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Authors: Peter D.

Karp Ingrid Keseler Alexander Shearer Anamika Kothari

Suzanne Paley Markus Krummenacker Tomer Altman Ian Paulsen

Amanda Mackie Aaron Johnson Julio Collado-Vides Cesar Bonavides-Martinez

Robert Gunsalus Socorro Gama-Castro Martin Peralta Alberto Santos-Zavaleta John L Ingraham

EcoCyc: Escherichia coli K-12 MG1655 Cellular Overview


xanthine xanthosine xanthine D-sorbitol D-gluconate D-gluconate L-idonate D-gluconate D-fructuronate D-gluconate beta-Dglucose-6phosphate beta-Dglucose putrescine putrescine putrescine spermidine putrescine D-xylose L-ornithine L-rhamnose L-lyxose D-xylose cellobiose chitobiose XylF/XylG/ XylH xylose ABC transporter D-allose D-fructose L-fucose N-acetyl-D-glucosamine glucosamine D-fructose beta-D-glucose D-mannose 2,3-diketoL-gulonate melibiose melibiose melibiose Li+ D-galactitol beta-Dgalactose beta-Dribopyranose trehalose lactose beta-Dgalactose taurine D-galactonate 2-dehydro3-deoxy-Dgluconate D-mannitol D-mannitol YiaMNO Binding Proteindependent Secondary (TRAP) Transporter nitrite nitrite nitrate H2O nitrate YjcD YejM RseP YagU QmcA MurJ GfcA MdoC RhtB YnfA RsxB RsxD RsxE YedZ YgaZ/YgaH L-valine exporter complex YegH ZipA YfhM YfjS YgdQ YgjV EamB EamA YhgN HemX TisB NapD YgfO XapB YicE YiaF DcuB DcuC DcuA EIIGut GntU GntT IdnT GntP UhpT EIIGlc PuuP putrescine ABC transporter FocA PotE putrescine/ spermidine ABC transporter PotE RhaT XylE EIIChb D-allose ABC transporter EIIFru FucP EIIMan MelB MelB EIIGat GalP ribose ABC transporter EIITre LacY SetA SetB galactose ABC transporter taurine ABC transporter DgoT KdgT EIIMtl CmtAB mannitol PTS permease TatABCE protein export complex CbdAB NirC NarK NarK NarU AqpZ NarU NarK NRZ N-acetylmuramoyl-Lalanyl-D-glutamyl-meso2,6-diaminopimelylD-alanyl-D-alaninediphosphoundecaprenylN-acetylglucosamine homoserine lactone homoserine L-valine L-cysteine O-acetyl-L-serine L-cysteine O-acetyl-L-serine a C4-dicarboxylate a C4-dicarboxylate a C4-dicarboxylate a C4-dicarboxylate a C4-dicarboxylate a C4-dicarboxylate D-sorbitol6-phosphate beta-Dglucose-6phosphate formate putrescine cellobiose-6-phosphate diacetylchitobiose-6-phosphate fructose-1phosphate

An online version of this diagram is available through EcoCyc.org and may be used for analysis of omics datasets. Lines in the diagram 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 other membrane proteins. In the periplasm are periplasmic enzymes and other periplasmic proteins. Connections between pathways are omitted for legibility.

L-glutamate

L-galactonate

GadC

ArgO

YfaV

YgfU

MinD

PspC

PsiE

EptA

NfrB

NRA

cytochrome bo terminal oxidase

YjjL

FtsQ

HcaT

YojI

YeiM

agmatine AdiC L-arginine

4-aminobutyrate

AMINOACYL-TRNA CHARGING tRNA charging pathway


L-arginine

CELL STRUCTURES BIOSYNTHESIS purine nucleotides de novo biosynthesis I NUCLEOSIDES AND NUCLEOTIDES BIOSYNTHESIS pyrimidine ribonucleotides de novo biosynthesis
bicarbonate

FATTY ACIDS AND LIPIDS BIOSYNTHESIS peptidoglycan biosynthesis I palmitate biosynthesis II (bacteria and plants)
an acetoacetyl-[acp]

AROMATIC COMPOUNDS BIOSYNTHESIS enterobactin biosynthesis


chorismate

TCA CYCLE FERMENTATION mixed acid fermentation


phosphoenolpyruvate

CARBOHYDRATES L-lyxose degradation


L-lyxose D-arabinose L-rhamnose isomerase: rhaA L-xylulose L-xylulose kinase: lyxK L-xylulose5-phosphate predicted Lxylulose 5phosphate 3-epimerase: sgbU L-ribulose5-phosphate L-ribulose-5phosphate 4-epimerase: sgbE L-ribulose 5phosphate 4-epimerase: araD D-xylulose5-phosphate L-fucose isomerase: fucI D-allose D-allose kinase: alsK D-allose-6phosphate allose-6phosphate isomerase / ribose-5phosphate isomerase B: rpiB D-allulose-6phosphate allulose-6phosphate 3-epimerase: alsE D-fructose6-phosphate glycolate dihydroxyacetone phosphate

N-acetyl-D-glucosamine-6-phosphate D-glucosamine-6-phosphate D-fructose-6-phosphate beta-D-glucose-6-phosphate DEGRADATIOND-mannose-6-phosphate

lactose galactitol-1phosphate trehalose 6phosphate

lactose mannitol-1phosphate a polypeptide mannitol-1phosphate

H+

nitrite

nitrite

nitrite

nitrite

H+

H+ H+ a lipopolysaccharide MsbA a longlinear glucan a singlestranded RNA

L-ornithine L-lysine L-arginine

lysine/ arginine/ ornithine ABC Transporter arginine ABC transporter

pyrimidine deoxyribonucleotides de novo biosynthesis


CDP ribonucleoside- CDP reductase: diphosphate nrdB nrdA reductase 2: nrdF nrdE dCDP CTP ribonucleosidetriphosphate reductase: nrdD UDP reductase: ribonucleosidediphosphate nrdB nrdA reductase 2: nrdF nrdE dUDP nucleoside diphosphate kinase: ndk UTP ribonucleosidetriphosphate reductase: nrdD 2,3-dihydro-2,3dihydroxybenzoate 2,3-dihydro-2,3dihydroxybenzoate dehydrogenase: entA fumarase A: fumA fumarase B: fumB fumarase C: fumC isochorismate malate dehydrogenase: mdh malate

C1 COMPOUNDS UTILIZATION AND ASSIMILATION L-arabinose degradation I


L-arabinose L-arabinose isomerase: araA L-ribulose L-ribulokinase: araB L-ribulose5-phosphate L-ribulose 5phosphate 4epimerase: araD D-xylulose5-phosphate

colanic acid building blocks biosynthesis


D-fructose6-phosphate D-galactose UTP UDP-Dgalactose UDPgalactopyranose mutase: glf UDP-Dgalacto-1,4furanose

O-antigen biosynthesis
dTTP alpha-Dglucose 1phosphate dTDP-glucose pyrophosphorylase: rfbA dTDP-Dglucose dTDPglucose 4,6dehydratase: rfbB dTDP-4dehydro6-deoxyD-glucose dTDP-4dehydrorhamnose 3,5-epimerase: rfbC dTDP-4dehydro6-deoxyL-mannose dTDP-4dehydrorhamnose reductase: rfbD dTDPalpha-Lrhamnose D-fructose6-phosphate L-glutamine:Dfructose-6phosphate aminotransferase: glmS D-glucosamine6-phosphate phosphoglucosamine mutase: glmM D-glucosamine 1-phosphate fused Nacetylglucosamine1-phosphate uridyltransferase and glucosamine1-phosphate acetyltransferase: glmU N-acetylglucosamine1-phosphate fused Nacetylglucosamine1-phosphate uridyltransferase and glucosamine1-phosphate acetyltransferase: glmU UDP-Nacetyl-Dglucosamine

arginyl-tRNA synthetase: argS

superpathway of lipopolysaccharide biosynthesis


UDP-Nacetyl-Dglucosamine an (R)-3hydroxymyristoyl[acp] UDP-Nacetylglucosamine acyltransferase: lpxA UDP-3-O-(3hydroxymyristoyl)N-acetylglucosamine UDP-3-O-acyl-Nacetylglucosamine deacetylase: lpxC UDP-3-O-(3hydroxymyristoyl) glucosamine UDP-3-O-[3hydroxymyristoyl]glucosamine N-acetyltransferase: lpxD

phospholipid biosynthesis I
dihydroxyacetone phosphate glycerol-3-phosphate dehydrogenase, biosynthetic: gpsA

UDP-N-acetyl-D-glucosamine UDP-N-acetylglucosamine enolpyruvoyl transferase: murA UDP-GlcNAc-enolpyruvate UDP-Nacetylenolpyruvoylglucosamine reductase: murB L-glutamate UDP-N-acetylmuramate L-alanine glutamate racemase: murI UDP-N-acetylmuramatealanine ligase: murC UDP-N-acetylmuramoylL-alanine D-glutamate

L-arginine

L-arginyltRNAarg

tRNAarg D-ribulose5-phosphate cysteinyltRNA synthetase: cysS L-cysteinyltRNAcys an (R)-3hydroxybutanoyl[acp] beta-hydroxyacylACP dehydrase [multifunctional]: fabA beta-hydroxyacylACP dehydratase: fabZ D-arabinose 5-phosphate isomerase: gutQ D-arabinose 5-phosphate isomerase: kdsD D-arabinose 5-phosphate 3-deoxyD-mannooctulosonate 8-phosphate synthase: kdsA 3-deoxyD-mannooctulosonate 8-P 3-deoxyD-mannooctulosonate 8-phosphate phosphatase: kdsC 3-deoxyD-mannooctulosonate 3-deoxy-D-mannooctulosonate cytidylyltransferase: kdsB

mannose-6phosphate isomerase: manA D-mannose6-phosphate

galactokinase: galK

glucose-1-phosphate uridylyltransferase: galU galF UDP-D-glucose

biosynthesis of 4-amino4-deoxy-LarabinoseUDP-Dmodified lipid A glucuronate


UDP-GlcA C-4"decarboxylase: arnA UDP-L-Ara4O

5-phosphoribosyl 1-pyrophosphate amidophosphoribosyl transferase: purF 5-phosphobeta-Dribosylamine phosphoribosylamineglycine ligase: purD 5-phosphoribosylglycineamide GAR transformylase 2: purT 5-phosphoribosylN-formylglycineamide phosphoribosylglycinamide formyltransferase: purN

pyruvate oxidation pathway


pyruvate kinase I: pykF pyruvate kinase II: pykA pyruvate pyruvate oxidase: poxB acetate

D-arabinose degradation I

D-allose degradation

rhamnose degradation
L-rhamnose

phosphoenolpyruvate carboxylase: ppc uridine-5diphosphate isochorismate synthase 1: entC

2-O-alphamannosylD-glycerate 2-O-(6degradation
phosphoalphamannosyl)D-glycerate

alpha-Lfucose L-fucose mutarotase: fucU beta-Lfucose

1-deoxyD-xylulose xylulokinase: xylB 1-deoxy-Dxylulose 5phosphate

D-fructose manno(fructo) kinase: mak D-fructose6-phosphate

a beta-Dgalactoside galactoside Oacetyltransferase: lacA a 6-acetylbeta-Dgalactoside

maltose maltose acetyltransferase: maa acetylmaltose

dihydrouracil NADH NAD-dependent dihydropyrimidine dehydrogenase: yeiA yeiT uracil NAD+ H+ nitrite H2O inorganic pyrophosphatase: ppa

a maltodextrin amylomaltase: malQ beta-Dglucose a maltodextrin

phenylhydantoin phenylhydantoinase: hyuA corresponding carbamoyl amino acid

a carboxylic ester carboxylesterase: bioH a carboxylate an alcohol

formaldehyde oxidation II (glutathionedependent)


formaldehyde

a DNA containing 6-Omethylguanine

a protein L-cysteine Ogt: ogt

an N-acetyl-Dhexosaminide beta-Nacetylglucosaminidase: nagZ an Nacetyl-Dhexosamine an organic molecule

dCTP pyrimidine deoxynucleoside triphosphate pyrophosphohydrolase: nudI dCMP

UDP-Dgalacto-1,4furanose

DNA (without 6O-methylguanine)

a proteinS-methylL-cysteine

2-O-(6phosphobeta-1,6alphagalactofuranosyltransferase: wbbI mannosyl)D-glycerate octyl beta-1,6-Dgalactofuranosylalpha-Dglucopyranoside

octyl alpha-Dglucopyranoside

1,4dihydroxy-2naphthoate

all-transoctaprenyl diphosphate

L-glutamate

p-aminobenzoate

2-O-alpha-mannosyl-Dglycerate transporting phosphotransferase system

mannosylglycerate

a short glucan

a short glucan

a singlestranded RNA

a singlestranded RNA

demethylmenaquinone-8

p-aminobenzoyl glutamate

uridine-5diphosphate

carbamoyl phosphate synthetase: carA carB

L-rhamnose isomerase: rhaA

H+

oxaloacetate pyruvate

D-ribulose L-fuculokinase: fucK

alpha-D-galactose 1-phosphate

fucose degradation
L-fucose

L-rhamnulose

ribose degradation
beta-Dribopyranose ribose pyranase: rbsD beta-Dribofuranose

pyridine nucleotide transhydrogenase

beta-Dgalactose aldose-1epimerase: galM

a quinone

dihydroorotate

all-transfarnesyl diphosphate

protoheme IX

a phosphatidylcholine

carbamoyl-phosphate nucleoside diphosphate kinase: ndk

alphamannosidase: mngB S-hydroxymethylglutathione D-glycerate glycerate kinase I: garK D-mannose6-phosphate formaldehyde dehydrogenase, glutathionedependent: frmA S-formylglutathione 2-phosphoglycerate S-formylglutathione hydrolase: yeiG S-formylglutathione hydrolase: frmB

an oxidized electron acceptor

D-mannose mannose isomerase: yihS

D-mannose

a 1,2diacylglycerol diacylglycerol kinase: dgkA a 1,2diacylglycerol3-phosphate

a polypeptide aminopeptidase N: pepN

an acyl phosphate acylphosphatase: yccX

hydroxypyruvate hydroxypyruvate isomerase: hyi tartronate semialdehyde

an acetic ester acetylesterase: aes acetate an alcohol

citrate citrate lyase: citE citF citD

S-ureidoglycolate ureidoglycolase: allA glyoxylate urea

alpha-Nacetylneuraminate N-acetylneuraminate mutarotase: nanM beta-Nacetylneuraminate

4-nitrobenzaldehyde 4-nitrobenzaldehyde reductase: dkgB 4-nitrobenzyl alcohol

7,8dihydroneopterin triphosphate

7-aminomethyl7-deazaguanine

7-cyano-7carbaguanine 7-cyano-7deazaguanine reductase: queF

dTTP pyrimidine deoxynucleoside triphosphate pyrophosphohydrolase: nudI dTMP

UDP-Dglucose

a lipopolysaccharide UDP-glucose:(glucosyl) LPS alpha-1,2glucosyltransferase: rfaJ H+ cytochrome bd-I terminal oxidase

sn-glycerol-3-phosphate phosphomannomutase: cpsG alpha-D-mannose 1-phosphate UDP-glucosehexose-1-phosphate uridylyltransferase: galT UDP-glucose 6dehydrogenase: ugd UDP-Dglucuronate

L-cysteine

enterobacterial common antigen biosynthesis


dTTP alpha-D-glucose 1-phosphate dTDP-glucose pyrophosphorylase 2: rffH

aspartate carbamoyltransferase: pyrI pyrB

isochorismatase: entB

citrate synthase: gltA citrate bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase: acnB aconitate hydratase 1: acnA cis-aconitate acetylphosphate bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase: acnB aconitate hydratase 1: acnA acetaldehyde

YneN

glycerol-3-phosphate acyltransferase: plsB a 1-acyl-sn-glycerol3-phosphate 1-acylglycerol3-phosphate acyltransferase: plsC

glycerol-3-phosphate acyltransferase: plsB a 1-acyl-sn-glycerol3-phosphate 1-acylglycerol3-phosphate acyltransferase: plsC

UDP-L-Ara4O C4" transaminase: arnB UDP-4-amino4-deoxy-Larabinose UDP-L-Ara4N formyltransferase: arnA

dCTP N-carbamoyl-L-aspartate dCTP deaminase: dcd dihydroorotase: pyrC

pyruvate formatelyase: pflB pyruvate formatelyase: tdcE acetyl-CoA formate

D-lactate dehydrogenase: ldhA D-lactate

L-rhamnulose kinase: rhaB L-fucose isomerase: fucI L-fuculose rhamnulose1-phosphate aldolase: rhaD dihydroxyacetone phosphate L-rhamnulose1-phosphate

a quinol alpha-Dgalactose

orotate

mannokinase

heme o

a carboxylate

a 1-lyso-2-acylsn-glycero-3phosphocholine

D-ribulose-1-phosphate

a reduced electron acceptor

D-fructose

D-mannose6-phosphate

a polypeptide

6-pyruvoyl tetrahydropterin

PPPi 7-cyano-7carbaguanine 7-aminomethyl7-deazaguanine

a carboxylate

oxaloacetate

acetate

UDP-D-galactose

L-fuculose-phosphate aldolase: fucA

uridine-5diphosphate

D-glucosyllipopolysaccharide

oxidized thioredoxin

trehalose periplasmic trehalase: treA beta-Dglucose

NADPH

NAD+

an L-1phosphatidylglycerol

an MDOO-glucose

a longlinear glucan endo-1,4-Dglucanase: bcsZ

tRNAcys SugE glutaminyltRNA synthetase: glnS L-glutaminyltRNAgln

L-glutamine L-glutamine glutamine ABC transporter tRNAgln L-glutamate GltS

a crotonyl-[acp]

UDP-2,32,3-bis(3-diacylglucosamine hydroxymyristoyl)hydrolase: UDP-2,3-bis(3lpxH beta-D-glucosaminyl hydroxymyristoyl) 1-phosphate glucosamine lipid A disaccharide synthase: lpxB

UDP-N-acetylmuramoylL-alanine:Dglutamate ligase: murD UDP-N-acetylmuramoylL-alanyl-D-glutamate

mannose-1-phosphate guanylyltransferase: cpsB D-alanine GDP-alphaD-mannose D-alanine-D-alanine ligase B: ddlB D-alanine-D-alanine ligase A: ddlA

UDP-glucose 4epimerase: galE UDP-D-glucose

dUTP dihydroorotate pyrimidine deoxynucleoside triphosphate pyrophosphohydrolase: nudI deoxyuridine triphosphatase: dut dUMP thymidylate synthase: thyA dTMP orotidine-5-phosphate dTMP kinase: tmk orotidine-5-phosphatedecarboxylase: pyrF uridine-5-phosphate 2,3dihydroxybenzoate L-serine

fumarate fumarate reductase: frdD frdC frdB frdA succinate

UDP-N-acetylD-glucosamine UDP-Nacetylglucosamine2-epimerase: rffE UDP-N-acetylD-mannosamine di-trans,poly-cisundecaprenyl phosphate

phosphate acetyltransferase: pta

acetaldehyde dehydrogenase: adhE

dTDP-D-glucose dTDP-glucose 4,6-dehydratase 2: rffG dTDP-4dehydro-6deoxy-D-glucose dTDP-4-oxo-6deoxy-D-glucose transaminase: rffA dTDP-Dfucosamine dTDP-fucosamine acetyltransferase: rffC dTDP-4acetamido4,6-dideoxyD-galactose 4-acetamido4,6-dideoxyD-galactose transferase: rffT undecaprenyl N-acetylglucosaminyl-N-acetylmannosaminuronate4-acetamido-4,6dideoxy-D-galactose pyrophosphate

phosphoribosylformylglycinamide synthetase: purL UDP-L-Ara4FN 5-phosphoribosyl-Nformylglycineamidine phosphoribosylformylglycinamide cyclo-ligase: purM 5-aminoimidazole ribonucleotide N5-carboxyaminoimidazole ribonucleotide synthetase: purK N5-carboxyaminoimidazole ribonucleotide N5-carboxyaminoimidazole ribonucleotide mutase: purE 4-carboxyaminoimidazole ribonucleotide phosphoribosylaminoimidazolesuccinocarboxamide synthase: purC dihydroorotate oxidase: pyrD

formate hydrogenlyase complex: hycD hycC hycF hycG hycB hycE fdhF

dihydroxyacetone phosphate

glycolaldehyde aldehyde dehydrogenase A, NAD-linked: aldA

L-fuculokinase: fucK L-fuculose1-phosphate L-fuculosephosphate aldolase: fucA

transaconitate

L-rhamnose L-rhamnose mutarotase: rhaM

xyloglucan oligosaccharide alphaxylosidase: yicI D-xylose

L-rhamnonate L-rhamnonate dehydratase: yfaW 2-keto-3deoxy-Lrhamnonate

a polypeptide aminopeptidase N: pepN a polypeptide

L-lactaldehyde

dihydroxyacetone phosphate methylglyoxal synthase: mgsA methylglyoxal

a 1,4-alphaD-glucan maltodextrin glucosidase: malZ alpha-Dglucose a 1,4-alphaD-glucan

