekinase: lyxK
2-oxobutanoate
a protein-L-methionine-(R)-S-oxide
GDP-mannosemannosylhydrolase:gmm
beta-D-galactose
correspondingcarbamoylamino acid
carnitine degradation I
a cis,trans-polyisoprenyln-PP
5-aminoimidazoleribonucleotide
uridine-5’-diphosphate
predicted alpha-ribazole-5’-Pphosphatase: cobC
D-erythrose-4-phosphate
phosphoproteinphosphatase: pphB
glutamate-1-semialdehyde
ADP
dGTP
ribulosephosphate3-epimerase:rpe
homoserine
di-trans,poly-cis-nonaprenyl
diphosphate
AlkB repairsystem foralkylatedDNA andRNA: alkB
methionylpeptide
inosine-5’-phosphate
uroporphyrinogen-III
MdtJIspermidine
SMRtransporter
EIIChb
D-xylulose
2-aceto-2-hydroxy-butyrate
fructoselysine 3-epimerase: frlC
L,D-transpeptidaseErfK: erfK
UhpBA Two-Component
SignalTransduction
System
TrkH
precorrin-1
D-ribose
methylglyoxalreductase(NADPH-dependent)
L-cysteine
a fatty acid
predicted acetoindehydrogenase:yohF
sn-glycerol-3-phosphate
O-succinylhomoserinelyase: metB
pre-cofactor
IdnT
bifunctional NadRtranscriptionalrepressor and NMNadenylyltransferase:nadR
CO2
N-acetylmuramicacid PTSpermease
phosphoribosylamine-glycine ligase: purD
thiamin(thiazolemoiety)biosynthesisprotein: thiF
MdtO
thiaminemonophosphatekinase: thiL
thiaminbiosynthesis
ThiGHcomplex:thiH thiG
4,5-dihydroxy-2,3-pentanedione
L-glutamate
adenylosuccinatesynthetase: purA
phospholipid biosynthesis I
palmitoleatebiosynthesis
beta-D-glucose-6-phosphate
N5-carboxyaminoimidazoleribonucleotidesynthetase: purK
phosphoribosylaminoimidazole-succinocarboxamide synthase: purC
nucleosidediphosphatekinase: ndk
multifunctional2-keto-3-deoxygluconate 6-phosphate aldolaseand 2-keto-4-hydroxyglutaratealdolase andoxaloacetatedecarboxylase: eda
L-Ala-D-Glu-meso-A2pm
ribonucleoside-diphosphatereductase 2:nrdF nrdE
a 6-acetyl-beta-D-
galactoside
crRNA
2-keto-isovalerate
phosphoenolpyruvatecarboxylase: ppc
dTMP
ethyl-2-methylacetoacetate
leucine ABCtransporter
pyruvatekinase I: pykF
HlyE
tRNAile
OuterMembrane
FerrichromeTransportSystem
YhhS
2-trans,5-cis-tetradecadienoyl-
CoA
fumarase B: fumB
NarQ Nitrate/Nitrite-DependentTwo-Component Regulatory System
aspartateaminotransferase,PLP-dependent: aspC
imidazoleacetol-
phosphate
an (R)-3-hydroxyhexanoyl-
[acp]
an N-acetylspermidine
HYD1
formate
a drug
pyridoxalphosphatase:cof
N-acetylglutamatesynthase: argA
RcsF
Zn2+
a holo-[acp]
UDP-4-amino-4-deoxy-L-arabinose
ATP
23S rRNAcontaining
C5-methylatedcytosine
ornithinedecarboxylase,biosynthetic:speC
octaprenyldiphosphatesynthase: ispB
partially N-deacetylated
poly-beta-1,6-N-acetyl-D-glucosamine
NarP
a holo-[acp]
5’-deoxyadenosine
tRNA containing 5-methylaminomethyl-
2-selenouridine
aldehydedehydrogenase A,NAD-linked: aldA
L-tryptophanyl-tRNAtrp
16S rRNAcontaining
N3-methylated
uridine
a 3-oxo-cis-vaccenoyl-
[acp]
YagU
N-acetyl-D-glucosamine-6-phosphate
5-amino-6-(5’-phosphoribosylamino)
uracil
fatty acid oxidationcomplex, alphacomponent: fadB
heme dsynthase:katE
short chain acyl-CoAsynthetase: fadK
polynucleotidephosphorylase:pnp
pyruvate
L-glutamategamma-
semialdehyde
an acyl-[acp]
DNA Cleavedat Recognition
Site
L-tartrate
N-acetyl-D-glucosamine-6-phosphate
dihydroxyacetonephosphate
dTDP-4-dehydro-6-deoxy-
L-mannose
sulfate
methanol
tRNAtyr
TorSR Two-Component Signal Transduction System
NarK
