modeling and understanding metabolism

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

Outline

1 Background: what is metabolism

2 Systems Biology

3 A step back: modeling gene regulation

4 Modeling 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] )

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

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

L-Ala-gamma-D-Glu-DAP-

alpha-amylase:malS

an octanoyl-[acp]

phenylacetaldehyde

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

alpha-D-glucose-1-

phosphatase:yihX

cytochromeC552: nrfA

L-lactate

N-acetyl-anhydromuramyl-L-alanine-amidase: ampD

aminoacetoneoxidase: tynA

multicopperoxidase withrole in copperhomeostasis:cueO

L-lactate

a carboxylate

a peptidoglycan

a phospholipidolefinic

fatty acid

peptidyl-prolylcis-transisomerase:ppiD

peptidylprolylisomerase: fkpB

a palmitoleoyl-[acp]

argininedecarboxylase,degradative: adiA

D-lactate

a single-stranded

1,4-dihydroxy-2-naphthoate

beta-D-glucose

an acyl-[acp]

beta-D-glucose-6-phosphate

a glucosylatedglucose

acceptor

nitrite

holo-EntB

serineproteaseDo: degP

soluble lytic mureintransglycosylase: slt

uridine-5’-phosphate

a shortglucan

phenylethylamineoxidase: tynA

nitrite

a leadersequence

phytate

D-alanine

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:

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:

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

an acyl-[acp]

DsbDoxidized

-D-glucose

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

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

thioesteraseII: tesB

an L-1-phosphatidyl-ethanolamine

N-acetylmuramate

pyruvate

diguanylatecyclase: yeaP

a tRNAprecursor

a holo-[acp]

trimethylamine

a single-stranded

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

diphosphoundecaprenol

a holo-[acp]

phosphatidate

peptidoglycanDAP-DAPcrosslink

a holo-[acp]

UDP-sugarhydrolase:ushA

N-acetylmuramoyl-L-alanineamidase 1: amiA

a polypeptide

a quinone

serineendoprotease,periplasmic: degQ

tetrahydrothiophene

argininedecarboxylase,biosynthetic:speA

a phospholipidcyclopropane

fatty acid

di-trans,poly-cis-

a CDP-diacylglycerol

-D-glucose

a dodecanoyl-[acp]

ubiquinol-8

a 1,2-diacylglycerol

a polypeptide

glycan chain 2

a proteinwith

oxidizeddisulfidebonds

superoxidedismutase(Mn): sodA

sulfite

broadspecificity 5’(3’)-nucleotidase andpolyphosphatase:surE

coenzyme A

acyl-CoAthioesterase:yciA

oxidizedcytochrome

phosphoethanolamine

a holo-[acp]

L-arginine

di-trans,poly-cis-

an oxidizedelectronacceptor

a shortglucan

murein DD-endopeptidase,penicillin-insensitive: mepA

a 2,3,4-saturated

fattyacyl-[acp]

O: fdoI fdoH fdoG

alpha-D-galactose

thiosulfate

protoheme IX

beta-D-glucosideglucohydrolase,periplasmic: bglX

penicillin-bindingprotein6: dacC

orotate

UDP-2,3-diacylglucosaminehydrolase: lpxH

a proteinL-tyrosine

2,3-bis(3-hydroxymyristoyl)-

beta-D-glucosaminyl1-phosphate

uridine-5’-diphosphate

a ribonucleosidemonophosphate

trehalose

O: fdoI fdoH fdoG

nitritereductasecomplex:nrfA nrfBnrfC nrfD

a shortglucan

D-alanyl-D-alanine

a UDP-sugara reducedelectronacceptor

KDO2-lipid IVA

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

a peptidoglycan

di-trans,poly-cis-

a holo-[acp]

ubiquinone-8

a 1,2-diacylglycerol-3-phosphate

a D-amino acid

glucose-1-phosphatase:

phosphocholine

a 2,3,4-saturated

fattyacyl-[acp]

p-aminobenzoate

pyruvate

L-aspartate

2’,3’-cyclic nucleotide2’-phosphodiesterase:cpdB

a single-stranded

peptidoglycantripeptide,

glycan chain 1

an L-1-phosphatidylglycerol-

phosphate

KDO2-lipid A

a nonglucosylated

glucoseacceptor

D-fructose-6-phosphate

a proteinwith

reducedsulfidegroups

5’-nucleotidase:ushA

di-trans,poly-cis-

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

a diacylglycerolpyrophosphate

alpha-D-glucose 1-phosphate

glycerol

disulfideoxidoreductase:dsbC

GlcNAc-1,6-anhMurNAc

KDO2-lipidA, coldadapted

a tRNA

L-glutamate

adenosine 3’,5’-bisphosphate

a holo-[acp]

a ribonucleoside

all-trans-octaprenyl

diphosphate

maltohexaose

heme o

tetrahydrothiophene1-oxide

periplasmicnitratereductase:napGnapH napCnapA napB

a peptide

a carboxylate

N-acetylmuramyl-L-alanineamidase: amiC

nitrate

thiosulfatesulfurtransferase:glpE

UDP-N-acetylmuramoyl-

L-alanyl-D-glutamyl-meso-2,6-

diaminopimelyl-D-alanyl-D-alanine

ferritin iron-storagecomplex:ftnA

an aldehyde

trimethylamineN-oxide

3-octaprenyl-4-hydroxybenzoate

all transundecaprenyl

phosphate

D-glucose

phosphatidylglycerophosphataseB: pgpB

a peptide

putative p-aminobenzoyl-glutmatehydrolase: abgB

D-Glu-DAP-D-Ala

malate

2-carboxymuconate

agmatine

an aliphaticamine

p-aminobenzoate

NADP+beta-D-glucose

KDO2-lipid IVA

pyrimidinenucleotidase:yjjG

phosphocholine

glycerol

thiosulfatesulfurtransferase:pspE

di-trans,poly-cis-

4-hydroxybenzoate

a proteinL-tyrosine

beta-D-galactose

cardiolipin

a beta-lactam

sugarphosphatase:

asparaginaseIII: iaaA

phosphatidylethanolamine-KDO2-lipidA

aldose-1-epimerase:galM

superoxidedismutaseprecursor(Cu-Zn): sodC

a 2-oxo acid

aminoacetone

diguanylatecyclase: ydeH

succinate

diphosphoundecaprenyl-[GlcNAc-MurNAc-

pentapeptide]n

L-asparagine

hydrogenperoxide

phosphoglyceroltransferase II: mdoB

lipid Adisaccharide

agmatine

diphosphate

hydrogencyanide

agmatine

L-Ara4N-modifiedKDO2-Lipid A

a carboxylate

KDO2-lipid A

fumarate

a myristoyl-[acp]

hydrogenperoxide

peptidyl-prolylcis-transisomerase;in proteinfolding:fkpA

CmtABmannitol

PTSpermease

pyruvate

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

L-asparaginyl-tRNAasn

a beta-ketoacyl-[acp]

geranylfarnesyldiphosphate

L-lyxose

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-

lipoatebiosynthesis

andincorporation I

deoxyadenosine adenosine

inosine deoxyuridine thymidine deoxyinosine

uridine deoxycytidine

cytidine

tRNApro

1-ethyladenine

ALCOHOLS DEGRADATION

1,3-diphosphateglycerate

chorismate

L-glutaminyl-tRNAgln

a (R)-3-hydroxy-cis-vaccenoyl-

octaprenyldiphosphatesynthase: ispB

PFL-deactivase:adhE

phosphoglycerate mutase,cofactor independent: gpmM

L-serine

NADPphosphatase

2-phosphoglycerate

gluconokinaseII: idnK

fructoselysine6-kinase: frlD

guaninedeaminase:

L-valine

salicin-6-phosphatearbutin-6-phosphate

alpha-D-glucose1-phosphate

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]

o-succinylbenzoate-CoA ligase: menE

L-valyl-tRNAval

tryptophan synthase,alpha subunit: trpA

beta-D-ribopyranose

glycerophosphodiesterphosphodiesterase,cytosolic: ugpQ

PRPPbiosynthesis II

6-phospho-D-gluconate

shikimatedehydrogenase: aroE

N-acetylneuraminatelyase: nanA

shikimatedehydrogenase: ydiB

glutathionylspermidine

quinolinatephosphoribosyltransferase:nadC

nucleosidediphosphatekinase: ndk

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

L-aspartate

a 5,10-methylene-tetrahydrofolate

menadione

phosphatidylglycerophosphataseA: pgpA

enoyl-CoAhydratase: fadJ

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

lipoate acetyltransferaseN6-(dihydrolipoyl)lysine

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

a trans hex-2-enoyl-[acp]

octanoate

a (3R)-3-hydroxyacyl-CoA

glutamate-1-semialdehydeaminotransferase:hemL

molybdenumcofactor

exopolyphosphatase: ppx

alpha-ribazole-5’-P

an aliphaticomega-

aminoaldehyde

formate

an aldehydeor ketone

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

succinyl-CoA

di-trans,poly-cis-undecaprenyl

phosphate

a reducedthioredoxin

L-fucose isomerase: fucI

deoxyribose-phosphatealdolase: deoC

fused 4’-phosphopantothenoylcysteinedecarboxylase andphosphopantothenoylcysteinesynthetase: dfp

cholinedehydrogenase:betA

RESPIRATION

superpathway of arginineand polyamine biosynthesis

purine nucleosidephosphorylase:

purine deoxyribonucleosides degradation

pyruvate

L-methionine

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

beta-D-galactose

phosphotyrosine-proteinphosphatase: etp

alanineracemase2, PLP-binding:dadX

D-fructose

L-valine

formate

lysinedecarboxylase2: ldcC

formate

7,8-dihydroneopterin

triphosphate

D-mannitol

O-acetyl-L-serine

formatedehydrogenase:fdhF

nicotinate

DNAcontaining

a basewith lesion

3-hydroxyacyl-CoAdehydrogenase: fadJ

L-cystathionine

poly-beta-1,6-N-acetyl-D-glucosamine

methioninesulfoxidereductaseB: msrB

HMP-PPhydrolase:nudJ

L-threonine

an oxidizedcytochrome c

riboflavin

an inactiveribonucleosidetriphosphatereductase

adenosyl-cobinamidephosphate

superpathway of phenylalanine,tyrosine, and tryptophan biosynthesis

a beta-keto-cis-delta5-dodecenoyl-[acp]

N-substitutedaminoacyl-

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

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

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

a tRNA

C1 COMPOUNDSUTILIZATION AND

ASSIMILATION

glyceratekinase I: garK

glycerol-3-phosphateacyltransferase: plsB

L-aspartate

tartronatesemialdehyde

a trans tetradec-2-enoyl-[acp]

xanthine

phospho-TorR

nitrite

L-isoleucine

UDP-N-acetyl-D-mannosamine

Targlu

AtoS-Phis

L-proline

BarA-Pasp

L-ribulose

formylTHF biosynthesis I

serinehydroxymethyltransferase: glyA

2-deoxy-D-glucose 6-phosphate

aconitate hydratase 1: acnA

UDP-N-acetylmuramate

tetrahydrofolate

dihydrolipoamideacetyltransferase:aceF

fructose-1,6-bisphosphatase I: fbp

N5-carboxyaminoimidazoleribonucleotide mutase: purE

a reducedferredoxin

rRNAcontaining N6-methyladenine

guanylatekinase: gmk

L-Ala-D/L-Gluepimerase:ycjG

indole

L-tryptophan

phosphoribosylglycinamideformyltransferase: purN

a [citrate(pro-3S)-

lyase](citrylform)

methanol

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

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:

phosphohydroxythreonineaminotransferase: serC

asparaginyl-tRNA

synthetase:asnS

L-lactaldehydedegradation(anaerobic)

pyridoxalkinase2: pdxY

a 3’-terminalunsaturated

RNaseD: rnd

EmrKY-TolC

putativemultidrug

effluxtransportsystem

[+ 6 isozymes]

imidazoleglycerol-phosphatedehydratase: hisB

a quinone

ATPphosphoribosyltransferase: hisG

UDP-glucose 6-dehydrogenase:ugd

GDP-mannose 4,6-dehydratase: gmd

2-ketoaldonatereductase: ghrB

N-hydroxyarylamineO-acetyltransferase:nhoA

7-keto-8-aminopelargonate

salvage pathways of adenine,hypoxanthine, and their nucleosides

L-glutamate

23Sribosomal

a carboxylated-biotinylated-

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

propionyl-CoA

23S rRNA 2’-O-ribose C2498methyltransferase:rlmM

phenylacetaldehyde

menaquinone-8

molybdate

a ribosomalprotein-

N-acetyl-L-alanine

betaine aldehydedehydrogenase:betB

acetaldehydedehydrogenase:adhE

ribonucleosidehydrolase 3: rihC

cytidinedeaminase:cdd

triphosphate

CheB-Pasp: cheB

CRISPR-associatedcomplexfor antiviraldefense:casEcasD casCcasB casA

D-galacturonateisomerase: uxaC

tagatose-1,6-bisphosphatealdolase 2: gatZ gatY

DNAcontaining arecognition

acyl-CoAdehydrogenase: fadE

phospho-RcsB

acetylphosphate

D-allosedegradation

coenzyme A

citrate lyasesynthetase:citC

dTDP-L-rhamnosesynthetase:rfbD rfbC

methyleneTHFenzyme: folD

an (R)-3-hydroxydecanoyl-

2-oxoglutarate

dihydrolipoyltranssuccinylaseN6-(lipoyl)lysine

fructose-1-phosphate

OuterMembrane

FerricEnterobactinTransportSystem

an oxidizednitroaromatic

compound

phosphopentomutase:deoB

L-aspartate

NAD synthetase,NH3-dependent: nadE

Trgglu

trehalosedegradationII (trehalase)

NMN amidohydrolase

50Sribosomalsubunit

protein L7

orotatephosphoribosyltransferase: pyrE

D-alanine

malatedehydrogenase:mdh

aconitatehydratase1: acnA

(2S)-2-amino-3-oxo-4-phosphonooxybutanoate

L-leucyl-tRNAleu

histidyl-tRNA

synthetase:hisS

(2R,4S)-2-methyl-2,4-dihydroxydihydrofuran-

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

EIIAsc

mannosylglycerate

NarQ-Phis

L-threonine

L-methionine

CheB-Pasp: cheB

2-oxobutanoate

an rRNA

e14 prophage;site-specificDNArecombinase:pinE

Tapglu

lipoyl-proteinligase: lipB

freemethionine-(R)-sulfoxidereductase:yebR

trehalosebiosynthesis I

delta(2)-isopentenylpyrophosphatetRNA-adenosinetransferase: miaA

phosphatidylserinesynthase: pssA

transketolaseI: tktA

acetyl-CoA

6-phosphogluconatedehydrogenase(decarboxylating): gnd

L-threonine

hybrid-cluster

proteinox

prephenate

ubiquinol-8

alpha-xylosidase:yicI

a myristoyl-[acp]

KASI: fabB

Tsrglu

dihydroneopterinphosphate

PhoB-Pasp

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

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

chorismate

2-octaprenyl-6-methoxy-

1,4-benzoquinol

dimethylbenzimidazole

pyruvateformate-lyase: pflB

L-lactatedehydrogenase:

quinolinate

pyridoxamine5’-phosphate

maltotetraose

laurate

tRNApseudouridine65 synthase: truC

peptidoglycantripeptide-

Lpp crosslink

endonucleaseIV: nfo

RNApyrophosphohydrolase:rppH

xyloseisomerase:xylA

deoxyribodipyrimidinephotolyase(photoreactivation): phr

UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelateligase: mpl

NADkinase: nadK

tetrahydrodipicolinate

L-aspartyl-4-phosphate

a purineribonucleoside

putrescine

an oxidizedelectron

acceptor

rhamnosedegradation

a reducedelectronacceptor

glycerol-3-phosphatedehydrogenase,biosynthetic: gpsA

pyridoxal 5’-phosphate

alkanesulfonatemonooxygenase,FMNH2-dependent: ssuD

beta-D-glucose

amidophosphoribosyltransferase: purF

UvrABCNucleotideExcisionRepairComplex:uvrB uvrCuvrA uvrD

RecG, DNAhelicase,resolutionof Hollidayjunctions,branchmigration:recG

autoinducer AI-2 biosynthesis

5,10-methenyltetrahydrofolate

glutathione S-transferase:gst

(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran

2-dehydro-3-deoxygalactonatekinase: dgoK

L-Ala-gamma-D-Glu-Dap

diacetylreductase

uridylyltransferase:glnD

cob(I)alamin

guanylatecyclase

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

L-threoninehomoserine

deoxyribose-1-phosphate

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

L-glyceraldehyde3-phosphatereductase: yghZ

nicotinate mononucleotide

L-isoleucine

NADHdehydrogenase(quinone)

DNAligase: ligA

L-alanine

D-ribulose

ThiS-COAMP

chorismate

lipoamidedehydrogenase: lpd

L-aspartate

triphosphate

a reducedglutaredoxin

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

a tRNAcontaining

glutamylatedqueuosine

acetyl-CoA

quinolmonooxygenase:ygiN

tRNAcontainingqueuine

dihydrofolatereductase: folA

beta-D-glucose

L-aspartateL-glutamate

glutathione

a trans dodec-2-enoyl-[acp]

tRNAasp

D-alloseD-fructuronateD-gluconate

D-ribose

methanol

ClpP serineprotease:clpP

glycinebetaine

poly-beta-1,6-N-acetyl-D-glucosamineN-deacetylase:pgaB

2,3-dihydroxy-3-methylvalerate

thioglycolate

diphosphate

D-fructose

cobinamide-Pguanylyltransferase: cobU

cysteinesynthase B: cysM

cobinamideadenosyltransferase:btuR

crotonobetainyl-CoA

hydratase: caiD

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

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

5-ketogluconate

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

deoxyadenosinedeaminase: add

hypoxanthinephosphoribosyltransferase: hpt

formyltetrahydrofolatedeformylase: purU

bifunctional NadRtranscriptionalrepressor and NMNadenylyltransferase:nadR

3-phosphoglycerate

glyceratekinaseI: garK

a palmitoyl-[acp]

L-glycerol 3-phosphate

ribonucleoside-diphosphatereductase:nrdB nrdA

purinenucleotidase:yrfG

pantothenate

dTDP-glucosepyrophosphorylase2: rffH

chorismatelyase: ubiC

3-phosphoglycerate

2-ketobutyrateformate-lyase: tdcE

superpathway ofphenylethylamine

degradation

a 3-oxo-dodecanoyl-[acp]

dihydromonapterin-triphosphate

a dodecanoyl-[acp]

indole-3-glycerol-phosphate

a deamineatedamine donor

a reducedcytochrome c

maltotriose

L-galactonate

chorismate

alanine racemase2, PLP-binding: dadX

ribonucleoside-diphosphatereductase 2:nrdF nrdE

L-alanine

(R)-pantolactone

thiaminediphosphate

long chainpolyphosphate

an alcohol

2-oxoglutarate

phosphate

branched-chainamino-acidaminotransferase:ilvE

succinate

D-lactate

a tRNAcontaining 7-

aminomethyl-7-deazaguanineat position 34

a tRNA

UDP-D-galactose

D-malatedehydrogenase(decarboxylating): yeaU

D-4-hydroxy-2-keto-

glutarate

glutamine synthetaseadenylyltransferase:

folate polyglutamylation I

fumarase A: fumA

L-fuculose-phosphatealdolase: fucA

L-aspartate

L-serine

L-seryl-tRNAser

formaldehydedehydrogenase,glutathione-dependent: frmA

L-serine

nicotinamidemononucleotide

3-phosphoserineaminotransferase: serC

lipoamide

KASI: fabB

L-aspartate

D-fructose

a tRNA

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

methyl red

a tRNA

selenocysteinelyase: sufS

a phosphatemonoester

beta-D-glucose

Trgglu-Me

allantoate

pyruvate

adeninephosphoribosyltransferase: apt

GTPcyclohydrolaseII: ribA

D-ribose-5-phosphate

ribonucleosidehydrolase 2(pyrimidine-specific): rihB

L- and D-methionineuptake ABCpermease

UDP-N-acetyl-D-mannosaminuronicaciddehydrogenase: rffD

2-amino-3-oxobutanoate

tRNAMet cytidineacetyltransferase:tmcA

L-alanyl-tRNAala

nitrite

glutamineABC

transporter

predicted L-xylulose 5-phosphate3-epimerase:sgbU

D-glucosyl-lipopolysaccharide

glutaminase A

D-4’-phosphopantothenate

reducedflavorubredoxin:norV

L-isoleucine

glycyl-tRNAsynthetase:glyQ glyS

diaminopimelateepimerase: dapF

pseudouridine

thiamin ABCtransporter

beta-ketoadipyl-CoA thiolase: paaJ

ADP-sugarpyrophosphorylase:nudE

oligopeptideABC

transporter

cystathionine-beta-lyase: metC

alpha-ribazole

predictedpseudouridine5’-phosphateglycosidase:pscG

D-alloseABC

transporter

YgaZ/YgaHL-valineexportercomplex

tRNA containing 5-methylaminomethyl-

2-thiouridylate

AMINO ACIDS DEGRADATION

malonyl-CoA-ACPtransacylase: fabD

(R)-methylmalonyl-

acetoacetatedegradation

(to acetyl CoA)

tRNA m6A37methyltransferase:yfiC

ethanoldehydrogenase:adhP

uridylyl-removingenzyme: glnD

tRNAasn

biosynthesisof 4-amino-4-deoxy-L-arabinose-

modified lipid A

L-methioninesulfoxide

UDP-D-galactose

a peptideantibiotic

aldehydedehydrogenaseA, NAD-linked: aldA

carnitine-CoAligase: caiC

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

a ribosomalprotein-

L-alanine

pyridoxine5’-phosphate

synthase:pdxJ

iron dicitrateABC

transporter

3-(3-hydroxyphenyl)propionate 2-hydroxylase:mhpA

a 3-oxo-palmitoyl-[acp]

4-hydroxy-2-ketovaleratealdolase: mhpE

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

RNase R: rnr

ribose ABCtransporter

D-glycerate

hypoxanthine

lipid Adisaccharidesynthase: lpxB

a ribonucleosidediphosphate

UDP-N-acetylglucosamineacyltransferase: lpxA

a phospholipid

an isocitratedehydrogenase

L-alanine

L-cysteine

a macrolideantibiotic

6-phospho-beta-glucosidaseB; cryptic:bglB

SucB-lipoate

3-phospho-hydroxypyruvate

diacylglycerolkinase: dgkA

acetaldehyde

KDO2-lipid IVA

3-deoxy-D-manno-octulosonatecytidylyltransferase:kdsB

vitaminB12 ABC

transporter

adenosine

dipeptideABC

transporter

thiosulfateABC

transporter

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

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

L-tartrate

16S rRNAcontaining

C5-methylatedcytosine

O-antigenligase: rfaL

KDO2-lipid A

D-tyrosyl-tRNATyr

a sugar

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:

poly(A)polymeraseI: pcnB

resolvasome:ruvA ruvB ruvC

arginyl-tRNAsynthetase:

tyrosyl-tRNAsynthetase:

S-adenosyl-L-methioninamine

adenosylcobinamide-GDP

cellobiosesalicinarbutin

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

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

ArcAB Two-Component

SignalTransduction

System

succinate

pantothenatekinase: coaA

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

cyanate

di-trans,poly-cis-decaprenyldiphosphate

mannitol-1-phosphate 5-dehydrogenase:mtlD

ITPase: yjjX

arylsulfatase:aslA

quinatedehydrogenase:ydiB

acetyl-CoAbiosynthesis

(from pyruvate)

uracil

NarP-Pasp

KASIII: fabH

ribose 1,5-bisphosphokinase:phnN

beta-hydroxyacyl-ACP dehydratase: fabZ

L-glutamine

phenylalanyl-tRNA

synthetase:pheT pheS

(R)-methylmalonyl-CoA

molybdopteringuaninedinucleotidesynthase: mobA

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

folylpoly-alpha-glutamatesynthetase

4-aminobutyrate

a trans-2-enoyl-CoA

a proteinL-cysteine

dihydroxyacetonephosphate

Nitrogen RegulationTwo-Component System

glutathionebiosynthesis

L-ribulose 5-phosphate 4-epimerase: araD

putrescine

fructosebisphosphatealdolaseclass II: fbaA

uracil

NADH pyrophosphatase: nudC

ClpAXP:clpXclpA clpP

tryptophansynthase:trpB trpA

thymidylatesynthase:

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

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

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

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

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

6-phosphofructokinase I: pfkA

D-ribulose-5-phosphate

acetyl-CoA

phosphateABC

transporter

As3H3O6

citrate

alcoholdehydrogenase:adhE

phosphoglycerate kinase: pgk

selenite

pyruvate

fumarase B: fumB

pyridoxamine

a tRNA

L-arabinosedegradation I

tRNApseudouridine

inosine

nicotinamide

guanosine-5’-triphosphate,3’-diphosphatepyrophosphatase: gpp

adenosylmethioninedecarboxylase: speD

5’-deoxyadenosine

5-phospho-beta-D-ribosyl-amine

CDP-diglyceridesynthetase: cdsA

phosphatidylglycerophosphatase C

pyruvate

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

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

thiaminediphosphate

tRNAArg2

AcrAD-TolCmultidrug

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

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

L-aspartate

beta-hydroxyacyl-ACPdehydratase:fabZ

lysinedecarboxylase:cadA

a holo-[acp]

L-arginino-succinate

tyrosineaminotransferase: tyrB

7-aminomethyl-7-deazaguanine

prephenatedehydrogenase: tyrA

dihydrouracil

S-lactoylglutathionehydrolase: yeiG

NAD(P)H:quinoneoxidoreductase:wrbA

an L-1-phosphatidylserine

16S-rRNAs

1-amino-propan-2-ol

galactaratedehydratase: garD

a hexanoyl-[acp]