1,3propanediol

an rRNA 23S rRNA m2A2503 methyltransferase: rlmN

xanthosine ribonucleoside hydrolase 3: rihC xanthine D-ribose

DcuSPhis349

DcuR

transaconitate trans-aconitate methyltransferase: tam

beta-Dglucose 1phosphate betaphosphoglucomutase: ycjU beta-Dglucose-6phosphate

a DNA cyclobutadipyrimidine deoxyribodipyrimidine photolyase (photoreactivation): phr a DNA pair of adjacent pyrimidines

3-hydroxypropionaldehyde gamma-glutamyl-gammaaminobutyraldehyde dehydrogenase: puuC 3-hydroxypropionate CO

a quercetin pirin-like protein: yhhW 2-protocatechuoylphloroglucinolcarboxylate

MdtO

D-ribose ribokinase: rbsK D-ribose-5phosphate

NADP+

NADH

an MDO-6(glycerophospho) -D-glucose

a 1,2diacylglycerol

a short glucan

a short glucan

a 1,2-diacylglycerol3-phosphate CDP-diglyceride synthetase: cdsA

a butyryl-[acp]

UDP-N-acetylmuramoylalanylD-glutamate 2,6diaminopimelate ligase: murE UDP-N-acetylmuramoylL-alanyl-D-glutamylmeso-2,6-diaminopimelate

GDP-mannose 4,6dehydratase: gmd

5-phosphoribosyl 1-pyrophosphate

orotate

enterobactin synthase multienzyme complex: entE entF entD entB enterobactin

H2 acetate kinase: ackA acetate kinase B: ackB ethanol dehydrogenase: adhP alcohol dehydrogenase: adhE ethanol

CO2

L-lactaldehyde

D-alanyl-D-alanine GDP-4-dehydro6-deoxyD-mannose

L-glutamate

GltIJKL glutamate ABC transporter

L-glutamate

glutamyltRNA synthetase: gltX L-glutamyltRNAGlu

KASI: fabB

lipid A disaccharide a CDP-diacylglycerol tetraacyldisaccharide 4-kinase: lpxK phosphatidylglycerophosphate synthase: pgsA lipid IVA an L-1phosphatidylglycerolphosphate phosphatidylglycerophosphatase C phosphatidylglycerophosphatase B: pgpB phosphatidylglycerophosphatase A: pgpA an L-1-phosphatidylglycerol cardiolipin synthase: cls an L-1phosphatidylserine phosphatidylserine synthase: pssA

a 3-oxohexanoyl-[acp] beta-ketoacyl[acyl-carrierprotein] reductase: fabG

D-alanyl-D-alanineadding enzyme: murF UDP-N-acetylmuramoylL-alanyl-D-glutamylmeso-2,6-diaminopimelylD-alanyl-D-alanine phospho-N-acetylmuramoylpentapeptide transferase: mraY N-acetylmuramoyl-Lalanyl-D-glutamyl-meso2,6-diaminopimelylD-alanyl-D-alaninediphosphoundecaprenol N-acetylglucosaminyl transferase: murG N-acetylmuramoyl-Lalanyl-D-glutamyl-meso2,6-diaminopimelylD-alanyl-D-alaninediphosphoundecaprenylN-acetylglucosamine

UDP-N-acetyl-Dmannosaminuronic acid dehydrogenase: rffD undecaprenylN-acetyl-alphaUDP-N-acetyl-beta-DD-glucosaminylmannosaminouronate pyrophosphate UDP-N-acetyl-Dmannosaminuronic acid transferase: rffM undecaprenyl N-acetylglucosaminyl-N-acetylmannosaminuronate pyrophosphate

undecaprenyl phosphatealpha-L-Ara4FN

trehalose degradation II (trehalase)


trehalose

trehalose degradation I (low osmolarity) trehalose 6phosphate trehalose-6phosphate hydrolase: treC beta-Dglucose

formate

cis-aconitate

beta-Lrhamnose

3-hydroxypropionaldehyde

rRNA containing 2methyladenine

DcuS

DcuRPasp56

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

FtsE/ FtsX ABC transporter

L-lactate

undecaprenyl phosphatealpha-L-Ara4N

KDO2lipid A

a 2,3,4saturated Lphosphatidate

CTP

di-trans,polycisundecaprenyl diphosphate

orotate phosphoribosyltransferase: pyrE

nigerose glycoside hydrolase: ygjK alpha-Dglucose

pre-cofactor caiE protein: caiE

lactose betagalactosidase: lacZ allolactose

acetate D-threo-isocitrate isocitrate dehydrogenase: icd

PENTOSE PHOSPHATE PATHWAYS pentose phosphate pathway


beta-Dglucose-6phosphate

xylose degradation I
D-xylose xylose isomerase: xylA D-xylulose xylulokinase: xylB D-xylulose5-phosphate

an aliphatic alpha,omegadiamine diamine transaminase: ygjG an aliphatic omegaaminoaldehyde

pyrazinamide pyrazinamidase: pncA

an aliphatic alpha,omegadiamine spermidine acetyltransferase: speG an aliphatic N-acetyldiamine

formyl-Lmethionyl peptide peptide deformylase: def formate methionyl peptide

enterobactin enterochelin esterase: fes

acetaldehyde

pyruvate acetoin synthesis: poxB

colanic acid

Lipid A-core

a 1,4-alphaD-glucan maltodextrin phosphorylase: malP alpha-Dglucose 1phosphate a 1,4-alphaD-glucan

an oxidized cytochrome c

trimethylamine

an alkylhydroperoxide alkylhydroperoxide reductase: ahpF ahpC

an rRNA 16S rRNA m62A1518,m62A1519 dimethyltransferase: ksgA rRNA containing N6,N6dimethyladenine

GlcNAc-1,6anhMurNAc beta-Nacetylglucosaminidase: nagZ N-acetyl-Dglucosamine 1,6-anhydro-Nacetylmuramate

3,4-dihydroxyphenylacetylCoA hydroxyphenylacetylCoA thioesterase: paaI

AmpG

GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-DAP-D-Ala GlcNAc-1,6-anhMurNAc pyruvate

chitobiose degradation
diacetylchitobiose6-phosphate

all trans undecaprenyl phosphate

L-Ara4Nmodified KDO2Lipid A

a CDP-2,3,4saturateddiacylglycerol

tRNAGlu L-aspartate L-glutamate GltP

GDP-fucose synthase: fcl

undecaprenyl phosphatealpha-L-Ara4N

D-mannose degradation
D-mannose6-phosphate mannose-6phosphate isomerase: manA D-fructose6-phosphate

cytoplasmic trehalase: treF beta-Dglucose glucokinase: glk beta-Dglucose-6phosphate

glucose and glucose-1phosphate degradation


alpha-D-glucose-1phosphatase: yihX sugar phosphatase: ybiV sugar phosphatase: yidA sugar phosphatase: yigL

O-antigen ligase: rfaL

di-trans,polycisundecaprenyl phosphate GlcNAc-1,6anhMurNAcL-Ala-gammaD-GluDAP-D-Ala N-acetylanhydromuramylL-alanineamidase: ampD L-Alagamma-DGlu-DAPD-Ala GlcNAc-1,6anhMurNAc

YhjE Cu2+ beta-Dglucose-6phosphate phosphoglucose isomerase: pgi D-fructose6-phosphate CMP a 1,2diacylglycerol3-phosphate a CDPdiacylglycerol

cofactor

pyrazinoate

2,3-dihydroxybenzoylserine acetoin

MLPS

a reduced cytochrome c

trimethylamine N-oxide

an alcohol

coenzyme A

3,4-dihydroxyphenylacetate

dTDP nucleoside diphosphate kinase: ndk xanthosine

2-oxoglutarate

salvage pathways of guanine, xanthine, and their nucleosides RESPIRATION


guanine xanthosine phosphorylase: xapA guanine deaminase: guaD purine nucleoside phosphorylase: deoD hypoxanthine phosphoribosyltransferase: hpt xanthine-guanine phosphoribosyltransferase: gpt

GDP-L-fucose

L-valine L-leucine L-isoleucine

branched chain amino acids ABC transporter

L-isoleucine

isoleucyltRNA synthetase: ileS L-isoleucyltRNAile

an (R)-3hydroxyhexanoyl[acp] beta-hydroxyacylACP dehydrase [multifunctional]: fabA beta-hydroxyacylACP dehydratase: fabZ

KDO transferase: waaA (KDO)lipid IVA

uridylate kinase: pyrH

glucose 6phosphate-1dehydrogenase: zwf D-gluconodeltalactone-6phosphate 6-phosphogluconolactonase: pgl

diacetylchitobiose6-phosphate hydrolase: chbF N-acetyl-Dglucosamine N-acetyl-Dkinase: nagK N-acetyl-Dglucosamineglucosamine 6-phosphate

alpha-D-glucose 1-phosphate

D-glucose

glucokinase: glk beta-Dglucose-6phosphate a 1,4-alphaD-glucan alphaamylase: amyA maltopentaose 3-keto-Lgulonate L-xylulose kinase: lyxK 3-keto-Lgulonate 6phosphate an aromatic sulfate arylsulfatase: aslA a phenol an oxidized nitroaromatic compound NADPH nitroreductase: nfsA a reduced nitroaromatic compound gluconodelta-lactone gluconolactonase 4-hydroxybutyrate succinate semialdehyde reductase: yihU succinate semialdehyde spermidine spermidine acetyltransferase: speG an Nacetylspermidine a quinone quinone oxidoreductase: qor a semiquinone an rRNA 23S rRNA m6A1618 methyltransferase: rlmF rRNA containing N6methyladenine 2-phosphoglycolate an oxidized electron acceptor formate formate dehydrogenase: fdhF a reduced electron acceptor a nucleoside monophosphate DNAn exonuclease III: xthA SucB-Ssuccinyldihydrolipoate SucB-lipoate 2-oxoglutarate an amineated amine donor 2-oxobutanoate valine-pyruvate aminotransferase: avtA a deamineated amine donor 2-aminobutyrate UTP

YjhB alpha-Dgalactose 1phosphate galactose-1phosphate uridylyltransferase: galT UDP-Dgalactose colanic acid

CMP-3-deoxyD-mannooctulosonate

phosphatidylserine decarboxylase: psd an L-1-phosphatidylethanolamine

salvage pathways of adenine, hypoxanthine, and their nucleosides


uridine-5-diphosphate

dTTP

alpha-D-glucose 1-phosphate

phosphoglucomutase: pgm alpha-D-glucose glucose 6-phosphate dehydrogenase: gcd

GDP-Lfucose

UDP-Dglucose

UDP-Dgalactose

UDP-Dglucuronate YjeM

Cu+

respiration (anaerobic)
phosphoenolpyruvate purine nucleoside phosphorylase: deoD 2-phosphoglycerate

phosphoglycolate phosphatase: gph glycolate

beta-D-glucose glucokinase: glk beta-D-glucose6-phosphate

malate

D-gluconate

L-valine L-leucine L-isoleucine

DNAn

beta-Dglucose-6phosphate phosphoglucose isomerase: pgi

an MDOO-glucose

an MDO-6(glycerophospho) -D-glucose phosphoglycerol transferase II: mdoB

BrnQ

tRNAile

nucleoside diphosphate kinase: ndk UTP

AMP

melibiose degradation fructose degradation


fructose-1phosphate 1-phosphofructokinase: fruK fructose-1,6bisphosphate beta-Dgalactose melibiose alphagalactosidase: melA beta-Dglucose

lactose degradation III


lactose

AtpI

KDO transferase: waaA

L-leucine

leucine ABC transporter

L-leucine

superpathway of fatty acid biosynthesis

METABOLIC REGULATORS BIOSYNTHESIS ppGpp biosynthesis

5-phosphoribosyl-4(N-succinocarboxamide) -5-aminoimidazole 5-phosphoribosyl-4(N-succinocarboxamide) -5-aminoimidazole lyase: purB aminoimidazole carboxamide ribonucleotide

AMP adenine phosphoribosyltransferase: apt nucleosidase: amn CTP synthetase: pyrG

xanthine

leucyl-tRNA synthetase: leuS

L-leucyltRNAleu

a trans hex2-enoyl-[acp]

xanthine-guanine phosphoribosyltransferase: gpt adenine xanthosine5-phosphate

deoxyguanosine guanosine5-phosphate

KDO2lipid IVA lauroyl acyltransferase: lpxL

acetyl-CoA

cardiolipin

guanosine kinase: gsk

guanosine

pyruvate kinase I: pykF pyruvate kinase II: pykA pyruvate

enolase: eno 6-phosphoD-gluconate phosphoenolpyruvate 6-phosphogluconate dehydrogenase (decarboxylating): gnd D-ribulose5-phosphate ammonium hydroxide betagalactosidase: lacZ beta-Dglucose beta-Dgalactose nitrite reductase: nirB nirD nitrite ribose-5phosphate isomerase A: rpiA allose-6phosphate isomerase / ribose-5phosphate isomerase B: rpiB D-ribose-5phosphate protoheme IX heme d synthase: katE heme d ammonia hybridcluster protein: hcp hydroxylamine ethanolamine ethanolamine ammonia-lyase: eutC eutB acetaldehyde acetaldehyde acetaldehyde dehydrogenase: aldB acetate L-quinate quinate dehydrogenase: ydiB 3-dehydroquinate rRNA containing pseudouridine 23S rRNA m3psi1915 methyltransferase: rlmH rRNA containing N3-methylated pseudouridine a nucleoside 3,5-cyclic phosphate phosphodiesterase, heme-regulated: dos AlsR-allose a nucleoside5-phosphate a nucleic acid with a terminal 5phosphate a DNA containing abasic site endonuclease VIII: nei a 3-terminal unsaturated sugar dihydrolipoamide dihydrolipoamide acetyltransferase: aceF S-acetyldihydrolipoamide tRNA containing a thionucleotide activated tRNA CTP L-cysteine pyrimidine (deoxy) nucleoside triphosphate pyrophosphohydrolase: nudG CMP oxaloacetate long chain polyphosphate exopolyphosphatase: ppx succinate 2-oxobutanoate pyridoxal 5phosphate D-alanine Lit trimethylamine N-oxide MinE pyruvate a reduced electron acceptor hydroperoxidase I: katG an oxidized electron acceptor D-fructose6-phosphate

peptidoglycan polymer lytic murein transglycosylase E: emtA membrane-bound lytic murein transglycosylase C: mltC membrane-bound lytic murein transglycosylase B: mltB peptidoglycan polymer with GlcNAc end peptidoglycan polymer with 1,6anhydromuropeptide end

D-allose

AlsR

an MDO-6(glycerophospho) -D-glucose

an MDOO-glucose

ThiI: thiI

CTP

phosphoenolpyruvate carboxylase: ppc

O-succinylhomoserine lyase: metB O-succinyl-Lhomoserine

serine hydroxymethyltransferase: glyA pyridoxamine 5-phosphate

a UDP-sugar UDP-sugar hydrolase: ushA an alpha-Daldose-1phosphate uridine-5phosphate

uracil

UraA

tRNAleu

KASIII: fabH

acetyl-CoA carboxylase: accB accC accA accD

L-serine

GTP

a hexanoyl-[acp] cytosine deoxyadenosine adenosine inosine deoxyuridine thymidine deoxyinosine uridine deoxycytidine D-cycloserine cytidine beta-alanine D-serine D-alanine glycine L-alanine CodB L-valine

nucleoside diphosphate kinase: ndk CDP purine nucleoside phosphorylase: deoxyadenosine deoD

valyl-tRNA synthetase: valS

KASI: fabB L-valyltRNAval a 3-oxooctanoyl-[acp] beta-ketoacyl[acyl-carrierprotein] reductase: fabG

KDO2(lauroyl)lipid IVA myristoyl-acyl carrier protein (ACP)-dependent acyltransferase: lpxM KDO2lipid A ADPheptose:LPS heptosyl transferase I: rfaC

malonyl-CoA an acetyl-[acp] KASI: fabB KASI: fabB KASII: fabF malonyl-CoA-ACP transacylase: fabD

GTP pyrophosphokinase: relA

AICAR transformylase: purH phosphoribosylformamidocarboxamide IMP cyclohydrolase: purH

purine nucleoside phosphorylase: deoD

pyruvate dehydrogenase multienzyme complex: lpd aceF aceE

palmitoleate biosynthesis
a palmitoyl[acp]

salvage pathways of pyrimidine ribonucleotides


adenosine acetyl-CoA cytidine citrate synthase: gltA citrate bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase: acnB aconitate hydratase 1: acnA cis-aconitate bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase: acnB aconitate hydratase 1: acnA D-threoisocitrate isocitrate dehydrogenase: icd

pyruvate formatelyase: pflB pyruvate formatelyase: tdcE

oxaloacetate malate dehydrogenase: mdh malate fumarase A: fumA fumarase B: fumB fumarase C: fumC D-glyceraldehyde3-phosphate fumarate fumarate reductase: frdD frdC frdB frdA succinate D-erythrose4-phosphate transketolase II: tktB transketolase I: tktA transaldolase A: talA transaldolase B: talB agmatine agmatinase: speB L-ornithine ribulose phosphate 3-epimerase: rpe D-xylulose5-phosphate transketolase II: tktB transketolase I: tktA

long chain polyphosphate

trimethylamine

AMINO ACIDS DEGRADATION


arsenate D-serine D-serine deaminase: dsdA pyruvate L-tartrate L-tartrate dehydratase: ttdB ttdA oxaloacetate homoserine

nitrous oxide reduced flavorubredoxin: norV nitric oxide

2-hydroxyglutarate alphaketoglutarate reductase: serA 2-oxoglutarate

L-glyceraldehyde 3-phosphate L-glyceraldehyde 3-phosphate reductase: yghZ L-glycerol 3phosphate

6-phosphoD-gluconate 6-phosphogluconate phosphatase: yieH

23S ribosomal RNA 23S rRNA m5C1962 methyltransferase: rlmI 23S rRNA containing C5methylated cytosine

lipoamide

pyruvate pyruvate dehydrogenase: aceE

an N-Dribosylpyrimidine ribonucleoside hydrolase 2 (pyrimidinespecific): rihB a pyrimidine D-ribose

PspD menadiol quinol monooxygenase: ygiN superoxide menadione thioglycolate 3-chloroD-alanine 3-chloro-D-alanine dehydrochlorinase: dcyD S-carboxymethylD-cysteine L-cysteine L-cystathionine TDPrhamnose a lipopolysaccharide CTP a tRNA a phospholipid olefinic fatty acid