arsenatereductase:arsC
DNA (without 6-O-methylguanine)
oxidizedribonucleoside-
triphosphatereductase
tRNAval
YfhM
L-cysteinedesulfhydrase
succinate
protein-tyrosine-phosphatase:pphB
L-valine L-leucineL-isoleucine
bifunctional 3-demethylubiquinone-83-O-methyltransferaseand 2-octaprenyl-6-hydroxyphenolmethylase: ubiG nicotinate
mononucleotide
L-homocysteine
AraJ
tetrahydrofolate
EcoCyc: Escherichia coli K-12 MG1655 Cellular OverviewAuthors: Peter D. Karp
Ingrid KeselerAlexander ShearerAnamika Kothari
Suzanne PaleyMarkus KrummenackerTomer AltmanIan Paulsen
Amanda MackieAaron JohnsonJulio Collado-VidesCesar Bonavides-Martinez
Socorro Gama-CastroMartin PeraltaAlberto Santos-ZavaletaJohn L Ingraham
Robert GunsalusAn online version of this diagram is available through EcoCyc.org and may be used for analysis of omics datasets. Lines in thediagram correspond to reactions; nodes correspond to metabolites. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways in the right, signaling pathways in the bottom-left.Pathways are colored according to their cellular function, such as biosynthesis of cofactors. Reactions not assigned to any pathway are in the far right of the cytoplasm. In the inner and outer membranes are transporters (with arrows) and othermembrane proteins. In the periplasm are periplasmic enzymes and other periplasmic proteins. Connections between pathways are omitted for legibility.
Copyright ' 2009 SRI International. All Rights Reserved. This diagram was automatically generated by SRI International Pathway Tools version 13.0, authors S. Paley and P. Karp.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Metabolism has been mainly studied through the reductionist approach that characterized theBiological sciences in the XXth century.In recent times, full genome sequencing and the newly developed high-throughput techniquesallowed a more realistic approach i.e. systems biology.
A possible definition
A biology-based inter-disciplinary study field that focuses on the systematic study of complexinteractions in biological systems, thus using a new perspective (holism instead of reduction) tostudy them.
Goals
The discovery of new emergent properties that may arise from the systemic view used by thisdiscipline in order to understand better the entirety of processes that happen in a biologicalsystem.
Good book to start with: Foundations of Systems Biology by Hiroaki Kitano, available onAmazon.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling Gene Regulatory Networks (GRN)
g
x
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling Gene Regulatory Networks (GRN)
g
Regulated synthesis
Degrada1on and
dilu1on
a transcrip1on factor x
1 2 3 4 5
0
0.2
0.4
0.6
0.8
1
x
y=
xn
xn+
!n
Positive Hill
1 2 3 4 5
0
0.2
0.4
0.6
0.8
1
x
y=
!n
xn+
!n
Negative Hill
n=1n=2n=3n=4n=5n=6
A) TF effect on the transcription rate:- Positive regulation:
A(x, p) = κmax h+(x, θ, n) = κmaxxn
θn + xn,
with κmax the maximum transcription rate of thepromoter, θ the activation threshold, n the steepnessparameter and p = [θ, n] the vector of parameters;- Negative regulation:
A(x, p) = κmaxh−(x, θ, n) = κmax(1− h+(x, θ, n)
);
B) Degradation rate γ;
C) Dilution µ.
A guide to modeling GRN and a literature review:de Jong [2002].