ZnuA/ZnuB/ZnuC ABCtransporter

UDP-L-Ara4O

L-galactonate

menadiol

2-oxobutanoate

a ThiSsulfur-carrier

protein

methylglyoxal

allantoindegradation

IV (anaerobic)

an apo-GcvHprotein

2-oxoglutarate

H-Gcv-protein-(dihydrolipoyl)lysine

L-serineL-threonine

an mRNA with 5’-monophosphate

L-rhamnoseL-lyxose

D-sorbitol

cis-aconitate

putrescineABC

transporter

ferredoxinNAD+reductase:hcaD

KDO2-(lauroyl)-lipid IVA

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

pyridoxal

sulfatereduction I

(assimilatory)

formyl-CoAtransferase: frc

AcrAB-TolCmultidrug

L-xylulose-5-phosphate

N-ethylmaleimide

a tRNAArg2containinginosine atthe wobble

position

L-idonate 5-dehydrogenase:idnD

2-dehydropantoate2-reductase: panE

4-hydroxy-L-threoninephosphatedehydrogenase,NAD-dependent: pdxA

erythrose 4-phosphatedehydrogenase:epd

ZraSR Two-Component

SignalTransduction

System

carboxylesterase:bioH

phenylacetate

OTHER BIOSYNTHESIS

ornithine decarboxylase,biosynthetic: speC

UDP-GlcA C-4"-decarboxylase:arnA

a 2,3,4-saturated

fattyacyl-[acp]

fatty acidoxidationcomplex,alphacomponent:fadB

UDP-[N-acetyl-D-

glucosamine]n

CheB-Pasp: cheB

gamma-glutamylkinase-GP-reductasemultienzymecomplex:proA proB

4-aminobutyrateaminotransferase: puuE

TorS-Phis443

CheB-Pasp: cheB

1,4-alpha-glucanbranchingenzyme:glgB

succinate

aspartate 1-decarboxylase:panD

dihydrodipicolinatereductase: dapB

isochorismate

L-serine

an rRNA

cyclopropanefatty acylphospholipidsynthase: cfa

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

1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatereductase: ispH

D-glycerate

CcmABCDEprotoheme

IX ABCtransporter

L-fucose

propionyl-CoA

UDP-N-acetyl-D-

glucosamine

uracilphosphorylase:deoA

branchedchain aminoacids ABCtransporter

bicarbonate

a tRNA

D-erythrose-4-phosphate

cyclic-AMP

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

isomerase: idi

ethanol

NarX-Phis

N-6-isopentyl

adenosine-37 tRNA

acetohydroxybutanoatesynthase: ilvH ilvI

a cis-vaccen-2-enoyl-[acp]

all-trans-heptaprenyldiphosphate

glutamate-pyruvateaminotransferase:alaB

glucosyl-heptosyl3-

KDO2-lipid A-

phosphate

glutathionedisulfide

uridinephosphorylase:udp

dihydroneopterinaldolase: folB

2-dehydropantoyl-lactone reductase(B-specific)

phosphoenolpyruvatecarboxylase: ppc

phosphoenolpyruvatecarboxykinase (ATP): pck

L-threo-3-phenylserine

propionyl-P

tRNAlys

glyceraldehyde3-phosphatedehydrogenase-A complex: gapA

EIITre

23S rRNA 2’-O-ribose G2251methyltransferase:rlmB

acetyl-CoA

melibiose

HMP-PPhydrolase/ thiaminpyrophosphatehydrolase: nudJ

p-aminobenzoate

a (3R)-3-hydroxyacyl-[acp]

UhpB-Phis

fumaraseA: fumA

ethyl-(2R)-methyl-(3S)-

hydroxybutanoate

pyruvatekinaseI: pykF

multifunctional 2-keto-3-deoxygluconate

6-phosphatealdolase and 2-keto-4-hydroxyglutarate

aldolase andoxaloacetate

decarboxylase: eda

BarA-Phis

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

L-lysine

a damagedDNA

(purine orpyrimidine)

cytosine

glycogenbiosynthesis I (from

ADP-D-Glucose)

a DNAsegment

a tetrahydrofolatepolyglutamate

alpha-L-arabinose

gluconokinaseI: gntK

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate

rRNAcontaining 2’-O-methylcytosine

a thioredoxin

allantoateamidohydrolase:allC

glycolaldehyde

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

inosine

fructose 6-phosphatealdolase2: fsaB

tartronatesemialdehydereductase: garR

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

N-succinyl-L-diaminopimelatedesuccinylase:dapE

biotin

2-thiouridylate

homoserinekinase: thrB

anaerobicnucleoside-triphosphatereductaseactivatingsystem: fprnrdG nrdD

beta-N-acetylglucosaminidase:nagZ

anhydro-N-acetylmuramicacid kinase: anmK

orotate

sn-glycerol-3-phosphate

choline

succinyl-CoA synthetase: sucC sucD

3-keto-L-gulonate 6-phosphate

oleate beta-oxidation

beta-D-glucose

fatty acid beta-oxidation I

serineacetyltransferase:cysE

ferriccoprogen

H-Gcv-protein-

(lipoyl)lysine

acetaldehyde

lipid kinase:yegS

L-asparagine

a tRNA

phosphoribosyl-ATPpyrophosphatase: hisI

6-carboxy-5,6,7,8-tetrahydropterin

BaeR-Pasp

histidinol-phosphatase:hisB

mannose-6-phosphateisomerase: manA

(deoxynucleotides)(m)

UDP-glucose 4-epimerase: galE

1,4-dihydroxy-2-naphthoyl-CoA

a nucleoside

guanosine-3’,5’-bis(diphosphate) 3’-diphosphatase: spoT

D-alanine-D-alanineligase B: ddlB

7,8-dihydropteroate

crotonobetainyl-CoA

tRNAsec

a 3-oxo-hexanoyl-[acp]

a glycerophosphodiester

UDP-galactose biosynthesis(salvage pathway from

galactose using UDP-glucose)

an ADP-sugar

GTPpyrophosphokinase: relA

maltose

glutaminase:yneH

OuterMembrane

FerricCitrate

TransportSystem

fosmidomycin

L-idonate

undecaprenyldiphosphatesynthase: ispU

dihydrodipicolinatesynthase: dapA

xanthine

methyltransferasefor 50S ribosomalsubunit proteinL11: prmA

putrescine/spermidine

ABCtransporter

selenate

xanthosine

thymidinephosphorylase:deoA

glutamate racemase: murI

glycerol-3-P ABC

transporter

deoxyuridinekinase: tdk

FtsE/FtsX ABCtransporter

glycine

3-chloro-D-alaninedehydrochlorinase:dcyD

potassiumion P-typeATPase

transporter

precursor-Z

homoserinedehydrogenase:metL

pyruvateoxidase:poxB

dehydrogenase

diaminopimelatedecarboxylase: lysA

cytidine

folylpoly-gamma-glutamatesynthetase:folC

2-octaprenylphenol

thiaminpyrophosphatehydrolase: nudJ

low-specificityL-threoninealdolase: ltaE

tetraacyldisaccharide4’-kinase: lpxK

L-ascorbate-6-phosphate

DNA withlesion

catabolicthreoninedehydratase: tdcB

lipoate

a citryl-[acp]succinylglutamatedesuccinylase: astE

pyridoxal

fumarase A: fumA

gamma-butyrobetaine

AP siteremoved

from DNA

a drug

succinyl-CoA

ammoniumhydroxide

a FeS-protein

D-aminopropanoldehydrogenase:gldA

superpathway of KDO2-lipid A biosynthesis

dihydroxy-aciddehydratase: ilvD

phosphateacetyltransferase: pta

2-methylcitratecycle I

L-aspartate

citratesynthase: gltA

serineactivatingenzyme: entF

cadaverine

pyruvateformate-lyase: tdcE

cobalamin-independent

homocysteinetransmethylase:

2,3-diketo-L-gulonate

pyruvatedehydrogenasemultienzymecomplex: lpdaceF aceE

acetylglutamatekinase: argB

isocitratedehydrogenase: icd

2-hydroxyglutarate

mannose-6-phosphateisomerase:manA

propionate

guanosine-5’-diphosphate

vitaminB12 outermembranetransportcomplex

succinate

AlsR-allose

a DNAadenine

DNA withlesion

spermidine

L-tryptophan

S-formylglutathionehydrolase: yeiG

dihydropteridinereductase: nfsB

L-alanine

ThDPadenylyltransferase

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

CheY-Pasp

Tsrglu-Me

RcsB-phosphate

tyrosineaminotransferase:tyrB

ADP-L-glycero-D-mannoheptose-6-epimerase: rfaD

methylerythritolphosphate pathway

phosphoenolpyruvate

glyceratekinaseII: glxK

D-gluconate

a reducedferredoxin

acetaldehyde

diadenosinetetraphosphatase:apaH

CPS-53 (KpLE1)prophage;deoxyribonucleoside5’-monophosphatephosphatase: yfdR

aminomethyltransferase: gcvT

Osmoregulatory Two-ComponentSignal Transduction System

Lipid A-core

pryidoxinetranporter

L-methionine

lipoate

proteindisulfideisomerase:dsbC

uroporphyrinogendecarboxylase: hemE

GDP-alpha-D-mannose

phosphoribosyl-formamido-carboxamide

deoxyguanosine

isethionate

6-carboxy-5,6,7,8-tetrahydropterinsynthase: queD

meso-diaminopimelate

GDP-mannosemannosylhydrolase:gmm

cadaverine

purine nucleotides de novo biosynthesis I

spermidinesynthase:

glutaminase B

N-acetyl-L-glutamate 5-

semialdehyde

succinylornithinetransaminase: astC

pyruvatekinaseII: pykA

fumaraseB: fumB

L-tyrosine

a malonyl-[acp]

adenylyl-[glutaminesynthetase]

glycerol

1,6-anhydro-N-acetylmuramicacid recycling

phenylacetyl-CoA

3,5-tetradecadienoate

RstB-Phis

3-phenylpropionate-2’,3’-dihydrodioldehydrogenase: hcaB

chorismate

L-glutamine

D-gluconate

2-dehydro-3-deoxy-D-gluconate

acetyl-CoA

transaldolaseA: talA

multidrug

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

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

NAD-dependentdihydropyrimidinedehydrogenase:yeiA yeiT

pyridine nucleotidetranshydrogenase

enterochelinesterase: fes

L-arginine

D-glycerate

methylmalonyl-CoAdecarboxylase: scpB

CMP-3-deoxy-D-manno-

octulosonate

glycolate

D-xylulose-5-phosphate

L-glutamate

acetyl-CoA

hydroquinone

L-glutamate

L-aspartate

L-1,2-propanediol

cyclopropanefatty acid

(CFA)biosynthesis

BarA-Phis

cAMPphosphodiesterase:cpdA

S-formylglutathione

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

glyoxylate

a tRNA

deoxycytidine

beta-D-glucose

acetatekinase B: ackB

lipidhydroperoxideperoxidase: tpx

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

an acetoacetyl-[acp]

propionyl-CoA

isovaleryl-CoAdehydrogenase/ predictedacyl-CoAdehydrogenase:aidB

phosphorylatedserine/threonine

kinase HipA

UDP-3-O-(3-hydroxymyristoyl)

glucosamine

phosphoglycolatephosphatase: gph

ThiI: thiI

seryl-tRNAsynthetase:serS

rRNAcontaining N1-methylguanine

L-valine

L-carnitinyl-CoA

colanic acid

methionineadenosyltransferase:metK

cyanase:cynS

5’-deoxyadenosine

L-ornithine

GMP-N-epsilon-(N-alpha-acetyl lysinemethyl ester) 5’-phosphoramidate

methylglyoxal

3-mercaptopyruvate

N-acetylneuraminate

glutaminesynthetase:glnA

D-alanine

oxaloacetate

L-methionine

glycogenphosphorylase-limit dextrinalpha-1,6-glucohydrolase:glgX

lactose

D-ribose

EvgS-Phis

L-lactaldehyde

L-glutamate

S-acetyldihydrolipoamide

sulfite reductase-(NADPH): cysI cysJ

cadaverine

a beta-D-glucuronoside

3-oxoacyl-CoA

O-succinylhomoserine(thiol)-lyase: metB

protoporphyrinogen IX

D-lactate

L-glutamate

N-acetylglucosamine-6-phosphatedeacetylase: nagA

acetolactatesynthase: ilvMilvG_2 ilvG_1

superpathwayof hexuronide

and hexuronatedegradation

L-homocysteine

phosphoenolpyruvate

pyruvatedehydrogenase:aceE

enoyl-ACP reductase(NADPH): fabI

dihydroneopterintriphosphatepyrophosphohydrolase:nudB

a DNA withalkylatedadenine

enoyl-ACP reductase(NAD[P]H): fabI

beta-hydroxydecanoyl-ACP dehydrase: fabA

dihydrofolatereductase: folM

RNasePH: rph

L-ascorbate

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

7,8-diaminopelargonicacid synthase: bioA

D-ribose

uracil-DNA-glycosylase:ung

a 2’,3’-cyclic-phosphate-terminated

KDO2-(palmitoleoyl)

-lipid IVA

Mg2+Co2+Ni2+

a DNAcontainingabasic site

cobalamin-dependenthomocysteinetransmethylase:metH

pyruvatekinase II: pykA

orotidine-5’-phosphate

alpha-L-arabinose

KASI: fabB

phosphoribosylformylglycinamidesynthetase: purL

carbamate

a pyrimidine

N-succinyldiaminopimelate-aminotransferase: argD

threoninesynthase:thrC

a protein

L-citrulline

acetatekinase: ackA

asparaginaseI: ansA

an rRNA

dTDP-D-fucosamine

superpathway of glycolysisand Entner-Doudoroff

acetate

malate

sugarphosphatase:yidA

coenzyme A

palmitoleate

16S rRNA m7G527methyltransferase:rsmG

ThiS-COAMP

5-phosphoribosyl-N-formylglycineamidine

phosphoribulosylformimino-AICAR-P

pyridoxamine

glycerol

nitrite

D-sedoheptulose-7-phosphate

psicoselysine

L-phenylalanine

KdpDE Two-Component

SignalTransduction

System

EIINag

an (R)-3-hydroxymyristoyl-

argininosuccinatesynthase: argG

23S rRNAand tRNApseudouridinesynthase: rluA

dethiobiotin

acetyl-CoAcarboxyltransferase:accD accA

chloride

maltodextringlucosidase:malZ

undecaprenyl-N-acetyl-alpha-

D-glucosaminyl-pyrophosphate

L,D-transpeptidaseYcbB: ycbB

1-deoxy-D-xylulose

a trans-2-enoyl-CoA

a nucleotide

gamma-butyrobetainyl-

beta-D-glucuronidase:uidA queuine

altronateoxidoreductase:uxaB

a tRNA

a non-methylatedribosomalprotein L11

tRNAcontaininguridine at

position 54

pyridoxaltransporter

YejA/YejB/YejE/YejF ABCtransporter

pyruvate

GDP-L-fucose

chromatereductase:yieF

an (R)-3-hydroxybutanoyl-

iron (III)hydroxamate

ABCtransporter

ADP-L-glycero-

D-manno-heptose

a quinone

L-serine

ADP-D-glucose

protoheme IX

isochorismate

aminodeoxychorismatelyase: pabC

pyridine nucleotidetranshydrogenase,soluble: sthA

formaldehyde

an RNA

glutathioneredox

reactions II

L-leucyl-tRNAleu

N-acetyl-D-mannosamine-6-phosphate

Tsrglu

shikimate

L-carnitinyl-CoA

lipoylateddomain

2-cis,6-trans,10-trans-geranylgeranyldiphosphate

D-ribose

L-ribulose 5-phosphate4-epimerase:araD

transaldolaseB: talB

maltose ABCtransporter

a reducednitroaromatic

compound

L-methionine

di-trans,poly-cis-octaprenyldiphosphate

S-lactoyl-glutathione

L-glutamate

phosphatidylglycerol-prolipoproteindiacylglyceryltransferase; amajor membranephospholipid: lgt

glutamate-putrescineligase: puuA

putativenucleoside (IDP)diphosphatase:yibQ

pyrazinoate

adenosylcobalamin salvagefrom cobinamide and cobalamin

Lipid A-core

guanine

diphosphate

bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinonemethylase and S-adenosylmethionine:2-DMKmethyltransferase: ubiE

dihydroneopterinmonophosphatedephosphorylase

L,L-diaminopimelate

nitrite

proline ABCtransporter

salicin-6-phosphate

ureidoglycine

bifunctionalbiotin-[acetyl-CoA-carboxylase]ligase andtranscriptionalrepressor: birA

alpha-N-acetylneuraminate

a single-stranded

aliphaticsulfonate

ABCtransporter

D-carnitinyl-CoA

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

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

D-arabinose5-phosphateisomerase:kdsD

L,D-carboxypeptidaseA: ldcA

phosphoadenosine-5’-phosphosulfate

glycinecleavagesystem:gcvT gcvHgcvP lpd

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

pyruvateformate-lyaseactivatingenzyme: pflA

a stabilizedRecA

filament-DNA

complex

L-lactaldehyde

L-arginine

N-acetylglutamyl-phosphate

methylcitratesynthase: prpC

fatty acid oxidationcomplex, alphacomponent: fadB

3-hydroxybutyryl-CoA epimerase: fadJ

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

3-demethylubiquinol-8

allulose-6-phosphate3-epimerase:alsE

EIISga

pyruvate

23S rRNA m2A2503methyltransferase:rlmN

NtrB-P

N-succinyl-2-amino-6-ketopimelate

threoninedeaminase: ilvA

undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-

4-acetamido-4,6-dideoxy-D-galactose

pyrophosphate

N2-succinyl-L-ornithine

D-lactatedehydrogenase: dld

GDP-fucosesynthase: fcl

dimethylallyldiphosphate

serine/threonineproteinkinase: rdoA

galactokinase: galK

a phosphoprotein

D-allose

tRNAcontaining a

thionucleotide

L-methionine

low-specificityL-threoninealdolase:ltaE

superpathway ofD-glucarate and

D-galactaratedegradation

PENTOSE PHOSPHATE PATHWAYS

D-altronate

EnvZ-Phis

3-(3-hydroxyphenyl)propionate

pyruvate dehydrogenase: aceE

5-phosphoribosyl1-pyrophosphate

L-rhamnonate

ThiI: thiI

L-histidine

diaminetransaminase:ygjG

a thioredoxin

tRNAthr

3-phospho-L-serine

D-arabinose

FMNphosphatase:ybjI

D-tagaturonate

pre-crRNA

molybdopterinsynthase

D-glucosamine1-phosphate

2-oxobutanoate

2-phosphoglycerate

homoserine

6-phosphofructokinaseII: pfkB

thiosulfatesulfate

argininosuccinatelyase: argH

glycine

4-hydroxyphenylpyruvate

L-alanine

tetrahydrofolate

TatABCEproteinexport

complex

ribonucleaseII: rnb

L-glutamate

phenylethylamine

3-dehydro-shikimate

tRNAleu

acetate kinase: ackA

hydrogenase4: hyfH hyfFhyfE hyfDhyfC hyfBhyfA hyfG hyfI

glycine

citrate

3-isopropylmalatedehydrogenase:leuB

2,3-diaminopropionateammonia-lyase: ygeX

L-selenocysteinyl-tRNAsec

D-arabinose5-phosphateisomerase:gutQ

argininedegradation

II (ASTpathway)

an AP(apurinicor apyrimidinic)

site createdby glycosylic

bond cleavage

a tRNA

(R)-malate

phosphoglucomutase: pgm

D-mannonatedehydratase:uxuA

D-tyrosine

fucosedegradation

ammonia

acetyl-CoA

1-deoxy-D-xylulose 5-phosphate

(2R,3S)-3-isopropylmalate

acetyl-CoA

nicotinate adeninedinucleotide

a [citrate(pro-3S)-

lyase](acetylform)

XTPase: yjjX

tryptophandegradation

II (viapyruvate)

2-aceto-2-hydroxy-butyrate

putativephenylacetate-CoA oxygenase:paaE paaDpaaC paaB paaA

EIIGut

lipoate acetyltransferaseN6-(lipoyl)lysine

acetaldehydedehydrogenase:aldB

acetaldehyde

non-specific ion/solutemaltose

L-histidine

glutaredoxinreductase

L-arginyl-tRNAarg

3-chloro-D-alanine

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

L-cysteinedesulfhydrase:tnaA

galactosyl-glucosyl3-heptosyl3-

KDO2-lipid A-bisphosphate

D-allose-6-phosphate

guanosine

2-deoxy-D-glucose

protoheme IX

hydroxymethylpyrimidine

bond cleavage

pyruvate

tagatose-1,6-bisphosphate

7-alpha-hydroxysteroiddehydrogenase:hdhA

a sugarphosphate

SECONDARY METABOLITES DEGRADATION

L-glutamate

homocysteinemethyltransferase:mmuM

N-(5’-phospho-L-ribosyl-formimino)-5-amino-1-(5’-phosphoribosyl)-4-imidazolecarboxamideisomerase: hisA

histidinoldehydrogenase:hisD

tyrosinephosphatase:wzb

2-methylisocitratelyase: prpB

fused heptose7-phosphatekinase/heptose1-phosphateadenyltransferase:rfaE

L-lactaldehyde

N-acetylmuramicacid 6-phosphateetherase: murQ

D-gluconate

3-keto-L-gulonate 6-phosphatedecarboxylase:ulaD

tRNA(m5U54)methyltransferase:trmA

D-glucaratedehydratase:gudD

hydroxymethylpyrimidinephosphate

acetate

2-O-alpha-mannosyl-D-glyceratedegradation

mannose-1-phosphateguanylyltransferase:cpsB

mureintripeptide

ABCtransporter

superpathway ofalanine biosynthesis

glycerol

UDP-glucose-hexose-1-phosphateuridylyltransferase:galT

an alkanesulfonate

2-oxoglutarate

a deoxynucleotideD-alanine

monophosphate

aryl carrierprotein/ serine

activatingenzyme

superoxide

glycolate

4-diphosphocytidyl-2C-methyl-D-erythritolsynthase: ispD

dihydroxyacetone phosphate

1-deoxyxylulose-5-phosphatesynthase: dxs

N-acetylmuramate6-phosphate

D-galactose

PhoB-Pasp

prephenatedehydratase: pheA

a drug

a reducedferredoxin

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

deoxyadenosine

fructoselysine-6-phosphate

TCA CYCLE

dTDP-4-dehydrorhamnose3,5-epimerase: rfbC

glycine betainebiosynthesis

I (Gram-negativebacteria)

D-glucose

deoxyguanylatekinase: gmk

bond cleavage

S-adenosylmethionine:tRNAribosyltransferase-isomerase: queA

propionatekinase: ackA

fumarate

L-methionine-(S)-S-oxide

a phosphoprotein

inosine-5’-phosphate

pyruvate

a 3-oxo-meristoyl-[acp]

thymidinekinase: tdk

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

D-fructuronate

dihydrolipoyltranssuccinylase: sucB

uridine

pentakisphosphate

betainealdehyde

shikimate-3-phosphate

tRNAtrp

a tRNA containingepoxyqueuosineat position 34

ADP-L-glycero-beta-

D-manno-heptose

biosynthesis

a tRNA

cadaverine

3-deoxy-D-arabino-heptulosonate-7-phosphate

L-alanine

fructoselysineand

psicoselysinedegradation

4-(glutamylamino)butanoate

nitric oxide

cob(I)alamin

RNA 3’-terminalphosphatecyclase: rtcA

adenineglycosylase;G.C --> T.Atransversions:mutY

GDP-alpha-D-mannose

INORGANIC NUTRIENTS METABOLISM

shikimate kinase I: aroK

malate

pentose phosphate pathway

2-dehydro-3-deoxyphosphoheptonatealdolase: aroH

alpha-D-galactose1-phosphate

a quaternary amine L-proline

phosphoribosyl-AMP

thymidine

L-proline

2,3-dihydroxybenzoyl-

cytosine

NADphosphorylation anddephosphorylation

16S rRNA m5C967methyltransferase:rsmB

L-cysteinedesulfhydrase

melibiosemelibiose

trans-delta2,cis-delta4-

decadienoyl-CoA

3,4-dihydroxyphenylacetate

pyruvate

lineardimeric GMP

UDP-3-O-(3-hydroxymyristoyl)-

N-acetylglucosamine

23S rRNA 2’-O-ribose U2552methyltransferase:rlmE

aminopeptidaseA/I: pepA

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-

EIIMtl

PhoP-Pasp

ribonucleosidehydrolase 1(pyrimidine-specific): rihA

oxalurate

(KDO)-lipid IVA

L-glyceraldehyde3-phosphate

L-fuculokinase:fucK

hydrogenase3: hycE hycBhycG hycFhycC hycD

nitrousoxide

D-glycerate

KASI: fabB

glyceroldehydrogenase:gldA

cytidine

D-galacturonateD-glucuronate

fused diaminohydroxyphosphoribosylaminopyrimidinedeaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase: ribD

thiamin(thiazolemoiety)biosynthesisprotein: thiF

an alcohol

indole-3-glycerolphosphatesynthase: trpC

adenine

a standardalpha

amino acid

tryptophan synthase,beta subunit dimer: trpB

chorismatesynthase: aroC

nicotinamide

3-dehydroquinatedehydratase: aroD

N-(5’-phosphoribosyl)-anthranilate

5-keto-D-gluconate 5-reductase:idnO

pyruvate

D-glucarate

aspartatekinaseIII: lysC

acetylmaltose

16S-rRNAs

hydroxymethylbilane

adenine

2,5-diamino-6-(ribosylamino)