NupC

tRNAval

a malonyl-[acp] KASIII: fabH an acetoacetyl-[acp]

guanosine 3diphosphate 5-triphosphate

guanosine-5diphosphate

formate formate hydrogenlyase complex: hycD hycC hycF hycG hycB hycE fdhF

superpathway of arginine and ornithine degradation


L-arginine

CycA

L-alanine alanyl-tRNA synthetase: alaS L-alanyltRNAala

guanosine-5triphosphate,3diphosphate pyrophosphatase: gpp a palmitoleoyl[acp]

GDP pyrophosphokinase: relA GDP diphosphokinase: spoT

adenosine deaminase: add deoxyadenosine deaminase: add deoxyinosine

cytidine deaminase: cdd cytosine cytosine deaminase: codA uridine

cytidine kinase: udk CMP cytidylate kinase: cmk

arginine degradation II (AST pathway)


L-arginine

alanine degradation I
L-alanine

2-ketoglutarate dehydrogenase complex


dihydrolipoyltranssuccinylase N6-(lipoyl)lysine

tryptophan degradation II (via pyruvate)


L-tryptophan

arsenate reductase: arsC arsenite

L-cysteine desulfhydrase

L-cysteine desulfhydrase

lipopolysaccharide core biosynthesis protein: rfaS dTDP a rhamnosyl lipopolysaccharide

phenylethylamine phenylethylamine oxidase: tynA

tRNA nucleotidyltransferase: cca

YiaB

a peptide with a leader sequence

peptidylproline (omega = 180) trigger factor; a molecular chaperone involved in cell division: tig peptidylprolyl isomerase: fkpB peptidylprolyl cis-trans isomerase C (rotamase C): ppiC FKBP-type peptidyl prolyl cis-trans isomerase: slyD peptidylproline (omega = 0)

2-oxobutanoate

D-gluconate

S-acetyldihydrolipoamide

2-oxobutanoate

a tRNA multidrug

an (R)-3hydroxyoctanoyl[acp] beta-hydroxyacylACP dehydrase [multifunctional]: fabA beta-hydroxyacylACP dehydratase: fabZ

inosine-5phosphate

CO2

D-sedoheptulose7-phosphate

inosine inosine kinase: gsk

L-alanine

YaaJ tRNAala

a beta-ketoacyl-[acp] heptosylKDO2lipid A ADP-heptose:LPS heptosyltransferase II: rfaF heptosyl2KDO2lipid A lipopolysaccharide glucosyltransferase I: rfaG glucosylheptosyl2KDO2lipid A lipopolysaccharide core biosynthesis; phosphorylation of core heptose: rfaP glucosylheptosyl2KDO2lipid Aphosphate lipopolysaccharide core biosynthesis protein; heptosyl transferase III: rfaQ glucosylheptosyl3KDO2lipid Aphosphate lipopolysaccharide core biosynthesis protein: rfaY glucosylheptosyl3KDO2-lipid Abisphosphate UDP-Dgalactose:(glucosyl) lipopolysaccharide-1,6D-galactosyltransferase: rfaB galactosylglucosylheptosyl3KDO2-lipid Abisphosphate UDP-Dglucose:(glucosyl) LPS alpha-1,3glucosyltransferase: rfaI galactosylglucosyl2heptosyl3KDO2-lipid Abisphosphate UDP-glucose:(glucosyl) LPS alpha-1,2glucosyltransferase: rfaJ galactosylglucosyl3heptosyl3KDO2-lipid Abisphosphate lipopolysaccharide core biosynthesis; heptosyl transferse IV; probably hexose transferase: waaU an (R)-3hydroxydecanoyl-[acp] beta-hydroxydecanoylACP dehydrase: fabA beta-hydroxyacylACP dehydratase: fabZ KASII: fabF KASI: fabB a 2,3,4-saturated fatty acyl-[acp] palmitoleate beta-ketoacyl-[acyl-carrierprotein] reductase: fabG

ppGpp IMP dehydrogenase: guaB guanosine-3,5bis(diphosphate) 3diphosphatase: spoT xanthosine5-phosphate GMP GMP synthetase: synthetase: guaA guaA adenylosuccinate synthetase: purA purine nucleoside phosphorylase: deoD

uridine phosphorylase: udp uracil phosphoribosyltransferase: upp

uridine kinase: udk

CDP nucleoside diphosphate kinase: ndk CTP

arginine succinyltransferase: astA N2-succinylL-arginine succinylarginine dihydrolase: astB N2-succinylL-ornithine succinylornithine transaminase: astC

L-asparagine

AnsP L-asparagine asparaginyltRNA synthetase: asnS L-asparaginyltRNAasn tRNAasn GltIJKL glutamate ABC transporter

purine nucleoside phosphorylase: deoD

uridine-5phosphate

ornithine decarboxylase, biosynthetic: speC

proline degradation I
L-proline

alanine racemase 2, PLPbinding: dadX alanine racemase 1, PLP-binding, biosynthetic: alr

tryptophanase: tnaA lipoamide dehydrogenase: lpd dihydrolipoyltranssuccinylase dihydrolipoyltranssuccinylase N6(S-succinyldihydrolipoyl)lysine N6-(dihydrolipoyl)lysine pyruvate indole

Cr6+ chromate reductase: yieF Cr3+

L-idarate D-glucarate dehydratase: gudD D-glucarate

H2O acyl-CoA thioesterase: yciA a carboxylate

dTDP-4dehydro6-deoxyD-glucose dTDP-Lrhamnose synthetase: rfbD rfbC dTDPalpha-Lrhamnose

EmrABTolC multidrug efflux transport system

a phospholipid cyclopropane fatty acid

phenylacetaldehyde

a leader sequence

a peptide

a quinone NADH dehydrogenase (quinone) a hydroquinone

methyl-1,4benzoquinone NAD(P)H:quinone oxidoreductase: ytfG methyl-1,4benzoquinol

a tRNA

2-hydroxyglutarate L-2hydroxyglutarate oxidase: lhgO 2-oxoglutarate

Tapglu-Me

an rRNA 16S rRNA m7G527 methyltransferase: rsmG rRNA containing 7-methylguanosine

a tRNA

(R)pantolactone 2-dehydropantoyllactone reductase (B-specific) 2-dehydropantolactone

a mRNA

isopentenyl diphosphate

a transpolyisoprenyln-PP octaprenyl diphosphate synthase: ispB

P-DPD

CDP-choline

a 1,2diacylglycerol Cd2+ YiiP putative diacylglycerol cholinephosphotransferase: ynbA CorA Mg2+ Co2+ Ni2+

tetrahydrothiophene 1-oxide

a holo-[acp]

octanoate

DsbD

DsbGoxidized

uracil

D-alanine dihydrolipoyltranssuccinylase: sucB

tRNA (m1G37) methyltransferase: trmD tRNA containing N1methylguanine

CheBPasp: cheB

tRNA (m7G46) methyltransferase: trmI a tRNA containing N7methylguanine

RNA pyrophosphohydrolase: rppH an mRNA with 5monophosphate

Autoinducer 2-degrading protein: lsrG an unknown C3 fragment CMP

adenylosuccinate hypoxanthine inosine-5phosphate

D-fructose6-phosphate

putrescine

malate fumarate succinate orotate L-aspartate

DctA

a trans oct2-enoyl-[acp]

guanosine-5diphosphate a (3R)-3-hydroxyacyl-[acp] beta-hydroxyacylACP dehydratase: fabZ beta-hydroxydecanoylACP dehydrase: fabA

adenylosuccinate lyase: purB

glutamate-putrescine ligase: puuA

L-aspartate

an octanoyl-[acp] L-aspartate aspartyltRNA synthetase: aspS

enoyl-ACP reductase (NADH): fabI enoyl-ACP reductase (NADPH): fabI

guanosine5-phosphate

AMP

xanthine-guanine phosphoribosyltransferase: gpt hypoxanthine phosphoribosyltransferase: hpt xanthine dehydrogenase: xdhC xdhB xdhA xanthine

superpathway of glycolysis and Entner-Doudoroff


beta-D-glucose6-phosphate

D-glyceraldehyde3-phosphate

gamma-glutamylL-putrescine gammaglutamylputrescine oxidase: puuB putrescine aminotransferase: ygjG

fused PutA transcriptional repressor / proline dehydrogenase / 1-pyrroline5-carboxylate dehydrogenase: putA (S)-1pyrroline-5carboxylate fused PutA transcriptional repressor / proline dehydrogenase / 1-pyrroline5-carboxylate dehydrogenase: putA

D-amino acid dehydrogenase: dadA pyruvate

Tapglu

methanol

a transpolyisoprenyln-PP

2-phosphoglycolate

a phosphatidylcholine

tetrahydrothiophene

an octanoyl[acp]

DsbDoxidized

DsbG

lysine degradation I
L-lysine

taurine degradation IV
taurine taurine dioxygenase: tauD aminoacetaldehyde L-carnitinylCoA D-carnitinylCoA 2,3-diketoL-gulonate 2,3-diketoL-gulonate reductase: yiaK 3-keto-Lgulonate XTP an AP(apurinic or apyrimidinic) site created by glycosylic bond cleavage endonuclease IV: nfo AP site removed from DNA an alcohol NADP-dependent dehydrogenase: yqhD an aldehyde glycerol 2phosphate inositol monophosphatase: suhB glycerol a tRNA N-ethylmaleimide N-ethylmaleimide reductase, FMNlinked: nemA N-ethylsuccinimide Targlu-Me an Nhydroxyarylamine N-hydroxyarylamine O-acetyltransferase: nhoA an Nacetoxyarylamine MgtA lipoyl-ACP AceF 2,3diaminopropionate 2,3diaminopropionate ammonia-lyase: ygeX pyruvate a holo-[acp] AceF-lipoate a nucleoside5-phosphate a tRNA precursor isopentenyl diphosphate a cis,transpolyisoprenyln-PP undecaprenyl diphosphate synthase: ispU a cis,transpolyisoprenyln-PP pyruvate phosphoenolpyruvate dihydroxyacetone allothreonine

Ni2+ Mg2+

aminoacetone aminoacetone oxidase: tynA

a fatty acid

a holo-[acp]

DsbCoxidized

DsbD

N2-succinylL-glutamate 5semialdehyde aldehyde dehydrogenase: astD N2succinylglutamate succinylglutamate desuccinylase: astE

XTPase: yjjX

malate fumarate L-aspartate L-aspartate

L-aspartyltRNAasp

KASI: fabB

guanylate kinase: gmk

adenylate kinase: adk

salvage pathways of pyrimidine deoxyribonucleotides


deoxycytidine cytidine deaminase: cdd

glucose 6-phosphate1-dehydrogenase: zwf phosphoglucose isomerase: pgi D-glucono-deltalactone-6-phosphate 6-phosphogluconolactonase: pgl

L-serine degradation
L-serine

tRNA m6A37 methyltransferase: yfiC tRNA containing N6methyladenine

CheBPasp: cheB

lipoylprotein ligase: lipB

RNase D: rnd

dihydroxyacetone kinase: dhaL dhaK dhaM dihydroxyacetone phosphate glycine

serine hydroxymethyltransferase: glyA

NupG

a nucleoside methylglyoxal

gamma-glutamyl-gammaaminobutyraldehyde gamma-glutamyl-gammaaminobutyraldehyde dehydrogenase: puuC 4-(glutamylamino) butanoate

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

DcuB

tRNAasp

a 3-oxodecanoyl-[acp] beta-ketoacyl[acyl-carrierprotein] reductase: fabG L-tyrosyltRNAtyr an (R)-3hydroxydecanoyl[acp] beta-hydroxyacylACP dehydrase [multifunctional]: fabA beta-hydroxyacylACP dehydratase: fabZ

guanosine-5diphosphate

lysine decarboxylase 2: ldcC lysine decarboxylase: cadA cadaverine

a 2,3,4saturated fatty acyl-[acp]

DsbC

DsbDoxidized

YebF

XDP

Targlu

methanol

a tRNA

acetaldehyde Na+ NhaA a 1,4-alphaD-glucan alphaamylase: malS maltohexaose a nucleoside 2,3-cyclic phosphate 2,3-cyclic nucleotide 2-phosphodiesterase: cpdB holo-EntB a nucleoside 3-phosphate KDO2lipid IVA an L-1phosphatidylethanolamine

coenzyme A

EntB

ADP xanthine dehydrogenase: xdhC xdhB xdhA ribonucleosideADP reductase: diphosphate nrdB nrdA reductase 2: nrdF nrdE urate

2-oxoglutarate

deoxyuridine uracil phosphorylase: deoA deoxyribose1-phosphate thymidine phosphorylase: deoA thymidine thymidine kinase: tdk dTMP fructose bisphosphate aldolase class I: fbaB fructose bisphosphate aldolase class II: fbaA

L-tyrosine tyrosyl-tRNA synthetase: tyrS

nucleoside diphosphate kinase: ndk

malate fumarate L-aspartate L-aspartate

GDP reductase: nrdB nrdA

ribonucleosidediphosphate reductase 2: nrdF nrdE

deoxyuridine kinase: tdk dUMP

4-aminobutanal L-glutamate succinate gammaaminobutyraldehyde dehydrogenase: ydcW

L-glutamate

DcuA

GTP

tRNAtyr

2-deoxyguanosine5-diphosphate

2-deoxyadenosine5-diphosphate

ATP

a trans-delta2-decenoyl-[acp]

ribonucleosidetriphosphate reductase: nrdD

tRNAtrp malate fumarate L-aspartate L-aspartate

tryptophanyltRNA synthetase: trpS L-tryptophanyltRNAtrp

nucleoside diphosphate kinase: ndk

trans-2-decenoylACP isomerase: fabA

nucleoside diphosphate kinase: ndk

D-fructose-6-phosphate fructose-1,6bisphosphatase: yggF fructose 1,6bisphosphatase: ybhA fructose 1,6bisphosphatase II: glpX fructose-1,6bisphosphatase I: fbp fructose-1,6bisphosphate

6-phospho-D-gluconate

6-phosphofructokinasephosphogluconate I: pfkA dehydratase: edd 6-phosphofructokinase II: pfkB 2-dehydro-3-deoxy-Dgluconate-6-phosphate multifunctional 2-keto3-deoxygluconate 6-phosphate aldolase and 2-keto4-hydroxyglutarate aldolase and oxaloacetate decarboxylase: eda

superpathway of gluconate degradation


D-gluconate gluconokinase I: gntK gluconokinase II: idnK 6-phosphoD-gluconate

gamma-glutamylgamma-aminobutyrate hydrolase: puuD

4-aminobutyrate 4-aminobutyrate aminotransferase: puuE 4-aminobutyrate transaminase: gabT succinate semialdehyde

glutamine degradation I
L-glutamine

catabolic threonine dehydratase: tdcB L-serine deaminase III: tdcG L-serine deaminase II: sdaB L-serine deaminase I: sdaA

L-cysteine degradation II
L-cysteine

a reduced thioredoxin

L-AlagammaD-Glu L-AlaD/L-Glu epimerase: ycjG

a phosphate monoester alkaline phosphatase: phoA an alcohol

4,5dihydroxy-2,3pentanedione predicted Autoinducer2 kinase: lsrK

an aldehyde NADP-dependent dehydrogenase: yqhD an acid

tRNA containing uridine at position 54 tRNA(m5U54) methyltransferase: trmA tRNA containing ribothymidine at position 54

Targlu

an rRNA 23S rRNA m1G745 methyltransferase: rrmA rRNA containing N1methylguanine

Trgglu-Me

oxalate

formyl-CoA

a citryl-[acp]

a [citrate (pro-3S)lyase](citryl form) citrate lyase: citE citF citD

a damaged DNA (purine or pyrimidine) formamidopyrimidine DNA glycosylase: mutM an AP(apurinic or apyrimidinic) site created by glycosylic bond cleavage

nitric oxide

oxidized flavorubredoxin flavorubredoxin reductase: norW

N-methyltryptophan

EntF

coenzyme A

7,8dihydroneopterin triphosphate 6-carboxy-5,6,7,8tetrahydropterin synthase: queD

As3H3O6

ArsB

chemotaxis protein methyltransferase: cheR

CheBPasp: cheB oxalyl-CoA

formyl-CoA transferase: frc

N-methyltryptophan oxidase: solA aryl carrier protein / serine activating enzyme

phosphopantetheinyl transferase: entD

adenosine 3,5bisphosphate

phosphatidylethanolamineKDO2-lipidA

a 1,2diacylglycerol

pyruvate

ribonucleosidetriphosphate reductase: nrdD

L-cysteine desulfhydrase: metC L-cysteine desulfhydrase: tnaA L-cysteine desulfhydrase pyruvate

glycine cleavage complex


H-Gcv-protein-(lipoyl)lysine

an oxidized thioredoxin

L-Ala-L-Glu

P-DPD

Trgglu

methanol

formate

Targlu-Me

a [citrate (pro-3S)lyase](acetyl form)

oxaloacetate

nitrous oxide

MQH2 adenosine 3,5bisphosphate acetaldehyde PPPi 6-carboxy-5,6,7,8tetrahydropterin

HYD1

H2 a protein L-tyrosine 2,3dihydroxybenzoate multicopper oxidase with role in copper homeostasis: cueO 2-carboxymuconate a 2,3,4saturated fatty acyl-[acp] all-transoctaprenyl diphosphate

NorV

formaldehyde

L-tryptophan

a 2,3,4-saturated 2lysophosphatidate

4-hydroxybenzoate

GabP an oxidized ferredoxin glycine decarboxylase: gcvP H-protein-Slipoamide dehydrogenase: lpd H-Gcv-protein(aminomethyldihydrolipoyl) (dihydrolipoyl)lysine lysine YgjD a tRNA pseudouridine an L-1phosphatidylglycerol lipid kinase: yegS an L-1phosphatidylglycerolphosphate L-serine Trgglu a phosphate monoester acid phosphatase/ phosphotransferase: aphA an alcohol Tsrglu Tsrglu-Me D-myo-inositol (1) -monophosphate inositol monophosphatase: suhB myo-inositol 4-coumarate coenzyme A a peptide a nucleoside triphosphate nucleoside triphosphate pyrophosphohydrolase: mazG a nucleoside monophosphate a DNA with uracil uracil-DNAglycosylase: ung an AP(apurinic or apyrimidinic) site created by glycosylic bond cleavage selenophosphate tRNA containing 5methylaminomethyl2-thiouridylate tRNA 2selenouridine synthase: ybbB tRNA containing 5methylaminomethyl2-selenouridine N-formyl-LmethionyltRNAfmet L-methionyltRNAfmet 10-formyltetrahydrofolate 10-formyltetrahydrofolate:Lmethionyl-tRNA(fMet) N-formyltransferase: fmt EriC

4-aminobutyrate

1,4dihydroxy-2naphthoate

DcuC L-tryptophan

a trans-delta2decenoyl-[acp]

a cis-delta3-decenoyl-[acp] dGTP dATP KASI: fabB

6-phosphogluconate dehydrogenase (decarboxylating): gnd D-ribulose5-phosphate ribose-5phosphate isomerase A: rpiA allose-6phosphate isomerase / ribose-5phosphate isomerase B: rpiB pyruvate D-ribose-5phosphate

phosphogluconate dehydratase: edd 2-dehydro3-deoxy-Dgluconate-6phosphate multifunctional 2-keto-3deoxygluconate 6phosphate aldolase and 2-keto-4hydroxyglutarate aldolase and oxaloacetate decarboxylase: eda D-glyceraldehyde3-phosphate

succinate semialdehyde succinate semialdehyde dehydrogenase, dehydrogenase, NADP+NAD+-dependent: sad dependent: gabD

glutaminase: ybaS glutaminase: yneH glutaminase B glutaminase A

protease specific for YgjD: yeaZ a reduced ferredoxin YgjD degradation products tRNA containing 5methylaminomethyl2-thiouridylate

predicted pseudouridine kinase: pscK pseudouridine 5-phosphate

3-hydroxy acid dehydrogenase: ydfG 2-aminomalonatesemialdehyde

chemotaxis protein methyltransferase: cheR

CheBPasp: cheB

acetyl-CoA synthetase (AMPforming): acs a peptide 4-coumaroylCoA

aminopeptidase A/I: pepA a standard alpha amino acid

chloride

a proteinL-tyrosine phosphate

a holo-[acp]

a 2,3,4saturated Lphosphatidate

3-octaprenyl-4hydroxybenzoate

demethylmenaquinone-8

methanol

Trgglu-Me

uracil

unknown

tetrahydrofolate

PitB

phosphate D-alanine a diacylglycerol pyrophosphate diacylglycerol pyrophosphate phosphatase: pgpB pyruvate a 1,2diacylglycerol3-phosphate