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling Gene Regulatory Networks (GRN)
g
Regulated synthesis
Degrada1on and
dilu1on
a transcrip1on factor x
1 2 3 4 5
0
0.2
0.4
0.6
0.8
1
x
y=
xn
xn+
!n
Positive Hill
1 2 3 4 5
0
0.2
0.4
0.6
0.8
1
x
y=
!n
xn+
!n
Negative Hill
n=1n=2n=3n=4n=5n=6
A) TF effect on the transcription rate:- Positive regulation:
A(x, p) = κmax h+(x, θ, n) = κmaxxn
θn + xn,
with κmax the maximum transcription rate of thepromoter, θ the activation threshold, n the steepnessparameter and p = [θ, n] the vector of parameters;- Negative regulation:
A(x, p) = κmaxh−(x, θ, n) = κmax(1− h+(x, θ, n)
);
B) Degradation rate γ;
C) Dilution µ.
A guide to modeling GRN and a literature review:de Jong [2002].
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling Gene Regulatory Networks (GRN)
g
Regulated synthesis
Degrada1on and
dilu1on
a transcrip1on factor x
1 2 3 4 5
0
0.2
0.4
0.6
0.8
1
x
y=
xn
xn+
!n
Positive Hill
1 2 3 4 5
0
0.2
0.4
0.6
0.8
1
x
y=
!n
xn+
!n
Negative Hill
n=1n=2n=3n=4n=5n=6
A) TF effect on the transcription rate:- Positive regulation:
A(x, p) = κmax h+(x, θ, n) = κmaxxn
θn + xn,
with κmax the maximum transcription rate of thepromoter, θ the activation threshold, n the steepnessparameter and p = [θ, n] the vector of parameters;- Negative regulation:
A(x, p) = κmaxh−(x, θ, n) = κmax(1− h+(x, θ, n)
);
B) Degradation rate γ;
C) Dilution µ.
A guide to modeling GRN and a literature review:de Jong [2002].
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
For each gene there are (at least) three terms in the model:
dgdt
= Ag(x,p)− µ[g]− γ[g]
where µ is the growth rate and µ[g] accounts for the dilution of the transcriptby growth, γ is the degradation rate.
Hereinafter I will indicateA(x, p) simply withA.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Promoters as logic gates
g
promoter
g
g
x1
x1 x2
x2
g
x1
A)
B)
C)
A) Simple regulation:
Ag = κmaxh+(x1, θ1, n1);
B) AND configuration (both regulators must bepresent to affect transcription):
Ag = κmax h+(x1, θ1, n1) ∗ h+(x2, θ2, n2);
C) OR configuration (one regulator is sufficient toaffect transcription):
Ag = κ1max h+(x1, θ1, n1)+κ
2maxh+(x2, θ2, n2);
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Network motifs
Figure : Feed Forward Loops [Shoval and Alon[2010]].
Summary on Network Motifs
• Transcription regulation andsignaling networks are composed ofrecurring patterns called networkmotifs;
• Highly abundant in gene regulatorynetworks from bacteria to humans;
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling the feedforward loop
-1-1
I-1
System of equations for the FFLC-1 AND
dYdt
=
Regulated synthesis︷ ︸︸ ︷κ
Xn
θn + Xn− (γ + µ)︸ ︷︷ ︸
Degr. and dil.
Y (1)
dZdt
= κXn
θn + Xn
Yn
θn + Yn︸ ︷︷ ︸AND logic
−(γ + µ)Z. (2)
Let’s put:α = γ + µ.