-4-(3H)-pyrimidinone5’-phosphate

cyanatedegradation

D-ribose

Tsrglu

inorganicpyrophosphatase: ppa

ribosomal-protein-S5-alanine N-acetyltransferase:rimJ

a glycerolester

acetolactatesynthase: ilvN ilvB

2-isopropylmalatesynthase: leuA

cobalamin-independenthomocysteinetransmethylase:metE

an (R)-3-hydroxypalmitoyl-

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

L-tryptophan

bifunctional beta-cystathionase,PLP-dependentand regulatorof maltoseregulon: malY

a properlymatched

DNAbase pair

homoserinedehydrogenase:thrA

L-lysine

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

2-ketobutyrateformate-lyase

/ pyruvateformate-lyase

ferricenterobactin

ABCtransporter

a nucleoside-5’-phosphate

carbamoyl phosphatesynthetase: carA carB

a DNAwith uracil

a purine base

L-serine

dihydroorotate oxidase: pyrD

tRNA withGU(N)

anticodon

predicted L-galactonateoxidoreductase:yjjN

sulfate ABCtransporter

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

tetrapyrrolebiosynthesis I

lipopolysaccharidecore biosynthesis;heptosyl transferseIV; probably hexosetransferase: waaU

glutathione

7,8-diaminopelargonate

lipopolysaccharidecore biosynthesisprotein; heptosyltransferase III: rfaQ

L-phenylalanyl-tRNAphe

a prolipoprotein

sirohydrochlorin

L-serine

D-alanine

H-Gcv-protein-(lipoyl)lysine

UDP-N-acetyl-D-glucosaminebeta-1,6-N-acetyl-D-glucosaminyltransferase:pgaC

di-trans,poly-cis-hexaprenyldiphosphate

farnesyldiphosphatesynthase: ispA

2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol

D-tagaturonate

bicarbonate

spermidine

di-trans,poly-cis-

aminodeoxychorismatesynthase: pabA pabB

acetoacetyl-CoA

hybrid-cluster

proteinred

3-hydroxypropionaldehyde

L-lysine

O-phospho-L-homoserine

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

diamine

uridylyl-glutaminesynthase PII

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

a debranchedlimit dextrin

enterobactinbiosynthesis

lipoyl-ACP

Chemotactic SignalTransduction System

2-oxo-3-deoxygalactonate6-phosphatealdolase: dgoA

pyruvate

2-dehydro-3-deoxy-D-galactonate

precorrin-2dehydrogenase:cysG

acetate

Cd2+Zn2+

superpathwayof glycol

metabolismand degradation

tagatose-6-phosphate

acyl carrier proteinphosphodiesterase:acpH

D-galactitol

hydrogen sulfide

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-aminobutyrate

beta-D-ribopyranose

a fatty acid

acetolactatesynthase: ilvH ilvI

L-methionyl-tRNAmet

isopropylmalateisomerase:leuD leuC

5-aminoimidazoleribonucleotide

acetate

coenzyme A

alaninedegradation I

agmatine

3-phosphoglycerate

dTDP-alpha-L-

rhamnose

D-galactose

2’-deoxyadenosine-5’-diphosphate

GDP-alpha-D-mannose

AtoSC Two-Component

SignalTransduction

System

octyl beta-1,6-D-galactofuranosyl-

alpha-D-glucopyranoside

GMPsynthetase:guaA

asparaginesynthetaseA: asnA

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

porphobilinogen

pyruvate

aspartateammonia-lyase: aspA

beta-L-rhamnose

pyridoxalphosphatase:ybhA

dihydroorotase: pyrC

L-tryptophan

Trgglu-Me

phosphoribosyl-AMPcyclohydrolase: hisI

hypoxanthine

cis-aconitate

anaerobiccoproporphyrinogenIII oxidase: hemN

citratelyase: citEcitF citD

histidinol-phosphateaminotransferase:hisC

2-oxoglutarate

succinate semialdehydedehydrogenase,NAD+-dependent: sad

a cis,trans-polyisoprenyln-PP

nucleosidediphosphate kinase: ndk

N-acetylglucosaminyltransferase: murG

a singlestranded

L-arginine

thiamine-phosphate

4-methyl-2-oxopentanoate

23S rRNAm3psi1915methyltransferase:rlmH

D-arabinose5-phosphate

pyruvate

pyridoxine-5’-phosphate

carbamoylphosphatesynthetase:carA carB

replicativeDNAhelicase:dnaB

DNA combinedwith exogenousDNA to form a

recombinationaljunction

L-methionine

formate

DcuR-Pasp56

(KDO)-lipid IVA

pyrimidinedione

L-asparagine

L-alanine

3-octaprenyl-4-hydroxybenzoatedecarboxylasetogether withUbiG: ubiX

a (3S)-3-hydroxyacyl-CoA

2-phosphoglycolate

4-coumaroyl-CoA

acetyl-CoA

adenine

N-acetyl-L-glutamate

riboflavin

malate

D-allose

2-phospho-4-(cytidine 5’-diphospho)

a polypeptide

a tRNAcontainingqueuosine

acetaldehyde

rep helicase,a single-strandedDNAdependentATPase: rep

2-keto-3-deoxy-L-

rhamnonate

UDP-N-acetylmuramoylalanyl-D-glutamate 2,6-diaminopimelate ligase: murE

maltodextrinphosphorylase:malP

(S)-methylmalonyl-

CpxAR Two-Component

SignalTransduction

System

malate dehydrogenase: mdh

UDP-2,3-diacylglucosamine

hydrolase: lpxH

a tRNA

L-cysteinedesulfhydrase:metC

KASI: fabB

galactokinase: galK

KASI: fabB

KDO2-lipid A

chitobiosedegradation

methylglyoxalreductase(NADH-dependent): ydjG

phosphoglyceromutase1: gpmA

colanic acid building blocks biosynthesis

adenylylsulfatekinase: cysC

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

UDP reductase:nrdB nrdA

glucosyl-heptosyl2-

KDO2-lipid A-

phosphate

(S)-1-pyrroline-5-carboxylate fructose-1,6-

bisphosphate

7,8-dihydro-D-neopterin

glycerol

an RNA

ethyleneglycol

6-hydroxymethyl-7,8-dihydropterinpyrophosphokinase: folK

glutamyl-QtRNA(Asp)synthetase:yadB

GMPreductase:guaC

a hydroquinone

alpha-L-Ara4FN

acetylphosphate

acetaldehyde

nickel ABCtransporter

agmatinase:speB

3-phenylpropionatedioxygenasesystem: hcaDhcaC hcaF hcaE

2-dehydro-3-deoxy-D-

gluconate-6-phosphate

ALDEHYDE DEGRADATION

L-alanine

nicotinamide mononucleotide

ArcB-Phis292

protoporphyrin IX

S-ribosylhomocysteinelyase: luxS

acetate

succinate

precorrin-2

choline

beta-D-glucose

pyruvate

23Sribosomal

lactose

geranyldiphosphatesynthase: ispA

D-xylose

glutamate-cysteineligase: gshA

a trans-delta2-enoyl-acyl-[acp]

homoserine lactonehomoserine

5,10-methylene-

trehalose-6-phosphatephosphatase,biosynthetic:otsB

S-hydroxymethylglutathione

L-ornithine

diacetyl

selenophosphate

pyruvate

tRNAgln

RcsC-Phis

a proteinL-tyrosine

16S rRNAm62A1518,m62A1519dimethyltransferase: ksgA

nucleoside triphosphatepyrophosphohydrolase:mazG

tryptophanase:tnaA

ribose-1,5-bisphosphate

an (R)-3-hydroxyoctanoyl-

an (R)-3-hydroxydecanoyl-[acp]

lactosedegradation III

L-cysteine

fumarate

DcuS-Phis349

tetraphosphate

DNAcytosinemethylase:dcm

glycan chain 1

TDP-rhamnose

o-succinylbenzoate

KDO2-lipid IVA

L-fuculokinase: fucK

propionyl-CoA

2-keto-isovalerate

superpathwayof asparaginebiosynthesis

2-keto-3-deoxy-L-rhamnonatealdolase: yfaU

mannokinase

L-lysine

8-amino-7-oxononanoatesynthase: bioF

L-proline

2-oxobutanoate

L-ribulose-5-phosphate4-epimerase:sgbE

L-aspartate

gamma-aminobutyraldehydedehydrogenase: ydcW

N-acetylneuraminate

a carbohydrate

myo-inositol

L-glutamyl-tRNAGlu

D-alanyl-D-alanine-adding enzyme: murF

complex

dephospho-CoA kinase: coaE

23S rRNA m2G1835methyltransferase:rlmG

diphosphate

propionate

adenine

16S rRNA m5C1407methyltransferase:rsmF

inosine kinase: gsk

HMP-PPhydrolase:cof

protein with lowundecaprenylpyrophosphatephosphataseactivity: lpxT

cysteinesulfinatedesulfinase:csdA csdE

a 3’-phosphate-terminated

trehalose

L-alanine

GDP-L-fucose

CARBOXYLATES DEGRADATION

oxaloacetate

agmatinase: speB

glucosamine

4-hydroxybenzoateoctaprenyltransferase:ubiA

alpha-iminosuccinate

apo-citrate lyasephosphoribosyl-dephospho-CoAtransferase: citX

cytidinedeaminase: cdd

2-octaprenyl-6-methoxyphenolhydroxylase: ubiH

benzaldehyde

colanic acid

2-oxoglutarate

L-cysteine

molybdopterin

succinatesemialdehydereductase: yihU

dihydroneopterintriphosphate 2’-epimerase: folX

4-aminobutyrate

galactitoldegradation

L-glutamategamma-

semialdehyde

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

alpha-L-Ara4N

an apo-GcvHprotein

ferricdicitrate

fructose-1,6-bisphosphatase: yggF

L-glutamine:D-fructose-6-phosphateaminotransferase:glmS

glycogen

lipoatebiosynthesis

andincorporation II

succinate

dTDP-4-dehydrorhamnosereductase: rfbD

L-homocysteine

thymidylatesynthase: thyA

4-methyl-5-(beta-

hydroxyethyl)thiazole

N5-glutaminemethyltransferase:prmB

UDP-D-glucose

MutHLScomplex,methyl-directedmismatchrepair: mutHmutS mutL

alpha-D-glucose

acetaldehyde

rRNAcontaining

pseudouridine

a holo-[acp]

glycine

methylglyoxal

DNAadeninemethylase:dam

4-aminobutanal

nicotinatemononucleotide

dihydrofolatesynthetase: folC

L-rhamnose

pyrimidine deoxynucleosidetriphosphatepyrophosphohydrolase: nudI

nitrousoxide

2,3-diaminopropionate

di-trans,poly-cis-

methylmalonyl-CoA epimerase

tRNA-specificadenosinedeaminase:tadA

L-asparagine

L-glutamate

a peptide

3-phosphoglycerate

superpathway ofgluconate degradation

lipopolysaccharidecore biosynthesisprotein: rfaS

arsenate

CheB-Pasp: cheB

galactosyl-glucosyl-heptosyl3-

tRNAcontaining N6-methyladenine

uracil

L-cystathionine

acetyl-CoA carboxylase:accB accC accA accD

hemebiosynthesis fromuroporphyrinogen II

phosphate

a tRNA containing 5-carboxymethylaminomethyl-

2-thiouridine

phosphoenolpyruvate synthase: pps

phosphopantetheinyltransferase: entD

prolyl-tRNAsynthetase:

carbamoyl-phosphate

L-pantoate

isoleucyl-tRNA

synthetase:ileS

aspartyl-tRNA

synthetase:aspS

Tsrgln

putative enoyl-CoA hydratase/isomerase ofphenylacetatedegradation: paaG

Targln

succinate

N-acetyl-glucosamine-1-phosphate

D-galactonatedegradation

23Sribosomal

triose phosphate isomerase: tpiA

enolase: eno

succinate

beta-D-galactose

citrate synthase: gltA

oxaloacetate

L-1,2-propanediol

a DNAsegment

in reverseorientation

acetoin

ribosomal-protein-S18-alanine N-acetyltransferase: rimI

23S rRNA m5C1962methyltransferase: rlmI

beta-D-glucose

23S rRNA m1G745methyltransferase:rrmA

D-methionineL-methionine

an aldehyde

2-oxoglutarate

D-altronatedehydratase:uxaA

riboflavinsynthase:ribC

6-pyruvoyltetrahydropterin

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

a DNA pairof adjacentpyrimidines

bifunctional aconitate hydratase2 and 2-methylisocitrate

dehydratase: acnB

D-mannonateoxidoreductase:uxuB

D-threo-isocitrate

isocitrate dehydrogenase: icd

a glutaminesynthetase PII

an N-acetyl-D-hexosaminide

fructosedegradation

D-xylose

gamma-glutamyl-gamma-aminobutyraldehydedehydrogenase: puuC

dihydroxyacetonekinase: dhaLdhaK dhaM

superpathway of threonine metabolism

D-mannose

pyruvate kinase I: pykF

alanine racemase1, PLP-binding,biosynthetic: alr

aminoacetone

phosphohydroxymethylpyrimidinekinase: thiD

malate fumarate succinate orotateL-aspartate

an acid

UDP-N-acetylmuramoyl-L-alanyl-D-

glutamyl-meso-2,6-diaminoheptanedioate-

D-alanine

YgjDdegradation

products

propionyl-CoA:succinateCoA transferase: scpC

acidphosphatase:appA

7,8-dihydroneopterintriphosphate

a dipeptide

3-(2,3-dihydroxyphenyl)

propionate

putative ring-cleavage enzymeof phenylacetatedegradation: maoC

2-oxoglutarate

5-phospho-ribosyl-

glycineamide

tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:mnmA

phenylacetaldehydedehydrogenase: feaB

D-fructose-6-phosphateL-glutamine

3,5-tetradecadienoyl-

diphosphate

L-serine

D-galactonate

sirohemebiosynthesis

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

D-erythro-imidazole-glycerol-phosphate

protoporphyrinogenoxidase: hemG

KASI: fabB

L-valine

anamineated

amine donor

cobalamin-dependent

thioredoxinreductase:trxB

glycolateL-lactate

acetate

AMPnucleosidase: amn

cis-3-(carboxyethyl)-3,5-

cyclohexadiene-1,2-diol

16S rRNA m2G1207methyltransferase:rsmC

alpha-D-galactose 1-phosphate

tetrahydrofolate

rRNAcontaining 2-methyladenine

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

glycosidehydrolase:ygjK

N-ethylmaleimidereductase, FMN-linked: nemA

thiocyanate

cytosine

3-phosphoglycerate

2,3-dihydroxy-isovalerate

cytosinedeaminase:

glyoxylatecarboligase:gcl

hypoxanthine

chorismate mutase: pheA

tryptophanyl-tRNA

synthetase: trpS

glucokinase: glk

valyl-tRNAsynthetase:

UDP-D-glucose

cysteinyl-tRNA

synthetase:cysS

an rRNA

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

shikimate kinase II: aroL

PRPPbiosynthesis I

hydroxyphenylacetyl-CoA thioesterase: paaI

L-fucose

5’-deoxyadenosine

alkylhydroperoxidereductase: ahpF ahpC

phosphate

putativeoxidoreductaseFe-S subunit;possiblecomponentof selenatereductase: ygfK

oxalate

enterobactin

2-dehydro-3-deoxyphosphoheptonatealdolase: aroG

D-galactonatedehydratase: dgoD

pyruvate

anthranilate synthasecomponent II: trpD

superpathway of leucine, valine,and isoleucine biosynthesis

PII-UMP

deoxyguanosine

argininesuccinyltransferase:astA

3-deoxy-D-manno-

octulosonate

cytidine

maltose

UDP-N-acetyl-beta-D-mannosaminouronate

L-methionine

glutamatedehydrogenase:gdhA

2-oxobutanoate

sorbitol-6-phosphatedehydrogenase:srlD

ethanolamine

COFACTORS, PROSTHETIC GROUPS, ELECTRON CARRIERS BIOSYNTHESIS

cytidinekinase: udk

cytidylatekinase: cmk

ketogluconate metabolism

tetrahydrofolate

a DNAsegment

citratesynthase:gltA

lipoate acetyltransferase: aceF

hydroxymethylbilanesynthase: hemC

N5-methyl-L-glutamine

pyruvate

glucose and glucose-1-phosphate degradation

tRNA (Gm18) 2’-O-methyltransferase:trmH

methionyl-tRNA

synthetase:metG

trans-aconitate

DNAwithoutlesion

N-acetylneuraminatemutarotase: nanM

xanthosinephosphorylase:xapA

taurine

methylglyoxal

diphosphate

UDP-N-acetyl-D-

glucosamine

uroporphyrin III C-methyltransferase:cysG

NUCLEOSIDES AND NUCLEOTIDES BIOSYNTHESIS

elongatortRNAmet

D-galactono-1,4-lactone

BglG-P

3-keto-L-gulonate

pantothenateand coenzyme

A biosynthesis I

lipoylateddomain

L-lysyl-tRNAlys

a [citrate(pro-3S)-

lyase](citrylform)

triose phosphateisomerase: tpiA

L-rhamnulose-1-phosphate

acetaldehyde

enolase: eno

nitric oxide

alpha-L-arabinose

D-galacturonate

phosphoenolpyruvatesynthase: pps

malate

phosphoserinephosphatase: serB

L-tyrosyl-tRNAtyr

lipid Adisaccharide

a cis-delta5-dodecenoyl-[acp]

4-coumarate

superpathway of arginineand ornithine degradation

phenylacetate-CoA ligase: paaK

enterobactin

superpathway of aspartateand asparagine biosynthesis;

interconversion ofaspartate and asparagine

N-acetyl-D-glucosamine

Ni2+Mg2+

unknown

ferricenterobactin

ribonucleosidetriphosphatereductaseactivase: nrdG

3’-phospho-adenylylsulfatereductase: cysH

an rRNA

a cis-vaccenoyl-

pyrimidinedeoxyribonucleosides

degradation

crypticadeninedeaminase:ade

pyrazinamide

L-Ala-gamma-D-Glu

polyisoprenoidbiosynthesis (E. coli)

L-tyrosine

all-trans-farnesyl

diphosphate

a biotinylatedBCCP (dimer)

predicted 3-hydroxy-acyl-CoAdehydrogenaseof phenylacetatedegradation: paaH

FERMENTATION

2,4-dienoyl-CoAreductase:fadH

pyruvate

2-methylcitratedehydratase: prpD

ribose-5-phosphateisomeraseA: rpiA

cobinamide

fumaratereductase:frdD frdCfrdB frdA

lipoyl-ACP

a holo-[acp]

beta-alanine

5-methyluridine-modified 23S

ribosomal RNA

3-hydroxy-5-cis-tetradecenoyl-

a proteinL-beta-

isoaspartatealpha-

methyl ester

L-threonyl-tRNAthr

a [citrate(pro-3S)-lyase](thiol

N-acetyl-D-glucosamine-6-phosphate

D-gluconate

lipoatesalvage andmodification

a phosphatemonoester N-methyltryptophan

catabolicthreoninedehydratase:tdcB

D-alanine-D-alanineligase A: ddlA

anthranilate

beta-D-glucose

RstBA Two-Component

SignalTransduction

System

L-proline

a drug

UDP-3-O-[3-hydroxymyristoyl]glucosamineN-acetyltransferase: lpxD

phosphodiesterase,heme-regulated: dos

L-aspartyl-tRNAasp

tRNA uridine

cholate

formate

acetohydroxy acidisomeroreductase:ilvC

KDOtransferase:waaA

EvgA-Pasp

glutaminedegradation I

CheB-Pasp: cheB

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

D-glucono-delta-lactone-6-phosphate

acetate

a thioredoxin

agmatine

glycolate

1-phosphofructokinase:fruK

putative diacylglycerolcholinephosphotransferase:ynbA

gamma-glutamyl-L-putrescine

N-carbamoyl-L-aspartate

an RNA

trehalose

acetyl-esterase: aes

L-arginine

deoxyinosine

pyruvate

isochorismatesynthase 1: entC

a [citrate(pro-3S)-

lyase](acetylform)

pirin-likeprotein:yhhW

3-dehydroquinate

2,3-dihydroxybenzoate-AMP ligase: entE

cytoplasmictrehalase: treF

nitrite

2-isopropylmaleate

2,3-dihydro-2,3-dihydroxybenzoate

3-deoxy-D-manno-

octulosonate8-P

ThiS-COSH

UDP-N-acetyl-D-glucosamine

hydroxylamine

acetyl-CoA

pyruvate

citrate

chemotaxis proteinmethyltransferase:

uracil

deoxyuridine

L-rhamnonatedehydratase:yfaW

glucosedehydrogenase: gcd

a DNAcontaining aapyrimidinic

a deoxynucleoside

L-asparagine

cysteinedesulfurase:iscS

putrescine

formate

an oxidizedflavodoxin

Trgglu

aspartatecarbamoyltransferase: pyrI pyrB

glycolateoxidase:glcFglcE glcD

1-amino-propan-2-one-3-

phosphate

L-glutamate

glycerol 2-phosphate

a deoxynucleotide

predictedthiosulfatesulfurtransferase:ynjE

a DNAcontaining

a purinic site

D-mannose

thiosulfatesulfate

CDP-choline

phosphate

coproporphyrinogenoxidase, aerobic: hemF

UDP-D-galactose

SIGNAL TRANSDUCTION PATHWAYS

nicotinate-nucleotidedimethylbenzimidazolephosphoribosyltransferase: cobT

2-deoxygluconate

tRNAcontainingguanine

cobalaminadenosyltransferase:

pyrimidinephosphatase

trans-2-decenoyl-ACP isomerase: fabA

enoyl-ACP reductase(NADH): fabI

glycolaldehyde

alpha-D-glucose

DNAligase: ligB

phosphoenolpyruvate

2-aminobutyrate

beta-hydroxyacyl-ACP dehydrase: fabA

dihydroxy-acetone

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

uracil

anadenylated

ThiS sulfur-carrierprotein

ubiquinone-8

threoninedehydrogenase: tdh

octulosonate

crotonobetainyl-CoA reductase: caiA

L-ornithine

thymidine

diphosphate

glyoxylate

phosphoribosylformylglycinamidecyclo-ligase: purM

UDP-D-glucose

acetaldehyde

acetyl-CoAsynthetase (AMP-forming): acs

cobalamin 5’-phosphatesynthase:cobS

BaeS-Phis

GMPsynthetase:guaA

2-oxoglutarate

adenylatekinase: adk

a rhamnosyllipopolysaccharide

degradationof pyrimidine

ribonucleosides

uridinekinase: udk

L-gamma-glutamylcysteine

glucosamine

AICARtransformylase:purH

AceF-lipoate

erythronate-4-phosphatedehydrogenase:pdxB

xanthosine

predicted N-acetylmannosamine-6-phosphateepimerase: nanE

acetoin

acetaldehyde

superpathwayof glutamatebiosynthesis

oxaloacetate

D-galactonate

S-adenosyl-dependentmethyltransferase:mraW

a decanoyl-[acp]

3-keto-L-gulonate

RcsCB Two-ComponentSignal Transduction System

4-hydroxybutyrate

a protein-L-glutamate--O5-methyl-

L-arabinose

EIIBgl

adenine

D-glucono-delta-

lactone-6-phosphate

porphobilinogensynthase: hemB

a transhexadecenoyl-[acp]

DNAcontaining

a basewith lesion

chloride

lactose

EIIFru

KDOtransferase:waaA

isovaleryl-CoAdehydrogenase /predicted acyl-CoAdehydrogenase: aidB

cob(I)alamin

subunit of fatty acidoxidation complex: fadI

5’-methylthioadenosine/S-adenosylhomocysteine

nucleosidase: mtn

CARBOHYDRATES BIOSYNTHESIS

lysyl-tRNAsynthetase,constitutive:

D-allosekinase: alsK

glycine cleavagecomplex

AMINOACYL-TRNA CHARGING

xanthine

an N-hydroxy-

arylamine

adenosine 5’-phosphosulfate

phenylhydantoinase:hyuA

an acylphosphate

CreB-Pasp

spermidineacetyltransferase:speG

D-beta-D-heptose-1,7-bisphosphate

leucyl,phenylalanyl-tRNA-proteintransferase: aat

NarX Nitrate/Nitrite-DependentTwo-Component Regulatory System

phosphoribosylformiminoAICAR-phosphate

manno(fructo)kinase: mak

D-beta-D-heptose-1-phosphate

ribose 1-phosphokinase

aspartatekinase III: lysC

L-methionine

d-biotin d-sulfoxide

2-O-(6- phospho-

alpha-mannosyl)-

D-glycerate

glucosamine

2-phosphoglycerate

acid phosphatase/phosphotransferase:aphA

CheB-Pasp: cheB

ATP-dependentDNAhelicase: recQ

N-formyl-L-methionyl-tRNAfmet

N-methyltryptophanoxidase: solA

an N-D-ribosylpyrimidine

hybrid-clusterprotein: hcp

AMINES AND POLYAMINES BIOSYNTHESIS

L-2-hydroxyglutarateoxidase: lhgO

acetate kinase B: ackB

S-formylglutathionehydrolase: frmB

beta-ketoesterreductase:dkgA

allolactose

UhpA-Pasp

phosphoglucose isomerase: pgi

L-histidyl-tRNAhis

peptidedeformylase:def

5-ketogluconate

ribose-phosphatediphosphokinase: prs

nitritereductase:nirB nirD

L-threonine

1,3-propanediol

thiamin

glyceraldehyde 3-phosphatedehydrogenase-A complex: gapA

4-(2-aminophenyl)-2,4-

dioxobutanoate

uracil

adenosine-3’(2’),5’-bisphosphatenucleotidase:cysQ

dehydratase: acnB

phenylhydantoin

D-amino aciddehydrogenase:dadA

ATPsynthase

an alcohol

isochorismatesynthase 2: menF

’activated’tRNA

1,4-dihydroxy-2-naphthoateoctaprenyltransferase:menA

a peptide

L-rhamnoseisomerase:rhaA

a fatty acid

ppGpp biosynthesis

CDP reductase:nrdB nrdA

L-aspartate

tRNApseudouridine13 synthase: truD

2-oxoglutarate

2-deoxy-D-gluconate 3-dehydrogenase:kduD

pyridoxal

acetyl-CoA

indole

a proteinwith

incorrectdisulfidebonds

acetyl-CoAsynthetase(AMP-forming): acs

tRNAdihydrouridinesynthase: dusC

Ap3Asynthetase:lysU

enterobactin

lipopolysaccharidecore biosynthesisprotein: rfaY

citrate

glutaminesynthetase

deadenylylatingenzyme: glnE

lipid IVA

L-seryl-tRNAsec

CARBOHYDRATES DEGRADATION

CoA:carnitine CoAtransferase: caiB

nicotinate adenine dinucleotide

L-allo-threonine

NUCLEOSIDES AND NUCLEOTIDES DEGRADATION AND RECYCLINGL-histidinol-phosphate

carbamoyl-phosphate

thiaminbiosynthesisproteinThiC: thiC

a DNAcontaining 6-O-methylguanine

thiaminkinase: thiK

maltoseacetyltransferase:maa

tartronatesemialdehydereductase2: glxR

histidinol

putativepyruvatesynthase:ydbK

caiEprotein: caiE

L-lysine

polynucleotidephosphorylase:pnp

L-cysteine

(1R,6R)-6-hydroxy-2-succinylcyclohexa-

2,4-diene-1-carboxylate

4-methyl-5-(beta-

phosphate

pyridoxamine

salvage pathways of guanine, xanthine, and their nucleosides

nucleotide-sugarhydrolase:nudK

UDP-GlcNAc-enolpyruvate

Tapgln

a crotonyl-[acp]

acetoinsynthesis:poxB

trans-delta2-decenoyl-

L-lysine

protoheme IX

L-fuculose-1-phosphate

tRNAala

a reducedFeS-protein

gluconeogenesis I

phosphodiesterase, c-di-GMP-specific: yahA

acetyl-CoA

glycerolkinase: glpK

UDP-D-galactose

UDP-D-glucose

alpha-galactosidase:melA

xylulokinase:xylB

sirohydrochlorinferrochelatase: cysG

isocitratedehydrogenasephosphatase: aceK

BarA-UvrY Two-Component

SignalTransduction

System

lysidine-modifiedtRNAileX

succinate

a tripeptide

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)