L-phenylalanine L-tryptophan L-tyrosine

L-threonine AroP

threonyltRNA synthetase: thrS

a decanoyl-[acp] L-threonyltRNAthr

a beta-keto-cis-delta5dodecenoyl-[acp] beta-ketoacyl-[acyl-carrierprotein] reductase: fabG a beta-hydroxy cis delta5-dodecenoyl-[acp] beta-hydroxyacylACP dehydratase: fabZ beta-hydroxyacylACP dehydrase: fabA a trans-delta3-cisdelta5-dodecenoyl-[acp] enoyl-ACP reductase (NAD[P]H): fabI

gluconeogenesis I superpathway of phenylalanine, tyrosine, and tryptophan biosynthesis


D-erythrose4-phosphate 2-dehydro-3deoxyphosphoheptonate aldolase: aroF 2-dehydro-3deoxyphosphoheptonate aldolase: aroH 2-dehydro-3deoxyphosphoheptonate aldolase: aroG 5-phosphoribosyl 1-pyrophosphate ATP aspartate aminotransferase, PLPdependent: aspC

CARBOHYDRATES BIOSYNTHESIS glycogen biosynthesis I (from ADP-D-Glucose)


ATP malate dehydrogenase, NADrequiring: maeA alpha-Dglucose 1phosphate

succinate

L-glutamate

aminomethyltransferase: gcvT ethyl-2methylacetoacetate beta-keto ester reductase: dkgA ethyl-(2R)methyl-(3S)hydroxybutanoate hybridcluster proteinox NADH oxidoreductase: hcr hybridcluster proteinred 2-keto-3deoxy-Lrhamnonate 2-keto-3deoxy-Lrhamnonate aldolase: yfaU DLlactaldehyde pyruvate a nucleoside diphosphate KDO2lipid A a [citrate (pro-3S)lyase](acetyl form) citrate lyase: citE citF citD a [citrate (pro-3S)lyase](citryl form) Cu+ 2-deoxy-Dglucose 6phosphate 2-deoxyglucose6-phosphatase: yniC 2-deoxyD-glucose tRNA containing guanine uridine ribonucleoside hydrolase 3: rihC ribonucleoside hydrolase 1 (pyrimidinespecific): rihA a protein L-betaisoaspartate L-isoaspartate protein carboxylmethyltransferase type II: pcm a protein L-betaisoaspartate alphamethyl ester indole-3glycerolphosphate tryptophan synthase: trpB trpA D-glyceraldehyde3-phosphate CopA

a 1-lyso-2-acylsn-glycero-3phosphoethanolamine

an acyl-[acp]

lipid A disaccharide

UDP-2,3-bis(3hydroxymyristoyl) glucosamine UDP-2,3diacylglucosamine hydrolase: lpxH

KDO2lipid IVA

a dodecanoyl[acp]

a myristoyl[acp]

KASI: fabB

AMINO ACIDS BIOSYNTHESIS histidine biosynthesis superpathway of lysine, threonine and methionine biosynthesis I
oxaloacetate L-aspartate threonine dehydrogenase: tdh low-specificity L-threonine aldolase: ltaE 2-amino-3oxobutanoate 2-amino-3ketobutyrate CoA ligase: kbl catabolic threonine dehydratase: tdcB threonine deaminase: ilvA

malate

trehalose biosynthesis I
alpha-Dglucose 6phosphate UDP-Dglucose trehalose-6phosphate synthase: otsA trehalose 6phosphate

triose phosphate isomerase: tpiA D-glyceraldehydedihydroxyacetone 3-phosphate phosphate glyceraldehyde 3-phosphate dehydrogenaseA complex: gapA

SECONDARY METABOLITES DEGRADATION ketogluconate metabolism


2,5didehydroD-gluconate 2,5-diketoD-gluconate reductase A: dkgA 2,5-diketoD-gluconate reductase B: dkgB

DcuS

Tapgln

L-lysine

long chain polyphosphate polyphosphate kinase: ppk long chain polyphosphate

2-deoxygluconate 2-deoxy-Dgluconate 3dehydrogenase: kduD 3-dehydro2-deoxy-Dgluconate

Tsrglu

an RNA

a phospholipid

oxaloacetate

pyridoxamine

NADPH

NAD+

L-homocysteine

S-methyl-Lmethionine homocysteine methyltransferase: mmuM

a holo-[acp]

citrate

multidrug

YdhE

tRNAthr L-tyrosine TyrP a 3-oxododecanoyl-[acp] beta-ketoacyl[acyl-carrierprotein] reductase: fabG L-seryltRNAser an (R)-3hydroxydodecanoyl[acp] beta-hydroxyacylACP dehydrase [multifunctional]: fabA beta-hydroxyacylACP dehydratase: fabZ

superpathway of asparagine biosynthesis

superpathway of threonine metabolism

L-threonine

superpathway of glutamate biosynthesis


L-glutamate

malate dehydrogenase: mdh oxaloacetate

CheBPasp: cheB

indole L-tryptophan

L-serine Mtr seryl-tRNA synthetase: serS

malate dehydrogenase (oxaloacetatedecarboxylating) (NADP+): maeB pyruvate

ATP phosphoribosyltransferase: hisG

asparagine synthetase B: asnB

L-aspartate phosphoribosylATP L-asparagine

L-tryptophan

TnaB

tRNAser

asparagine synthetase B: asnB asparagine synthetase A: asnA acetaldehyde L-asparagine

glutamine synthetase: glnA

glucose-1-phosphate adenylyltransferase: glgC

1,3-diphosphateglycerate

superpathway of hexuronide and hexuronate degradationbeta-Da


glucuronoside beta-Dglucuronidase: uidA D-glucuronate

superpathway of D-glucarate and D-galactarate degradation


D-glucarate D-galactarate galactarate dehydratase: garD

fructoselysine and psicoselysine degradation


psicoselysine

lysine 2,3aminomutase: yjeK (R)-betalysine

chemotaxis protein methyltransferase: cheR

polynucleotide phosphorylase: pnp heptaacylated KDO2lipid A

palmitoyl transferase for Lipid A: pagP a glycerol ester L-aspartate

pyridoxamineoxaloacetate transaminase

pyridine nucleotide transhydrogenase, soluble: sthA

an L-1phosphatidylethanolamine

a holo-[acp] uridine-5lipid IVA phosphate

acyl carrier protein phosphodiesterase: acpH

2,3-bis(3hydroxymyristoyl)beta-D-glucosaminyl 1-phosphate

a holo-[acp]

a holo-[acp]

KDO2lipid A

YdgR

a tripeptide

DcuSPhis349

Tapglu

an RNA

Tsrglu-Me

pyridoxal

NADP+

NADH

L-methionine

4-phosphopantetheine

an apo-[acp]

acetate

a citryl-[acp]

a Damino acid

UQ or MQ

UQH2 or MQH2

a phosphatidylcholine

lipid A disaccharide

UDP-2,3-bis(3hydroxymyristoyl) glucosamine UDP-2,3diacylglucosamine hydrolase: lpxH 2,3-bis(3hydroxymyristoyl)beta-D-glucosaminyl 1-phosphate

KDO2lipid IVA

a dodecanoyl[acp]

a myristoyl[acp]

KDO2lipid IVA

a palmitoleoyl[acp]

a myristoyl[acp]

phosphoenolpyruvate phosphoenolpyruvate carboxykinase (ATP): pck carboxylase: ppc

glycogen degradation I
phosphoenolpyruvate synthase: pps a glycogen a 1,4-alphaD-glucan glycogen synthase: glgA a 1,4-alphaD-glucan 1,4-alphaglucan branching enzyme: glgB glycogen

ADP-Dglucose

phosphoglycerate kinase: pgk trehalose-6phosphate phosphatase, biosynthetic: otsB trehalose

L-glutamine 2-oxobutanoate phosphoenolpyruvate pyruvate formatelyase: pflB 2-ketobutyrate formatelyase: tdcE acetohydroxybutanoate synthase: ilvM ilvG_2 ilvG_1 acetohydroxybutanoate synthase: ilvN ilvB acetohydroxybutanoate synthase: ilvH ilvI 2-aceto-2hydroxy-butyrate phosphate acetyltransferase: pta acetohydroxy acid isomeroreductase: ilvC 2,3-dihydroxy3-methylvalerate dihydroxy-acid dehydratase: ilvD 2-keto-3methyl-valerate branched-chain amino-acid aminotransferase: ilvE glutamate synthase: gltD gltB

D-glucarate dehydratase: gudD

fructoselysine 3epimerase: frlC

an oxidized glutaredoxin

Trggln

a deoxyribonucleic acid DNA cytosine methylase: dcm DNA containing 5-methylcytosine

a ribonucleoside diphosphate nucleoside diphosphate kinase: ndk a ribonucleoside triphosphate

an isocitrate dehydrogenase isocitrate dehydrogenase kinase: aceK a phosphorylated isocitrate dehydrogenase

a mRNA toxin of the YafQDinJ toxinantitoxin system: yafQ a singlestranded RNA a singlestranded RNA

an rRNA 23S rRNA 2-Oribose U2552 methyltransferase: rlmE rRNA containing 2O-methyluridine

queuine

an RNA

dCMP dCMP phosphohydrolase: yfbR CPS-53 (KpLE1) prophage; deoxyribonucleoside 5-monophosphate phosphatase: yfdR deoxycytidine

L-serine

2-oxoglutarate 2,3dihydroxybenzoate ATP

N3methylcytosine AlkB repair system for alkylated DNA and RNA: alkB ExuT D-galacturonate D-glucuronate a 2-oxo acid

phospholipase A1: pldA D-lactate pyruvate a carboxylate L-lactate Kch K+ a glucosylated glucose acceptor beta-D-glucoside glucohydrolase, periplasmic: bglX beta-Dglucose a non glucosylated glucose acceptor pyruvate a 1-lyso-2-acylsn-glycero-3phosphocholine

3-phosphoglycerate

a holo-[acp]

a holo-[acp]

L-serine L-threonine

TdcC

L-proline

prolyl-tRNA synthetase: proS

cyclopropane fatty acid (CFA) biosynthesis a phospholipid


olefinic fatty acid

superpathway of KDO2lipid A biosynthesis


UDP-Nacetyl-Dglucosamine an (R)-3hydroxymyristoyl[acp]

3-deoxy-D-arabinoheptulosonate7-phosphate 3-dehydroquinate synthase: aroB

a cis-delta5-dodecenoyl-[acp]

phosphoribosyl-ATP pyrophosphatase: hisI

L-prolyltRNApro

methionine and methyldonormolecule biosynthesis


L-aspartate

aspartate kinase III: lysC aspartate kinase: metL aspartate kinase: thrA

glycine

L-serine NmpC

SdaC

tRNApro

a trans dodec2-enoyl-[acp]

Lipid A-core cyclopropane fatty acyl phospholipid synthase: cfa a phospholipid cyclopropane fatty acid UDP-Nacetylglucosamine acyltransferase: lpxA UDP-3-O-(3hydroxymyristoyl)N-acetylglucosamine UDP-3-O-acyl-Nacetylglucosamine deacetylase: lpxC UDP-3-O-(3hydroxymyristoyl) glucosamine UDP-3-O-[3hydroxymyristoyl]glucosamine N-acetyltransferase: lpxD UDP-2,3-bis(3hydroxymyristoyl) glucosamine lipid A disaccharide synthase: lpxB lipid A disaccharide tetraacyldisaccharide 4-kinase: lpxK UDP-2,3diacylglucosamine hydrolase: lpxH 2,3-bis(3hydroxymyristoyl)beta-D-glucosaminyl 1-phosphate

3-dehydroquinate 3-dehydroquinate dehydratase: aroD

acetaldehyde dehydrogenase 2: mhpF acetaldehyde dehydrogenase: adhE

aminoacetone

enolase: eno

phosphoribosylAMP

D-aminopropanol dehydrogenase: gldA methylglyoxal 1-aminopropan-2-ol

L-glutamate 2-phosphoglycerate

L-aspartyl4-phosphate aspartate kinase III: lysC aspartate kinase: metL aspartate kinase: thrA

propionyl-CoA acetyl-CoA phosphoglycerate mutase, cofactor independent: gpmM phosphoglycerate mutase 2: ytjC phosphoglyceromutase 1: gpmA

ADP-Lglycero-betaD-mannoheptose D-sedoheptulosebiosynthesis
7-phosphate D-sedoheptulose 7-phosphate isomerase: lpcA D-alpha,betaD-heptose7-phosphate fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase: rfaE D-beta-Dheptose-1,7bisphosphate D,D-heptose 1,7bisphosphate phosphatase: gmhB D-beta-Dheptose-1phosphate fused heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase: rfaE ADP-DglyceroD-mannoheptose ADP-L-glyceroD-mannoheptose6-epimerase: rfaD ADP-LglyceroD-mannoheptose a debranched limit dextrin

glycogen phosphorylase: glgP a limit dextrin glycogen phosphorylaselimit dextrin alpha-1,6glucohydrolase: glgX

phosphoglycerate mutase, cofactor independent: gpmM phosphoglycerate mutase 2: ytjC phosphoglyceromutase 1: gpmA

D-galacturonate 2-keto-Lgulonate 2-ketoaldonate reductase: ghrB 2-ketoaldonate reductase: ghrB D-galacturonate isomerase: uxaC D-tagaturonate L-idonate altronate oxidoreductase: uxaB D-altronate 5-ketogluconate D-altronate dehydratase: uxaA 2-dehydro3-deoxy-Dgluconate 2-keto-3deoxygluconokinase: kdgK 2-dehydro3-deoxy-Dgluconate-6phosphate D-glucuronate isomerase: uxaC D-fructuronate D-mannonate oxidoreductase: uxuB D-mannonate D-mannonate dehydratase: uxuA

fructoselysine 5-dehydro-4deoxy-D-glucarate alpha-dehydrobeta-deoxyD-glucarate aldolase: garL tartronate semialdehyde tartronate semialdehyde reductase: garR

CheBPasp: cheB

ribonuclease II: rnb RNase R: rnr tRNA containing queuine guanine a nucleoside5-phosphate

uridine-5lipid IVA phosphate

KDO2lipid A

a holo-[acp]

a holo-[acp]

KDO2-lipid A, cold adapted

galactitol degradation
galactitol-1-phosphate

2,3-dihydroxybenzoateAMP ligase: entE 2,3dihydroxybenzoylAMP

fructoselysine 6-kinase: frlD fructoselysine6-phosphate fructoselysine 6-phosphate deglycase: frlB beta-Dglucose-6phosphate

D-galactonate degradation
D-galactonate

a reduced glutaredoxin

Trgglu

an RNA

uracil

D-ribose

L-tryptophan

succinate

formaldehyde

cytosine phytate nitrate ubiquinol-8 periplasmic nitrate reductase: napG napH napC napA napB nitrite ubiquinone-8

2-phosphoglycerate L-idonate 5dehydrogenase: idnD

D-ribulose5-phosphate D-arabinose 5-phosphate isomerase: gutQ D-arabinose 5-phosphate isomerase: kdsD D-arabinose 5-phosphate 3-deoxyD-mannooctulosonate 8-phosphate synthase: kdsA

L-serine NfrA a quaternary amine L-proline NlpD glycine betaine L-proline YaiO

SstT

3-dehydro-shikimate

phosphoribosylAMP cyclohydrolase: hisI phosphoribosylformiminoAICARphosphate N-(5-phospho-Lribosyl-formimino) -5-amino-1-(5phosphoribosyl)-4imidazolecarboxamide isomerase: hisA phosphoribulosylformiminoAICAR-P

L-phenylalanine phenylalanyltRNA synthetase: pheT pheS L-phenylalanyltRNAphe tRNAphe

aspartate semialdehyde dehydrogenase: asd L-aspartatesemialdehyde

superpathway of leucine, valine, and isoleucine biosynthesis


pyruvate acetolactate synthase: ilvH ilvI acetolactate synthase: ilvM ilvG_2 ilvG_1 acetolactate synthase: ilvN ilvB L-threonine

pyruvate

galactitol-1-phosphate dehydrogenase: gatD tagatose-6-phosphate L-lysine 6-phosphofructokinase II: pfkB tagatose-1,6bisphosphate tagatose-1,6bisphosphate aldolase 2: gatZ gatY tagatose-1,6bisphosphate aldolase 1: kbaZ kbaY D-glyceraldehyde3-phosphate dihydroxyacetone phosphate

D-galactonate dehydratase: dgoD 2-dehydro3-deoxy-Dgalactonate 2-dehydro-3deoxygalactonate kinase: dgoK 2-dehydro3-deoxy-Dgalactonate6-phosphate 2-oxo-3deoxygalactonate 6-phosphate aldolase: dgoA D-glyceraldehyde3-phosphate

cysteine biosynthesis I
L-serine

enolase: eno

a FeSprotein

Targln

D-alanylD-alanine D-Ala-D-Ala dipeptidase: ddpX

DNA containing a recognition site McrBC restriction endonuclease: mcrC mcrB Cleaved DNA

dihydrouracil Tapglu putative oxidoreductase Fe-S subunit; possible component of selenate reductase: ygfK uracil

salicin-6phosphate 6-phosphobetaglucosidase B; cryptic: bglB salicyl alcohol beta-Dglucose-6phosphate

an rRNA 23S rRNA 2-Oribose C2498 methyltransferase: rlmM rRNA containing 2-Omethylcytosine

a tRNA

L-selenocysteine

D-tyrosyltRNATyr D-TyrtRNATyr deacylase: dtd

cytidine ribonucleoside hydrolase 3: rihC ribonucleoside hydrolase 1 (pyrimidinespecific): rihA

L-Alagamma-DGlu-DAPD-Ala L,Dcarboxypeptidase A: ldcA L-Alagamma-DGlu-Dap

a DNA with alkylated adenine 3-methyladenine DNA glycosylase I, constitutive: tag 3-methyladenine a DNA containing a purinic site

7-aminomethyl7-deazaguanine

tRNA with GU(N) anticodon tRNA-guanine transglycosylase: tgt a tRNA containing 7aminomethyl-7deazaguanine at position 34

S-adenosylL-methionine

a tRNA containing 7aminomethyl-7deazaguanine at position 34 S-adenosylmethionine:tRNA ribosyltransferaseisomerase: queA

TrkH

K+ 3-phytase: agp D-myo-inositol (1,2,4,5,6)pentakisphosphate

N-acetylmuramoyl-Lalanyl-D-glutamyl-Llysyl-D-alanyl-D-alaninediphosphoundecaprenylN-acetylglucosamine

a dodecanoyl-[acp]

propionyl-P

maltotetraose

CheBPasp: cheB a reduced FeS-protein

proline ABC transporter

KASI: fabB

shikimate shikimate dehydrogenase: ydiB dehydrogenase: aroE shikimate dehydrogenase: ydiB