System of equations for the FFLI-1 ANDdYdt
= κXn
θn + Xn− αY (3)
dZdt
= κXn
θn + Xn
θn
θn + Yn− αZ. (4)
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Network motifs have special dynamical properties
0 5 10 15 20 25 30 35 40−0.5
0
0.5
1
1.5
[Z
]m
ax([Z
])
Feed-Forward Loop Coherent type I
0 5 10 15 20 25 30 35 40−0.5
0
0.5
1
1.5
T ime! +µ
[Z
]m
ax([Z
])
Feed-Forward Loop Incoherent type I
Faster response withrespect to simple regulation
Signed delayed response withrespect to simple regulation
No delayturningOFF
Sensitivetransient ONsignals
Insensitive totransient ONsignals
Sensitive totransientOFF signals
Sensitive totransientOFF signals
Figure : [Shen-Orr et al. [2002], Mangan and Alon [2003], Mangan et al. [2003]]
FFLC-1-1-1
• Sign-sensitive delay;• Persistence detector;• Noise reduction;
FFLI-1I-1
• Sign-sensitiveaccelerator;
• other incoherent FFL aregood pulsers;
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Metabolic network representations
A
A
B
B
G
GG
CCA
B
C
DD
D E
EE
FF
F
Compound graph Reaction graph
Bipartite graph Hypergraph
R3 R2
R1
R1
R3
R2
A + B C + DD + E F B G
R1R2R3
Every representations has its own pros andcons
1 Loss of information - 1: Only masstransfer encoded in the graph (can yousee the feedback regulation of R1?);
2 Loss of information - 2: Reaction R1 isa multi-substrate reaction; By lookingat some of the representation one maythink that there exist different reactionsi.e. A→ C and A→ D
A review about (some of) these things: Kleinet al. [2012].The Structural Network Properties of
Biological Systems, Brilli and Liò, Ch. 2 inBoccaletti et al. [2010];
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
A B C
E F OUT
IN
OUT
E1
E4
E3E2
E5
OUTD
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
OUTA B C D
E F OUT
IN
OUT
E1
E4
E3E2
E5
G2G1 G3
G5
G4
TF1
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
OUTA B C D
E F OUT
IN
OUT
E1
E4
E3E2
E5
G2G1 G3
G5
G4
TF1
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
OUTA B C D
E F OUT
IN
OUT
E1
E4
E3E2
E5
G2G1 G3
G5
G4
TF1
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Metabolism is not isolated...
Gene regulation
Metabolism
Transcription&
Translation
Effectormetabolites
Even this picture misses important regulatory mechanisms..
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
The stoichiometry matrix
A B C
E F OUT
IN
OUT
E1
E4
E3E2
E5
OUTD
The corresponding stoichiometry matrix Nm×r :
IN E1 E2 E3 E4 E5 OUTF OUTD OUTC
A 1 −1 0 0 0 0 0 0 0
B 0 1 −1 0 0 0 0 0 0
C 0 0 1 −1 −1 0 0 0 −1
D 0 0 0 1 0 0 0 −1 0
E 0 0 0 0 1 −1 0 0 0
F 0 0 0 0 0 1 −1 0 0
Evolution of the system: dx
dt = N · v(x, p).
i.e. dBdt = NB · v =
= [0, 1,−1, 0, 0, 0, 0, 0, 0] · [IN, vE1, vE2, vE3, vE4, vE5,OUTF,OUTD,OUTC]T = vE1 − vE2.
Steady state of the system: dxdt = N · v(x, p) = 0.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
The stoichiometry matrix
A B C
E F OUT
IN
OUT
E1
E4
E3E2
E5
OUTD
The corresponding stoichiometry matrix Nm×r :
IN E1 E2 E3 E4 E5 OUTF OUTD OUTC
A 1 −1 0 0 0 0 0 0 0
B 0 1 −1 0 0 0 0 0 0
C 0 0 1 −1 −1 0 0 0 −1
D 0 0 0 1 0 0 0 −1 0
E 0 0 0 0 1 −1 0 0 0
F 0 0 0 0 0 1 −1 0 0
Evolution of the system: dxdt = N · v(x, p).
i.e. dBdt = NB · v =
= [0, 1,−1, 0, 0, 0, 0, 0, 0] · [IN, vE1, vE2, vE3, vE4, vE5,OUTF,OUTD,OUTC]T = vE1 − vE2.
Steady state of the system: dxdt = N · v(x, p) = 0.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
The stoichiometry matrix
A B C
E F OUT
IN
OUT
E1
E4
E3E2
E5
OUTD
The corresponding stoichiometry matrix Nm×r :
IN E1 E2 E3 E4 E5 OUTF OUTD OUTC
A 1 −1 0 0 0 0 0 0 0
B 0 1 −1 0 0 0 0 0 0
C 0 0 1 −1 −1 0 0 0 −1
D 0 0 0 1 0 0 0 −1 0
E 0 0 0 0 1 −1 0 0 0
F 0 0 0 0 0 1 −1 0 0
Evolution of the system: dx
dt = N · v(x, p).
i.e. dBdt = NB · v =
= [0, 1,−1, 0, 0, 0, 0, 0, 0] · [IN, vE1, vE2, vE3, vE4, vE5,OUTF,OUTD,OUTC]T = vE1 − vE2.