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

salicinarbutin

L-lyxosedegradation

deoxyadenosine

L-xylulose 5-phosphate3-epimerase:ulaE

dTDP-D-glucose

pyruvate

L-idarate

glyceroldegradation V

4-nitrobenzylalcohol

tRNAarg

L-lactate

formaldehyde

succinate

L-serine

a proteinL-beta-

isoaspartate

pyridoxamine5’-phosphateoxidase: pdxH

D-galactarate

selenide

a beta-D-galactoside

2-keto-isovalerate

3-mercaptopyruvate:cyanidesulfurtransferase: sseA

a thioredoxin

glucose-1-phosphateuridylyltransferase:

galU galF

hydroxypyruvate

glucosyl-heptosyl3-

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

CreCB Two-ComponentSignal Transduction System

6-hydroxymethyl-7,8-dihydropterin

isopentenyldiphosphateisomerase: idi

a protein

2-thiouridylate

BasR-Pasp

(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylatesynthase: menH

xylulokinase:xylB

D-myo-inositol (1)-monophosphate

pyrimidineribonucleotides denovo biosynthesis

23S rRNA m5U1939methyltransferase:rlmD

glycerol-3-phosphate-dehydrogenase,anaerobic:glpC glpB glpA

RstA-Pasp

uridine

methioninesulfoxidereductaseA: msrA

EIIMan

2,5-didehydro-

D-gluconate

two-componentalkanesulfonatemonooxygenase

an octanoylateddomain

coproporphyrinogen III

5,6,7,8-tetrahydropteridine

inosine

exonucleaseIII: xthA

glycyl-tRNAgly

a 2,3,4-saturated

fattyacyl CoA

acetol

NtrC-P

glycerol

coenzyme A

sugar phosphatase: yidA

PhoQP Two-Component

SignalTransduction

System

2-oxoglutarate

superpathway ofhexitol degradation

tRNA chargingpathway

7,8-dihydrofolate

glutaminesynthetase: glnA

L-serine

CpxA-Phis

heptosyl-KDO2-

lipid IVA

methylmalonyl-CoAmutase: scpA

L-Ala-D-Glu-meso-

DcuS-Phis349

biotincarboxylase:accC

dihydroorotate

lipid Adisaccharide

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

diphosphate

glycine

an aromaticsulfate

5,10-methylene-

trimethylamine

nitrite

deoxyinosinetriphosphatepyrophosphatase:rdgB

pyrroline-5-carboxylatereductase:proC

2-hydroxyglutarate

a cis-3-enoyl-CoA

pyruvateformate-

2’-(5’-phosphoribosyl)-3’-dephospho-

CoA biosynthesisI (citrate lyase)

RNA(n)

D-alanine

an mRNA

D-mannose

cis-dihydrodiolderivative of

phenylacetyl-CoA

(2S,3S)-2-methylcitrate

pyruvate

an (R)-3-hydroxydodecanoyl-

S-allantoin

multidrug

lipoatesynthase: lipA

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

meso-2,6-diaminopimelyl-D-alanyl-D-alanine

glycogen degradation I

prolinebiosynthesis I

a 2,3,4-saturatedfatty acyl-[acp]

L-ornithine L-lysine L-arginine

glutaminase:ybaS

an octanoyl-[acp]

glucokinase:glk

Tsrglu-Me

pyruvate

biotinsynthase: bioB

glycogenphosphorylase:glgP

2-keto-3-deoxygluconokinase:kdgK

acetyl-CoA

D-glucuronateisomerase:uxaC

L-3,4-dihydroxybutan-2-one-4-phosphate

an N-substitutedamino acid

a ribonucleosidetriphosphate

glutamatesynthase:gltD gltB

guanosine

triphosphoribosyl-dephospho-CoAsynthase: citG

biotinbiosynthesis I

coenzyme A

N-alpha-acetyl lysinemethyl ester

3-(2,3-dihydroxyphenyl)propionatedioxygenase: mhpB

an aceticester

QseB-Phosphorylatedtranscriptional

activator

thiamine-phosphate

ribosomal-protein-L12-serineacetyltransferase:rimL

4-amino-4-deoxychorismate

cytochromebd-I terminal

oxidase

purine nucleosidephosphoramidase:hinT

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

GDPdiphosphokinase: spoT

GLYCOLYSIS

N-acetyl-D-mannosamine

L-prolyl-tRNApro

fused PutAtranscriptionalrepressor / prolinedehydrogenase/ 1-pyrroline-5-carboxylatedehydrogenase:putA

guanine

xanthosine

an RNA

fructoselysine

fructose 1,6-bisphosphatase:ybhA

degradation of purine ribonucleosides

lipoate

NADP-dependentdehydrogenase:yqhD

L-glutamate

nicotinatephosphoribosyltransferase: pncB

rRNAcontaining 2’-

O-methyluridine

tRNApseudouridine55 synthase: truB

propionyl-CoAcarboxylase

methylmalonylpathway

cobalaminsynthase: cobS

xanthine

di-trans,poly-cis-

heptaprenyldiphosphate

a peptide

D-Ala-D-Aladipeptidase:ddpX

pyruvate formate-lyase: tdcE

UDP-D-galacto-1,4-

furanose

4-(phosphonooxy)-threonine

a deoxyribonucleicacid

acetaldehyde

lipoylated domain

putrescine

pyrimidine (deoxy)nucleoside triphosphatepyrophosphohydrolase:nudG

nitrate

L-rhamnose

3-hydroxy aciddehydrogenase:ydfG

cyclicdi-3’,5’-

guanylate

fumarate

L-phenylalanine

UDP-D-galactose

a proteinwith correct

disulfidebonds

D-glucaratedehydratase: gudD

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

peptideuptake ABCtransporter

23S rRNA m6A1618methyltransferase:rlmF

pyridoxaminekinase: pdxK

endonucleaseVIII: nei

glycan chain 1

AROMATIC COMPOUNDSBIOSYNTHESIS

flavorubredoxinreductase: norW

carbamoyl-phosphate

galactoside O-acetyltransferase:lacA

a mRNA

6-phosphogluconatephosphatase: yieH

spermidine

triphosphate

L-lactaldehyde

beta-D-glucose

superpathway of lysine, threonineand methionine biosynthesis I

lysinedegradation I

threonyl-tRNA

synthetase:thrS

alanyl-tRNAsynthetase:

KASI: fabB

isochorismatase:entB

glycine betaine L-proline

glutaminyl-tRNA

synthetase:glnS

a semiquinone

predictedgalactose 1-dehydrogenase:yhhX

N,N’-dimethyl-p-phenylenediamine

acylphosphatase:yccX

3-hydroxyadipyl-CoA

dTDP-4-dehydro-6-

deoxy-D-glucose

isocitrate lyase: aceA

succinate dehydrogenase:sdhA sdhB sdhC sdhD

conversionof succinate

to propionate

fumarase C: fumC

6,7-dihydropteridine

tRNA:Cm32/Um32methyltransferase:trmJ

Mn2+Fe2+

palmitate

N2-succinylglutamate

inosine

6-phosphofructokinase II: pfkB

cofactor

oxidizedthioredoxin

a tRNA

23Sribosomal

RNAmethylatedat position

D-glucose

tRNApseudouridinesynthase I: truA

guanine

an alcohol

melibiosedegradation

3-sulfinoalanine

L-serinedegradation

L-aspartate

L,D-transpeptidaseYnhG: ynhG

an rRNA

a carboxylicester

a tRNAcontaining 2’-O-methylcytosine

or 2’-O-methyluridine

L-ascorbatedegradation,

anaerobic

enterobactin

molybdateABC

transporter

Ogt: ogt

2,5-diketo-D-gluconatereductaseA: dkgA

NarL-Pasp

tetrahydrofolate biosynthesis

pyridoxal

a protein

2-phosphoglycerate

D-mannosedegradation

DNA containing5-methylcytosine

L-leucyl-protein

glutathione

O-antigen biosynthesis

L-serine

galactose-1-phosphateuridylyltransferase:galT

phospho-N-acetylmuramoyl-pentapeptide transferase: mraY

a tRNA

tRNA (m7G46)methyltransferase: trmI

lysyl-tRNAsynthetase:

L-ribulose 5-phosphate4-epimerase:ulaF

cis-2-methylaconitate

malatedehydrogenase,NAD-requiring: maeA

cyclic-AMP

tRNAdihydrouridinesynthase: dusB

tRNAcys

an activeribonucleosidetriphosphatereductase

Targlu-Me

a protein-L-methionine-(S)-S-oxide

2-octaprenyl-6-methoxyphenol

methylmalonyl-CoA mutase: scpA

nicotinamidase: pncA

L-glutamate

Trggln

rhamnulose-1-phosphatealdolase: rhaD

deoxyuridinetriphosphatase: dut

an alcohol

L-quinate

ribokinase:rbsK

dGTPpyrophosphohydrolase: mutT

CurliSecretion

andAssemblyComplex

tRNAtyr

D-allulose-6-phosphate

L,D-transpeptidaseYcfS: ycfS

a peptide

AtoC-Pasp

L-isoleucyl-tRNAile

heptosyl-KDO2-lipid A

BasSR Two-Component

SignalTransduction

System

dTMP kinase: tmk

shikimate

UDP-N-acetyl-D-mannosaminuronicacid transferase: rffM

D-alanine

fatty acyl-CoAsynthetase: fadD

pantothenate

a DNA withunresolved

recombitionalor holidayjunctions,

created by RecA

phosphoenolpyruvate

dephospho-CoA

BasS-Phis

BaeSR Two-Component

SignalTransduction

System

succinate

2,3-diketo-L-gulonatereductase:yiaK

EvgSA Two-Component

SignalTransduction

System

phosphatidylglycerophosphatesynthase: pgsA

transketolaseII: tktB

dTDP-4-oxo-6-deoxy-D-glucosetransaminase: rffA

2-dehydropantoate

(S)-1-pyrroline-5-carboxylate

oxalyl-CoA

a cis-delta3-decenoyl-

D-glucarate

a dipeptide

3-deoxy-D-manno-

octulosonate8-P

L-arabinoseisomerase: araA

cis-aconitate

D-alanine

GTPase thatinteracts withmethylmalonyl-CoA mutase: argK

formamidopyrimidineDNA glycosylase: mutM

glyoxalase III

acetyl-CoAacetyltransferase:atoB

pyruvate dehydrogenasemultienzyme complex: lpd aceF aceE

RssB-P

protein N6-(lipoyl)lysine

coenzyme A

aminoacetaldehyde

cis-vaccenatebiosynthesis

nitrate

KDOtransferase:waaA

2-O-(6-phospho-alpha-

mannosyl)-D-glycerate

alpha-ketoglutaratereductase: serA

beta-D-galactose

L-tyrosine

5’-phosphoribosyl-4-(N-succinocarboxamide)

-5-aminoimidazole

lipopolysaccharideglucosyltransferaseI: rfaG

RcsF-P

UDP-D-glucose:(glucosyl)LPS alpha-1,3-glucosyltransferase: rfaI

alpha-D-glucose-1-phosphatase: yihX

Tapglu

a limitdextrin

DNApolymeraseV: umuDumuC

formyl-L-methionylpeptide

an aromaticamino acid

lactose

bicarbonate

octanoate

KefAfructose-1,6-bisphosphataseI: fbp

guanosine 3’-diphosphate

5’-triphosphate

an apo-[acp]

UDP-N-acetylmuramoyl-L-alanine

Targlu

flavodoxinNADP+reductase: fpr

pyruvate

anthranilatesynthase: trpD trpE

2-dehydro-3-deoxyphosphoheptonatealdolase: aroF

histidinal

tRNAcontaining

ribothymidineat position 54

pyridoxamine-phosphatetransaminase

L-homocysteine

methyl-1,4-benzoquinol

a ThiI sulfur-carrierprotein

tetrahydrodipicolinatesuccinylase: dapD

cysteinebiosynthesis I

an oxidizedglutaredoxin

anthranilate

gamma-glutamyl-gamma-aminobutyraldehyde

D-threo-isocitrate

octulosonate

NADH-azoreductase,FMN-dependent:azoR

ADP-heptose:LPSheptosyltransferaseII: rfaF

ornithinecarbamoyltransferase: argI

a 3-oxo-octanoyl-[acp]

dihydroxy-acetone

rRNA containingN6,N6-

dimethyladenine

trehalosedegradation

I (lowosmolarity)

KDOtransferase:waaA

R-4’-phosphopantothenoyl-

L-cysteine

heptosyl2-KDO2-lipid A

a phenol

glycine

tRNA-guaninetransglycosylase: tgt

UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6-D-galactosyltransferase:rfaB

2-phosphoglycolate

methionineadenosyltransferase:

glycan chain 2

thioredoxinpathway

23S rRNApseudouridine2605synthase: rluB

deoxycytidine

multidrug

L-methionine

DNApolymeraseIII, alphasubunit: dnaE

N-acetylmannosaminekinase: nanK

DL-lactaldehyde

fatty acid

pyruvate

a single-stranded

multidrug

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

UDP-N-acetyl-D-

glucosamine

L-arginine

D-glutamate

23S rRNApseudouridinesynthase: rluC

Targlu

2-C-methyl-D-

erythritol-4-phosphate

a protein-L-glutamine

hydrogencyanide

L-homocysteine

glycerol

pyruvate

pyrazinamidase:pncA

2-hydroxyglutaratesynthase

a polypeptide

glyoxalaseII: gloB

trehalose-6-phosphatehydrolase:treC

a tRNAcontaining 7-

a 2,3-dehydroacyl-CoA

6,7-dimethyl-8-(1-D-ribityl)lumazine

DNA withremovedadenine

mismatchleaving

an AP site

gluconolactonase

thiolperoxidase:bcp

o-succinylbenzoatesynthase: menC

excised base

tRNAhis

chorismate mutase: tyrA

methylglyoxalreductase: yeaE

5-methylaminomethyl-2-thiouridinemethyltransferase:mnmC

L-tartratedehydratase:ttdB ttdA

multidrug

Autoinducer2-degradingprotein: lsrG

Trgglu

adenosylcobinamide

hydroxyethylthiazolekinase: thiM

an organicmolecule

S-ureidoglycolate

dihydrolipoyltranssuccinylaseN6-(dihydrolipoyl)lysine

FATTY ACID AND LIPIDS DEGRADATION

a ThiS-ThiF acyl-disulfide

oxaloacetate

thioesteraseIII: ybaW

dTDP-D-glucose

a protein-S-methyl-L-cysteine

glycine decarboxylase: gcvP

an L-1-phosphatidyl-glycerol

glucokinase:glk

L-glutamate-5-phosphate

a damagedDNA

pyrimidine

enterobacterial commonantigen biosynthesis

citrate

glutathione S-transferase:yfcF

selenophosphate

D-cysteinedesulfhydrase,PLP-dependent: dcyD

uridine

D-ribose

dihydrouracil

lipoate acetyltransferase N6-(S-acetyldihydrolipoyl)lysine

KASI: fabB

3-methylcrotonyl-CoA

TorT-TMAO

UDP-L-Ara4FN

fatty acid

acetate CoA-transferase

Co2+Fe2+

Tapglu-Me

orotidine-5’-phosphate-decarboxylase: pyrF

uracil

restrictionof DNA at 5-methylcytosineresidues: mcrA

oxaloacetate

DNA adeninemethyltransferase:yhdJ

[+ 3 isozymes]

xyloglucanoligosaccharide

thiamin biosynthesis I

an aldehyde

ureidoglycolatedehydrogenase:allD

base withlesion

biotin

an aliphaticN-acetyl-diamine

citrate

uracil

amylomaltase:malQ

superpathway of pyridoxal 5’-phosphate biosynthesis and salvage

uridine

L-alanine

UDP-D-glucuronate

5’,5’-diadenosinetriphosphate

a glucoronide

phosphoenolpyruvate

2-hydroxyglutarate

23S rRNA m2G2445methyltransferase:rlmL

dihydropteroatesynthase: folP

probable 6-phospho-beta-glucosidase:glvG

N-acetylglucosamine

NADPHnitroreductase:nfsA

glycerophosphoryldiesterphosphodiesterase,periplasmic: glpQ

UDP-D-glucuronate

glycerol degradation I

ubiquinone-8biosynthesis(prokaryotic)

MdtABC-TolC

multidrugefflux

transportsystem

pyruvate

L-rhamnosemutarotase:rhaM

fumarase C: fumC

fumaratereductase: frdDfrdC frdB frdA

tRNAphe

UDP-L-Ara4Nformyltransferase:arnA

alpha-D-mannose1-phosphate

arbutin-6-phosphate

Ca2+ Na+ K+

a tRNA

c-di-GMPphosphodiesterase:yhjH

acetate

taurine

2-oxobutanoate

a protein-L-methionine-(R)-S-oxide

beta-D-galactose

correspondingcarbamoylamino acid

carnitine degradation I

predicted alpha-ribazole-5’-Pphosphatase: cobC

phosphoproteinphosphatase: pphB

glutamate-1-semialdehyde

ribulosephosphate3-epimerase:rpe

homoserine

di-trans,poly-cis-nonaprenyl

diphosphate

methionylpeptide

MdtJIspermidine

SMRtransporter

EIIChb

D-xylulose

fructoselysine 3-epimerase: frlC

L,D-transpeptidaseErfK: erfK

UhpBA Two-Component

SignalTransduction

System

precorrin-1

D-ribose

methylglyoxalreductase(NADPH-dependent)

L-cysteine

a fatty acid

predicted acetoindehydrogenase:yohF

O-succinylhomoserinelyase: metB

pre-cofactor

N-acetylmuramicacid PTSpermease

phosphoribosylamine-glycine ligase: purD

thiaminemonophosphatekinase: thiL

thiaminbiosynthesis

ThiGHcomplex:thiH thiG

L-glutamate

adenylosuccinatesynthetase: purA

phospholipid biosynthesis I

palmitoleatebiosynthesis

N5-carboxyaminoimidazoleribonucleotidesynthetase: purK

phosphoribosylaminoimidazole-succinocarboxamide synthase: purC

L-Ala-D-Glu-meso-A2pm

a 6-acetyl-beta-D-

galactoside

2-keto-isovalerate

ethyl-2-methylacetoacetate

leucine ABCtransporter

pyruvatekinase I: pykF

tRNAile

OuterMembrane

FerrichromeTransportSystem

2-trans,5-cis-tetradecadienoyl-

fumarase B: fumB

NarQ Nitrate/Nitrite-DependentTwo-Component Regulatory System

imidazoleacetol-

phosphate

an (R)-3-hydroxyhexanoyl-

an N-acetylspermidine

formate

a drug

pyridoxalphosphatase:cof

N-acetylglutamatesynthase: argA

a holo-[acp]

UDP-4-amino-4-deoxy-L-arabinose

23S rRNAcontaining

ornithinedecarboxylase,biosynthetic:speC

partially N-deacetylated

a holo-[acp]

5’-deoxyadenosine

2-selenouridine

aldehydedehydrogenase A,NAD-linked: aldA

L-tryptophanyl-tRNAtrp

16S rRNAcontaining

N3-methylated

uridine

a 3-oxo-cis-vaccenoyl-

5-amino-6-(5’-phosphoribosylamino)

uracil

heme dsynthase:katE

short chain acyl-CoAsynthetase: fadK

pyruvate

L-glutamategamma-

semialdehyde

an acyl-[acp]

DNA Cleavedat Recognition

L-tartrate

L-mannose

sulfate

methanol

tRNAtyr

TorSR Two-Component Signal Transduction System

arsenatereductase:arsC

DNA (without 6-O-methylguanine)

oxidizedribonucleoside-

triphosphatereductase

tRNAval

succinate

protein-tyrosine-phosphatase:pphB

bifunctional 3-demethylubiquinone-83-O-methyltransferaseand 2-octaprenyl-6-hydroxyphenolmethylase: ubiG nicotinate

mononucleotide

L-homocysteine

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.

The most studied metabolic network, Escherichia coli:

a CDP-2,3,4-saturated-

diacylglycerol

a holo-[acp]

peptidoglycanD-alanyl-

DAP crosslink

KDO2-lipid IVA

disulfideoxidoreductase:dsbG

lipid IVA

a peptide

3-phytase:agp

a shortglucan

oxaloacetate

tyrosine kinaseinvolved incolanic acidbiosynthesis:wzc

N-acetylmuramoyl-L-alanineamidase 2: amiB

disulfideoxidoreductase:dsbA

KDO2-lipid A

a fatty acid

glucosamine

membrane-boundlytic mureintransglycosylaseF: mltF

glycan chain 1

alpha-amylase:malS

an octanoyl-[acp]

phenylacetaldehyde

glucosamine

an MDO-O-glucose

di-trans,poly-cis-

peptidyl-prolylcis-transisomerase(PPIase): surA

a peptidewith a leadersequence

an MDO-O-glucose

a peptidoglycan

alpha-D-glucose-1-

phosphatase:yihX

cytochromeC552: nrfA

L-lactate

aminoacetoneoxidase: tynA

L-lactate

a carboxylate

a peptidoglycan

fatty acid

peptidyl-prolylcis-transisomerase:ppiD

D-lactate

a single-stranded

beta-D-glucose

an acyl-[acp]

a glucosylatedglucose

acceptor

nitrite

holo-EntB

serineproteaseDo: degP

soluble lytic mureintransglycosylase: slt

a shortglucan

phenylethylamineoxidase: tynA

nitrite

a leadersequence

phytate

D-alanine

glycan chain 2

superoxide

a holo-[acp]

phosphocholine

sugarphosphatase:

penicillin-bindingprotein7: pbpG

glycerol

-D-glucose

O: fdoI fdoH fdoG

aldose sugardehydrogenase: yliI

periplasmictrehalase:treA

anhydro-N-acetylmuramoyl-L-alanineamidase: amiD

DsbGoxidized

(5-L-glutamyl)-L-peptide

sugarphosphatase:

L-glutamate

gamma-glutamyltranspeptidase: ggt

a dodecanoyl-[acp]

all-trans-farnesyl

diphosphate

a myristoyl-[acp]

diphosphoundecaprenyl-[GlcNAc-MurNAc-pentapeptide]n+1

diacylglycerolpyrophosphatephosphatase:pgpB

pentakisphosphate

beta-D-glucose

UQ or MQ UQH2or MQH2

pyruvate di-trans,poly-cis-

lipid IVA

thiocyanate

L-arginine

an acyl-[acp]

DsbDoxidized

-D-glucose

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

phenylethylamine

phosphatidate

[+ 4 isozymes]

membrane-boundlytic mureintransglycosylaseA: mltA

methylglyoxal

a fatty acid

a myristoyl-[acp]

L-1-glycero-3-phosphocholine

KDO2-lipid IVA

D-Glu-DAP-D-Ala

thioesteraseII: tesB

N-acetylmuramate

pyruvate

diguanylatecyclase: yeaP

a tRNAprecursor

a holo-[acp]

trimethylamine

a single-stranded

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

alpha-L-Ara4N

a holo-[acp]

phosphatidate

a holo-[acp]

UDP-sugarhydrolase:ushA

N-acetylmuramoyl-L-alanineamidase 1: amiA

a polypeptide

a quinone

serineendoprotease,periplasmic: degQ

tetrahydrothiophene

fatty acid

di-trans,poly-cis-

-D-glucose

a dodecanoyl-[acp]

ubiquinol-8

a polypeptide

glycan chain 2

a proteinwith

oxidizeddisulfidebonds

superoxidedismutase(Mn): sodA

sulfite

coenzyme A

oxidizedcytochrome

phosphoethanolamine

a holo-[acp]

L-arginine

di-trans,poly-cis-

a shortglucan

a 2,3,4-saturated

fattyacyl-[acp]