L-aspartyl4-phosphate homoserine dehydrogenase: metL homoserine dehydrogenase: thrA

threonine deaminase: ilvA

proline biosynthesis I
L-glutamate

chemotaxis protein methyltransferase: cheR

tRNA (Gm18) 2-Omethyltransferase: trmH a tRNA containing 2-Omethylguanosine selenide

selenocysteine lyase: sufS

IdnT

5-ketogluconate

a peptidoglycan

shikimate shikimate kinase I: aroK shikimate kinase II: aroL

a 3-oxomeristoyl-[acp] ProP L-methionine methionyltRNA synthetase: metG L-methionyltRNAmet beta-ketoacyl[acyl-carrierprotein] reductase: fabG an (R)-3hydroxymyristoyl[acp] lysyl-tRNA synthetase, constitutive: lysS lysyl-tRNA synthetase: lysU beta-hydroxyacylACP dehydrase [multifunctional]: fabA beta-hydroxyacylACP dehydratase: fabZ

laurate

aspartate semialdehyde dehydrogenase: asd L-aspartatesemialdehyde

dihydrodipicolinate synthase: dapA L-2,3dihydrodipicolinate

propionate kinase: ackA propionate kinase: tdcD

3-phosphoglycerate serine acetyltransferase: cysE O-acetyl-L-serine

maltodextrin phosphorylase: malP alpha-Dglucose 1phosphate phosphoglucomutase: pgm alpha-Dglucose 6phosphate

phosphoenolpyruvate

2-keto-Lgulonate 2-ketoaldonate reductase: ghrB

D-glycerate glycerate kinase I: garK

di-trans,polycisundecaprenyl diphosphate

a peptidoglycan FimD

2-oxobutanoate propionate acetohydroxybutanoate synthase: ilvM ilvG_2 ilvG_1 acetohydroxybutanoate synthase: ilvN ilvB acetohydroxybutanoate synthase: ilvH ilvI 2-aceto-2hydroxy-butyrate acetohydroxy acid isomeroreductase: ilvC 2,3-dihydroxy3-methylvalerate gammaglutamyl kinase: proB L-glutamate5-phosphate glutamate-5semialdehyde dehydrogenase: proA L-glutamate gammasemialdehyde

phosphoglycerate kinase: pgk

maltotriose

phosphoenolpyruvate pyruvate kinase I: pykF pyruvate kinase II: pykA synthase: pps

5-keto-Dgluconate 5reductase: idnO

Targlu

D-alanine

L-alanine D-tyrosine tRNAtyr cytosine D-ribose

Tapglu-Me

D-alanine

guanine

L-methionine

adenine

a tRNA containing epoxyqueuosine at position 34

K+

KefB a tRNA precursor alpha-Larabinose a polypeptide serine endoprotease, periplasmic: degQ serine protease Do: degP a polypeptide (5-Lglutamyl)L-peptide a standard alpha amino acid gammaglutamyltranspeptidase: ggt a 5-Lglutamyl-Lamino acid

formate dehydrogenaseO: fdoI fdoH fdoG

LolB

2-acetolactate dihydrodipicolinate reductase: dapB acetohydroxy acid isomeroreductase: ilvC 2,3-dihydroxyisovalerate dihydroxy-acid dehydratase: ilvD 2-keto-isovalerate

shikimate-3-phosphate imidazole glycerol phosphate synthase: hisF hisH aminoimidazole carboxamide ribonucleotide D-erythroimidazoleglycerolphosphate imidazoleglycerolphosphate dehydratase: hisB imidazole acetolphosphate histidinolphosphate aminotransferase: hisC L-histidinolphosphate histidinolphosphatase: hisB histidinol histidinol dehydrogenase: hisD histidinal histidinal dehydrogenase: hisD cobalaminindependent homocysteine transmethylase: metE L-methionine cobalamindependent homocysteine transmethylase: metH homoserine dehydrogenase: metL homoserine dehydrogenase: thrA

homoserine

L-proline YbgQ

PutP tRNAmet

cis-vaccenate biosynthesis
a palmitoleoyl[acp]

superpathway of serine and glycine biosynthesis I


3-phosphoglycerate

1,3-diphosphateglycerate

maltodextrin glucosidase: malZ maltose amylomaltase: malQ beta-Dglucose glucokinase: glk alpha-Dglucose

pyruvate

D-gluconate gluconokinase II: idnK 6-phosphoD-gluconate

2-phosphoglycerate

3-deoxyD-mannooctulosonate 8-P 3-deoxyD-mannooctulosonate 8-phosphate phosphatase: kdsC 3-deoxyD-mannooctulosonate 3-deoxy-D-mannooctulosonate cytidylyltransferase: kdsB

3-phosphoshikimate-1carboxyvinyltransferase: aroA 5-enolpyruvylshikimate-3-phosphate chorismate synthase: aroC

tetrahydrodipicolinate homoserine kinase: thrB homoserine Osuccinyltransferase: metA O-succinyl-Lhomoserine O-succinylhomoserine(thiol) -lyase: metB tetrahydrodipicolinate succinylase: dapD N-succinyl2-amino-6ketopimelate N-succinyldiaminopimelateaminotransferase: argD N-succinylL,L-2,6diaminopimelate N-succinyl-Ldiaminopimelate desuccinylase: dapE L,Ldiaminopimelate diaminopimelate epimerase: dapF

cysteine synthase B: cysM cysteine synthase A: cysK

glyceraldehyde 3-phosphate dehydrogenaseA complex: gapA dihydroxyacetone phosphate D-glyceraldehyde3-phosphate fructose bisphosphate aldolase class I: fbaB fructose bisphosphate aldolase class II: fbaA tRNAsec fructose-1,6bisphosphate fructose-1,6bisphosphatase: yggF fructose 1,6bisphosphatase: ybhA fructose 1,6bisphosphatase II: glpX fructose-1,6bisphosphatase I: fbp D-fructose6-phosphate phosphoglucose isomerase: pgi beta-Dglucose-6phosphate

GLYCOLYSIS superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass


beta-D-glucose-6-phosphate

1,6-anhydro-Nacetylmuramic acid recycling


1,6-anhydro-Nacetylmuramate anhydro-Nacetylmuramic acid kinase: anmK N-acetylmuramate 6-phosphate N-acetylmuramic acid 6-phosphate etherase: murQ D-lactate N-acetyl-Dglucosamine6-phosphate

RssB

Tsrgln

a DNA segment

DNA containing a recognition site

(R)-malate D-malate dehydrogenase (decarboxylating) : yeaU pyruvate

dITP

a 2deoxyribonucleoside diphosphate deoxyinosine triphosphate pyrophosphatase: rdgB ribonucleosidediphosphate reductase: nrdB nrdA a ribonucleoside diphosphate

kynurenine aspartate aminotransferase, PLPdependent: aspC 4-(2aminophenyl)-2,4dioxobutanoate

acetate

a [citrate (pro-3S)lyase](thiol form) citrate lyase synthetase: citC

a phosphorylated isocitrate dehydrogenase isocitrate dehydrogenase phosphatase: aceK an isocitrate dehydrogenase

N-substituted aminoacyltRNA peptidyltRNA hydrolase: pth an Nsubstituted amino acid

AraE lipoyl-ACP SucB 2-oxoglutarate pyridoxamine 5-phosphate pyridoxaminephosphate transaminase methyl red ATP NADHazoreductase, FMNdependent: azoR N,N-dimethyl-pphenylenediamine anthranilate a tRNA dGTP N-acetylmuramic acid PTS permease

LamB

pyruvate

CheBPasp: cheB

L-isoleucine L-cysteine

superpathway of hexitol degradation


mannitol-1phosphate mannitol-1phosphate 5dehydrogenase: mtlD D-sorbitol6-phosphate sorbitol-6phosphate dehydrogenase: srlD

L-proline YncD D-methionine L-methionine MipA

ProY

D-3-phosphoglycerate dehydrogenase: serA 3-phosphohydroxypyruvate

RssB-P

Tsrglu

KASII: fabF

homoserine

O-phosphoL-homoserine

tRNAlys L- and Dmethionine uptake ABC permease L-lysine cadaverine

L-lysyltRNAlys

a 3-oxo-cisvaccenoyl[acp] betaketoacyl[acyl-carrierprotein] reductase: fabG a (R)-3hydroxy-cisvaccenoyl[acp] beta-hydroxyacylACP dehydrase [multifunctional]: fabA betahydroxyacylACP dehydratase: fabZ a cisvaccen-2enoyl-[acp]

a trans tetradec2-enoyl-[acp]

biotincarboxyl carrier protein


a BCCP (monomer) bifunctional biotin[acetyl-CoAcarboxylase] ligase and transcriptional repressor: birA a biotinylated BCCP (monomer)

lipid IVA

chorismate

homoserine Osuccinyltransferase: metA O-succinyl-Lhomoserine

threonine synthase: thrC

L-cystathionine L-threonine bifunctional betacystathionase, PLP-dependent and regulator of maltose regulon: malY cystathioninebeta-lyase: metC

2-isopropylmalate synthase: leuA (2S)-2isopropylmalate isopropylmalate isomerase: leuD leuC 2-isopropylmaleate

branched-chain amino-acid aminotransferase: ilvE

dihydroxy-acid dehydratase: ilvD 2-keto-3methyl-valerate

3-phosphoserine aminotransferase: serC (S)-1pyrroline-5carboxylate pyrroline-5carboxylate reductase: proC

selenocysteine biosynthesis
selenide selenide, water dikinase: selD L-serine

beta-Dglucose-6phosphate D-galactose

UDP-galactose biosynthesis (salvage pathway from galactose using UDP-glucose)


alpha-D-glucose 1-phosphate galactokinase: galK glucose-1-phosphate uridylyltransferase: galU galF UDP-D-glucose

phosphoglucose isomerase: pgi

L-galactonate degradation
L-galactonate QseB predicted Lgalactonate oxidoreductase: yjjN D-tagaturonate QseBPhosphorylated transcriptional activator pyruvate formatelyase PFLdeactivase: adhE

restriction e14 prophage; of DNA at 5site-specific methylcytosine DNA residues: mcrA recombinase: pinE DNA Cleaved a DNA at Recognition segment Site in reverse orientation

a tRNA 1,6-anhydro-Nacetylmuramate

a peptide

non-specific ion/solute maltose

lipoylprotein ligase: lipB

tRNA nucleotidyltransferase: cca

deoxyguanosinetriphosphate triphosphohydrolase: dgt

dIMP

a [citrate (pro-3S)lyase](acetyl form)

NlpE YidY peptidoglycan DAP-DAP crosslink murein DDendopeptidase, penicillininsensitive: mepA peptidoglycan tetrapeptide, glycan chain 2 peptidoglycan tripeptide, glycan chain 1 formate dehydrogenaseO: fdoI fdoH fdoG CsgA

a holo-[acp] a tRNA

SucB-lipoate

D-glutamate

pyridoxal 5phosphate

a tRNA

deoxyguanosine

PPPi

a drug

an aliphatic amine amine oxidase (Cu containing) : tynA an aldehyde

a nucleoside 3-phosphate broad specificity 5(3)nucleotidase and polyphosphatase: surE 3-nucleotidase: cpdB

a 3phosphateterminated RNA RNA 3terminal phosphate cyclase: rtcA a 2,3-cyclicphosphateterminated RNA

methylglyoxal methylglyoxal reductase (NADHdependent) : ydjG acetol

nitric oxide fused nitric oxide dioxygenase and dihydropteridine reductase 2: hmp nitrate

XTP

DNA containing a base with lesion xanthosine triphosphate pyrophosphatase: rdgB stationary phase mismatch/ uracil DNA glycosylase: mug base with lesion a DNA containing abasic site

Curli Secretion and Assembly Complex

protein N6(dihydrolipoyl) lysine lipoamide dehydrogenase: lpd protein N6(lipoyl)lysine

lipoate

AceF

NADP+

a reduced flavodoxin flavodoxin NADP+ reductase: fpr an oxidized flavodoxin

an oxidized thioredoxin

a protein Lmethionine methionine sulfoxide reductase A: msrA a protein-Lmethionine(S)-S-oxide

a lipoyl-[acp]

an apoGcvH protein lipoylprotein ligase: lipB H-Gcvprotein(lipoyl)lysine

molybdopterin synthase

precursor-Z

glutathionylspermidine fused glutathionylspermidine amidase / glutathionylspermidine synthetase: gsp spermidine glutathione

isopentenyl diphosphate

a tRNA

3-mercaptopyruvate

hydrogen cyanide

a drug

MdtM

D-fructose-6-phosphate

anthranilate synthase: trpD trpE

chorismate mutase: tyrA chorismate mutase: pheA

3-phospho-L-serine

D-fructose6-phosphate

lipoylprotein ligase A: lplA

molybdopterin synthase: moaE moaD molybdopterin synthase

YfaZ L-lysine

CadB L-histidine histidyltRNA synthetase: hisS a myristoyl-[acp] L-histidyltRNAhis KASI: fabB tRNAhis L-lysine LysP a 3-oxopalmitoyl-[acp] histidine ABC transporter glycine glycyl-tRNA synthetase: glyQ glyS glycyltRNAgly beta-ketoacyl[acyl-carrierprotein] reductase: fabG an (R)-3hydroxypalmitoyl[acp] beta-hydroxyacylACP dehydrase [multifunctional]: fabA beta-hydroxyacylACP dehydratase: fabZ L-threonine homoserine

CMP-3-deoxyD-mannooctulosonate

anthranilate anthranilate synthase component II: trpD KDO transferase: waaA N-(5-phosphoribosyl) -anthranilate phosphoribosylanthranilate isomerase: trpC 1-(ocarboxyphenylamino) -1-deoxyribulose5-phosphate indole-3-glycerol phosphate synthase: trpC indole-3-glycerolphosphate

prephenate

O-succinylhomoserine(thiol) -lyase: metB

L-valine branched-chain amino-acid aminotransferase: ilvE

phosphoserine phosphatase: serB

Blc

prephenate dehydratase: pheA phenylpyruvate

prephenate dehydrogenase: tyrA 4-hydroxyphenylpyruvate tyrosine aminotransferase: tyrB

L-cystathionine

superpathway of alanine biosynthesis


2-ketoisovalerate

seryl-tRNA synthetase: serS L-seryltRNAsec

alpha-D-galactose 1-phosphate

fructose-1,6-bisphosphatase: yggF fructose 1,6-bisphosphatase: ybhA fructose 1,6-bisphosphatase II: glpX fructose-1,6-bisphosphatase I: fbp

6-phosphofructokinase I: pfkA 6-phosphofructokinase II: pfkB

delta(2)isopentenylpyrophosphate tRNA-adenosine transferase: miaA tRNA containing 6Isopentenyladenosine thiocyanate

PflB

xanthosine5-phosphate

AceF-lipoate

NADPH

a holo-[acp]

molybdopterin

predicted thiosulfate sulfur transferase: ynjE 3-mercaptopyruvate:cyanide sulfurtransferase: sseA non-specific ion/solute

CirA

ferric dihydroxybenzoylserine

FeoB

Fe2+ a ribonucleoside OmpG mono-, di-, or trisaccharide < 600 Da

a thioredoxin

NUCLEOSIDES AND NUCLEOTIDES DEGRADATION AND RECYCLING pyrimidine deoxyribonucleosides degradation


deoxycytidine deoxyadenosine cytidine deaminase: cdd deoxyuridine uracil phosphorylase: deoA thymidine thymidine phosphorylase: deoA deoxyadenosine deaminase: add purine nucleoside phosphorylase: deoD purine nucleoside phosphorylase: deoD deoxyguanosine xanthosine xanthosine phosphorylase: xapA purine nucleoside phosphorylase: deoD purine nucleoside phosphorylase: deoD purine nucleoside phosphorylase: deoD

MscS a beta-lactam betalactamase; penicillin resistance: ampC a substituted betaamino acid L-arginine L-glutamate p-aminobenzoate

pyruvate

L-proline L-isoleucine

L-serine

formate dehydrogenaseO: fdoI fdoH fdoG OmpC hydrophilic solute or ion < 600 Da

selenophosphate

YtfM

(KDO)lipid IVA KDO transferase: waaA KDO2lipid IVA biotin acetyl-CoA carboxyltransferase: carboxylase: accC accD accA a carboxylatedbiotinylatedBCCP

L-histidine OmpL

aspartate aminotransferase, PLP-dependent: aspC tyrosine aminotransferase: tyrB

bifunctional betacystathionase, PLP-dependent and regulator of maltose regulon: malY cystathioninebeta-lyase: metC

L-homocysteine mesodiaminopimelate diaminopimelate decarboxylase: lysA

isopropylmalate isomerase: leuD leuC (2R,3S)-3isopropylmalate 3-isopropylmalate dehydrogenase: leuB (2S)-2-isopropyl3-oxosuccinate

serine hydroxymethyltransferase: glyA

cobalamincobalaminindependent dependent homocysteine homocysteine transmethylase: transmethylase: metH metE

glycine

branched-chain amino-acid aminotransferase: ilvE

selenocysteine synthase: selA

fructose-1,6-bisphosphate

purine deoxyribonucleosides degradation

degradation of purine ribonucleosides


d-biotin dsulfoxide adenosine adenosine deaminase: add inosine guanosine biotin sulfoxide reductase: bisC biotin

L-tyrosine

L-homocysteine

L-phenylalanine Ag43

PheP

tRNAgly

a biotinylated BCCP (dimer)

L-phenylalanine

tetrahydrofolate

L-lysine L-methionine

superpathway of aspartate and asparagine biosynthesis; interconversion of aspartate and asparagine


L-glutamate L-aspartate L-asparagine

L-selenocysteinyltRNAsec L-cysteine pyruvate glutamate-pyruvate aminotransferase: alaB

L-valine

UDP-glucosehexose-1-phosphate uridylyltransferase: galT alpha-D-glucose 1-phosphate

UDP-glucose 4epimerase: galE

fructose bisphosphate aldolase class I: fbaB fructose bisphosphate aldolase class II: fbaA

a 2,3,4saturated fatty acyl CoA trans-2enoyl-CoA reductase (NADPH) a trans-2enoyl-CoA

D-glycerate

a damaged DNA pyrimidine endonuclease III; specific for apurinic and/ or apyrimidinic sites: nth a DNA containing a apyrimidinic site

thiamine diphosphate thiamin pyrophosphate hydrolase: nudJ thiaminephosphate

a nonmethylated ribosomal protein L11 methyltransferase for 50S ribosomal subunit protein L11: prmA a methylated ribosomal protein L11

a quinone

a ribonucleoside triphosphate ribonucleosidetriphosphate reductase: nrdD a 2deoxyribonucleoside triphosphate

lipoate

an apoGcvH protein lipoylprotein ligase A: lplA

nicotinamide riboside bifunctional NadR transcriptional repressor and NMN adenylyltransferase: nadR nicotinamide mononucleotide

an oxidized thioredoxin

a protein Lmethionine methionine sulfoxide reductase B: msrB a protein-Lmethionine(R)-S-oxide

L-Alagamma-DGlu-Dap murein peptide amidase A: mpaA L-AlagammaD-Glu

a protein

S-adenosylL-methionine S-adenosyldependent methyltransferase: mraW

glutathione

spermidine fused glutathionylspermidine amidase / glutathionylspermidine synthetase: gsp