Steady state of the system: dxdt = N · v(x, p) = 0.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
The stoichiometry matrix
A B C
E F OUT
IN
OUT
E1
E4
E3E2
E5
OUTD
The corresponding stoichiometry matrix Nm×r :
IN E1 E2 E3 E4 E5 OUTF OUTD OUTC
A 1 −1 0 0 0 0 0 0 0
B 0 1 −1 0 0 0 0 0 0
C 0 0 1 −1 −1 0 0 0 −1
D 0 0 0 1 0 0 0 −1 0
E 0 0 0 0 1 −1 0 0 0
F 0 0 0 0 0 1 −1 0 0
Evolution of the system: dx
dt = N · v(x, p).
i.e. dBdt = NB · v =
= [0, 1,−1, 0, 0, 0, 0, 0, 0] · [IN, vE1, vE2, vE3, vE4, vE5,OUTF,OUTD,OUTC]T = vE1 − vE2.
Steady state of the system: dxdt = N · v(x, p) = 0.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
The stoichiometry matrix
A B C
E F OUT
IN
OUT
E1
E4
E3E2
E5
OUTD
The corresponding stoichiometry matrix Nm×r :
IN E1 E2 E3 E4 E5 OUTF OUTD OUTC
A 1 −1 0 0 0 0 0 0 0
B 0 1 −1 0 0 0 0 0 0
C 0 0 1 −1 −1 0 0 0 −1
D 0 0 0 1 0 0 0 −1 0
E 0 0 0 0 1 −1 0 0 0
F 0 0 0 0 0 1 −1 0 0
Evolution of the system: dx
dt = N · v(x, p).
i.e. dBdt = NB · v =
= [0, 1,−1, 0, 0, 0, 0, 0, 0] · [IN, vE1, vE2, vE3, vE4, vE5,OUTF,OUTD,OUTC]T = vE1 − vE2.
Steady state of the system: dxdt = N · v(x, p) = 0.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
The stoichiometry matrix
A B C
E F OUT
IN
OUT
E1
E4
E3E2
E5
OUTD
The corresponding stoichiometry matrix Nm×r :
IN E1 E2 E3 E4 E5 OUTF OUTD OUTC
A 1 −1 0 0 0 0 0 0 0
B 0 1 −1 0 0 0 0 0 0
C 0 0 1 −1 −1 0 0 0 −1
D 0 0 0 1 0 0 0 −1 0
E 0 0 0 0 1 −1 0 0 0
F 0 0 0 0 0 1 −1 0 0
Evolution of the system: dx
dt = N · v(x, p).
i.e. dBdt = NB · v =
= [0, 1,−1, 0, 0, 0, 0, 0, 0] · [IN, vE1, vE2, vE3, vE4, vE5,OUTF,OUTD,OUTC]T = vE1 − vE2.
Steady state of the system: dxdt = N · v(x, p) = 0.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
plot_1
[1,3-diphosphosphoglycerate]|Time [6-Phosphogluconate]|Time [Fructose-1,6-bisphosphate]|Time
[Glucose-6-Phosphate]|Time [Pyruvate]|Time
mmol/
l
0
1
2
3
4
5
6
s0 1,000 2,000 3,000 4,000 5,000 6,000
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling in different flavours
Modeling of metabolic systems have been approached with different strategies:
1 Flux Balance Analysis (FBA) on genome-scale metabolic systems; only steadystate flux distributions can be predicted (Palsson [2008]);
2 Hybrid cases FBA+rate functions (e.g. Jamshidi and Palsson [2010], Smallboneet al. [2007]);
3 Modeling of small to medium-scale systems (one or a few pathways) withmechanistic rate functions. This allows a full characterization of the system in atime dependent way;
4 Approximations of the full kinetic rate equations (e.g. Visser et al. [2004], Pozoet al. [2011]).
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
FBA - Concept
Given the inputs to this network(easily measurable e.g. the glucoseconsumption rate), how the internalfluxes distribute between the differentpossible paths at steady state?