O: fdoI fdoH fdoG

alpha-D-galactose

thiosulfate

protoheme IX

beta-D-glucosideglucohydrolase,periplasmic: bglX

penicillin-bindingprotein6: dacC

orotate

a proteinL-tyrosine

a ribonucleosidemonophosphate

trehalose

O: fdoI fdoH fdoG

nitritereductasecomplex:nrfA nrfBnrfC nrfD

a shortglucan

D-alanyl-D-alanine

a UDP-sugara reducedelectronacceptor

KDO2-lipid IVA

a holo-[acp]

asparaginaseII: ansB

diguanylatecyclase: yddV

dihydroorotate

an MDO-O-glucose

phospholipaseA1: pldA

reducedcytochrome

a peptidoglycan

di-trans,poly-cis-

a holo-[acp]

ubiquinone-8

a D-amino acid

glucose-1-phosphatase:

phosphocholine

a 2,3,4-saturated

fattyacyl-[acp]

p-aminobenzoate

pyruvate

L-aspartate

2’,3’-cyclic nucleotide2’-phosphodiesterase:cpdB

a single-stranded

peptidoglycantripeptide,

glycan chain 1

phosphate

KDO2-lipid A

a nonglucosylated

glucoseacceptor

a proteinwith

reducedsulfidegroups

5’-nucleotidase:ushA

di-trans,poly-cis-

cyclicdi-3’,5’-

guanylate

endo-1,4-D-glucanase:bcsZ

octanoate

pyruvate

undecaprenylpyrophosphatephosphatase:pgpB

DsbDoxidized

DsbCoxidized

beta-lactamase;penicillinresistance:ampC

amineoxidase (Cucontaining): tynA

a diacylglycerolpyrophosphate

glycerol

disulfideoxidoreductase:dsbC

a tRNA

L-glutamate

a holo-[acp]

a ribonucleoside

diphosphate

maltohexaose

heme o

tetrahydrothiophene1-oxide

periplasmicnitratereductase:napGnapH napCnapA napB

a peptide

a carboxylate

N-acetylmuramyl-L-alanineamidase: amiC

nitrate

thiosulfatesulfurtransferase:glpE

UDP-N-acetylmuramoyl-

L-alanyl-D-glutamyl-meso-2,6-

diaminopimelyl-D-alanyl-D-alanine

ferritin iron-storagecomplex:ftnA

an aldehyde

all transundecaprenyl

phosphate

D-glucose

a peptide

putative p-aminobenzoyl-glutmatehydrolase: abgB

D-Glu-DAP-D-Ala

malate

2-carboxymuconate

agmatine

an aliphaticamine

p-aminobenzoate

NADP+beta-D-glucose

KDO2-lipid IVA

pyrimidinenucleotidase:yjjG

phosphocholine

glycerol

thiosulfatesulfurtransferase:pspE

di-trans,poly-cis-

4-hydroxybenzoate

a proteinL-tyrosine

beta-D-galactose

cardiolipin

a beta-lactam

sugarphosphatase:

phosphatidylethanolamine-KDO2-lipidA

aldose-1-epimerase:galM

superoxidedismutaseprecursor(Cu-Zn): sodC

a 2-oxo acid

aminoacetone

diguanylatecyclase: ydeH

succinate

diphosphoundecaprenyl-[GlcNAc-MurNAc-

pentapeptide]n

L-asparagine

hydrogenperoxide

phosphoglyceroltransferase II: mdoB

lipid Adisaccharide

agmatine

diphosphate

hydrogencyanide

agmatine

L-Ara4N-modifiedKDO2-Lipid A

a carboxylate

KDO2-lipid A

fumarate

a myristoyl-[acp]

hydrogenperoxide

peptidyl-prolylcis-transisomerase;in proteinfolding:fkpA

CmtABmannitol

PTSpermease

pyruvate

DNApolymeraseIV (Y-family DNApolymerase;translesionDNAsynthesis): dinB

L-lactate

a hydroquinone

H-protein-S-(aminomethyldihydrolipoyl)

lysine

D-serinedeaminase:dsdA

L-asparaginyl-tRNAasn

a beta-ketoacyl-[acp]

L-lyxose

alkalinephosphatase:phoA

6-phospho-beta-D-

glucosyl-(1,4)-D-glucose

acetylornithinetransaminase:argD

RecFORcomplex:recOrecR recF

a trans-delta3-cis-delta5-dodecenoyl-[acp]

a citryl-[acp]

METABOLIC REGULATORSBIOSYNTHESIS

ribonucleotide

di-trans,poly-cis-

lipoatebiosynthesis

andincorporation I

deoxyadenosine adenosine

inosine deoxyuridine thymidine deoxyinosine

uridine deoxycytidine

cytidine

tRNApro

1-ethyladenine

ALCOHOLS DEGRADATION

chorismate

L-glutaminyl-tRNAgln

a (R)-3-hydroxy-cis-vaccenoyl-

PFL-deactivase:adhE

phosphoglycerate mutase,cofactor independent: gpmM

L-serine

NADPphosphatase

2-phosphoglycerate

fructoselysine6-kinase: frlD

guaninedeaminase:

L-valine

salicin-6-phosphatearbutin-6-phosphate

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]

o-succinylbenzoate-CoA ligase: menE

L-valyl-tRNAval

tryptophan synthase,alpha subunit: trpA

beta-D-ribopyranose

glycerophosphodiesterphosphodiesterase,cytosolic: ugpQ

PRPPbiosynthesis II

shikimatedehydrogenase: aroE

N-acetylneuraminatelyase: nanA

quinolinatephosphoribosyltransferase:nadC

respiration (anaerobic)

a DNA 6-methylaminopurine

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

L-aspartate

menadione

phosphatidylglycerophosphataseA: pgpA

enoyl-CoAhydratase: fadJ

Targlu-Me

glyoxylate

cytosine

NAD salvage pathway I

a lipoyl-[acp]

D-fructose

polyphosphatekinase: ppk

L-cysteinyl-tRNAcys

PhoR-Phis

selenocysteinebiosynthesis

an rRNA

GDPpyrophosphokinase: relA

L-histidine

glutamate-5-semialdehydedehydrogenase:proA

lipoate acetyltransferaseN6-(dihydrolipoyl)lysine

phosphoribosyl-ATP

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

acetol

phosphatidylserinedecarboxylase: psd

NADHpyrophosphatase:nudC

a trans hex-2-enoyl-[acp]

octanoate

a (3R)-3-hydroxyacyl-CoA

glutamate-1-semialdehydeaminotransferase:hemL

molybdenumcofactor

exopolyphosphatase: ppx

an aliphaticomega-

aminoaldehyde

formate

an aldehydeor ketone

pantothenatesynthetase: panC

a quinone

methylglyoxalreductase: dkgA

methionineand methyl-

donor-molecule

biosynthesis

formyl-CoA

FATTY ACIDS AND LIPIDS BIOSYNTHESIS

L-fucosemutarotase:fucU

pyruvate

succinyl-CoA

di-trans,poly-cis-undecaprenyl

phosphate

L-fucose isomerase: fucI

cholinedehydrogenase:betA

RESPIRATION

superpathway of arginineand polyamine biosynthesis

purine deoxyribonucleosides degradation

pyruvate

L-methionine

2-hydroxy-6-oxonona-2,4-diene-1,9-dioate

carbonicanhydrase1: cynT

trehalose

D-mannonate

GltIJKLglutamate

ABCtransporter

acetyl-CoA:acetoacetyl-CoA transferase,

alpha subunit: atoD

L-lysine

superpathway oflipopolysaccharide biosynthesis

agmatine

beta-D-galactose

phosphotyrosine-proteinphosphatase: etp

alanineracemase2, PLP-binding:dadX

D-fructose

L-valine

formate

triphosphate

D-mannitol

O-acetyl-L-serine

formatedehydrogenase:fdhF

nicotinate

DNAcontaining

a basewith lesion

3-hydroxyacyl-CoAdehydrogenase: fadJ

L-cystathionine

HMP-PPhydrolase:nudJ

L-threonine

an oxidizedcytochrome c

riboflavin

an inactiveribonucleosidetriphosphatereductase

adenosyl-cobinamidephosphate

superpathway of phenylalanine,tyrosine, and tryptophan biosynthesis

a beta-keto-cis-delta5-dodecenoyl-[acp]

N-substitutedaminoacyl-

L-Ala-gamma-D-Glu

adenine

dTDP-glucosepyrophosphorylase:rfbA

nicotinate-mononucleotideadenylyltransferase:nadD

lipopolysaccharidecore biosynthesis;phosphorylation ofcore heptose: rfaP

L-aspartateoxidase: nadB

adenosinethiamine

triphosphate

5’-phosphoribosyl-N-formylglycineamide

fructoselysine6-phosphatedeglycase: frlB

L-glutamine

indoleL-tryptophan

2-oxopentenoate

pyruvate

NAD(P)H:quinoneoxidoreductase:ytfG

3-oxoadipyl-CoA

alpha-mannosidase:mngB

peptidyl-tRNAhydrolase:pth

a tRNA

RstACheB

L-glutamate

deoxyguanosinetriphosphatetriphosphohydrolase: dgt

(R)-beta-lysine

NADHoxidoreductase: hcr

UDP-L-Ara4O C-4" transaminase:arnB

CELL STRUCTURES BIOSYNTHESIS

galactitol-1-phosphatedehydrogenase: gatD

phosphoenolpyruvate

D-serine

xylosedegradation I

a hydroquinone

tagatose-1,6-bisphosphatealdolase 1: kbaZ kbaY

3-deoxy-D-manno-

octulosonate

molybdopterinsynthase:moaE moaD

UDP-N-acetylglucosamine-2-epimerase: rffE

geranyl-diphosphate

a tRNA

C1 COMPOUNDSUTILIZATION AND

ASSIMILATION

glyceratekinase I: garK

L-aspartate

a trans tetradec-2-enoyl-[acp]

xanthine

phospho-TorR

nitrite

L-isoleucine

UDP-N-acetyl-D-mannosamine

Targlu

AtoS-Phis

L-proline

BarA-Pasp

L-ribulose

formylTHF biosynthesis I

2-deoxy-D-glucose 6-phosphate

tetrahydrofolate

dihydrolipoamideacetyltransferase:aceF

N5-carboxyaminoimidazoleribonucleotide mutase: purE

a reducedferredoxin

rRNAcontaining N6-methyladenine

guanylatekinase: gmk

L-Ala-D/L-Gluepimerase:ycjG

indole

L-tryptophan

a [citrate(pro-3S)-

lyase](citrylform)

methanol

nitric oxide

(2S)-2-isopropyl-3-oxosuccinate

adenylatecyclase: cyaA

ADP-ribose

glutathione

proteasespecific forYgjD: yeaZ

UDP-D-glucose

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:

phosphohydroxythreonineaminotransferase: serC

asparaginyl-tRNA

synthetase:asnS

L-lactaldehydedegradation(anaerobic)

pyridoxalkinase2: pdxY

a 3’-terminalunsaturated

RNaseD: rnd

EmrKY-TolC

putativemultidrug

[+ 6 isozymes]

imidazoleglycerol-phosphatedehydratase: hisB

a quinone

ATPphosphoribosyltransferase: hisG

UDP-glucose 6-dehydrogenase:ugd

GDP-mannose 4,6-dehydratase: gmd

N-hydroxyarylamineO-acetyltransferase:nhoA

7-keto-8-aminopelargonate

salvage pathways of adenine,hypoxanthine, and their nucleosides

L-glutamate

23Sribosomal

a carboxylated-biotinylated-

CheB-Pasp: cheB

tRNAser

a quinone

oxaloacetate

sulfite

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

propionyl-CoA

23S rRNA 2’-O-ribose C2498methyltransferase:rlmM

phenylacetaldehyde

menaquinone-8

molybdate

a ribosomalprotein-

N-acetyl-L-alanine

betaine aldehydedehydrogenase:betB

triphosphate

CheB-Pasp: cheB

CRISPR-associatedcomplexfor antiviraldefense:casEcasD casCcasB casA

D-galacturonateisomerase: uxaC

tagatose-1,6-bisphosphatealdolase 2: gatZ gatY

acyl-CoAdehydrogenase: fadE

phospho-RcsB

acetylphosphate

D-allosedegradation

coenzyme A

citrate lyasesynthetase:citC

dTDP-L-rhamnosesynthetase:rfbD rfbC

an (R)-3-hydroxydecanoyl-

2-oxoglutarate

dihydrolipoyltranssuccinylaseN6-(lipoyl)lysine

OuterMembrane

FerricEnterobactinTransportSystem

an oxidizednitroaromatic

compound

L-aspartate

NAD synthetase,NH3-dependent: nadE

Trgglu

trehalosedegradationII (trehalase)

NMN amidohydrolase

50Sribosomalsubunit

protein L7

orotatephosphoribosyltransferase: pyrE

D-alanine

(2S)-2-amino-3-oxo-4-phosphonooxybutanoate

L-leucyl-tRNAleu

histidyl-tRNA

synthetase:hisS

(2R,4S)-2-methyl-2,4-dihydroxydihydrofuran-

CheB-Pasp

N1-methyladenine

acetylornithinetransaminase,catabolic: astC

ferricdicitrate

spermidine

D-xylose

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

EIIAsc

mannosylglycerate

NarQ-Phis

L-threonine

L-methionine

CheB-Pasp: cheB

2-oxobutanoate

an rRNA

e14 prophage;site-specificDNArecombinase:pinE

Tapglu

freemethionine-(R)-sulfoxidereductase:yebR

trehalosebiosynthesis I

delta(2)-isopentenylpyrophosphatetRNA-adenosinetransferase: miaA

phosphatidylserinesynthase: pssA

acetyl-CoA

L-threonine

hybrid-cluster

proteinox

prephenate

ubiquinol-8

alpha-xylosidase:yicI

a myristoyl-[acp]

KASI: fabB

Tsrglu

dihydroneopterinphosphate

PhoB-Pasp

spermidine

GTPaseassociatedwith the50S subunitof theribosome:hflX

2-dehydropantolactone

phytate

acetoacetyl-CoAtransferase:atoD atoA

pyridoxine5’-phosphateoxidase:pdxH

a biotinylatedBCCP

(monomer)

formate

oxaloacetate

kynurenine

a protein

glyoxalaseI: gloA

6,7-dimethyl-8-ribityllumazinesynthase: ribE

methylglyoxalreductase: dkgB

a BCCP(monomer)

DNApolymeraseII: polB

TorS-Pasp723

glutamyl-tRNAreductase: hemA

succinyl-CoA

chorismate

2-octaprenyl-6-methoxy-

1,4-benzoquinol

dimethylbenzimidazole

pyruvateformate-lyase: pflB

L-lactatedehydrogenase:

quinolinate

maltotetraose

laurate

tRNApseudouridine65 synthase: truC

peptidoglycantripeptide-

Lpp crosslink

endonucleaseIV: nfo

RNApyrophosphohydrolase:rppH

xyloseisomerase:xylA

deoxyribodipyrimidinephotolyase(photoreactivation): phr

UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelateligase: mpl

NADkinase: nadK

tetrahydrodipicolinate

a purineribonucleoside

putrescine

an oxidizedelectron

acceptor

rhamnosedegradation

glycerol-3-phosphatedehydrogenase,biosynthetic: gpsA

alkanesulfonatemonooxygenase,FMNH2-dependent: ssuD

beta-D-glucose

amidophosphoribosyltransferase: purF

UvrABCNucleotideExcisionRepairComplex:uvrB uvrCuvrA uvrD

RecG, DNAhelicase,resolutionof Hollidayjunctions,branchmigration:recG

autoinducer AI-2 biosynthesis

glutathione S-transferase:gst

(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran

2-dehydro-3-deoxygalactonatekinase: dgoK

diacetylreductase

cob(I)alamin

guanylatecyclase

dihydrolipoyltranssuccinylase N6-(S-succinyldihydrolipoyl)lysine

glyoxylate

L-ornithine

trehalose-6-phosphatesynthase:otsA

L-selenocysteine

quinoneoxidoreductase: qor

pyruvate

D-mannitol

2,3-dihydro-2,3-dihydroxybenzoatedehydrogenase: entA

D-glucuronate

4-hydroxybenzoate

D-lactatedehydrogenase:ldhA

diphosphate

L-threoninehomoserine

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

nicotinate mononucleotide

L-isoleucine

NADHdehydrogenase(quinone)

DNAligase: ligA

L-alanine

D-ribulose

ThiS-COAMP

chorismate

L-aspartate

triphosphate

a reducedglutaredoxin

acetyl-CoA

oxaloacetate

acetylornithinedeacetylase: argE

superpathway of glycolysis, pyruvatedehydrogenase, TCA, and glyoxylate bypass

all-trans-farnesyldiphosphate

a peptide

3-phenylpropionate

tRNAcontaining N1-methylguanine

a tRNAcontaining

glutamylatedqueuosine

acetyl-CoA

quinolmonooxygenase:ygiN

tRNAcontainingqueuine

beta-D-glucose

L-aspartateL-glutamate

glutathione

a trans dodec-2-enoyl-[acp]

tRNAasp

D-alloseD-fructuronateD-gluconate

D-ribose

methanol

ClpP serineprotease:clpP

glycinebetaine

poly-beta-1,6-N-acetyl-D-glucosamineN-deacetylase:pgaB

thioglycolate

diphosphate

D-fructose

cobinamide-Pguanylyltransferase: cobU

cysteinesynthase B: cysM

cobinamideadenosyltransferase:btuR

crotonobetainyl-CoA

hydratase: caiD

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

KASII: fabF

L-serine

2-oxo-3-hydroxy-4-phosphobutanoate

[GlnK]

glutamyl-tRNAsynthetase: gltX

lipoatesynthase:lipA

glycogensynthase:glgA

predictedAutoinducer-2 kinase: lsrK

5-ketogluconate

2-phosphoglycerate

a mRNA

an unknownC3 fragment

2-amino-3-ketobutyrate

CoA ligase: kbl

enolase: eno

propionatekinase: tdcD

lysine 2,3-aminomutase:yjeK

formyltetrahydrofolatedeformylase: purU

3-phosphoglycerate

glyceratekinaseI: garK

a palmitoyl-[acp]

L-glycerol 3-phosphate

pantothenate

dTDP-glucosepyrophosphorylase2: rffH

chorismatelyase: ubiC

3-phosphoglycerate

2-ketobutyrateformate-lyase: tdcE

superpathway ofphenylethylamine

degradation

a 3-oxo-dodecanoyl-[acp]

dihydromonapterin-triphosphate

a dodecanoyl-[acp]

a deamineatedamine donor

a reducedcytochrome c

maltotriose

L-galactonate

chorismate

alanine racemase2, PLP-binding: dadX

L-alanine

(R)-pantolactone

thiaminediphosphate

an alcohol

2-oxoglutarate

phosphate

succinate

D-lactate

a tRNAcontaining 7-

a tRNA

UDP-D-galactose

D-malatedehydrogenase(decarboxylating): yeaU

D-4-hydroxy-2-keto-

glutarate

glutamine synthetaseadenylyltransferase:

folate polyglutamylation I

fumarase A: fumA

L-aspartate

L-serine

L-seryl-tRNAser

formaldehydedehydrogenase,glutathione-dependent: frmA

L-serine

3-phosphoserineaminotransferase: serC

lipoamide

KASI: fabB

L-aspartate

D-fructose

a tRNA

L-xylulose

D-alpha,beta-D-heptose-7-phosphate

4-(cytidine 5’-diphospho)

SucB-S-succinyldihydrolipoate

cellobiosechitobiose

tRNA 2-selenouridinesynthase: ybbB

hepta-acylatedKDO2-lipid A

methyl red

a tRNA

selenocysteinelyase: sufS

a phosphatemonoester

beta-D-glucose

Trgglu-Me

allantoate

pyruvate

adeninephosphoribosyltransferase: apt

GTPcyclohydrolaseII: ribA

ribonucleosidehydrolase 2(pyrimidine-specific): rihB

L- and D-methionineuptake ABCpermease

UDP-N-acetyl-D-mannosaminuronicaciddehydrogenase: rffD

2-amino-3-oxobutanoate

tRNAMet cytidineacetyltransferase:tmcA

L-alanyl-tRNAala

nitrite

glutamineABC

transporter

predicted L-xylulose 5-phosphate3-epimerase:sgbU

D-glucosyl-lipopolysaccharide

glutaminase A

D-4’-phosphopantothenate

reducedflavorubredoxin:norV

L-isoleucine

glycyl-tRNAsynthetase:glyQ glyS

diaminopimelateepimerase: dapF

pseudouridine

thiamin ABCtransporter

ADP-sugarpyrophosphorylase:nudE

oligopeptideABC

transporter

alpha-ribazole

predictedpseudouridine5’-phosphateglycosidase:pscG

D-alloseABC

transporter

YgaZ/YgaHL-valineexportercomplex

2-thiouridylate

AMINO ACIDS DEGRADATION

malonyl-CoA-ACPtransacylase: fabD

(R)-methylmalonyl-

acetoacetatedegradation

(to acetyl CoA)

tRNA m6A37methyltransferase:yfiC

uridylyl-removingenzyme: glnD

tRNAasn

biosynthesisof 4-amino-4-deoxy-L-arabinose-

modified lipid A

L-methioninesulfoxide

UDP-D-galactose

a peptideantibiotic

carnitine-CoAligase: caiC

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

a ribosomalprotein-

L-alanine

pyridoxine5’-phosphate

synthase:pdxJ

iron dicitrateABC

transporter

3-(3-hydroxyphenyl)propionate 2-hydroxylase:mhpA

a 3-oxo-palmitoyl-[acp]

4-hydroxy-2-ketovaleratealdolase: mhpE

AMINO ACIDS BIOSYNTHESIS

isocitratedehydrogenasekinase: aceK

L-carnitine

L-methionine

superpathway of N-acetylglucosamine, N-acetylmannosamine

and N-acetylneuraminate

degradation

RNase R: rnr

ribose ABCtransporter

D-glycerate

hypoxanthine

a phospholipid

L-alanine

L-cysteine

a macrolideantibiotic

SucB-lipoate

3-phospho-hydroxypyruvate

diacylglycerolkinase: dgkA

acetaldehyde

KDO2-lipid IVA

vitaminB12 ABC

transporter

adenosine

dipeptideABC

transporter

thiosulfateABC

transporter

GDP-alpha-D-glucose

a proteinL-glutamate

an apo-[acp]

taurinedegradation IV

AceF-lipoate

L-phenylalanine L-tryptophan

L-tyrosine

TorS-Phis850

5’-deoxyadenosine

L-cysteine

lipid A-core 1-diphosphate

ClpXP:clpX clpP

L-tartrate

16S rRNAcontaining

O-antigenligase: rfaL

KDO2-lipid A

D-tyrosyl-tRNATyr

a sugar

pyruvateoxidationpathway

H-Gcv-protein-

(lipoyl)lysine

protein involvedin KdoIIIattachment duringlipopolysaccharidecore biosynthesis: rfaZ

multidrug

pyridoxamine-oxaloacetatetransaminase

a maltodextrin

enterobactinsynthasemultienzymecomplex: entEentF entD entB

leucyl-tRNAsynthetase:

poly(A)polymeraseI: pcnB

resolvasome:ruvA ruvB ruvC

arginyl-tRNAsynthetase:

tyrosyl-tRNAsynthetase:

S-adenosyl-L-methioninamine

cellobiosesalicinarbutin

an alkylphosphate

oxamate

cis-vaccenate

S-methyl-L-methionine

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

quinolinatesynthase: nadA

2-acetolactate

holo-[acyl-carrier-protein]synthase:acpS

lysine/arginine/ornithine

ABCTransporter

disulfideisomerase,periplasmic:dsbG

arabinoseABC

transporter

SucB-lipoate

arginineABC

transporter

a carboxylate

ArcAB Two-Component

SignalTransduction

System

succinate

pantothenatekinase: coaA

RNApolymerase,core enzyme:rpoBrpoC rpoA

ethanoldegradation

beta-ketoacyl-[acyl-carrier-protein]reductase:fabG

N-succinyl-L,L-2,6-

diaminopimelate

glucokinase:glk

gamma-glutamylputrescineoxidase: puuB

beta-D-ribofuranose

tRNAIle-lysidinesynthetase:tilS

NarUYgfU

L-methionine-(R)-S-oxide

glycolate

cyanate

di-trans,poly-cis-decaprenyldiphosphate

mannitol-1-phosphate 5-dehydrogenase:mtlD

ITPase: yjjX

arylsulfatase:aslA

quinatedehydrogenase:ydiB

acetyl-CoAbiosynthesis

(from pyruvate)

uracil

NarP-Pasp

KASIII: fabH

ribose 1,5-bisphosphokinase:phnN

L-glutamine

phenylalanyl-tRNA

synthetase:pheT pheS

(R)-methylmalonyl-CoA

molybdopteringuaninedinucleotidesynthase: mobA

coenzyme B12

tetraphosphate

deoxyuridine

fused predictedacetyl-

CoA:acetoacetyl-CoA transferase:

alpha subunit/beta subunit: ydiF

superpathway ofacetate utilization

and formation

L-glutamate

4-aminobutyrate

a trans-2-enoyl-CoA

a proteinL-cysteine

Nitrogen RegulationTwo-Component System

glutathionebiosynthesis

L-ribulose 5-phosphate 4-epimerase: araD

putrescine

fructosebisphosphatealdolaseclass II: fbaA

uracil

NADH pyrophosphatase: nudC

ClpAXP:clpXclpA clpP

tryptophansynthase:trpB trpA

thymidylatesynthase:

sulfateadenylyltransferase:cysD cysN

beta-L-fucose

KDO2-lipid A

octyl alpha-D-glucopyranoside

L-methionine

an alcohol

L-proline

2,3-dihydroxybenzoylserine

AROMATIC COMPOUNDS DEGRADATION

acetate

xanthosine

imidazoleglycerolphosphatesynthase:hisF hisH

histidinaldehydrogenase:hisD

pyridoxine

a maltodextrin

predictedpseudouridinekinase: pscK

trans-aconitatemethyltransferase: tam

glutathione S-transferase:yfcG

trans-2-decenoyl-ACPisomerase:fabA

pyrimidinedione5’-phosphate

CheA-Phis

putrescineaminotransferase: ygjG

D-gluconate

ethanolamineammonia-lyase:eutC eutB

cyanate

spermidinesynthase:speE

xanthosinetriphosphatepyrophosphatase:rdgB

a DNAcyclobutadipyrimidine

L-2,3-dihydrodipicolinate

putrescine

D-cysteine

L-glutamate

ornithinecarbamoyltransferase:argF

UDP-N-acetylmuramate-alanine ligase: murC

beta-1,6-galactofuranosyltransferase: wbbI

2-oxopent-4-enoatehydratase:mhpD

dehydrogenase

a beta-hydroxy cisdelta5-dodecenoyl-[acp]

2-hydroxy-6-ketonona-2,4-dienedioatehydrolase:mhpC

6-phosphofructokinase I: pfkA

acetyl-CoA

phosphateABC

transporter

As3H3O6

citrate

phosphoglycerate kinase: pgk

selenite

pyruvate

fumarase B: fumB

pyridoxamine

a tRNA

L-arabinosedegradation I

tRNApseudouridine

inosine

nicotinamide

guanosine-5’-triphosphate,3’-diphosphatepyrophosphatase: gpp

adenosylmethioninedecarboxylase: speD

5’-deoxyadenosine

5-phospho-beta-D-ribosyl-amine

CDP-diglyceridesynthetase: cdsA

phosphatidylglycerophosphatase C

pyruvate

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

enolase: eno

fructosebisphosphatealdolaseclass I: fbaB

fructose 6-phosphatealdolase1: fsaA

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

thiaminediphosphate

tRNAArg2

AcrAD-TolCmultidrug

nicotinate-mononucleotideadenylyltransferase: nadD

NMN nucleosidase

4-nitrobenzaldehyde

lipoate

N5-carboxyaminoimidazoleribonucleotide

diacetylchitobiose-6-phosphate

methylglyoxalsynthase: mgsA

triphosphate

3,4-dihydroxy-2-butanone 4-phosphatesynthase:ribB

OmpR-Pasp

sulphurdioxide

a polypeptide

cobinamide kinase: cobU

spermidineputrescine

phosphoribosylanthranilateisomerase: trpC

guanosine

L-aspartate

beta-hydroxyacyl-ACPdehydratase:fabZ

a holo-[acp]