L-cysteine

uridine

a 2,3,4saturated fatty acyl-[acp]

non-specific sn-glycerolion/solute 3-phosphate

KefA

dihydroxyacetone phosphate UDP-D-galactose triose phosphate isomerase: tpiA

glyoxylate reductase B: ghrB glyoxylate reductase: ghrA hydroxypyruvate

NAD(P)H:quinone oxidoreductase: wrbA chromate reductase: yieF a hydroquinone

valine-pyruvate aminotransferase: avtA

cysteine desulfurase: iscS

purine nucleoside phosphorylase: deoD

H-Gcvprotein(lipoyl)lysine

tRNA (5methylaminomethyl2-thiouridylate)methyltransferase: mnmA an acyl-[acp] L-alanine 2-thiouridine a holo-[acp]

glycerol-3phosphate acyltransferase: plsB a 2,3,4-saturated 2lysophosphatidate

non-specific ion/solute

arginine decarboxylase, degradative: adiA arginine decarboxylase, biosynthetic: speA agmatine

putative paminobenzoylglutmate hydrolase: abgB OmpN p-aminobenzoyl glutamate

hydrophilic solute or ion < 600 Da

MscL

PhoE a 1-acyl-snglycerol-3phosphate ZitB Cu+ multicopper oxidase with role in copper homeostasis: cueO Cu2+ L-arginine thiosulfate hydrogen cyanide thiosulfate sulfurtransferase: pspE thiosulfate sulfurtransferase: glpE sulfite agmatine thiocyanate

a thioredoxin

mesodiaminopimelate

a methylated protein

glutathionylspermidine

hydrophilic solute or ion < 600 Da

Zn2+

deoxyinosine

ALCOHOLS DEGRADATION
deoxyribose1-phosphate alpha-D-ribose1-phosphate phosphopentomutase: deoB D-ribose-5phosphate

shikimate UidC

ShiA

a cisvaccenoyl[acp]

lauroyl acyltransferase: lpxL KDO2(lauroyl)lipid IVA myristoyl-acyl carrier protein (ACP)-dependent acyltransferase: lpxM KDO2lipid A

palmitoleoyl acyltransferase: lpxP KDO2(palmitoleoyl) -lipid IVA myristoyl-acyl carrier protein (ACP)-dependent acyltransferase: lpxM KDO2-lipid A, cold adapted

tryptophan synthase, alpha subunit: trpA

glutamate biosynthesis III


2-oxoglutarate

4-methyl-2oxopentanoate tyrosine aminotransferase: tyrB branched-chain amino-acid aminotransferase: ilvE

aspartate aminotransferase, PLPdependent: aspC

L-histidine

asparagine synthetase B: asnB asparagine synthetase A: asnA

asparaginase III: iaaA asparaginase I: ansA

L-alanine

AMINES AND POLYAMINES BIOSYNTHESIS


D-glyceraldehyde-3-phosphate

L-aspartate L-asparagine aspartate ammonialyase: aspA fumarate

L-aspartate

RhtA CsgB maltose YbfM RhtC YbhC ZnuA/ZnuB/ ZnuC ABC transporter maltose ABC transporter

L-serine

indole

a trans hexadecenoyl-[acp]

cisvaccenate

tryptophan synthase, beta subunit dimer: trpB

glutamate dehydrogenase: gdhA

methionine adenosyltransferase: metK S-adenosylL-methionine

alanine racemase 2, PLPbinding: dadX alanine racemase 1, PLP-binding, biosynthetic: alr

superpathway of arginine and polyamine biosynthesis


L-glutamate

deoxyribose1-phosphate phosphopentomutase: deoB deoxyribose5-phosphate

phosphopentomutase: deoB deoxyribose5-phosphate deoxyribosephosphate aldolase: deoC

N-acetylglutamate synthase: argA D-alanine N-acetyl-Lglutamate acetylglutamate kinase: argB

glycine betaine biosynthesis I (Gramnegative bacteria) choline


choline dehydrogenase: betA betaine aldehyde betaine aldehyde dehydrogenase: betB glycine betaine

glyceraldehyde 3-phosphate dehydrogenase-A complex: gapA

degradation of pyrimidine ribonucleosides


cytidine cytidine deaminase: cdd uridine uridine phosphorylase: udp alpha-D-ribose1-phosphate phosphopentomutase: deoB D-ribose-5phosphate uracil

superpathway of glycol metabolism and degradation


ethylene glycol

ethanol degradation
ethanol

RcsB

trans-delta2decenoylCoA 2,4-dienoylCoA reductase: fadH

an alcohol ATP ethanol dehydrogenase: adhP alcohol dehydrogenase: adhE an aldehyde or ketone

phytate

RplL ADP

thiamine diphosphate

7,8dihydroneopterin triphosphate dihydroneopterin triphosphate 2epimerase: folX dihydromonapterintriphosphate

lipoate

SucB

a reduced ferredoxin

NAD+

inosine

pseudouridine 5-phosphate predicted pseudouridine 5-phosphate glycosidase: pscG uracil D-ribose-5phosphate

a purine ribonucleoside

UDP-N-acetylmuramoylL-alanyl-Dglutamyl-meso-2,6diaminoheptanedioateD-alanine L,Dcarboxypeptidase A: ldcA UDP-Nacetylmuramoyl-Lalanyl-D-glutamylmeso-2,6diaminopimelate

UDP-[Nacetyl-Dglucosamine]n

UDP-Nacetyl-Dglucosamine UDP-N-acetylD-glucosamine beta-1,6N-acetyl-Dglucosaminyl transferase: pgaC

an inactive ribonucleoside triphosphate reductase

S-adenosylL-methionine

a drug

HsrA

L-1,2-propanediol oxidoreductase: fucO

1,3-diphosphateglycerate deoxyribosephosphate aldolase: deoC phosphoglycerate kinase: pgk acetaldehyde acetaldehyde dehydrogenase 2: mhpF acetaldehyde dehydrogenase: adhE D-glyceraldehyde3-phosphate acetaldehyde dehydrogenase 2: mhpF acetaldehyde dehydrogenase: adhE acetaldehyde D-glyceraldehyde3-phosphate

glycerol degradation I
glycolaldehyde aldehyde dehydrogenase A, NADlinked: aldA glycerol glycolate glycolate oxidase: glcF glcE glcD glycerol kinase: glpK a glycerophosphodiester

L-tryptophan

L-glutamate

L-leucine

ethanol dehydrogenase: adhP alcohol dehydrogenase: adhE acetaldehyde

RcsBphosphate

trans-delta2, cis-delta4decadienoylCoA

Ap4A synthetase: lysU 5,5diadenosine tetraphosphate

acid phosphatase: appA D-myo-inositol (1,2,3,4,5)pentakisphosphate

ribosomal-proteinL12-serine acetyltransferase: rimL 50S ribosomal subunit protein L7

ThDP adenylyl transferase adenosine thiamine triphosphate

lipoylprotein ligase A: lplA

ferredoxin NAD+ reductase: hcaD an oxidized ferredoxin

ribonucleoside hydrolase 3: rihC

purine nucleoside phosphorylase: deoD alpha-Dribose-1phosphate a purine base

ribonucleoside triphosphate reductase activase: nrdG an active ribonucleoside triphosphate reductase

a drug

YdhC

arginine decarboxylase, degradative: adiA arginine decarboxylase, biosynthetic: speA

N-acetylmuramoyl-Lalanyl-D-glutamyl-meso2,6-diaminopimelylD-alanyl-D-alaninediphosphoundecaprenylN-acetylglucosamine

diphosphoundecaprenyl[GlcNAc-MurNAcpentapeptide]n penicillinbinding protein 1A: mrcA

Fiu

ferric dihydroxybenzoylserine

FhuE

ferric coprogen

di-trans,polycisundecaprenyl diphosphate

diphosphoundecaprenyl[GlcNAc-MurNAcpentapeptide]n+1 BglH a carbohydrate

SucB-lipoate

NADH

hypoxanthine

D-ribose

L-alanine uridine-5diphosphate

poly-beta-1,6N-acetyl-Dglucosamine

L-methionine

5-deoxyadenosine

a drug

YceE di-trans,polycisundecaprenyl diphosphate L-arginine a 1-lyso-2-acylsn-glycero-3phosphocholine multifunctional acylCoA thioesterase I and protease I and lysophospholipase L1: tesA L-1-glycero-3phosphocholine superoxide hydrogen peroxide hydroperoxidase I: katG Slp YehA

a palmitoyl-[acp]

L-threonine

palmitate

Zn2+ HtrE

N-acetylglutamylphosphate N-acetylglutamylphosphate reductase: argC N-acetyl-Lglutamate 5semialdehyde acetylornithine transaminase, catabolic: astC acetylornithine transaminase: argD bicarbonate N-acetyl-Lornithine NAD+ L-glutamyltRNAGlu carbamoyl phosphate synthetase: carA carB carbamoylphosphate acetylornithine deacetylase: argE

3-phosphoglycerate

COFACTORS, PROSTHETIC GROUPS, ELECTRON CARRIERS BIOSYNTHESIS


PhnC/PhnD/PhnE alkylphosphonate ABC transporter EmrKYTolC putative multidrug efflux transport system [+ 6 isozymes] MdoH 4-hydroxybenzoate

phosphoglycerate mutase, cofactor independent: gpmM phosphoglycerate mutase 2: ytjC phosphoglyceromutase 1: gpmA

acetyl-CoA

glycerophosphodiester phosphodiesterase, cytosolic: ugpQ glycerophosphoryl diester phosphodiesterase, periplasmic: glpQ

acetaldehyde dehydrogenase 2: mhpF acetaldehyde dehydrogenase: adhE

BglG

L-methionine sulfoxide biotin sulfoxide reductase: bisC

FMN

a protein

acetyl-CoA sn-glycerol3-phosphate glycerol-3phosphatedehydrogenase, anaerobic: glpC glpB glpA dihydroxyacetone phosphate

BglG-P L-methionine

FMN phosphatase: ybjI FMN phosphatase: yigB riboflavin

acetyl-CoA

an alkylphosphate Tsx

ubiquinone-8 biosynthesis (prokaryotic)


multidrug chorismate

polyisoprenoid biosynthesis (E. coli)


isopentenyl diphosphate isopentenyl diphosphate isomerase: idi dimethylallyl diphosphate geranyl diphosphate synthase: ispA geranyldiphosphate farnesyl diphosphate synthase: ispA all-transfarnesyl diphosphate undecaprenyl diphosphate synthase: ispU 2-cis,6trans,10-transgeranylgeranyl diphosphate undecaprenyl diphosphate synthase: ispU di-trans,polycispentaprenyl diphosphate undecaprenyl diphosphate synthase: ispU di-trans,polycis-hexaprenyl diphosphate undecaprenyl diphosphate synthase: ispU di-trans,polycisheptaprenyl diphosphate undecaprenyl diphosphate synthase: ispU di-trans,polycis-octaprenyl diphosphate undecaprenyl diphosphate synthase: ispU di-trans,polycis-nonaprenyl diphosphate octaprenyl diphosphate synthase: ispB all-transgeranylgeranyl diphosphate octaprenyl diphosphate synthase: ispB geranylfarnesyl diphosphate octaprenyl diphosphate synthase: ispB all-transhexaprenyl diphosphate octaprenyl diphosphate synthase: ispB all-transheptaprenyl diphosphate octaprenyl diphosphate synthase: ispB all-transoctaprenyl diphosphate

superpathway of menaquinone8 biosynthesis


chorismate isochorismate synthase 2: menF

methylerythritol phosphate pathway


D-glyceraldehyde3-phosphate pyruvate GTP

flavin biosynthesis I (bacteria)

pantothenate and coenzyme A biosynthesis I


2-keto-isovalerate 3-methyl-2-oxobutanoate hydroxymethyltransferase: panB 2-dehydropantoate 2-dehydropantoate 2-reductase: panE aspartate 1decarboxylase: panD

superpathway of pyridoxal 5phosphate biosynthesis and salvage


D-erythrose4-phosphate erythrose 4phosphate dehydrogenase: epd erythronate4-phosphate erythronate4-phosphate dehydrogenase: pdxB

thiamin biosynthesis I
a ThiS sulfur-carrier protein thiamin (thiazole moiety) biosynthesis protein: thiF an adenylated ThiS sulfurcarrier protein

tetrapyrrole biosynthesis I
a ThiI sulfurcarrier protein cysteine desulfurase: iscS L-glutamate

NAD salvage pathway I


nicotinamide

autoinducer AI2 biosynthesis


S-adenosylL-methionine

OTHER BIOSYNTHESIS
2-phosphoglycerate

protein kinase: yeaG resolvasome: serine/ ruvA ruvB ruvC threonine resolution of protein kinase: rdoA recombinational junction formation of two intact strands a phosphoprotein

DNA combined with exogenous DNA to form a recombinational junction

23S ribosomal RNA 23S rRNA 2-Oribose G2251 methyltransferase: rlmB 23S ribosomal RNA methylated at position G2251

5,5diadenosine tetraphosphate

16S-rRNAs

an oxidized electron acceptor

NADPH

DNA containing a base with lesion stationary phase mismatch/ uracil DNA glycosylase: mug excised base a DNA containing abasic site

poly-beta-1,6N-acetyl-Dglucosamine poly-beta-1,6N-acetyl-Dglucosamine N-deacetylase: pgaB partially Ndeacetylated poly-beta-1,6N-acetyl-Dglucosamine

a protein

L-leucyltRNAleu leucyl, phenylalanyltRNA-protein transferase: aat L-leucylprotein

L-lysine

tRNAileX

a tRNA containing 5carboxymethylaminomethyl2-thiouridine 5-methylaminomethyl2-thiouridine methyltransferase: mnmC tRNA containing 5methylaminomethyl2-thiouridylate

an L-1phosphatidylglycerol

a prolipoprotein

an oxidized ferredoxin

alpha-Larabinose coenzyme A pyruvate

YdeA

undecaprenyl pyrophosphate phosphatase: pgpB di-trans,polycisundecaprenyl phosphate

16S rRNA m3U1498 methyltransferase: diadenosine rsmE tetraphosphatase: apaH 16S rRNA containing N3methylated uridine ADP

NADPH quinone reductase: mdaB a reduced electron acceptor

tRNAIlelysidine synthetase: tilS lysidinemodified tRNAileX

phosphatidylglycerolprolipoprotein diacylglyceryl transferase; a major membrane phospholipid: lgt sn-glycerol1-phosphate a diacylglycerol prolipoprotein

NADP+

putative pyruvate synthase: ydbK pyruvate synthase a reduced ferredoxin

K+

KefC

arginine decarboxylase, degradative: adiA arginine decarboxylase, biosynthetic: speA

a carboxylate

superoxide dismutase precursor (Cu-Zn) : sodC superoxide dismutase (Mn): sodA hydrogen peroxide

H2O

agmatine TrkG K+ D-alanylD-alanine Kup K+ penicillinbinding protein 6: dacC oxidized cytochrome c552 cytochrome C552: nrfA nitrite reductase complex: nrfA nrfB nrfC nrfD reduced cytochrome c552 succinate fumarate

OmpA

a tRNA

acetate

glyoxylate

acetyl-CoA di-trans,polycisundecaprenyl phosphate

enolase: eno

AMINES AND POLYAMINES DEGRADATION allantoin degradation IV (anaerobic)


urate pyruvate kinase I: pykF pyruvate kinase II: pykA

glyoxylate carboligase: gcl tartronate semialdehyde tartronate semialdehyde reductase 2: glxR D-glycerate glycerate kinase II: glxK

malate synthase G: glcB malate

selenite putative selenate reductase: ygfM xdhD ygfK selenate

HipA

a mismatched DNA base pair MutHLS complex, methyldirected mismatch repair: mutH mutS mutL a properly matched DNA base pair

cholate

a nucleoside diphosphate putative nucleoside (IDP) diphosphatase: yibQ a nucleotide

isovalerylCoA isovaleryl-CoA dehydrogenase / predicted acyl-CoA dehydrogenase: aidB 3-methylcrotonylCoA

L-homocysteine dGMP homocysteine methyltransferase: mmuM

a nucleoside triphosphate

RNA(n)

chorismate lyase: ubiC all-transoctaprenyl diphosphate 4-hydroxybenzoate octaprenyltransferase: ubiA 3-octaprenyl-4hydroxybenzoate

23S ribosomal RNA 23S rRNA m5U747 methyltransferase: rlmC 23S rRNA m5U1939 methyltransferase: rlmD 5-methyluridinemodified 23S ribosomal RNA

a phosphoprotein phosphoprotein phosphatase: pphB protein phosphatase 1 modulates phosphoproteins, signals protein misfolding: pphA

an oxidized thioredoxin

L-methionine

L-glutamate

1-deoxyxylulose5-phosphate synthase: dxs 1-deoxy-Dxylulose 5phosphate 1-deoxy-D-xylulose 5-phosphate reductoisomerase: dxr 2-Cmethyl-Derythritol-4phosphate 4-diphosphocytidyl2C-methylD-erythritol synthase: ispD 4-(cytidine 5diphospho) -2-C-methylD-erythritol 4-diphosphocytidyl2-C-methylerythritol kinase: ispE 2-phospho4-(cytidine 5diphospho) -2-C-methylD-erythritol 2C-methyl-Derythritol 2,4cyclodiphosphate synthase: ispF 2-C-methyl-Derythritol-2,4cyclodiphosphate 1-hydroxy-2methyl-2-(E) -butenyl 4diphosphate synthase: ispG 1-hydroxy-2methyl-2-(E) -butenyl 4diphosphate 1-hydroxy-2methyl-2-(E) -butenyl 4diphosphate reductase: ispH isopentenyl diphosphate

a tRNA containing queuosine glutamyl-Q tRNA(Asp) synthetase: yadB

L-seryl-AMP

2,3dihydroxybenzoylAMP aryl carrier protein: entF

GTP cyclohydrolase II: ribA 2,5-diamino-6(ribosylamino) -4-(3H)pyrimidinone 5-phosphate fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5phosphoribosylamino)uracil reductase: ribD 5-amino-6-(5phosphoribosylamino) uracil fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5D-ribulosephosphoribosylamino)uracil reductase: ribD 5-phosphate 5-amino-6ribitylamino2,4(1H,3H)pyrimidinedione 5-phosphate pyrimidine phosphatase 5-amino-6ribitylamino2,4(1H,3H)pyrimidinedione 6,7-dimethyl-8ribityllumazine synthase: ribE 6,7dimethyl-8(1-D-ribityl) lumazine riboflavin synthase: ribC riboflavin bifunctional riboflavin kinase / FMN adenylyltransferase: ribF 3,4dihydroxy-2butanone 4phosphate synthase: ribB L-3,4dihydroxybutan-2one-4-phosphate

glutamyl-tRNA synthetase: gltX

PRPP biosynthesis II
S-adenosyl-Lhomocysteine 5-methylthioadenosine/ S-adenosylhomocysteine nucleosidase: mtn S-ribosyl-Lhomocysteine S-ribosylhomocysteine lyase: luxS 4,5dihydroxy-2,3pentanedione D-ribose-5phosphate phosphopentomutase: deoB alpha-Dribose-1phosphate ribose 1phosphokinase ribose-1,5bisphosphate ribose 1,5bisphosphokinase: phnN (2R,4S)-2-methyl-2,4dihydroxydihydrofuran3-one 5-phosphoribosyl 1-pyrophosphate

L-aspartate

phosphoenolpyruvate

isochorismate 2-succinyl-5enolpyruvyl6-hydroxy-3cyclohexene1-carboxylate synthase: menD all-trans-farnesyl diphosphate octaprenyl diphosphate synthase: ispB all-transgeranyl-geranyl diphosphate octaprenyl diphosphate synthase: ispB geranylfarnesyl diphosphate octaprenyl diphosphate synthase: ispB all-transhexaprenyl diphosphate octaprenyl diphosphate synthase: ispB all-transheptaprenyl diphosphate octaprenyl diphosphate synthase: ispB all-transoctaprenyl diphosphate 2-succinyl-5enolpyruvyl6-hydroxy-3cyclohexene1-carboxylate (1R,6R)-2succinyl-6hydroxy-2,4cyclohexadiene1-carboxylate synthase: menH (1R,6R)-6-hydroxy2-succinylcyclohexa2,4-diene-1carboxylate o-succinylbenzoate synthase: menC

YidI

a ThiI persulfide

glutamyl-tRNA reductase: hemA glutamate-1semialdehyde glutamate-1semialdehyde aminotransferase: hemL 5-amino-levulinate NAD synthetase, NH3-dependent: nadE nicotinate adenine dinucleotide

NADH pyrophosphatase: nudC

L-ornithine

superpathway of Nacetylglucosamine, Nacetylmannosamine and Nacetylneuraminate N-acetylneuraminate degradation


N-acetylneuraminate lyase: nanA N-acetyl-Dmannosamine N-acetylmannosamine kinase: nanK N-acetyl-Dmannosamine6-phosphate predicted Nacetylmannosamine6-phosphate epimerase: nanE N-acetyl-Dglucosamine6-phosphate N-acetylglucosamine6-phosphate deacetylase: nagA