Solve: Nv = 0But for genome scale metabolicnetworks is an underdeterminedproblem, i.e. infinite solutions exist;
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
FBA - Concept
Given the inputs to this network(easily measurable e.g. the glucoseconsumption rate), how the internalfluxes distribute between the differentpossible paths at steady state?
Solve: Nv = 0
But for genome scale metabolicnetworks is an underdeterminedproblem, i.e. infinite solutions exist;
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
FBA - Concept
Given the inputs to this network(easily measurable e.g. the glucoseconsumption rate), how the internalfluxes distribute between the differentpossible paths at steady state?
Solve: Nv = 0But for genome scale metabolicnetworks is an underdeterminedproblem, i.e. infinite solutions exist;
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
FBA - Algo
Allowable solutions
Not allowablesolutions
v3
v2
v3v1
v2
v3v1
v2
v3*v1*
v2*
Unconstrained solution space
The solution space partitioned by the constraints
v1Solution: a vector of fluxes
satisfying Nv=0i.e. a flux distribution
The optimal solution
optimal solution:v*=[v1* v2* v3*]’ Example with 3 fluxes
maximize objectivefunction
e.g.
Constraints
Steady state
• To reduce the number of solutions, the problem is posed as Nv = 0subject to constraints.
• The best solution is picked among those such that minimizes ormaximizes some prespecified criterion.
• Alternatively an ensemble of satysfying solutions is chosen and furtheranalysed.
Varma and Palsson [1994], Edwards et al. [2001]Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
FBA - Objective function
Allowable solutions
Not allowablesolutions
v3
v2
v3v1
v2
v3v1
v2
v3*v1*
v2*
Unconstrained solution space
The solution space partitioned by the constraints
v1Solution: a vector of fluxes
satisfying Nv=0i.e. a flux distribution
The optimal solution
optimal solution:v*=[v1* v2* v3*]’ Example with 3 fluxes
maximize objectivefunction
e.g.
Constraints
Steady state
The objective function
many possible solutions satisfy the constraints
a, b and c can be combined into a single function to be maximized/minimized e.g.
Z=α a+β b+γ cwhere α, β and γ are weights.
Solution maximizing the objective function
Input fluxes Active fluxes
a b c
• The objective function is often the production of biomass i.e. the function to bemaximized is the growth rate;
• Maximizing the growth rate works for fast growing organisms (only a few...);
• Objective function is often chosen in a case-by-case manner e.g. Resendis-Antonio et al.[2007] modeled nitrogen fixation by Mesorhizobium loti and used an objective functiontailored on experimental information in that condition;
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling using detailed rate functions:
Advantages:1 Time can be taken into
account;2 Rate functions derive from
mechanistic information;
Limitations:1 Kinetic parameters;2 Non-linearity;3 No possible to obtain
analytical solutions(exceptions exist for verysimple systems);
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Modeling using detailed rate functions:
Advantages:1 Time can be taken into
account;2 Rate functions derive from
mechanistic information;
Limitations:1 Kinetic parameters;2 Non-linearity;3 No possible to obtain
analytical solutions(exceptions exist for verysimple systems);
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
Rate functions
1 Irreversible Michaelis-Menten: v = vmax[S]
Km+[S] ;
2 Reversible Michaelis-Menten: v =Vf ·[S]KmS− Vr·[P]
KmP
1+ [S]KmS
+[P]
KmP
;
3 Hill cooperativity: v = V·[S]hKh
h+[S]h ;
4 Allosteric inhibition: v =Vf ·[S]KmS− Vr·[P]
KmP
1+ [S]KmS
+[P]
KmP+(
[I]Ki)n
;
The "Bible" of enzyme kinetics: Fundamentals of Enzyme Kinetics by Athel Cornish-Bowden,available on Amazon.