L-arginino-succinate

prephenatedehydrogenase: tyrA

dihydrouracil

S-lactoylglutathionehydrolase: yeiG

an L-1-phosphatidylserine

16S-rRNAs

1-amino-propan-2-ol

galactaratedehydratase: garD

a hexanoyl-[acp]

ZnuA/ZnuB/ZnuC ABCtransporter

UDP-L-Ara4O

L-galactonate

menadiol

2-oxobutanoate

a ThiSsulfur-carrier

protein

methylglyoxal

allantoindegradation

IV (anaerobic)

an apo-GcvHprotein

2-oxoglutarate

H-Gcv-protein-(dihydrolipoyl)lysine

L-serineL-threonine

an mRNA with 5’-monophosphate

L-rhamnoseL-lyxose

D-sorbitol

cis-aconitate

putrescineABC

transporter

ferredoxinNAD+reductase:hcaD

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

pyridoxal

sulfatereduction I

(assimilatory)

formyl-CoAtransferase: frc

AcrAB-TolCmultidrug

N-ethylmaleimide

a tRNAArg2containinginosine atthe wobble

position

L-idonate 5-dehydrogenase:idnD

2-dehydropantoate2-reductase: panE

4-hydroxy-L-threoninephosphatedehydrogenase,NAD-dependent: pdxA

erythrose 4-phosphatedehydrogenase:epd

ZraSR Two-Component

SignalTransduction

System

carboxylesterase:bioH

phenylacetate

OTHER BIOSYNTHESIS

ornithine decarboxylase,biosynthetic: speC

UDP-GlcA C-4"-decarboxylase:arnA

a 2,3,4-saturated

fattyacyl-[acp]

UDP-[N-acetyl-D-

glucosamine]n

CheB-Pasp: cheB

gamma-glutamylkinase-GP-reductasemultienzymecomplex:proA proB

4-aminobutyrateaminotransferase: puuE

TorS-Phis443

CheB-Pasp: cheB

1,4-alpha-glucanbranchingenzyme:glgB

succinate

aspartate 1-decarboxylase:panD

dihydrodipicolinatereductase: dapB

isochorismate

L-serine

an rRNA

cyclopropanefatty acylphospholipidsynthase: cfa

malatesynthaseG: glcB

phosphopantetheineadenylyltransferase: coaD

an aldehyde

2-O-alpha-mannosyl-D-glycerate transportingphosphotransferase

system

putrescine

selenide

phosphate

5-dehydro-4-deoxy-D-glucarate

D-glycerate

CcmABCDEprotoheme

IX ABCtransporter

L-fucose

propionyl-CoA

UDP-N-acetyl-D-

glucosamine

branchedchain aminoacids ABCtransporter

bicarbonate

a tRNA

cyclic-AMP

NADP(H)-dependent FMNreductase: ssuE

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

isomerase: idi

ethanol

NarX-Phis

N-6-isopentyl

adenosine-37 tRNA

a cis-vaccen-2-enoyl-[acp]

glutamate-pyruvateaminotransferase:alaB

glucosyl-heptosyl3-

KDO2-lipid A-

phosphate

glutathionedisulfide

dihydroneopterinaldolase: folB

2-dehydropantoyl-lactone reductase(B-specific)

phosphoenolpyruvatecarboxykinase (ATP): pck

L-threo-3-phenylserine

propionyl-P

tRNAlys

EIITre

23S rRNA 2’-O-ribose G2251methyltransferase:rlmB

acetyl-CoA

melibiose

HMP-PPhydrolase/ thiaminpyrophosphatehydrolase: nudJ

p-aminobenzoate

a (3R)-3-hydroxyacyl-[acp]

UhpB-Phis

fumaraseA: fumA

ethyl-(2R)-methyl-(3S)-

hydroxybutanoate

pyruvatekinaseI: pykF

multifunctional 2-keto-3-deoxygluconate

6-phosphatealdolase and 2-keto-4-hydroxyglutarate

aldolase andoxaloacetate

decarboxylase: eda

BarA-Phis

fumarate

S-ureidoglycolate

D-glucose

a nucleicacid with aterminal 5’-phosphate

L-lysine

a damagedDNA

(purine orpyrimidine)

cytosine

glycogenbiosynthesis I (from

ADP-D-Glucose)

a DNAsegment

alpha-L-arabinose

gluconokinaseI: gntK

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate

rRNAcontaining 2’-O-methylcytosine

a thioredoxin

glycolaldehyde

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

inosine

fructose 6-phosphatealdolase2: fsaB

tartronatesemialdehydereductase: garR

dTDP-fucosamineacetyltransferase:rffC

alpha-D-glucose

dTDP-glucose4,6-dehydratase2: rffG

toxin ofthe YafQ-DinJ toxin-antitoxinsystem: yafQ

succinatesemialdehyde

6-phosphofructokinaseI: pfkA

N-succinyl-L-diaminopimelatedesuccinylase:dapE

biotin

2-thiouridylate

homoserinekinase: thrB

anaerobicnucleoside-triphosphatereductaseactivatingsystem: fprnrdG nrdD

anhydro-N-acetylmuramicacid kinase: anmK

orotate

choline

succinyl-CoA synthetase: sucC sucD

oleate beta-oxidation

beta-D-glucose

fatty acid beta-oxidation I

serineacetyltransferase:cysE

ferriccoprogen

H-Gcv-protein-

(lipoyl)lysine

acetaldehyde

lipid kinase:yegS

L-asparagine

a tRNA

phosphoribosyl-ATPpyrophosphatase: hisI

6-carboxy-5,6,7,8-tetrahydropterin

BaeR-Pasp

histidinol-phosphatase:hisB

mannose-6-phosphateisomerase: manA

(deoxynucleotides)(m)

1,4-dihydroxy-2-naphthoyl-CoA

a nucleoside

guanosine-3’,5’-bis(diphosphate) 3’-diphosphatase: spoT

D-alanine-D-alanineligase B: ddlB

7,8-dihydropteroate

crotonobetainyl-CoA

tRNAsec

a 3-oxo-hexanoyl-[acp]

a glycerophosphodiester

UDP-galactose biosynthesis(salvage pathway from

galactose using UDP-glucose)

an ADP-sugar

GTPpyrophosphokinase: relA

maltose

glutaminase:yneH

OuterMembrane

FerricCitrate

TransportSystem

fosmidomycin

L-idonate

dihydrodipicolinatesynthase: dapA

xanthine

methyltransferasefor 50S ribosomalsubunit proteinL11: prmA

putrescine/spermidine

ABCtransporter

selenate

xanthosine

glutamate racemase: murI

glycerol-3-P ABC

transporter

deoxyuridinekinase: tdk

FtsE/FtsX ABCtransporter

glycine

3-chloro-D-alaninedehydrochlorinase:dcyD

potassiumion P-typeATPase

transporter

precursor-Z

pyruvateoxidase:poxB

dehydrogenase

diaminopimelatedecarboxylase: lysA

cytidine

2-octaprenylphenol

thiaminpyrophosphatehydrolase: nudJ

low-specificityL-threoninealdolase: ltaE

DNA withlesion

catabolicthreoninedehydratase: tdcB

lipoate

a citryl-[acp]succinylglutamatedesuccinylase: astE

pyridoxal

fumarase A: fumA

gamma-butyrobetaine

AP siteremoved

from DNA

a drug

succinyl-CoA

ammoniumhydroxide

a FeS-protein

D-aminopropanoldehydrogenase:gldA

superpathway of KDO2-lipid A biosynthesis

2-methylcitratecycle I

L-aspartate

citratesynthase: gltA

serineactivatingenzyme: entF

cadaverine

pyruvateformate-lyase: tdcE

pyruvatedehydrogenasemultienzymecomplex: lpdaceF aceE

acetylglutamatekinase: argB

2-hydroxyglutarate

mannose-6-phosphateisomerase:manA

propionate

vitaminB12 outermembranetransportcomplex

succinate

AlsR-allose

a DNAadenine

DNA withlesion

spermidine

L-tryptophan

S-formylglutathionehydrolase: yeiG

dihydropteridinereductase: nfsB

L-alanine

ThDPadenylyltransferase

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

histidineABC

transporter

KDOIII-lipopolysaccharide

methanol

a 3-oxo-decanoyl-[acp]

an acyl-CoA

taurine ABCtransporter

glucosamine-6-phosphatedeaminase: nagB

CheY-Pasp

Tsrglu-Me

RcsB-phosphate

tyrosineaminotransferase:tyrB

ADP-L-glycero-D-mannoheptose-6-epimerase: rfaD

methylerythritolphosphate pathway

phosphoenolpyruvate

glyceratekinaseII: glxK

D-gluconate

a reducedferredoxin

acetaldehyde

diadenosinetetraphosphatase:apaH

aminomethyltransferase: gcvT

Osmoregulatory Two-ComponentSignal Transduction System

Lipid A-core

pryidoxinetranporter

L-methionine

lipoate

proteindisulfideisomerase:dsbC

uroporphyrinogendecarboxylase: hemE

GDP-alpha-D-mannose

phosphoribosyl-formamido-carboxamide

deoxyguanosine

isethionate

6-carboxy-5,6,7,8-tetrahydropterinsynthase: queD

cadaverine

purine nucleotides de novo biosynthesis I

spermidinesynthase:

glutaminase B

N-acetyl-L-glutamate 5-

semialdehyde

succinylornithinetransaminase: astC

pyruvatekinaseII: pykA

fumaraseB: fumB

L-tyrosine

a malonyl-[acp]

adenylyl-[glutaminesynthetase]

glycerol

1,6-anhydro-N-acetylmuramicacid recycling

phenylacetyl-CoA

3,5-tetradecadienoate

RstB-Phis

3-phenylpropionate-2’,3’-dihydrodioldehydrogenase: hcaB

chorismate

L-glutamine

D-gluconate

acetyl-CoA

transaldolaseA: talA

multidrug

modulatorof RNase IIstability: gmr

ZraS-Phis

ethanol

malonyl-CoA

uridylyl-[GlnK]

ADP-L-glycero-

D-manno-heptose

EIIGat

L-seryl-AMP

acetaldehyde

L-rhamnulosekinase: rhaB

superpathway of methylglyoxal degradation

L-tryptophan

beta-D-glucose 1-phosphate

dihydrolipoamideL-leucine

molybdopteringuanine

dinucleotide

allantoinase:allB

proteinkinase: yeaG

3-dehydroquinate

L-seryl-AMP

diphosphate

NAD-dependentdihydropyrimidinedehydrogenase:yeiA yeiT

pyridine nucleotidetranshydrogenase

enterochelinesterase: fes

L-arginine

D-glycerate

methylmalonyl-CoAdecarboxylase: scpB

octulosonate

glycolate

L-glutamate

acetyl-CoA

hydroquinone

L-glutamate

L-aspartate

L-1,2-propanediol

cyclopropanefatty acid

(CFA)biosynthesis

BarA-Phis

cAMPphosphodiesterase:cpdA

S-formylglutathione

a tRNAprecursor

superpathwayof menaquinone-8 biosynthesis

pimeloyl-CoA

PhnC/PhnD/PhnEalkylphosphonateABC transporter

PhoRB Two-Component

SignalTransduction

System

XylF/XylG/XylH

xylose ABCtransporter

4-carboxyaminoimidazoleribonucleotide

glyoxylate

a tRNA

deoxycytidine

beta-D-glucose

acetatekinase B: ackB

lipidhydroperoxideperoxidase: tpx

2-C-methyl-D-erythritol-2,4-

cyclodiphosphate

alpha-L-fucose

a citratelyase holo-[acyl-carrier

protein]

GltIJKLglutamate

ABCtransporter

propionyl-CoA

isovaleryl-CoAdehydrogenase/ predictedacyl-CoAdehydrogenase:aidB

phosphorylatedserine/threonine

kinase HipA

glucosamine

phosphoglycolatephosphatase: gph

ThiI: thiI

seryl-tRNAsynthetase:serS

L-valine

L-carnitinyl-CoA

colanic acid

methionineadenosyltransferase:metK

cyanase:cynS

5’-deoxyadenosine

L-ornithine

GMP-N-epsilon-(N-alpha-acetyl lysinemethyl ester) 5’-phosphoramidate

methylglyoxal

3-mercaptopyruvate

N-acetylneuraminate

glutaminesynthetase:glnA

D-alanine

oxaloacetate

L-methionine

glycogenphosphorylase-limit dextrinalpha-1,6-glucohydrolase:glgX

lactose

D-ribose

EvgS-Phis

L-lactaldehyde

L-glutamate

sulfite reductase-(NADPH): cysI cysJ

cadaverine

a beta-D-glucuronoside

3-oxoacyl-CoA

protoporphyrinogen IX

D-lactate

L-glutamate

N-acetylglucosamine-6-phosphatedeacetylase: nagA

acetolactatesynthase: ilvMilvG_2 ilvG_1

superpathwayof hexuronide

and hexuronatedegradation

L-homocysteine

phosphoenolpyruvate

pyruvatedehydrogenase:aceE

enoyl-ACP reductase(NADPH): fabI

a DNA withalkylatedadenine

enoyl-ACP reductase(NAD[P]H): fabI

RNasePH: rph

L-ascorbate

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

7,8-diaminopelargonicacid synthase: bioA

D-ribose

uracil-DNA-glycosylase:ung

a 2’,3’-cyclic-phosphate-terminated

KDO2-(palmitoleoyl)

-lipid IVA

Mg2+Co2+Ni2+

pyruvatekinase II: pykA

orotidine-5’-phosphate

alpha-L-arabinose

KASI: fabB

phosphoribosylformylglycinamidesynthetase: purL

carbamate

a pyrimidine

N-succinyldiaminopimelate-aminotransferase: argD

threoninesynthase:thrC

a protein

L-citrulline

acetatekinase: ackA

asparaginaseI: ansA

an rRNA

dTDP-D-fucosamine

superpathway of glycolysisand Entner-Doudoroff

acetate

malate

coenzyme A

palmitoleate

16S rRNA m7G527methyltransferase:rsmG

ThiS-COAMP

5-phosphoribosyl-N-formylglycineamidine

phosphoribulosylformimino-AICAR-P

pyridoxamine

glycerol

nitrite

psicoselysine

L-phenylalanine

KdpDE Two-Component

SignalTransduction

System

EIINag

argininosuccinatesynthase: argG

dethiobiotin

acetyl-CoAcarboxyltransferase:accD accA

chloride

undecaprenyl-N-acetyl-alpha-

D-glucosaminyl-pyrophosphate

L,D-transpeptidaseYcbB: ycbB

1-deoxy-D-xylulose

a trans-2-enoyl-CoA

a nucleotide

beta-D-glucuronidase:uidA queuine

altronateoxidoreductase:uxaB

a tRNA

a non-methylatedribosomalprotein L11

tRNAcontaininguridine at

position 54

pyridoxaltransporter

YejA/YejB/YejE/YejF ABCtransporter

pyruvate

GDP-L-fucose

an (R)-3-hydroxybutanoyl-

ABCtransporter

ADP-L-glycero-

D-manno-heptose

a quinone

L-serine

ADP-D-glucose

protoheme IX

isochorismate

aminodeoxychorismatelyase: pabC

pyridine nucleotidetranshydrogenase,soluble: sthA

formaldehyde

an RNA

glutathioneredox

reactions II

L-leucyl-tRNAleu

N-acetyl-D-mannosamine-6-phosphate

Tsrglu

shikimate

L-carnitinyl-CoA

lipoylateddomain

2-cis,6-trans,10-trans-geranylgeranyldiphosphate

D-ribose

L-ribulose 5-phosphate4-epimerase:araD

transaldolaseB: talB

maltose ABCtransporter

a reducednitroaromatic

compound

L-methionine

di-trans,poly-cis-octaprenyldiphosphate

S-lactoyl-glutathione

L-glutamate

phosphatidylglycerol-prolipoproteindiacylglyceryltransferase; amajor membranephospholipid: lgt

glutamate-putrescineligase: puuA

putativenucleoside (IDP)diphosphatase:yibQ

pyrazinoate

adenosylcobalamin salvagefrom cobinamide and cobalamin

Lipid A-core

guanine

diphosphate

dihydroneopterinmonophosphatedephosphorylase

L,L-diaminopimelate

nitrite

proline ABCtransporter

salicin-6-phosphate

ureidoglycine

bifunctionalbiotin-[acetyl-CoA-carboxylase]ligase andtranscriptionalrepressor: birA

alpha-N-acetylneuraminate

a single-stranded

aliphaticsulfonate

ABCtransporter

D-carnitinyl-CoA

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

endonucleaseIII; specific forapurinic and/or apyrimidinicsites: nth

3-hydroxypropionate

KASII: fabF

adenosine

acetyl-CoA

adenosine

N2-succinyl-L-glutamate 5-semialdehyde

N-acetylneuraminate

phosphoadenosine-5’-phosphosulfate

glycinecleavagesystem:gcvT gcvHgcvP lpd

S-methyl-5’-thioadenosine

UDP-galactopyranosemutase: glf

a peptide

cellobiose-6-phosphatesalicin-6-phosphatearbutin-6-phosphate

a stabilizedRecA

filament-DNA

complex

L-lactaldehyde

L-arginine

N-acetylglutamyl-phosphate

methylcitratesynthase: prpC

3-hydroxybutyryl-CoA epimerase: fadJ

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

3-demethylubiquinol-8

allulose-6-phosphate3-epimerase:alsE

EIISga

pyruvate

23S rRNA m2A2503methyltransferase:rlmN

NtrB-P

N-succinyl-2-amino-6-ketopimelate

undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-

4-acetamido-4,6-dideoxy-D-galactose

pyrophosphate

N2-succinyl-L-ornithine

D-lactatedehydrogenase: dld

GDP-fucosesynthase: fcl

serine/threonineproteinkinase: rdoA

galactokinase: galK

a phosphoprotein

D-allose

tRNAcontaining a

thionucleotide

L-methionine

superpathway ofD-glucarate and

D-galactaratedegradation

PENTOSE PHOSPHATE PATHWAYS

D-altronate

EnvZ-Phis

3-(3-hydroxyphenyl)propionate

pyruvate dehydrogenase: aceE

L-rhamnonate

ThiI: thiI

L-histidine

diaminetransaminase:ygjG

a thioredoxin

tRNAthr

3-phospho-L-serine

D-arabinose

FMNphosphatase:ybjI

D-tagaturonate

pre-crRNA

D-glucosamine1-phosphate

2-oxobutanoate

2-phosphoglycerate

homoserine

thiosulfatesulfate

argininosuccinatelyase: argH

glycine

4-hydroxyphenylpyruvate

L-alanine

tetrahydrofolate

TatABCEproteinexport

complex

ribonucleaseII: rnb

L-glutamate

phenylethylamine

3-dehydro-shikimate

tRNAleu

acetate kinase: ackA

hydrogenase4: hyfH hyfFhyfE hyfDhyfC hyfBhyfA hyfG hyfI

glycine

citrate

3-isopropylmalatedehydrogenase:leuB

2,3-diaminopropionateammonia-lyase: ygeX

L-selenocysteinyl-tRNAsec

argininedegradation

II (ASTpathway)

bond cleavage

a tRNA

(R)-malate

D-mannonatedehydratase:uxuA

D-tyrosine

fucosedegradation

ammonia

acetyl-CoA

(2R,3S)-3-isopropylmalate

acetyl-CoA

nicotinate adeninedinucleotide

a [citrate(pro-3S)-

lyase](acetylform)

XTPase: yjjX

tryptophandegradation

II (viapyruvate)

putativephenylacetate-CoA oxygenase:paaE paaDpaaC paaB paaA

EIIGut

lipoate acetyltransferaseN6-(lipoyl)lysine

acetaldehydedehydrogenase:aldB

acetaldehyde

non-specific ion/solutemaltose

L-histidine

glutaredoxinreductase

L-arginyl-tRNAarg

3-chloro-D-alanine

S-adenosyl-L-methioninecycle I (prokaryotic)

L-glutamine

5-amino-levulinate

a 2,3,4-saturated

fattyacyl CoA

cardiolipin

ureidoglycolase:allA

pyruvatesynthase

alpha-D-mannose 1-phosphate

serine/threoninekinaseHipA: hipA

EntS-TolCEnterobactin

EffluxTransportSystem

L-cysteinedesulfhydrase:tnaA

D-allose-6-phosphate

guanosine

2-deoxy-D-glucose

protoheme IX

hydroxymethylpyrimidine

bond cleavage

pyruvate

tagatose-1,6-bisphosphate

7-alpha-hydroxysteroiddehydrogenase:hdhA

a sugarphosphate

SECONDARY METABOLITES DEGRADATION

L-glutamate

N-(5’-phospho-L-ribosyl-formimino)-5-amino-1-(5’-phosphoribosyl)-4-imidazolecarboxamideisomerase: hisA

histidinoldehydrogenase:hisD

tyrosinephosphatase:wzb

2-methylisocitratelyase: prpB

L-lactaldehyde

N-acetylmuramicacid 6-phosphateetherase: murQ

D-gluconate

3-keto-L-gulonate 6-phosphatedecarboxylase:ulaD

tRNA(m5U54)methyltransferase:trmA

D-glucaratedehydratase:gudD

acetate

2-O-alpha-mannosyl-D-glyceratedegradation

mannose-1-phosphateguanylyltransferase:cpsB

mureintripeptide

ABCtransporter

superpathway ofalanine biosynthesis

glycerol

an alkanesulfonate

2-oxoglutarate

a deoxynucleotideD-alanine

monophosphate

aryl carrierprotein/ serine

activatingenzyme

superoxide

glycolate

4-diphosphocytidyl-2C-methyl-D-erythritolsynthase: ispD

dihydroxyacetone phosphate

N-acetylmuramate6-phosphate

D-galactose

PhoB-Pasp

prephenatedehydratase: pheA

a drug

a reducedferredoxin

diamine

acetoacetate

beta-D-galactose

formate

a ThiS-ThiI acyl-disulfide

resolution ofrecombinational

junctionformation of twointact strands

deoxyadenosine

fructoselysine-6-phosphate

TCA CYCLE

dTDP-4-dehydrorhamnose3,5-epimerase: rfbC

glycine betainebiosynthesis

I (Gram-negativebacteria)

D-glucose

deoxyguanylatekinase: gmk

bond cleavage

S-adenosylmethionine:tRNAribosyltransferase-isomerase: queA

propionatekinase: ackA

fumarate

L-methionine-(S)-S-oxide

a phosphoprotein

pyruvate

a 3-oxo-meristoyl-[acp]

thymidinekinase: tdk

D-sedoheptulose7-phosphateisomerase: lpcA

coenzyme A

2-keto-3-deoxy-L-

rhamnonate

mixed acid fermentation

ArcB-Phis717

phosphate acetyltransferase: pta

beta-N-acetylneuraminatea carboxylate

trans-2-enoyl-CoAreductase(NADPH)

a supercoiledduplex DNA

D-fructuronate

dihydrolipoyltranssuccinylase: sucB

uridine

pentakisphosphate

betainealdehyde

shikimate-3-phosphate

tRNAtrp

a tRNA containingepoxyqueuosineat position 34

ADP-L-glycero-beta-

D-manno-heptose

biosynthesis

a tRNA

cadaverine

3-deoxy-D-arabino-heptulosonate-7-phosphate

L-alanine

fructoselysineand

psicoselysinedegradation

4-(glutamylamino)butanoate

nitric oxide

cob(I)alamin

RNA 3’-terminalphosphatecyclase: rtcA

adenineglycosylase;G.C --> T.Atransversions:mutY

GDP-alpha-D-mannose

INORGANIC NUTRIENTS METABOLISM

shikimate kinase I: aroK

malate

pentose phosphate pathway

2-dehydro-3-deoxyphosphoheptonatealdolase: aroH

a quaternary amine L-proline

phosphoribosyl-AMP

thymidine

L-proline

cytosine

NADphosphorylation anddephosphorylation

16S rRNA m5C967methyltransferase:rsmB

melibiosemelibiose

trans-delta2,cis-delta4-

decadienoyl-CoA

3,4-dihydroxyphenylacetate

pyruvate

lineardimeric GMP

N-acetylglucosamine

23S rRNA 2’-O-ribose U2552methyltransferase:rlmE

aminopeptidaseA/I: pepA

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-

EIIMtl

PhoP-Pasp

oxalurate

(KDO)-lipid IVA

L-glyceraldehyde3-phosphate

L-fuculokinase:fucK

hydrogenase3: hycE hycBhycG hycFhycC hycD

nitrousoxide

D-glycerate

KASI: fabB

cytidine

D-galacturonateD-glucuronate

an alcohol

indole-3-glycerolphosphatesynthase: trpC

adenine

a standardalpha

amino acid

tryptophan synthase,beta subunit dimer: trpB

chorismatesynthase: aroC

nicotinamide

3-dehydroquinatedehydratase: aroD

N-(5’-phosphoribosyl)-anthranilate

pyruvate

D-glucarate

aspartatekinaseIII: lysC

acetylmaltose

16S-rRNAs

hydroxymethylbilane

adenine

2,5-diamino-6-(ribosylamino)