CMP-3-deoxyD-mannooctulosonate

a lipopolysaccharide

N-6isopentyl adenosine37 tRNA isopentenyladenosine A37 tRNA methylthiolase MiaB: miaB 2-methylthioN-6isopentyl adenosine37 tRNA

UDP-NacetylmuramoylL-alanyl-Dglutamylmeso-2,6diaminopimelyl-Dalanyl-D-alanine

partially Ndeacetylated poly-beta-1,6N-acetyl-Dglucosamine

PgaA

UQ

UQH2 N-acetylmuramoyl-Lalanyl-D-glutamyl-meso2,6-diaminopimelylD-alanyl-D-alaninediphosphoundecaprenol NanC N-acetylmuramoyl-Lalanyl-D-glutamyl-meso2,6-diaminopimelylD-alanyl-D-alaninediphosphoundecaprenylN-acetylglucosamine N-acetylneuraminate

glycerol degradation V
glycerol

serine/ threonine kinase HipA: hipA phosphorylated serine/threonine kinase HipA

phosphoenolpyruvate synthase: pps S-allantoin

L-pantoate

beta-alanine

nicotinamide mononucleotide

PnuC 3-octaprenyl-4hydroxybenzoate decarboxylase together with UbiG: ubiX 3-octaprenyl-4hydroxybenzoate carboxy-lyase: ubiD 2-octaprenylphenol

tetrahydrofolate biosynthesis
pantothenate synthetase: panC GTP pantothenate pantothenate kinase: coaA D-4phosphopantothenate fused 4phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase: dfp R-4phosphopantothenoylL-cysteine fused 4phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase: dfp chorismate 4-phosphopantetheine aminodeoxychorismate synthase: pabA pabB phosphopantetheine adenylyltransferase: coaD 4-amino-4deoxychorismate aminodeoxychorismate lyase: pabC bifunctional riboflavin kinase / FMN adenylyltransferase: ribF dephosphoCoA kinase: coaE dihydroneopterin aldolase: folB 6-hydroxymethyl7,8-dihydropterin 6-hydroxymethyl7,8-dihydropterin pyrophosphokinase: folK 6-hydroxymethyldihydropterin diphosphate dihydropteroate synthase: folP

2-oxo-3-hydroxy-4phosphobutanoate phosphohydroxythreonine aminotransferase: serC 4-(phosphonooxy) -threonine 5-aminoimidazole ribonucleotide hydroxymethylpyrimidine 4-hydroxyL-threonine phosphate dehydrogenase, NADdependent: pdxA D-glyceraldehyde3-phosphate pyruvate (2S)-2-amino-3-oxo-4phosphonooxybutanoate thiamin biosynthesis protein ThiC: thiC hydroxymethylpyrimidine kinase: thiD 4-methyl5-(betahydroxyethyl) thiazole hydroxyethylthiazole kinase: thiM 4-methyl5-(betahydroxyethyl) thiazole phosphate

thiamin (thiazole moiety) biosynthesis protein: thiF a ThiSThiI acyldisulfide

nicotinamide mononucleotide ornithine carbamoyltransferase: argF ornithine carbamoyltransferase: argI

glycerol dehydrogenase: gldA dihydroxyacetone an unstable RecA filamentDNA complex RecFOR complex: recO recR recF a transdelta2enoylacyl-[acp] trans-2decenoylACP isomerase: fabA a cis-delta3decenoyl[acp]

7-alphahydroxysteroid dehydrogenase: hdhA 3-alpha,12alphadihydroxy7-oxo5-betacholanate

deoxyguanylate kinase: gmk

RNA polymerase, core enzyme: rpoB rpoC rpoA RNA(n)

methionine sulfoxide reductase A: msrA L-methionine(S)-S-oxide

SbmA

a peptide antibiotic

L-methionine 2-deoxyguanosine5-diphosphate

a thioredoxin a protein

a tRNA containing glutamylated queuosine

AMP

enterobactin CMP

protein involved in KdoIII attachment during lipopolysaccharide core biosynthesis: rfaZ KDOIIIlipopolysaccharide 5-deoxyadenosine

D-alanine

beta-Dglucose-6phosphate

phosphoglucose isomerase: pgi D-fructose6-phosphate

nitrite uridine-5diphosphate

NanT

N-acetylneuraminate

L-methionine

nicotinate-mononucleotide adenylyltransferase: nadD

NMN nucleosidase NMN amidohydrolase

PRPP biosynthesis I
D-ribose-5phosphate

pyruvate

allantoinase: allB

pantothenate

PanF

D-glyceraldehyde3-phosphate

3-phosphoglycerate

DNA with GA mismatch ATP adenine glycosylase; G.C --> T.A transversions: mutY DNA with removed adenine mismatch leaving an AP site

beta-Dgalactose predicted galactose 1dehydrogenase: yhhX [+ 3 isozymes] D-galactono1,4-lactone

pyruvate

allantoate pyruvate dehydrogenase multienzyme complex: lpd aceF aceE allantoate amidohydrolase: allC ureidoglycine allantoate amidohydrolase: allC S-ureidoglycolate malate dehydrogenase: mdh ureidoglycolate dehydrogenase: allD oxaloacetate malate synthase A: aceB oxalurate citrate synthase: gltA

4-amino-5hydroxymethyl-2methylpyrimidinepyrophosphate HMP-PP hydrolase: cof HMP-PP hydrolase: nudJ hydroxymethylpyrimidine phosphate

a tRNA cyclic-AMP tRNA:Cm32/Um32 methyltransferase: trmJ a tRNA containing 2-Omethylcytosine or 2-Omethyluridine

3-sulfinoalanine

glyoxylate GTP molybdenum cofactor 2-succinyl-5enolpyruvyl6-hydroxy-3cyclohexene1-carboxylate synthase: menD 2-hydroxyglutarate synthase 2-hydroxyglutarate

L-threo-3phenylserine lowspecificity L-threonine aldolase: ltaE

di-trans,polycisundecaprenyl diphosphate

Lipid A-core

L-Ala-DGlu-mesoA2pm

UDP-Nacetylmuramate UDP-Nacetylmuramate:Lalanyl-gamma-Dglutamyl-mesodiaminopimelate ligase: mpl

murein tripeptide ABC transporter

L-Ala-DGlu-mesoA2pm

2-oxoglutarate

1-ethyladenine

S-adenosylL-methionine

PflB B3496 a dipeptide

a protein L-tyrosine tyrosine kinase involved in colanic acid biosynthesis: wzc a proteinL-tyrosine phosphate

H2O

nicotinate mononucleotide 1-deoxyxylulose5-phosphate synthase: dxs 1-deoxy-Dxylulose 5phosphate a ThiSThiF acyldisulfide nicotinate phosphoribosyltransferase: pncB porphobilinogen synthase: hemB porphobilinogen thiamin biosynthesis ThiGH complex: thiH thiG

nicotinamide nicotinamidase: pncA

L-citrulline argininosuccinate synthase: argG L-argininosuccinate

GTP cyclohydrolase I: folE 7,8-dihydroneopterin triphosphate dihydroneopterin triphosphate pyrophosphohydrolase: nudB dihydroneopterin phosphate dihydroneopterin monophosphate dephosphorylase pyridoxine 7,8-dihydro-D-neopterin pyridoxal kinase: pdxK pyridoxine 5-phosphate synthase: pdxJ pyridoxamine pyridoxamine kinase: pdxK pyridoxal pyridoxamine 5-phosphate pyridoxamine 5-phosphate oxidase: pdxH pyridoxal kinase 2: pdxY pyridoxal kinase: pdxK thiamin kinase: thiK

ribose-phosphate diphosphokinase: prs 5-phosphoribosyl 1-pyrophosphate acetyl-CoA

ALDEHYDE DEGRADATION superpathway of methylglyoxal degradation


methylglyoxal

adenylate cyclase: cyaA

MarC

2-octaprenylphenol hydroxylase: ubiB DjlA 2-octaprenyl-6hydroxyphenol bifunctional 3demethylubiquinone-8 3-O-methyltransferase and 2-octaprenyl6-hydroxyphenol methylase: ubiG 2-octaprenyl-6methoxyphenol 2-octaprenyl-6methoxyphenol hydroxylase: ubiH 2-octaprenyl6-methoxy1,4benzoquinol bifunctional 2octaprenyl-6-methoxy1,4-benzoquinone methylase and Sadenosylmethionine:2DMK methyltransferase: ubiE 2-octaprenyl3-methyl-6methoxy-1,4benzoquinol PspB 2-octaprenyl3-methyl-6methoxy-1,4benzoquinone hydroxylase: ubiF 3-demethylubiquinol-8

nicotinate

hydroxymethylpyrimidine phosphate phosphohydroxymethylpyrimidine kinase: thiD 4-amino-5hydroxymethyl-2methylpyrimidinepyrophosphate thiamin thiamine phosphate synthase: thiE

hydroxymethylbilane synthase: hemC

adenosylcobalamin salvage from cobinamide and cobalamin


cobinamide

argininosuccinate lyase: argH

L-lactaldehyde degradation (anaerobic)


L-lactaldehyde methylglyoxal reductase (NADPHdependent) L-lactaldehyde aldehyde dehydrogenase A, NADlinked: aldA L-lactate

a stabilized RecA filamentDNA complex

cAMP phosphodiesterase: cpdA

cysteine sulfinate desulfinase: csdA csdE sulphur dioxide

molybdopterin guanine dinucleotide synthase: mobA molybdopterin guanine dinucleotide glycine

protein with low undecaprenyl pyrophosphate phosphatase activity: lpxT di-trans,polycisundecaprenyl phosphate lipid A-core 1diphosphate

AlkB repair system for alkylated DNA and RNA: alkB

pyruvate formatelyase activating enzyme: pflA

L-alanine

cyclic-AMP

benzaldehyde

AMP

UDP-Nacetylmuramoyl-Lalanyl-D-glutamylmeso-2,6diaminopimelate

Pit succinate acetaldehyde adenine pyruvate formatelyase

phosphate

multifunctional acylCoA thioesterase I and protease I and lysophospholipase L1: tesA thioesterase II: tesB acyl-CoA thioesterase: yciA a fatty acid

GlcNAc-1,6anhMurNAcL-Ala-gammaD-GluDAP-D-Ala anhydro-NacetylmuramoylL-alanine amidase: amiD N-acetylanhydromuramylL-alanineamidase: ampD L-Alagamma-DGlu-DAPD-Ala GlcNAc-1,6anhMurNAc

UQ aldose sugar dehydrogenase: yliI beta-Dglucose

UQH2

gluconodelta-lactone

L-methionine

5-deoxyadenosine Ca2+ YrbG

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

o-succinylbenzoate o-succinylbenzoateCoA ligase: menE o-succinylbenzoylCoA naphthoate-CoA synthase: menB 1,4-dihydroxy-2naphthoyl-CoA

formylTHF biosynthesis I
hydroxymethylbilane tetrahydrofolate uroporphyrinogen III synthase: hemD

glyoxalase I: gloA S-lactoylglutathione glyoxalase III S-lactoylglutathione hydrolase: yeiG glyoxalase II: gloB D-lactate D-lactate dehydrogenase: dld

L-arginine

HflD

1-deoxyxylulose5-phosphate synthase: dxs 1-deoxy-Dxylulose 5phosphate 1-aminopropan2-one-3phosphate

pyridoxamine

pyridoxamine transporter

thiamin

thiamin ABC transporter

pyridoxine5-phosphate pyridoxine 5-phosphate oxidase: pdxH

thiaminephosphate thiamine monophosphate kinase: thiL thiamine diphosphate

biotin biosynthesis I
pimeloyl-CoA L-alanine

dihydrofolate reductase: folM glycine dihydrofolate cleavage reductase: folA cobalamin- serine system: dependent hydroxymethyltransferase: glyAgcvT gcvH homocysteine gcvP lpd transmethylase: dihydrofolate metH synthetase: folC 7,87,85-methyldihydropteroate dihydrofolate tetrahydrofolate 5,10methylenetetrahydrofolate reductase: metF

uroporphyrinogen-III

NAD biosynthesis I (from aspartate)


L-aspartate

cobinamide adenosyltransferase: btuR dimethylbenzimidazole adenosylcobinamide cobinamide kinase: cobU

carnitine degradation I
D-glucosamine6-phosphate glucosamine6-phosphate deaminase: nagB D-fructose6-phosphate gammabutyrobetainylCoA

nicotinate mononucleotide agmatine nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase: cobT agmatinase: speB

L-ornithine S-adenosylL-methionine adenosylmethionine decarboxylase: speD S-adenosyl-Lmethioninamine L-lysine

fumarase A: fumA fumarase B: fumB fumarate fumarase C: fumC

methylglyoxal reductase: yeaE methylglyoxal reductase: dkgA methylglyoxal reductase: dkgB L-glyceraldehyde 3-phosphate reductase: yghZ

L-1,2-propanediol oxidoreductase: fucO L-1,2propanediol

glycolate

tRNAArg2

L-glutamate GTP

D-cysteine

L-glutamine ATP ThiS

an alkylhydroperoxide guanosine thiol peroxidase: bcp lipid hydroperoxide peroxidase: tpx guanine an alcohol

a ribosomal proteinL-alanine ribosomal-proteinS5-alanine Nacetyltransferase: rimJ ribosomal-proteinS18-alanine Nacetyltransferase: rimI AMP a ribosomal proteinN-acetylL-alanine

NADH

a tRNA

peptidoglycan tetrapeptide, glycan chain 1

peptidoglycan tetrapeptide, glycan chain 2 L,Dtranspeptidase YnhG: ynhG L,Dtranspeptidase YcbB: ycbB peptidoglycan DAP-DAP crosslink

GMP-N-epsilon-(Nalpha-acetyl lysine methyl ester) 5phosphoramidate purine nucleoside phosphoramidase: hinT

2-oxoglutarate

N1methyladenine AlkB repair system for alkylated DNA and RNA: alkB

NAD+

(deoxynucleotides)(m)

a deoxynucleotide YnfJ chloride alpha-Dglucose 1phosphate Na+ NhaB a protein with reduced sulfide groups disulfide oxidoreductase: dsbG disulfide oxidoreductase: dsbC disulfide oxidoreductase: dsbA a protein with oxidized disulfide bonds peptidoglycan D-alanylDAP crosslink penicillinbinding protein 1A: mrcA murein DDendopeptidase, penicillininsensitive: mepA penicillinbinding protein 7: pbpG peptidoglycan tetrapeptide, glycan chain 1 peptidoglycan tetrapeptide, glycan chain 2

ornithine decarboxylase, biosynthetic: speC

acetol glycerol L-lactate dehydrogenase: dehydrogenase: lldD gldA

glyoxylate reductase B: ghrB glyoxylate reductase: ghrA glyoxylate

tRNAspecific adenosine deaminase: tadA a tRNAArg2 containing inosine at the wobble position

L-aspartate oxidase: nadB alphaiminosuccinate cob(I)alamin ATP quinolinate synthase: nadA

adenosyl-cobinamide phosphate cobinamide-P guanylyltransferase: cobU adenosylcobinamideGDP

alpha-ribazole-5-P

putrescine

lysine decarboxylase 2: ldcC lysine decarboxylase: cadA

succinate dehydrogenase: sdhA sdhB sdhC sdhD succinate citrate bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase: acnB aconitate hydratase 1: acnA

carbamoylphosphate

oxamate

gammabutyrobetainylCoA:carnitine CoA transferase: caiB crotonobetainylCoA reductase: caiA crotonobetainylL-carnitinyl-CoA CoA

gammaglutamyl kinase-GPreductase multienzyme complex: proA proB L-glutamate gammasemialdehyde

acid phosphatase: appA

D-cysteine desulfhydrase, PLPdependent: dcyD pyruvate

N5-glutamine methyltransferase: prmB protein(glutamine-N5) methyltransferase: prmC N5-methylL-glutamine

thiamin (thiazole moiety) biosynthesis protein: thiF ThiSCOAMP

ribonucleoside hydrolase 3: rihC

NADH pyrophosphatase: nudC

RNase PH: rph polynucleotide phosphorylase: pnp a nucleoside diphosphate

DNA ligase: ligA DNA ligase: ligB

alpha-Dglucose-1phosphatase: yihX glucose-1phosphatase: agp sugar phosphatase: ybiV sugar phosphatase: yidA sugar phosphatase: yigL

D-glucose

D-ribose

guanosine-5diphosphate

NMNH

a tRNA

D-alanine

N-alphaacetyl lysine methyl ester

guanosine5-phosphate

succinate

formaldehyde

adenine

AMP

nicotinamide mononucleotide

a deoxynucleotide MQH2 HYD2 H2

L-asparagine

an acyl-[acp]

a 1-acyl-snglycerol-3phosphate

pyruvate carnitine-CoA ligase: caiC

YfcA

predicted alpharibazole-5-P phosphatase: cobC alpha-ribazole S-methyl-5thioadenosine

cadaverine spermidine synthase: speE succinyl-CoA synthetase: sucC sucD spermidine synthase: speE succinyl-CoA

L-1,2propanediol DNA with lesion pre-crRNA CRISPRassociated complex for antiviral defense: casE casD casC casB casA crRNA H2 acetoacetylCoA transferase: atoD atoA acetoacetylCoA acetyl-CoA acetyltransferase: atoB DNA with lesion UvrABC Nucleotide Excision Repair Complex: uvrB uvrC uvrA uvrD DNA without lesion a DNA with unresolved recombitional or holiday junctions, created by RecA RecG, DNA helicase, resolution of Holliday junctions, branch migration: recG a DNA segment pyridoxal 5phosphate pyridoxal phosphatase: cof sugar phosphatase: yigL pyridoxal phosphatase: ybhA H+ hydrogenase 4: hyfH hyfF hyfE hyfD hyfC hyfB hyfA hyfG hyfI hydrogenase 3: hycE hycB hycG hycF hycC hycD adenosine 3,5bisphosphate an mRNA adenosine3(2),5bisphosphate nucleotidase: cysQ oxaloacetate multifunctional 2-keto-3deoxygluconate 6phosphate aldolase and 2-keto-4hydroxyglutarate aldolase and oxaloacetate decarboxylase: eda pyruvate 5,6,7,8tetrahydropteridine fused nitric oxide dioxygenase and dihydropteridine reductase 2: hmp dihydropteridine reductase: nfsB 6,7dihydropteridine adenine

glyoxylate

1,4-dihydroxy2-naphthoate 1,4-dihydroxy2-naphthoate octaprenyltransferase: menA

YtjB

1-hydroxy-2methyl-2-(E) -butenyl 4diphosphate reductase: ispH isopentenyl diphosphate isomerase: idi dimethylallyl diphosphate

FMN

dephospho-CoA

a tRNA ATP tRNA dihydrouridine synthase: dusC tRNA dihydrouridine synthase: dusB tRNAdihydrouridine synthase A: dusA tRNA containing 5,6dihydrouridine

8-amino-7oxononanoate synthase: bioF 7-keto-8aminopelargonate 7,8diaminopelargonic acid synthase: bioA 7,8diaminopelargonate dethiobiotin synthetase: bioD 5,10methyleneTHF

p-aminobenzoate

thymidylate synthase: thyA

CO2 cis-aconitate isocitrate lyase: aceA

crotonobetainylCoA hydratase: caiD

L-carnitine

coenzyme A

adenosine

FATTY ACID AND LIPIDS DEGRADATION


RecJ: recJ

ADP-LglyceroD-mannoheptose

KDO2lipid IVA

ADP-ribose

a 2deoxyribonucleoside monophosphate CPS-53 (KpLE1) prophage; deoxyribonucleoside 5-monophosphate phosphatase: yfdR dCMP phosphohydrolase: yfbR a deoxynucleoside