Matteo Brilli Metabolic modeling
Background: what is metabolismSystems Biology
A step back: modeling gene regulationModeling metabolism
[S] is fized at 1mM; [P] startsfrom 0mM;Reversible Michaelis-Menten:
v =Vf ·[S]KmS− Vr·[P]
KmP
1+ [S]KmS
+[P]
KmP
;
IrreversibleMichaelis-Menten:
v = vmax[S]
Km + [S];
0 2 4 6 8 100
2
4
6
8
10
Time
[P
](m
M)
Product of reversible Michaelis-Menten
0 2 4 6 8 100
2
4
6
8
10
Time
v(m
mol/s)
Rate Reversible Michaelis-Menten
0 2 4 6 8 100
20
40
60
80
100
Time
[P
](m
M)
Product of Irreversible Michaelis-Menten
0 2 4 6 8 108
8.5
9
9.5
10
10.5
Time
vm
mol/s
Rate Irreversible Michaelis-Menten
Matteo Brilli Metabolic modeling
AppendixReferences
Stefano Boccaletti, Vito Latora, and Yamir Moreno, editors. Handbook on biological networks. World Scientific Publishing Co. Pte. Ltd., Singapore,world scie edition, 2010. ISBN 9789812838797.
Hidde de Jong. Modeling and simulation of genetic regulatory systems: a literature review. Journal of Computational Biology, 9(1):67–103, 2002.
Eric Duchaud, Mekki Boussaha, Valentin Loux, Jean-François Bernardet, Christian Michel, Brigitte Kerouault, Stanislas Mondot, Pierre Nicolas, RobertBossy, Christophe Caron, Philippe Bessières, Jean-François Gibrat, Stéphane Claverol, Fabien Dumetz, Michel Le Hénaff, and AbdenourBenmansour. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nature biotechnology, 25(7):763–9, 2007.
J S Edwards, R U Ibarra, and Bernhard ØPalsson. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.Nature biotechnology, 19(2):125–30, 2001.
Neema Jamshidi and Bernhard ØPalsson. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometricmodels. Biophysical journal, 98(2):175–85, 2010.
Cecilia Klein, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu, and Matteo Brilli. Structural and dynamical analysis of biological networks.Briefings in functional genomics, 11(6):420–33, 2012.
Shmoolik Mangan and Uri Alon. Structure and function of the feed-forward loop network motif. Proceedings of the National Academy of Sciences of theUnited States of America, 100(21):11980–5, 2003.
Shmoolik Mangan, A Zaslaver, and Uri Alon. The Coherent Feedforward Loop Serves as a Sign- sensitive Delay Element in Transcription Networks.Journal of molecular biology, 334:197–204, 2003.
Bernhard ØPalsson. Collection of Homework Sets for Systems Biology : properties of reconstructed networks Capabilities of Reconstructed Networks.Technical report, 2008.
Carlos Pozo, Alberto Marin-Sanguino, Rui Alves, Gonzalo Guillen-Gosalbez, Laureano Jimenez, and Albert Sorribas. Steady-state global optimizationof metabolic non-linear dynamic models through recasting into power-law canonical models. BMC systems biology, 5(1):137, 2011.
Osbaldo Resendis-Antonio, Jennifer L Reed, Sergio Encarnación, Julio Collado-Vides, and Bernhard ØPalsson. Metabolic reconstruction and modelingof nitrogen fixation in Rhizobium etli. PLoS computational biology, 3(10):1887–95, 2007.
Shai S Shen-Orr, Ron Milo, Shmoolik Mangan, and Uri Alon. Network motifs in the transcriptional regulation network of Escherichia coli. NatureGenetics, 31(1):64–8, 2002.
Oren Shoval and Uri Alon. SnapShot: network motifs. Cell, 143(2):326–e1, 2010.
Kieran Smallbone, Evangelos Simeonidis, David S Broomhead, and Douglas B Kell. Something from nothing: bridging the gap betweenconstraint-based and kinetic modelling. The FEBS journal, 274(21):5576–85, 2007.
Amit Varma and Bernhard ØPalsson. Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use. Nature biotechnology, 12:994–998, 1994.
Diana Visser, Joachim W Schmid, Klaus Mauch, Matthias Reuss, and Joseph J Heijnen. Optimal re-design of primary metabolism in Escherichia coliusing linlog kinetics. Metabolic engineering, 6(4):378–90, 2004.
Matteo Brilli Metabolic modeling