-4-(3H)-pyrimidinone5’-phosphate

cyanatedegradation

D-ribose

Tsrglu

inorganicpyrophosphatase: ppa

ribosomal-protein-S5-alanine N-acetyltransferase:rimJ

a glycerolester

acetolactatesynthase: ilvN ilvB

2-isopropylmalatesynthase: leuA

cobalamin-independenthomocysteinetransmethylase:metE

an (R)-3-hydroxypalmitoyl-

L-leucine

an N-acetyl-D-

hexosamine

aminopropylcadaverine

an mRNA

AaeABHydroxylated,

AromaticCarboxylicAcid EffluxTransport

System

glycolate

CheB-Pasp: cheB

L-asparagine

(2S)-2-isopropylmalate

formaldehyde

L-tryptophan

a properlymatched

DNAbase pair

L-lysine

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

lipid IVA

2-ketobutyrateformate-lyase

/ pyruvateformate-lyase

ferricenterobactin

ABCtransporter

carbamoyl phosphatesynthetase: carA carB

a DNAwith uracil

a purine base

L-serine

dihydroorotate oxidase: pyrD

tRNA withGU(N)

anticodon

predicted L-galactonateoxidoreductase:yjjN

sulfate ABCtransporter

EmrAB-TolC

multidrugefflux

transportsystem

a methylatedribosomalprotein L11

taurinedioxygenase:tauD

hydroxypyruvate

beta-phosphoglucomutase: ycjU

[+ 2 isozymes]

a tRNAcontaining N7-methylguanine

LysP nicotinamideriboside

palmitoyltransferasefor LipidA: pagP

CreC-Phis

an alcohol

ferricenterobactin

an unstableRecA

filament-DNA

complex

putative enoyl-CoA hydratase/isomerase ofphenylacetatedegradation: paaF

tetrapyrrolebiosynthesis I

lipopolysaccharidecore biosynthesis;heptosyl transferseIV; probably hexosetransferase: waaU

glutathione

7,8-diaminopelargonate

lipopolysaccharidecore biosynthesisprotein; heptosyltransferase III: rfaQ

L-phenylalanyl-tRNAphe

a prolipoprotein

sirohydrochlorin

L-serine

D-alanine

H-Gcv-protein-(lipoyl)lysine

UDP-N-acetyl-D-glucosaminebeta-1,6-N-acetyl-D-glucosaminyltransferase:pgaC

di-trans,poly-cis-hexaprenyldiphosphate

farnesyldiphosphatesynthase: ispA

2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol

D-tagaturonate

bicarbonate

spermidine

di-trans,poly-cis-

aminodeoxychorismatesynthase: pabA pabB

acetoacetyl-CoA

hybrid-cluster

proteinred

L-lysine

O-phospho-L-homoserine

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

diamine

uridylyl-glutaminesynthase PII

a carboxylate

2,4-dinitrophenyl-S-glutathione

a trans oct-2-enoyl-[acp]

pyruvate

YiaMNOBindingProtein-

dependentSecondary(TRAP)

Transporter

4-hydroxybenzoate

isopentenyl-adenosineA37 tRNAmethylthiolaseMiaB: miaB

a debranchedlimit dextrin

enterobactinbiosynthesis

lipoyl-ACP

Chemotactic SignalTransduction System

2-oxo-3-deoxygalactonate6-phosphatealdolase: dgoA

pyruvate

2-dehydro-3-deoxy-D-galactonate

precorrin-2dehydrogenase:cysG

acetate

Cd2+Zn2+

superpathwayof glycol

metabolismand degradation

tagatose-6-phosphate

acyl carrier proteinphosphodiesterase:acpH

D-galactitol

hydrogen sulfide

NarP-Pasp

tRNAileX

salvage pathwaysof pyrimidine

deoxyribonucleotides

5’-methylthioadenosine/S-adenosylhomocysteinenucleosidase: mtn

L-phenylalanine

a glycogen

acetyl-CoA synthetase(AMP-forming): acs

formate

16S rRNA m3U1498methyltransferase:rsmE

4-aminobutyrate

beta-D-ribopyranose

a fatty acid

acetolactatesynthase: ilvH ilvI

L-methionyl-tRNAmet

acetate

coenzyme A

alaninedegradation I

agmatine

3-phosphoglycerate

dTDP-alpha-L-

rhamnose

D-galactose

2’-deoxyadenosine-5’-diphosphate

GDP-alpha-D-mannose

AtoSC Two-Component

SignalTransduction

System

octyl beta-1,6-D-galactofuranosyl-

alpha-D-glucopyranoside

GMPsynthetase:guaA

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

porphobilinogen

pyruvate

aspartateammonia-lyase: aspA

beta-L-rhamnose

pyridoxalphosphatase:ybhA

dihydroorotase: pyrC

L-tryptophan

Trgglu-Me

phosphoribosyl-AMPcyclohydrolase: hisI

hypoxanthine

cis-aconitate

anaerobiccoproporphyrinogenIII oxidase: hemN

histidinol-phosphateaminotransferase:hisC

2-oxoglutarate

succinate semialdehydedehydrogenase,NAD+-dependent: sad

N-acetylglucosaminyltransferase: murG

a singlestranded

L-arginine

thiamine-phosphate

4-methyl-2-oxopentanoate

23S rRNAm3psi1915methyltransferase:rlmH

pyruvate

pyridoxine-5’-phosphate

carbamoylphosphatesynthetase:carA carB

replicativeDNAhelicase:dnaB

DNA combinedwith exogenousDNA to form a

recombinationaljunction

L-methionine

formate

DcuR-Pasp56

(KDO)-lipid IVA

pyrimidinedione

L-asparagine

L-alanine

3-octaprenyl-4-hydroxybenzoatedecarboxylasetogether withUbiG: ubiX

2-phosphoglycolate

4-coumaroyl-CoA

acetyl-CoA

adenine

N-acetyl-L-glutamate

riboflavin

malate

D-allose

2-phospho-4-(cytidine 5’-diphospho)

a polypeptide

a tRNAcontainingqueuosine

acetaldehyde

rep helicase,a single-strandedDNAdependentATPase: rep

2-keto-3-deoxy-L-

rhamnonate

UDP-N-acetylmuramoylalanyl-D-glutamate 2,6-diaminopimelate ligase: murE

(S)-methylmalonyl-

CpxAR Two-Component

SignalTransduction

System

malate dehydrogenase: mdh

UDP-2,3-diacylglucosamine

hydrolase: lpxH

a tRNA

L-cysteinedesulfhydrase:metC

KASI: fabB

galactokinase: galK

KASI: fabB

KDO2-lipid A

chitobiosedegradation

methylglyoxalreductase(NADH-dependent): ydjG

colanic acid building blocks biosynthesis

adenylylsulfatekinase: cysC

glutathionesynthetase: gshB

UDP-N-acetyl-D-

glucosamine

partially N- deacetylatedpoly-beta-1,6-

N-acetyl-D- glucosamine

UDP reductase:nrdB nrdA

glucosyl-heptosyl2-

KDO2-lipid A-

phosphate

(S)-1-pyrroline-5-carboxylate fructose-1,6-

bisphosphate

7,8-dihydro-D-neopterin

glycerol

an RNA

ethyleneglycol

6-hydroxymethyl-7,8-dihydropterinpyrophosphokinase: folK

glutamyl-QtRNA(Asp)synthetase:yadB

GMPreductase:guaC

a hydroquinone

alpha-L-Ara4FN

acetylphosphate

acetaldehyde

nickel ABCtransporter

agmatinase:speB

3-phenylpropionatedioxygenasesystem: hcaDhcaC hcaF hcaE

ALDEHYDE DEGRADATION

L-alanine

nicotinamide mononucleotide

ArcB-Phis292

protoporphyrin IX

acetate

succinate

precorrin-2

choline

beta-D-glucose

pyruvate

23Sribosomal

lactose

geranyldiphosphatesynthase: ispA

D-xylose

glutamate-cysteineligase: gshA

a trans-delta2-enoyl-acyl-[acp]

homoserine lactonehomoserine

5,10-methylene-

trehalose-6-phosphatephosphatase,biosynthetic:otsB

S-hydroxymethylglutathione

L-ornithine

diacetyl

selenophosphate

pyruvate

tRNAgln

RcsC-Phis

a proteinL-tyrosine

16S rRNAm62A1518,m62A1519dimethyltransferase: ksgA

nucleoside triphosphatepyrophosphohydrolase:mazG

tryptophanase:tnaA

ribose-1,5-bisphosphate

an (R)-3-hydroxyoctanoyl-

an (R)-3-hydroxydecanoyl-[acp]

lactosedegradation III

L-cysteine

fumarate

DcuS-Phis349

tetraphosphate

DNAcytosinemethylase:dcm

glycan chain 1

TDP-rhamnose

o-succinylbenzoate

KDO2-lipid IVA

L-fuculokinase: fucK

propionyl-CoA

2-keto-isovalerate

superpathwayof asparaginebiosynthesis

2-keto-3-deoxy-L-rhamnonatealdolase: yfaU

mannokinase

L-lysine

8-amino-7-oxononanoatesynthase: bioF

L-proline

2-oxobutanoate

L-ribulose-5-phosphate4-epimerase:sgbE

L-aspartate

gamma-aminobutyraldehydedehydrogenase: ydcW

N-acetylneuraminate

a carbohydrate

myo-inositol

L-glutamyl-tRNAGlu

D-alanyl-D-alanine-adding enzyme: murF

complex

dephospho-CoA kinase: coaE

23S rRNA m2G1835methyltransferase:rlmG

diphosphate

propionate

adenine

16S rRNA m5C1407methyltransferase:rsmF

inosine kinase: gsk

HMP-PPhydrolase:cof

protein with lowundecaprenylpyrophosphatephosphataseactivity: lpxT

cysteinesulfinatedesulfinase:csdA csdE

a 3’-phosphate-terminated

trehalose

L-alanine

GDP-L-fucose

CARBOXYLATES DEGRADATION

oxaloacetate

agmatinase: speB

glucosamine

4-hydroxybenzoateoctaprenyltransferase:ubiA

alpha-iminosuccinate

apo-citrate lyasephosphoribosyl-dephospho-CoAtransferase: citX

2-octaprenyl-6-methoxyphenolhydroxylase: ubiH

benzaldehyde

colanic acid

2-oxoglutarate

L-cysteine

molybdopterin

succinatesemialdehydereductase: yihU

dihydroneopterintriphosphate 2’-epimerase: folX

4-aminobutyrate

galactitoldegradation

L-glutamategamma-

semialdehyde

PhoQ-Phis

holo-[acylcarrierprotein]synthase2: acpT

UDP-D-glucose

UDP-D-galacto-1,4-

furanose

(E)-3-(methoxycarbonyl)pent-2-enedioate

UvrY-Pasp

a drug

melibiose

alpha-L-Ara4N

an apo-GcvHprotein

ferricdicitrate

L-glutamine:D-fructose-6-phosphateaminotransferase:glmS

glycogen

lipoatebiosynthesis

andincorporation II

succinate

dTDP-4-dehydrorhamnosereductase: rfbD

L-homocysteine

thymidylatesynthase: thyA

4-methyl-5-(beta-

N5-glutaminemethyltransferase:prmB

UDP-D-glucose

MutHLScomplex,methyl-directedmismatchrepair: mutHmutS mutL

alpha-D-glucose

acetaldehyde

rRNAcontaining

pseudouridine

a holo-[acp]

glycine

methylglyoxal

DNAadeninemethylase:dam

4-aminobutanal

nicotinatemononucleotide

L-rhamnose

nitrousoxide

2,3-diaminopropionate

di-trans,poly-cis-

methylmalonyl-CoA epimerase

tRNA-specificadenosinedeaminase:tadA

L-asparagine

L-glutamate

a peptide

3-phosphoglycerate

superpathway ofgluconate degradation

lipopolysaccharidecore biosynthesisprotein: rfaS

arsenate

CheB-Pasp: cheB

galactosyl-glucosyl-heptosyl3-

tRNAcontaining N6-methyladenine

uracil

L-cystathionine

acetyl-CoA carboxylase:accB accC accA accD

hemebiosynthesis fromuroporphyrinogen II

phosphate

a tRNA containing 5-carboxymethylaminomethyl-

2-thiouridine

phosphoenolpyruvate synthase: pps

phosphopantetheinyltransferase: entD

prolyl-tRNAsynthetase:

carbamoyl-phosphate

L-pantoate

isoleucyl-tRNA

synthetase:ileS

aspartyl-tRNA

synthetase:aspS

Tsrgln

putative enoyl-CoA hydratase/isomerase ofphenylacetatedegradation: paaG

Targln

succinate

N-acetyl-glucosamine-1-phosphate

D-galactonatedegradation

23Sribosomal

triose phosphate isomerase: tpiA

enolase: eno

succinate

beta-D-galactose

citrate synthase: gltA

oxaloacetate

L-1,2-propanediol

a DNAsegment

in reverseorientation

acetoin

ribosomal-protein-S18-alanine N-acetyltransferase: rimI

23S rRNA m5C1962methyltransferase: rlmI

beta-D-glucose

23S rRNA m1G745methyltransferase:rrmA

D-methionineL-methionine

an aldehyde

2-oxoglutarate

D-altronatedehydratase:uxaA

riboflavinsynthase:ribC

6-pyruvoyltetrahydropterin

malate synthase A: aceB

o-succinylbenzoyl-CoA

L-glutamyl-tRNAGlu

KDO2-lipid IVA

phosphate

L-glutamine

UDP-D-glucuronate

phosphoglycerate mutase 2: ytjC

a DNA pairof adjacentpyrimidines

dehydratase: acnB

D-mannonateoxidoreductase:uxuB

D-threo-isocitrate

isocitrate dehydrogenase: icd

a glutaminesynthetase PII

an N-acetyl-D-hexosaminide

fructosedegradation

D-xylose

dihydroxyacetonekinase: dhaLdhaK dhaM

superpathway of threonine metabolism

D-mannose

alanine racemase1, PLP-binding,biosynthetic: alr

aminoacetone

phosphohydroxymethylpyrimidinekinase: thiD

malate fumarate succinate orotateL-aspartate

an acid

UDP-N-acetylmuramoyl-L-alanyl-D-

glutamyl-meso-2,6-diaminoheptanedioate-

D-alanine

YgjDdegradation

products

propionyl-CoA:succinateCoA transferase: scpC

7,8-dihydroneopterintriphosphate

a dipeptide

3-(2,3-dihydroxyphenyl)

propionate

2-oxoglutarate

5-phospho-ribosyl-

glycineamide

tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:mnmA

phenylacetaldehydedehydrogenase: feaB

D-fructose-6-phosphateL-glutamine

3,5-tetradecadienoyl-

diphosphate

L-serine

D-galactonate

sirohemebiosynthesis

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

D-erythro-imidazole-glycerol-phosphate

protoporphyrinogenoxidase: hemG

KASI: fabB

L-valine

anamineated

amine donor

cobalamin-dependent

thioredoxinreductase:trxB

glycolateL-lactate

acetate

AMPnucleosidase: amn

cis-3-(carboxyethyl)-3,5-

cyclohexadiene-1,2-diol

16S rRNA m2G1207methyltransferase:rsmC

alpha-D-galactose 1-phosphate

tetrahydrofolate

rRNAcontaining 2-methyladenine

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

glycosidehydrolase:ygjK

N-ethylmaleimidereductase, FMN-linked: nemA

thiocyanate

cytosine

3-phosphoglycerate

2,3-dihydroxy-isovalerate

cytosinedeaminase:

glyoxylatecarboligase:gcl

hypoxanthine

chorismate mutase: pheA

tryptophanyl-tRNA

synthetase: trpS

glucokinase: glk

valyl-tRNAsynthetase:

UDP-D-glucose

cysteinyl-tRNA

synthetase:cysS

an rRNA

uracilphosphoribosyltransferase: upp

Tapglu

siroheme

protein-(glutamine-N5)methyltransferase:prmC

2-octaprenyl-6-hydroxyphenol

shikimate kinase II: aroL

PRPPbiosynthesis I

hydroxyphenylacetyl-CoA thioesterase: paaI

L-fucose

5’-deoxyadenosine

alkylhydroperoxidereductase: ahpF ahpC

phosphate

putativeoxidoreductaseFe-S subunit;possiblecomponentof selenatereductase: ygfK

oxalate

enterobactin

2-dehydro-3-deoxyphosphoheptonatealdolase: aroG

D-galactonatedehydratase: dgoD

pyruvate

anthranilate synthasecomponent II: trpD

superpathway of leucine, valine,and isoleucine biosynthesis

PII-UMP

deoxyguanosine

argininesuccinyltransferase:astA

3-deoxy-D-manno-

octulosonate

cytidine

maltose

UDP-N-acetyl-beta-D-mannosaminouronate

L-methionine

glutamatedehydrogenase:gdhA

2-oxobutanoate

sorbitol-6-phosphatedehydrogenase:srlD

ethanolamine

COFACTORS, PROSTHETIC GROUPS, ELECTRON CARRIERS BIOSYNTHESIS

cytidinekinase: udk

cytidylatekinase: cmk

ketogluconate metabolism

tetrahydrofolate

a DNAsegment

citratesynthase:gltA

lipoate acetyltransferase: aceF

hydroxymethylbilanesynthase: hemC

N5-methyl-L-glutamine

pyruvate

glucose and glucose-1-phosphate degradation

tRNA (Gm18) 2’-O-methyltransferase:trmH

methionyl-tRNA

synthetase:metG

trans-aconitate

DNAwithoutlesion

N-acetylneuraminatemutarotase: nanM

taurine

methylglyoxal

diphosphate

UDP-N-acetyl-D-

glucosamine

NUCLEOSIDES AND NUCLEOTIDES BIOSYNTHESIS

elongatortRNAmet

D-galactono-1,4-lactone

BglG-P

3-keto-L-gulonate

pantothenateand coenzyme

A biosynthesis I

lipoylateddomain

L-lysyl-tRNAlys

a [citrate(pro-3S)-

lyase](citrylform)

triose phosphateisomerase: tpiA

L-rhamnulose-1-phosphate

acetaldehyde

enolase: eno

nitric oxide

alpha-L-arabinose

D-galacturonate

malate

phosphoserinephosphatase: serB

L-tyrosyl-tRNAtyr

lipid Adisaccharide

a cis-delta5-dodecenoyl-[acp]

4-coumarate

superpathway of arginineand ornithine degradation

phenylacetate-CoA ligase: paaK

enterobactin

superpathway of aspartateand asparagine biosynthesis;

interconversion ofaspartate and asparagine

Ni2+Mg2+

unknown

ferricenterobactin

ribonucleosidetriphosphatereductaseactivase: nrdG

3’-phospho-adenylylsulfatereductase: cysH

an rRNA

a cis-vaccenoyl-

pyrimidinedeoxyribonucleosides

degradation

crypticadeninedeaminase:ade

pyrazinamide

L-Ala-gamma-D-Glu

polyisoprenoidbiosynthesis (E. coli)

L-tyrosine

all-trans-farnesyl

diphosphate

a biotinylatedBCCP (dimer)

predicted 3-hydroxy-acyl-CoAdehydrogenaseof phenylacetatedegradation: paaH

FERMENTATION

2,4-dienoyl-CoAreductase:fadH

pyruvate

2-methylcitratedehydratase: prpD

cobinamide

fumaratereductase:frdD frdCfrdB frdA

lipoyl-ACP

a holo-[acp]

beta-alanine

5-methyluridine-modified 23S

ribosomal RNA

3-hydroxy-5-cis-tetradecenoyl-

a proteinL-beta-

isoaspartatealpha-

methyl ester

L-threonyl-tRNAthr

a [citrate(pro-3S)-lyase](thiol

D-gluconate

lipoatesalvage andmodification

a phosphatemonoester N-methyltryptophan

catabolicthreoninedehydratase:tdcB

D-alanine-D-alanineligase A: ddlA

anthranilate

beta-D-glucose

RstBA Two-Component

SignalTransduction

System

L-proline

a drug

L-aspartyl-tRNAasp

tRNA uridine

cholate

formate

KDOtransferase:waaA

EvgA-Pasp

glutaminedegradation I

CheB-Pasp: cheB

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

D-glucono-delta-lactone-6-phosphate

acetate

a thioredoxin

agmatine

glycolate

1-phosphofructokinase:fruK

putative diacylglycerolcholinephosphotransferase:ynbA

gamma-glutamyl-L-putrescine

N-carbamoyl-L-aspartate

an RNA

trehalose

acetyl-esterase: aes

L-arginine

deoxyinosine

pyruvate

isochorismatesynthase 1: entC

a [citrate(pro-3S)-

lyase](acetylform)

pirin-likeprotein:yhhW

3-dehydroquinate

2,3-dihydroxybenzoate-AMP ligase: entE

cytoplasmictrehalase: treF

nitrite

2-isopropylmaleate

2,3-dihydro-2,3-dihydroxybenzoate

3-deoxy-D-manno-

octulosonate8-P

ThiS-COSH

hydroxylamine

acetyl-CoA

pyruvate

citrate

chemotaxis proteinmethyltransferase:

uracil

deoxyuridine

L-rhamnonatedehydratase:yfaW

glucosedehydrogenase: gcd

a DNAcontaining aapyrimidinic

a deoxynucleoside

L-asparagine

putrescine

formate

an oxidizedflavodoxin

Trgglu

aspartatecarbamoyltransferase: pyrI pyrB

glycolateoxidase:glcFglcE glcD

1-amino-propan-2-one-3-

phosphate

L-glutamate

glycerol 2-phosphate

a deoxynucleotide

predictedthiosulfatesulfurtransferase:ynjE

a DNAcontaining

a purinic site

D-mannose

thiosulfatesulfate

CDP-choline

phosphate

coproporphyrinogenoxidase, aerobic: hemF

UDP-D-galactose

SIGNAL TRANSDUCTION PATHWAYS

nicotinate-nucleotidedimethylbenzimidazolephosphoribosyltransferase: cobT

2-deoxygluconate

tRNAcontainingguanine

cobalaminadenosyltransferase:

pyrimidinephosphatase

trans-2-decenoyl-ACP isomerase: fabA

enoyl-ACP reductase(NADH): fabI

glycolaldehyde

alpha-D-glucose

DNAligase: ligB

phosphoenolpyruvate

2-aminobutyrate

beta-hydroxyacyl-ACP dehydrase: fabA

dihydroxy-acetone

a holo-[acp]

3-methyladenine

salvage pathways of pyrimidine ribonucleotides

dTDP-4-acetamido-4,6-dideoxy-D-galactose

ZraR-phosphate

formaldehyde

uracil

anadenylated

ThiS sulfur-carrierprotein

ubiquinone-8

threoninedehydrogenase: tdh

octulosonate

crotonobetainyl-CoA reductase: caiA

L-ornithine

thymidine

diphosphate

glyoxylate

phosphoribosylformylglycinamidecyclo-ligase: purM

UDP-D-glucose

acetaldehyde

acetyl-CoAsynthetase (AMP-forming): acs

cobalamin 5’-phosphatesynthase:cobS

BaeS-Phis

GMPsynthetase:guaA

2-oxoglutarate

adenylatekinase: adk

a rhamnosyllipopolysaccharide

degradationof pyrimidine

ribonucleosides

uridinekinase: udk

L-gamma-glutamylcysteine

glucosamine

AICARtransformylase:purH

AceF-lipoate

erythronate-4-phosphatedehydrogenase:pdxB

xanthosine

predicted N-acetylmannosamine-6-phosphateepimerase: nanE

acetoin

acetaldehyde

superpathwayof glutamatebiosynthesis

oxaloacetate

D-galactonate

S-adenosyl-dependentmethyltransferase:mraW

a decanoyl-[acp]

3-keto-L-gulonate

RcsCB Two-ComponentSignal Transduction System

4-hydroxybutyrate

a protein-L-glutamate--O5-methyl-

L-arabinose

EIIBgl

adenine

D-glucono-delta-

lactone-6-phosphate

porphobilinogensynthase: hemB

a transhexadecenoyl-[acp]

DNAcontaining

a basewith lesion

chloride

lactose

EIIFru

KDOtransferase:waaA

isovaleryl-CoAdehydrogenase /predicted acyl-CoAdehydrogenase: aidB

cob(I)alamin

subunit of fatty acidoxidation complex: fadI

5’-methylthioadenosine/S-adenosylhomocysteine

nucleosidase: mtn

CARBOHYDRATES BIOSYNTHESIS

lysyl-tRNAsynthetase,constitutive:

D-allosekinase: alsK

glycine cleavagecomplex

AMINOACYL-TRNA CHARGING

xanthine

an N-hydroxy-

arylamine

adenosine 5’-phosphosulfate

phenylhydantoinase:hyuA

an acylphosphate

CreB-Pasp

D-beta-D-heptose-1,7-bisphosphate

leucyl,phenylalanyl-tRNA-proteintransferase: aat

NarX Nitrate/Nitrite-DependentTwo-Component Regulatory System

phosphoribosylformiminoAICAR-phosphate

manno(fructo)kinase: mak

D-beta-D-heptose-1-phosphate

ribose 1-phosphokinase

aspartatekinase III: lysC

L-methionine

d-biotin d-sulfoxide

2-O-(6- phospho-

alpha-mannosyl)-

D-glycerate

glucosamine

2-phosphoglycerate

acid phosphatase/phosphotransferase:aphA

CheB-Pasp: cheB

ATP-dependentDNAhelicase: recQ

N-formyl-L-methionyl-tRNAfmet

N-methyltryptophanoxidase: solA

an N-D-ribosylpyrimidine

hybrid-clusterprotein: hcp

AMINES AND POLYAMINES BIOSYNTHESIS

L-2-hydroxyglutarateoxidase: lhgO

acetate kinase B: ackB

S-formylglutathionehydrolase: frmB

beta-ketoesterreductase:dkgA

allolactose

UhpA-Pasp

phosphoglucose isomerase: pgi

L-histidyl-tRNAhis

peptidedeformylase:def

5-ketogluconate

ribose-phosphatediphosphokinase: prs

nitritereductase:nirB nirD

L-threonine

1,3-propanediol

thiamin

glyceraldehyde 3-phosphatedehydrogenase-A complex: gapA

4-(2-aminophenyl)-2,4-

dioxobutanoate

uracil

adenosine-3’(2’),5’-bisphosphatenucleotidase:cysQ

dehydratase: acnB

phenylhydantoin

D-amino aciddehydrogenase:dadA

ATPsynthase

an alcohol

isochorismatesynthase 2: menF

’activated’tRNA

1,4-dihydroxy-2-naphthoateoctaprenyltransferase:menA

a peptide

L-rhamnoseisomerase:rhaA

a fatty acid

ppGpp biosynthesis

CDP reductase:nrdB nrdA

L-aspartate

tRNApseudouridine13 synthase: truD

2-oxoglutarate

2-deoxy-D-gluconate 3-dehydrogenase:kduD

pyridoxal

acetyl-CoA

indole

a proteinwith

incorrectdisulfidebonds

acetyl-CoAsynthetase(AMP-forming): acs

tRNAdihydrouridinesynthase: dusC

Ap3Asynthetase:lysU

enterobactin

lipopolysaccharidecore biosynthesisprotein: rfaY

citrate

glutaminesynthetase

deadenylylatingenzyme: glnE

lipid IVA

L-seryl-tRNAsec

CARBOHYDRATES DEGRADATION

CoA:carnitine CoAtransferase: caiB

nicotinate adenine dinucleotide

L-allo-threonine

NUCLEOSIDES AND NUCLEOTIDES DEGRADATION AND RECYCLINGL-histidinol-phosphate

carbamoyl-phosphate

thiaminbiosynthesisproteinThiC: thiC

a DNAcontaining 6-O-methylguanine

thiaminkinase: thiK

maltoseacetyltransferase:maa

tartronatesemialdehydereductase2: glxR

histidinol

putativepyruvatesynthase:ydbK

caiEprotein: caiE

L-lysine

L-cysteine

(1R,6R)-6-hydroxy-2-succinylcyclohexa-

2,4-diene-1-carboxylate

4-methyl-5-(beta-

phosphate

pyridoxamine

salvage pathways of guanine, xanthine, and their nucleosides

nucleotide-sugarhydrolase:nudK

UDP-GlcNAc-enolpyruvate

Tapgln

a crotonyl-[acp]

acetoinsynthesis:poxB

trans-delta2-decenoyl-

L-lysine

protoheme IX

L-fuculose-1-phosphate

tRNAala

a reducedFeS-protein

gluconeogenesis I

phosphodiesterase, c-di-GMP-specific: yahA

acetyl-CoA

glycerolkinase: glpK

UDP-D-galactose

UDP-D-glucose

alpha-galactosidase:melA

xylulokinase:xylB

sirohydrochlorinferrochelatase: cysG

isocitratedehydrogenasephosphatase: aceK

BarA-UvrY Two-Component

SignalTransduction

System

lysidine-modifiedtRNAileX

succinate

a tripeptide

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)

L-methionine

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

salicinarbutin

L-lyxosedegradation

deoxyadenosine

L-xylulose 5-phosphate3-epimerase:ulaE

dTDP-D-glucose

pyruvate

L-idarate

glyceroldegradation V

4-nitrobenzylalcohol

tRNAarg

L-lactate

formaldehyde

succinate

L-serine

a proteinL-beta-

isoaspartate

pyridoxamine5’-phosphateoxidase: pdxH

D-galactarate

selenide

a beta-D-galactoside

2-keto-isovalerate

3-mercaptopyruvate:cyanidesulfurtransferase: sseA

a thioredoxin

glucose-1-phosphateuridylyltransferase:

galU galF

hydroxypyruvate

glucosyl-heptosyl3-

glutathionereductase: gor

a tRNAcontaining 2’-O-methylguanosine

tRNAGlu

1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatesynthase: ispG

2C-methyl-D-erythritol 2,4-cyclodiphosphatesynthase: ispF

L-isoaspartate proteincarboxylmethyltransferasetype II: pcm

deoxyinosine

CreCB Two-ComponentSignal Transduction System

6-hydroxymethyl-7,8-dihydropterin

isopentenyldiphosphateisomerase: idi

a protein

2-thiouridylate

BasR-Pasp

(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylatesynthase: menH

xylulokinase:xylB

D-myo-inositol (1)-monophosphate

pyrimidineribonucleotides denovo biosynthesis

23S rRNA m5U1939methyltransferase:rlmD

glycerol-3-phosphate-dehydrogenase,anaerobic:glpC glpB glpA

RstA-Pasp

uridine

EIIMan

2,5-didehydro-

D-gluconate

two-componentalkanesulfonatemonooxygenase

coproporphyrinogen III

5,6,7,8-tetrahydropteridine

inosine

exonucleaseIII: xthA

glycyl-tRNAgly

a 2,3,4-saturated

fattyacyl CoA

acetol

NtrC-P

glycerol

coenzyme A

sugar phosphatase: yidA

PhoQP Two-Component

SignalTransduction

System

2-oxoglutarate

superpathway ofhexitol degradation

tRNA chargingpathway

7,8-dihydrofolate

glutaminesynthetase: glnA

L-serine

CpxA-Phis

heptosyl-KDO2-

lipid IVA

methylmalonyl-CoAmutase: scpA

L-Ala-D-Glu-meso-

DcuS-Phis349

biotincarboxylase:accC

dihydroorotate

lipid Adisaccharide

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

diphosphate

glycine

an aromaticsulfate

5,10-methylene-

trimethylamine

nitrite

deoxyinosinetriphosphatepyrophosphatase:rdgB

pyrroline-5-carboxylatereductase:proC

2-hydroxyglutarate

a cis-3-enoyl-CoA

pyruvateformate-

2’-(5’-phosphoribosyl)-3’-dephospho-

CoA biosynthesisI (citrate lyase)

RNA(n)

D-alanine

an mRNA

D-mannose

cis-dihydrodiolderivative of

phenylacetyl-CoA

(2S,3S)-2-methylcitrate

pyruvate

an (R)-3-hydroxydodecanoyl-

S-allantoin

multidrug

lipoatesynthase: lipA

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

meso-2,6-diaminopimelyl-D-alanyl-D-alanine

glycogen degradation I

prolinebiosynthesis I

a 2,3,4-saturatedfatty acyl-[acp]

L-ornithine L-lysine L-arginine

glutaminase:ybaS

an octanoyl-[acp]

glucokinase:glk

Tsrglu-Me

pyruvate

biotinsynthase: bioB

glycogenphosphorylase:glgP

2-keto-3-deoxygluconokinase:kdgK

acetyl-CoA

D-glucuronateisomerase:uxaC

L-3,4-dihydroxybutan-2-one-4-phosphate

an N-substitutedamino acid

glutamatesynthase:gltD gltB

guanosine

triphosphoribosyl-dephospho-CoAsynthase: citG

biotinbiosynthesis I

coenzyme A

N-alpha-acetyl lysinemethyl ester

3-(2,3-dihydroxyphenyl)propionatedioxygenase: mhpB

an aceticester

QseB-Phosphorylatedtranscriptional

activator

thiamine-phosphate

ribosomal-protein-L12-serineacetyltransferase:rimL

4-amino-4-deoxychorismate

cytochromebd-I terminal

oxidase

purine nucleosidephosphoramidase:hinT

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

GDPdiphosphokinase: spoT

GLYCOLYSIS

N-acetyl-D-mannosamine

L-prolyl-tRNApro

guanine

xanthosine

an RNA

fructoselysine

fructose 1,6-bisphosphatase:ybhA

degradation of purine ribonucleosides

lipoate

L-glutamate

nicotinatephosphoribosyltransferase: pncB

rRNAcontaining 2’-

O-methyluridine

tRNApseudouridine55 synthase: truB

propionyl-CoAcarboxylase

methylmalonylpathway

cobalaminsynthase: cobS

xanthine

di-trans,poly-cis-

heptaprenyldiphosphate

a peptide

D-Ala-D-Aladipeptidase:ddpX

pyruvate formate-lyase: tdcE

UDP-D-galacto-1,4-

furanose

4-(phosphonooxy)-threonine

a deoxyribonucleicacid

acetaldehyde

lipoylated domain

putrescine

pyrimidine (deoxy)nucleoside triphosphatepyrophosphohydrolase:nudG

nitrate

L-rhamnose

3-hydroxy aciddehydrogenase:ydfG

cyclicdi-3’,5’-

guanylate

fumarate

L-phenylalanine

UDP-D-galactose

a proteinwith correct

disulfidebonds

D-glucaratedehydratase: gudD

salicylalcohol

dodecenoyl-CoAD-isomerase: fadJ

a tRNA

glucosyl-heptosyl2-

KDO2-lipid A

phosphoenolpyruvate

D,D-heptose 1,7-bisphosphatephosphatase:gmhB

succinyl-CoA

acetate

ArcB-Pasp

peptideuptake ABCtransporter

23S rRNA m6A1618methyltransferase:rlmF

pyridoxaminekinase: pdxK

endonucleaseVIII: nei

glycan chain 1

AROMATIC COMPOUNDSBIOSYNTHESIS

flavorubredoxinreductase: norW

carbamoyl-phosphate

galactoside O-acetyltransferase:lacA

a mRNA

6-phosphogluconatephosphatase: yieH

spermidine

triphosphate

L-lactaldehyde

beta-D-glucose

superpathway of lysine, threonineand methionine biosynthesis I

lysinedegradation I

threonyl-tRNA

synthetase:thrS

alanyl-tRNAsynthetase:

KASI: fabB

isochorismatase:entB

glycine betaine L-proline

glutaminyl-tRNA

synthetase:glnS

a semiquinone

predictedgalactose 1-dehydrogenase:yhhX

N,N’-dimethyl-p-phenylenediamine

acylphosphatase:yccX

3-hydroxyadipyl-CoA

dTDP-4-dehydro-6-

deoxy-D-glucose

isocitrate lyase: aceA

succinate dehydrogenase:sdhA sdhB sdhC sdhD

conversionof succinate

to propionate

fumarase C: fumC

6,7-dihydropteridine

tRNA:Cm32/Um32methyltransferase:trmJ

Mn2+Fe2+

palmitate

N2-succinylglutamate

inosine

6-phosphofructokinase II: pfkB

cofactor

oxidizedthioredoxin

a tRNA

23Sribosomal

RNAmethylatedat position

D-glucose

tRNApseudouridinesynthase I: truA

guanine

an alcohol

melibiosedegradation

3-sulfinoalanine

L-serinedegradation

L-aspartate

L,D-transpeptidaseYnhG: ynhG

an rRNA

a carboxylicester

a tRNAcontaining 2’-O-methylcytosine

or 2’-O-methyluridine

L-ascorbatedegradation,

anaerobic

enterobactin

molybdateABC

transporter

Ogt: ogt

2,5-diketo-D-gluconatereductaseA: dkgA

NarL-Pasp

tetrahydrofolate biosynthesis

pyridoxal

a protein

2-phosphoglycerate

D-mannosedegradation

DNA containing5-methylcytosine

L-leucyl-protein

glutathione

O-antigen biosynthesis

L-serine

galactose-1-phosphateuridylyltransferase:galT

phospho-N-acetylmuramoyl-pentapeptide transferase: mraY

a tRNA

tRNA (m7G46)methyltransferase: trmI

lysyl-tRNAsynthetase:

L-ribulose 5-phosphate4-epimerase:ulaF

cis-2-methylaconitate

malatedehydrogenase,NAD-requiring: maeA

cyclic-AMP

tRNAdihydrouridinesynthase: dusB

tRNAcys

an activeribonucleosidetriphosphatereductase

Targlu-Me

a protein-L-methionine-(S)-S-oxide

2-octaprenyl-6-methoxyphenol

methylmalonyl-CoA mutase: scpA

nicotinamidase: pncA

L-glutamate

Trggln

rhamnulose-1-phosphatealdolase: rhaD

deoxyuridinetriphosphatase: dut

an alcohol

L-quinate

ribokinase:rbsK

dGTPpyrophosphohydrolase: mutT

CurliSecretion

andAssemblyComplex

tRNAtyr

D-allulose-6-phosphate

L,D-transpeptidaseYcfS: ycfS

a peptide

AtoC-Pasp

L-isoleucyl-tRNAile

heptosyl-KDO2-lipid A

BasSR Two-Component

SignalTransduction

System

dTMP kinase: tmk

shikimate

UDP-N-acetyl-D-mannosaminuronicacid transferase: rffM

D-alanine

fatty acyl-CoAsynthetase: fadD

pantothenate

a DNA withunresolved

recombitionalor holidayjunctions,

created by RecA

phosphoenolpyruvate

dephospho-CoA

BasS-Phis

BaeSR Two-Component

SignalTransduction

System

succinate

2,3-diketo-L-gulonatereductase:yiaK

EvgSA Two-Component

SignalTransduction

System

phosphatidylglycerophosphatesynthase: pgsA

dTDP-4-oxo-6-deoxy-D-glucosetransaminase: rffA

2-dehydropantoate

(S)-1-pyrroline-5-carboxylate

oxalyl-CoA

a cis-delta3-decenoyl-

D-glucarate

a dipeptide

3-deoxy-D-manno-

octulosonate8-P

L-arabinoseisomerase: araA

cis-aconitate

D-alanine

GTPase thatinteracts withmethylmalonyl-CoA mutase: argK

formamidopyrimidineDNA glycosylase: mutM

glyoxalase III

acetyl-CoAacetyltransferase:atoB

pyruvate dehydrogenasemultienzyme complex: lpd aceF aceE

RssB-P

protein N6-(lipoyl)lysine

coenzyme A

aminoacetaldehyde

cis-vaccenatebiosynthesis

nitrate

KDOtransferase:waaA

2-O-(6-phospho-alpha-

mannosyl)-D-glycerate

alpha-ketoglutaratereductase: serA

beta-D-galactose

L-tyrosine

5’-phosphoribosyl-4-(N-succinocarboxamide)

-5-aminoimidazole

lipopolysaccharideglucosyltransferaseI: rfaG

RcsF-P

UDP-D-glucose:(glucosyl)LPS alpha-1,3-glucosyltransferase: rfaI

alpha-D-glucose-1-phosphatase: yihX

Tapglu

a limitdextrin

DNApolymeraseV: umuDumuC

formyl-L-methionylpeptide

an aromaticamino acid

lactose

bicarbonate

octanoate

KefAfructose-1,6-bisphosphataseI: fbp

guanosine 3’-diphosphate

5’-triphosphate

an apo-[acp]

UDP-N-acetylmuramoyl-L-alanine

Targlu

flavodoxinNADP+reductase: fpr

pyruvate

anthranilatesynthase: trpD trpE

2-dehydro-3-deoxyphosphoheptonatealdolase: aroF

histidinal

tRNAcontaining

ribothymidineat position 54

pyridoxamine-phosphatetransaminase

L-homocysteine

methyl-1,4-benzoquinol

a ThiI sulfur-carrierprotein

tetrahydrodipicolinatesuccinylase: dapD

cysteinebiosynthesis I

an oxidizedglutaredoxin

anthranilate

gamma-glutamyl-gamma-aminobutyraldehyde

D-threo-isocitrate

octulosonate

NADH-azoreductase,FMN-dependent:azoR

ADP-heptose:LPSheptosyltransferaseII: rfaF

ornithinecarbamoyltransferase: argI

a 3-oxo-octanoyl-[acp]

dihydroxy-acetone

rRNA containingN6,N6-

dimethyladenine

trehalosedegradation

I (lowosmolarity)

KDOtransferase:waaA

R-4’-phosphopantothenoyl-

L-cysteine

heptosyl2-KDO2-lipid A

a phenol

glycine

tRNA-guaninetransglycosylase: tgt

UDP-D-galactose:(glucosyl)lipopolysaccharide-1,6-D-galactosyltransferase:rfaB

2-phosphoglycolate

methionineadenosyltransferase:

glycan chain 2

thioredoxinpathway

23S rRNApseudouridine2605synthase: rluB

deoxycytidine

multidrug

L-methionine

DNApolymeraseIII, alphasubunit: dnaE

N-acetylmannosaminekinase: nanK

DL-lactaldehyde

fatty acid

pyruvate

a single-stranded

multidrug

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

UDP-N-acetyl-D-

glucosamine

L-arginine

D-glutamate

23S rRNApseudouridinesynthase: rluC

Targlu

2-C-methyl-D-

erythritol-4-phosphate

a protein-L-glutamine

hydrogencyanide

L-homocysteine

glycerol

pyruvate

pyrazinamidase:pncA

2-hydroxyglutaratesynthase

a polypeptide

glyoxalaseII: gloB

trehalose-6-phosphatehydrolase:treC

a tRNAcontaining 7-

a 2,3-dehydroacyl-CoA

6,7-dimethyl-8-(1-D-ribityl)lumazine

DNA withremovedadenine

mismatchleaving

an AP site

gluconolactonase

thiolperoxidase:bcp

o-succinylbenzoatesynthase: menC

excised base

tRNAhis

chorismate mutase: tyrA

methylglyoxalreductase: yeaE

5-methylaminomethyl-2-thiouridinemethyltransferase:mnmC

L-tartratedehydratase:ttdB ttdA

multidrug

Autoinducer2-degradingprotein: lsrG

Trgglu

adenosylcobinamide

hydroxyethylthiazolekinase: thiM

an organicmolecule

S-ureidoglycolate

dihydrolipoyltranssuccinylaseN6-(dihydrolipoyl)lysine

FATTY ACID AND LIPIDS DEGRADATION

a ThiS-ThiF acyl-disulfide

oxaloacetate

thioesteraseIII: ybaW

dTDP-D-glucose

a protein-S-methyl-L-cysteine

glycine decarboxylase: gcvP

an L-1-phosphatidyl-glycerol

glucokinase:glk

L-glutamate-5-phosphate

a damagedDNA

pyrimidine

enterobacterial commonantigen biosynthesis

citrate

glutathione S-transferase:yfcF

selenophosphate

D-cysteinedesulfhydrase,PLP-dependent: dcyD

uridine

D-ribose

dihydrouracil

lipoate acetyltransferase N6-(S-acetyldihydrolipoyl)lysine

KASI: fabB

3-methylcrotonyl-CoA

TorT-TMAO

UDP-L-Ara4FN

fatty acid

acetate CoA-transferase

Co2+Fe2+

Tapglu-Me

orotidine-5’-phosphate-decarboxylase: pyrF

uracil

restrictionof DNA at 5-methylcytosineresidues: mcrA

oxaloacetate

DNA adeninemethyltransferase:yhdJ

[+ 3 isozymes]

xyloglucanoligosaccharide

thiamin biosynthesis I

an aldehyde

ureidoglycolatedehydrogenase:allD

base withlesion

biotin

an aliphaticN-acetyl-diamine

citrate

uracil

amylomaltase:malQ

superpathway of pyridoxal 5’-phosphate biosynthesis and salvage

uridine

L-alanine

UDP-D-glucuronate

5’,5’-diadenosinetriphosphate

a glucoronide

phosphoenolpyruvate

2-hydroxyglutarate

23S rRNA m2G2445methyltransferase:rlmL

dihydropteroatesynthase: folP

probable 6-phospho-beta-glucosidase:glvG

N-acetylglucosamine

NADPHnitroreductase:nfsA

glycerophosphoryldiesterphosphodiesterase,periplasmic: glpQ

UDP-D-glucuronate

glycerol degradation I

ubiquinone-8biosynthesis(prokaryotic)

MdtABC-TolC

multidrugefflux

transportsystem

pyruvate

L-rhamnosemutarotase:rhaM

fumarase C: fumC

fumaratereductase: frdDfrdC frdB frdA

tRNAphe

UDP-L-Ara4Nformyltransferase:arnA

alpha-D-mannose1-phosphate

arbutin-6-phosphate

Ca2+ Na+ K+

a tRNA

c-di-GMPphosphodiesterase:yhjH

acetate

taurine

2-oxobutanoate

a protein-L-methionine-(R)-S-oxide

beta-D-galactose

correspondingcarbamoylamino acid

carnitine degradation I

predicted alpha-ribazole-5’-Pphosphatase: cobC

phosphoproteinphosphatase: pphB

glutamate-1-semialdehyde

ribulosephosphate3-epimerase:rpe

homoserine

di-trans,poly-cis-nonaprenyl

diphosphate

methionylpeptide

MdtJIspermidine

SMRtransporter

EIIChb

D-xylulose

fructoselysine 3-epimerase: frlC

L,D-transpeptidaseErfK: erfK

UhpBA Two-Component

SignalTransduction

System

precorrin-1

D-ribose

methylglyoxalreductase(NADPH-dependent)

L-cysteine

a fatty acid

predicted acetoindehydrogenase:yohF

O-succinylhomoserinelyase: metB

pre-cofactor

N-acetylmuramicacid PTSpermease

phosphoribosylamine-glycine ligase: purD

thiaminemonophosphatekinase: thiL

thiaminbiosynthesis

ThiGHcomplex:thiH thiG

L-glutamate

adenylosuccinatesynthetase: purA

phospholipid biosynthesis I

palmitoleatebiosynthesis

N5-carboxyaminoimidazoleribonucleotidesynthetase: purK

phosphoribosylaminoimidazole-succinocarboxamide synthase: purC

L-Ala-D-Glu-meso-A2pm

a 6-acetyl-beta-D-

galactoside

2-keto-isovalerate

ethyl-2-methylacetoacetate

leucine ABCtransporter

pyruvatekinase I: pykF

tRNAile

OuterMembrane

FerrichromeTransportSystem

2-trans,5-cis-tetradecadienoyl-

fumarase B: fumB

NarQ Nitrate/Nitrite-DependentTwo-Component Regulatory System

imidazoleacetol-

phosphate

an (R)-3-hydroxyhexanoyl-

an N-acetylspermidine

formate

a drug

pyridoxalphosphatase:cof

N-acetylglutamatesynthase: argA

a holo-[acp]

UDP-4-amino-4-deoxy-L-arabinose

23S rRNAcontaining

ornithinedecarboxylase,biosynthetic:speC

partially N-deacetylated

a holo-[acp]

5’-deoxyadenosine

2-selenouridine

aldehydedehydrogenase A,NAD-linked: aldA

L-tryptophanyl-tRNAtrp

16S rRNAcontaining

N3-methylated

uridine

a 3-oxo-cis-vaccenoyl-

5-amino-6-(5’-phosphoribosylamino)

uracil

heme dsynthase:katE

short chain acyl-CoAsynthetase: fadK

pyruvate

L-glutamategamma-

semialdehyde

an acyl-[acp]

DNA Cleavedat Recognition

L-tartrate

L-mannose

sulfate

methanol

tRNAtyr

TorSR Two-Component Signal Transduction System

arsenatereductase:arsC

DNA (without 6-O-methylguanine)

oxidizedribonucleoside-

triphosphatereductase

tRNAval

succinate

protein-tyrosine-phosphatase:pphB

bifunctional 3-demethylubiquinone-83-O-methyltransferaseand 2-octaprenyl-6-hydroxyphenolmethylase: ubiG nicotinate

mononucleotide

L-homocysteine

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.

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.

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.

Modeling Gene Regulatory Networks (GRN)

Regulated synthesis

Degrada1on and

dilu1on

a transcrip1on factor x

1 2 3 4 5

Positive Hill

1 2 3 4 5

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].

Regulated synthesis

Degrada1on and

dilu1on

1 2 3 4 5

Positive Hill

1 2 3 4 5

Negative Hill

n=1n=2n=3n=4n=5n=6

θn + xn,

C) Dilution µ.

Regulated synthesis

Degrada1on and

dilu1on

1 2 3 4 5

Positive Hill

1 2 3 4 5

Negative Hill

n=1n=2n=3n=4n=5n=6

θn + xn,

C) Dilution µ.

For each gene there are (at least) three terms in the model:

= 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.

Promoters as logic gates

promoter

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);

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;

Modeling the feedforward loop

System of equations for the FFLC-1 AND

Regulated synthesis︷︸︸︷κ

θn + Xn− (γ + µ)︸︷︷︸

Degr. and dil.

= κXn

θn + Xn

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)

= κXn

θn + Xn

θn + Yn− αZ. (4)

Network motifs have special dynamical properties

0 5 10 15 20 25 30 35 40−0.5

Feed-Forward Loop Coherent type I

0 5 10 15 20 25 30 35 40−0.5

T ime! +µ

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

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;

Metabolic network representations

Compound graph Reaction graph

Bipartite graph Hypergraph

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];

E F OUT

OUTA B C D

E F OUT

G2G1 G3

OUTA B C D

E F OUT

G2G1 G3

OUTA B C D

E F OUT

G2G1 G3

Metabolism is not isolated...

Gene regulation

Metabolism

Transcription&

Translation

Effectormetabolites

Even this picture misses important regulatory mechanisms..

The stoichiometry matrix

E F OUT

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.

E F OUT

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).

E F OUT

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

dt = N · v(x, p).

E F OUT

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

dt = N · v(x, p).

E F OUT

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

dt = N · v(x, p).

E F OUT

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

dt = N · v(x, p).

plot_1

[1,3-diphosphosphoglycerate]|Time [6-Phosphogluconate]|Time [Fructose-1,6-bisphosphate]|Time

[Glucose-6-Phosphate]|Time [Pyruvate]|Time

s0 1,000 2,000 3,000 4,000 5,000 6,000

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]).

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;

FBA - Concept

Solve: Nv = 0

But for genome scale metabolicnetworks is an underdeterminedproblem, i.e. infinite solutions exist;

FBA - Concept

Solve: Nv = 0But for genome scale metabolicnetworks is an underdeterminedproblem, i.e. infinite solutions exist;

FBA - Algo

Allowable solutions

Not allowablesolutions

v3*v1*

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

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

FBA - Objective function

Allowable solutions

Not allowablesolutions

v3*v1*

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

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

• 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;

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);

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);

Rate functions

1 Irreversible Michaelis-Menten: v = vmax[S]

Km+[S] ;

2 Reversible Michaelis-Menten: v =Vf ·[S]KmS− Vr·[P]

1+ [S]KmS

3 Hill cooperativity: v = V·[S]hKh

h+[S]h ;

4 Allosteric inhibition: v =Vf ·[S]KmS− Vr·[P]

1+ [S]KmS

[I]Ki)n

The "Bible" of enzyme kinetics: Fundamentals of Enzyme Kinetics by Athel Cornish-Bowden,available on Amazon.

[S] is fized at 1mM; [P] startsfrom 0mM;Reversible Michaelis-Menten:

v =Vf ·[S]KmS− Vr·[P]

1+ [S]KmS

IrreversibleMichaelis-Menten:

v = vmax[S]

Km + [S];

0 2 4 6 8 100

Product of reversible Michaelis-Menten

0 2 4 6 8 100

mol/s)

Rate Reversible Michaelis-Menten

0 2 4 6 8 100

Product of Irreversible Michaelis-Menten

0 2 4 6 8 108

Rate Irreversible Michaelis-Menten

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.