D-4hydroxy2-ketoglutarate multifunctional 2-keto-3deoxygluconate 6phosphate aldolase and 2-keto-4hydroxyglutarate aldolase and oxaloacetate decarboxylase: eda pyruvate glyoxylate

asparaginase III: iaaA asparaginase II: ansB

a 1,2diacylglycerol3-phosphate

dGTP

S-adenosylL-methionine

TdcE

L-allothreonine lowspecificity L-threonine aldolase: ltaE serine hydroxymethyltransferase: glyA

AmtB

NH4+ L-aspartate

pyridoxal 5phosphate

quinolinate cobalamin adenosyltransferase: btuR

coenzyme A FAD

cobalamin synthase: cobS

spermidine

aminopropylcadaverine

fatty acid beta-oxidation I INORGANIC NUTRIENTS METABOLISM


a (3R)-3hydroxyacyl-CoA

demethylmenaquinone-8 bifunctional 2octaprenyl-6-methoxy1,4-benzoquinone methylase and Sadenosylmethionine:2DMK methyltransferase: ubiE

siroheme biosynthesis
uroporphyrinogen-III 5,10methenyltetrahydrofolate methyleneTHF enzyme: folD uroporphyrin III Cmethyltransferase: cysG precorrin-1 uroporphyrin III Cmethyltransferase: cysG precorrin-2

folate polyglutamylation I
tetrahydrofolate

MrdB

lipoate biosynthesis and incorporation I


octanoate

7,8-dihydropteroate

S-adenosyl-L-methionine cycle I (prokaryotic)


S-adenosylL-methionine

methyleneTHF enzyme: folD 5,10methenyltetrahydrofolate methyleneTHF enzyme: folD 10-formyltetrahydrofolate an N10-formyltetrahydrofolate

quinolinate phosphoribosyltransferase: nadC nicotinate mononucleotide nicotinatemononucleotide adenylyltransferase: nadD nicotinate adenine dinucleotide

2-oxoglutarate dehydrogenase complex: lpd sucB sucA

coenzyme B12

heme biosynthesis from uroporphyrinogen II


uroporphyrinogen-III

bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase: acnB aconitate hydratase 1: acnA D-threo-isocitrate

a cis-3-enoyl-CoA

a trans-2-enoyl-CoA

acetoacetate degradation (to acetyl CoA)


acetoacetate

2-oxoglutarate

sulfate reduction I (assimilatory)


sulfate

cyanate degradation
cyanate cyanase: cynS

MinC

bifunctional 3demethylubiquinone-8 3-O-methyltransferase and 2-octaprenyl6-hydroxyphenol methylase: ubiG ubiquinol-8

glutathione biosynthesis
di-trans,polycis-decaprenyl diphosphate L-glutamate

menaquinone-8

formatetetrahydrofolate ligase a tetrahydrofolate polyglutamate folylpolyalphaglutamate synthetase folylpolygammaglutamate synthetase: folC a tetrahydrofolate polyglutamate 10-formyltetrahydrofolate

serine hydroxymethyltransferase: glyA 5,10methyleneTHF

acyl-ACP synthetase: aas an octanoyl[acp] lipoylprotein ligase: lipB an octanoylated domain lipoate synthase: lipA lipoylated domain

2-(5phosphoribosyl) -3-dephosphoCoA biosynthesis I dephospho(citrate lyase)


CoA triphosphoribosyldephospho-CoA synthase: citG 2-(5triphosphoribosyl)3-dephospho-CoA apo-citrate lyase phosphoribosyldephospho-CoA transferase: citX a citrate lyase holo[acyl-carrier protein]

dihydrofolate synthetase: folC

3-hydroxybutyrylCoA epimerase: fadJ fatty acid oxidation complex, alpha component: fadB a (3S)-3hydroxyacyl-CoA 3-hydroxyacyl-CoA dehydrogenase: fadJ fatty acid oxidation complex, alpha component: fadB

fatty acid oxidation complex, alpha component: fadB dodecenoyl-CoA D-isomerase: fadJ

7,8-dihydrofolate dihydrofolate reductase: folM dihydrofolate reductase: folA 10-formyltetrahydrofolate phosphoribosylglycinamide formyltransferase: purN

methionine adenosyltransferase: metK L-methionine

dethiobiotin S-adenosyl-Lhomocysteine 5-methylthioadenosine/ S-adenosylhomocysteine nucleosidase: mtn folylpolyalphaglutamate synthetase folylpolygammaglutamate synthetase: folC an N10-formyltetrahydrofolate

lipoate biosynthesis and incorporation II


octanoate

uroporphyrinogen decarboxylase: hemE

isocitrate dehydrogenase: icd

sulfate adenylyltransferase: cysD cysN adenosine 5phosphosulfate

a trans-2-enoyl-CoA

coproporphyrinogen III

carbamate

two-component alkanesulfonate monooxygenase


an alkanesulfonate FMNH2

fatty acid oxidation complex, alpha component: fadB enoyl-CoA hydratase: fadJ putative ringcleavage enzyme of phenylacetate degradation: maoC

DNA with lesion resolved through Recmediated pathway

poly(A) polymerase I: pcnB an mRNA

ribonucleoside hydrolase 3: rihC

ADPheptose:LPS heptosyl transferase I: rfaC

ADP-sugar pyrophosphatase: nudF

dGTP pyrophosphohydrolase: mutT

pyruvate formatelyase activating enzyme: pflA 2-ketobutyrate formate-lyase / pyruvate formate-lyase

ZupT

Co2+ Fe2+

a CDPdiacylglycerol

D-ribose ADP heptosylKDO2lipid IVA D-ribose-5phosphate AMP

dGMP

AMP

5-deoxyadenosine acetaldehyde glycine

MntH

Mn2+ Fe2+

an L-1phosphatidylglycerolphosphate phosphatidylglycerophosphatase B: pgpB an L-1phosphatidylglycerol

Cd2+ Zn2+ a 2deoxyribonucleoside diphosphate ribonucleosidediphosphate reductase 2: nrdF nrdE ribonucleosidediphosphate reductase: nrdB nrdA a ribonucleoside diphosphate a DNA adenine L-serine ATP DNA adenine methyltransferase: yhdJ DNA adenine methylase: dam a DNA 6methylaminopurine dATP glutathione GDP-alphaD-mannose 1-chloro-2,4dinitrobenzene glutathione Stransferase: yfcG glutathione Stransferase: yfcF glutathione Stransferase: gst 2,4dinitrophenylS-glutathione Lpp peptidoglycan tetrapeptide, glycan chain 1 L,Dtranspeptidase YbiS: ybiS L,Dtranspeptidase YcfS: ycfS L,Dtranspeptidase ErfK: erfK peptidoglycan tripeptideLpp crosslink alpharibazole-5-P adenosylcobinamideGDP S-adenosylL-methionine oxidized ribonucleosidetriphosphate reductase anaerobic nucleosidetriphosphate reductase activating system: fpr nrdG nrdD

ZntA

adenine

ADP

ATP

inosine-5phosphate

ATP

nicotinamide mononucleotide

a trans-2-enoyl-CoA

a (3S)-3hydroxyacyl-CoA

biotin synthase: bioB

formatetetrahydrofolate ligase

formyltetrahydrofolate deformylase: purU

HtpX

glutamate-cysteine ligase: gshA di-trans,polycisundecaprenyl diphosphate L-gammaglutamylcysteine

thioredoxin pathway
an oxidized thioredoxin

tetrahydrofolate a 5,10-methylenetetrahydrofolate folylpolyalphaglutamate synthetase folylpolygammaglutamate synthetase: folC a 5,10-methylenetetrahydrofolate NADP phosphatase precorrin-2 dehydrogenase: cysG sirohydrochlorin sirohydrochlorin ferrochelatase: cysG

glycine

an N10-formyltetrahydrofolate folylpolyalphaglutamate synthetase folylpolygammaglutamate synthetase: folC an N10-formyltetrahydrofolate

cobalaminindependent homocysteine transmethylase: metE L-homocysteine

biotin formate S-ribosylhomocysteine lyase: luxS tetrahydrofolate

NAD NAD synthetase, NH3- synthetase, NH3dependent: nadE dependent: nadE NAD+

lipoyl-protein ligase A: lplA an octanoylated domain lipoate synthase: lipA

anaerobic coproporphyrinogen coproporphyrinogen oxidase, aerobic: hemF III oxidase: hemN protoporphyrinogen IX protoporphyrinogen oxidase: hemG

adenylylsulfate kinase: cysC CO2 phosphoadenosine5-phosphosulfate 3-phosphoadenylylsulfate reductase: cysH sulfite carbonic anhydrase 1: cynT bicarbonate 3-oxoacyl-CoA

cryptic adenine deaminase: ade

Ap3A synthetase: lysU 5,5diadenosine triphosphate

acetyl-CoA

purine nucleotidase: yrfG ribonucleotide monophosphatase: nagD

serine activating enzyme: entF

dihydroneopterin triphosphate pyrophosphohydrolase: nudB

nucleotidesugar hydrolase: nudK

bifunctional NadR transcriptional repressor and NMN adenylyltransferase: nadR guanosine5-phosphate

cobalamin 5phosphate synthase: cobS

Ca2+ Na+ K+

ChaA glycerol cardiolipin

Zn2+

YiiP Fe2+ ferritin ironstorage complex: ftnA multicopper oxidase with role in copper homeostasis: cueO a ribonucleoside monophosphate ribonucleotide monophosphatase: nagD pyrimidine nucleotidase: yjjG broad specificity 5(3)nucleotidase and polyphosphatase: surE 5-nucleotidase: ushA a ribonucleoside 3-(3hydroxyphenyl) propionate peptidylproline (omega = 180) GTP FtsW diguanylate cyclase: ydeH diguanylate cyclase: yddV diguanylate cyclase: yeaP cyclic di-3,5guanylate trigger factor; a molecular chaperone involved in cell division: tig peptidylprolyl cis-trans isomerase (PPIase) : surA peptidylprolyl cis-trans isomerase; in protein folding: fkpA peptidylprolyl cis-trans isomerase: ppiD peptidylprolyl isomerase: fkpB [+ 4 isozymes] peptidylproline (omega = 0) membrane-bound lytic murein transglycosylase F: mltF lytic murein transglycosylase E: emtA membrane-bound lytic murein transglycosylase C: mltC soluble lytic murein transglycosylase: slt membrane-bound lytic murein transglycosylase A: mltA membrane-bound lytic murein transglycosylase B: mltB peptidoglycan polymer with GlcNAc end peptidoglycan polymer with 1,6anhydromuropeptide end peptidoglycan polymer SecM a peptidoglycan FtsP

L-seryl-AMP

hypoxanthine

Lnt ubiquinone-8

glutathione synthetase: gshB glutathione thioredoxin reductase: trxB

NAD phosphorylation and dephosphorylation


NAD+

S-ribosyl-Lhomocysteine

DsdX

glutathione redox reactions II


glutathione disulfide 4,5dihydroxy-2,3pentanedione

lipoate salvage and modification


lipoate

protoporphyrin IX ferrochelatase: hemH sulfite reductase(NADPH): cysI cysJ

alkanesulfonate monooxygenase, FMNH2dependent: ssuD

AROMATIC COMPOUNDS DEGRADATION


NADP(H)dependent FMN reductase: ssuE subunit of fatty acid oxidation complex: fadI fatty acid oxidation complex, beta component: fadA acetyl-CoA a 2,3,4-saturated fatty acyl CoA a fatty acid coenzyme A

dAMP

pyridoxal

inosine

alpha-Dmannose 1phosphate

guanosine5-phosphate

NAD+ D-alanine

adenosylcobalamin5-phosphate L-methionine NrdD 5-deoxyadenosine FtsN

oleate betaoxidation
2-trans,5-cistetradecadienoylCoA fatty acid oxidation complex, alpha component: fadB 3,5tetradecadienoylCoA thioesterase III: ybaW 3,5tetradecadienoate fatty acid oxidation complex, alpha component: fadB 3-hydroxy-5-cistetradecenoylCoA

lipoylated domain

superpathway of phenylethylamine degradation


phenylethylamine

3-phenylpropionate and 3-(3-hydroxyphenyl) propionate degradation


3-phenylpropionate 3-phenylpropionate dioxygenase system: hcaD hcaC hcaF hcaE GTP inosine-5phosphate

a sugar phosphate sugar phosphatase: yigL sugar phosphatase: yidA sugar phosphatase: yfbT sugar phosphatase: ybiV a sugar

a supercoiled duplex DNA ATPdependent DNA helicase: recQ rep helicase, a singlestranded DNA dependent ATPase: rep replicative DNA helicase: dnaB a single stranded DNA

diacetyl 5-keto-Dgluconate 5reductase: idnO predicted acetoin dehydrogenase: yohF diacetyl reductase

tRNA uridine

a quinone

16S-rRNAs

GDP-alphaD-glucose GDPmannose mannosyl hydrolase: gmm

siroheme

cyclic di-3,5guanylate c-di-GMP phosphodiesterase: yhjH modulator of RNase II stability: gmr phosphodiesterase, heme-regulated: dos phosphodiesterase, cdi-GMP-specific: yahA

GDP-alphaD-mannose

an oxidized thioredoxin

L-methionine

an ADPsugar

D-fructose6-phosphate acetyl-CoA fructose 6phosphate aldolase 2: fsaB fructose 6phosphate aldolase 1: fsaA D-glyceraldehyde3-phosphate AMP dihydroxyacetone coenzyme A ATP

elongator tRNAmet

a 2,3,4saturated fatty acyl CoA

acetate

YccA

CcmABCDE protoheme IX ABC transporter

protoheme IX glutathione glutaredoxin reductase: gor reductase lipoylprotein ligase A: lplA lipoylated domain

protoheme IX

a reduced thioredoxin

pyridine nucleotide NAD transhydrogenase: kinase: nadK pntA pntB

an aldehyde hydrogen sulfide

FMN

short chain acyl-CoA synthetase: fadK fatty acyl-CoA synthetase: fadD

guanylate cyclase

GMP reductase: guaC

phenylacetaldehyde cis-3(carboxyethyl)-3,5cyclohexadiene1,2-diol 3-phenylpropionate2,3-dihydrodiol dehydrogenase: hcaB 3-(3hydroxyphenyl) propionate 3-(3hydroxyphenyl) propionate 2hydroxylase: mhpA cyclic-GMP guanosine5-phosphate

YgjI glutathione NADP+

a 2,3,4-saturated fatty acyl CoA isovaleryl-CoA dehydrogenase / predicted acyl-CoA dehydrogenase: aidB predicted acyl-CoA dehydrogenase: ydiO acyl-CoA dehydrogenase: fadE CreC-Phis a 2,3-dehydroacyl-CoA

phenylacetaldehyde dehydrogenase: feaB

acetoin

phenylacetate

YeeF

Nitrogen Regulation Two-Component System


YihN a glutamine synthetase PII

SIGNAL TRANSDUCTION PATHWAYS Osmoregulatory Two-Component Signal Transduction System


BarA-Pasp EvgA

EvgSA TwoComponent Signal Transduction System


EvgA-Pasp BaeR

BaeSR TwoComponent Signal Transduction System


BaeR-Pasp BarA

BarA-UvrY TwoComponent Signal Transduction System


BarA-Phis

CreCB Two-Component Signal Transduction System


CreC

phenylacetateCoA ligase: paaK

NADPH 23S rRNA quinone and tRNA reductase: pseudouridine mdaB synthase: rluA chromate tRNA reductase: pseudouridine yieF 65 synthase: truC NAD(P)H:quinone tRNA oxidoreductase: pseudouridine wrbA 55 synthase: truB tRNA pseudouridine a hydroquinone synthase I: truA tRNA pseudouridine 13 synthase: truD tRNA pseudouridine

16S rRNA m5C1407 methyltransferase: rsmF 16S rRNA m5C967 methyltransferase: rsmB 16S rRNA containing C5methylated cytosine

GDPmannose mannosyl hydrolase: gmm

guanosine-5diphosphate

beta-Dglucose

methionine sulfoxide reductase B: msrB free methionine(R)-sulfoxide reductase: yebR L-methionine(R)-S-oxide an alpha-Daldose-1phosphate

Fe3+ tRNAMet cytidine acetyltransferase: tmcA PspA fused predicted an acyl-CoA acetylCoA:acetoacetylCoA transferase: alpha subunit/ beta subunit: ydiF acetylCoA:acetoacetylCoA transferase, alpha subunit: atoD acetylCoA:acetoacetylCoA transferase, beta subunit: atoA acetate CoAa fatty acid transferase

ADP-sugar pyrophosphorylase: nudE ADP-sugar pyrophosphatase: nudF

N-acetylmuramoylL-alanine amidase 1: amiA N-acetylmuramoylL-alanine amidase 2: amiB N-acetylmuramylL-alanine amidase: amiC N-acetylanhydromuramylL-alanineamidase: ampD

FadL

a fatty acid

a peptide

N-acetylmuramate

ADP

MhpT

D-mannose linear dimeric GMP

guanosine-5diphosphate

a thioredoxin

phenylacetyl-CoA

3-(2,3dihydroxyphenyl) propionate 3-(2,3dihydroxyphenyl) propionate dioxygenase: mhpB 2-hydroxy6-oxonona2,4-diene1,9-dioate 2-hydroxy-6ketonona-2,4dienedioate hydrolase: mhpC a protein with incorrect disulfide bonds disulfide isomerase, periplasmic: dsbG protein disulfide isomerase: dsbC a protein with correct disulfide bonds fructose-1phosphate fructose-1phosphatase: yqaB sugar phosphatase: ybiV sugar phosphatase: yfbT sugar phosphatase: yidA sugar phosphatase: yigL D-fructose a proteinL-tyrosine phosphate arbutin-6phosphate 6-phosphobetaglucosidase; cryptic: ascB 6-phosphobetaglucosidase A: bglA 6-phosphobetaglucosidase B; cryptic: bglB a peptide beta-Dglucose-6phosphate 6-phosphobeta-Dglucosyl(1,4)-Dglucose diacetylchitobiose6-phosphate hydrolase: chbF 6-phosphobetaglucosidase B; cryptic: bglB probable 6phospho-betaglucosidase: glvG 6-phosphobetaglucosidase; cryptic: ascB 6-phosphobetaglucosidase A: bglA beta-Dglucose beta-Dglucose-6phosphate a 2deoxyribonucleoside triphosphate DNA polymerase I, 3 --> 5 polymerase, 5 --> 3 and 3 --> 5 exonuclease: polA DNA polymerase V: umuD umuC DNA polymerase II: polB DNA polymerase III, alpha subunit: dnaE DNA polymerase IV (Yfamily DNA polymerase; translesion DNA synthesis) : dinB DNAn acetaldehyde dehydrogenase 2: mhpF acetaldehyde dehydrogenase: adhE

acetyl-CoA

TehA

AraJ

PII YhhS uridylyl-removing enzyme: glnD

uridylyltransferase: glnD glutamine synthetase adenylyltransferase: glnE uridylyl-glutamine synthase PII

Chemotactic Signal Transduction System


chemotaxis protein methyltransferase: cheR CheBPasp: cheB a protein-Lglutamate-O5-methylester CheBPasp: cheB BarA BarA-Phis EnvZ EnvZ-Phis EvgS-Phis EvgS BaeS-Phis BaeS UvrY-Pasp UvrY

PhoB-Pasp

PhoB

CreB-Pasp

CreB

putative phenylacetateCoA oxygenase: paaE paaD paaC paaB paaA cis-dihydrodiol derivative of phenylacetyl-CoA beta-ketoadipylCoA thiolase: paaJ putative ringcleavage enzyme of phenylacetate degradation: maoC putative enoylCoA hydratase/ isomerase of phenylacetate degradation: paaG 3-hydroxyadipylCoA predicted 3hydroxy-acyl-CoA dehydrogenase of phenylacetate degradation: paaH putative enoylCoA hydratase/ isomerase of phenylacetate degradation: paaF

an rRNA guanosine-5diphosphate 23S rRNA and tRNA pseudouridine synthase: rluA 23S rRNA pseudouridine synthase: rluD 23S rRNA pseudouridine 2604 synthase: rluF 23S rRNA pseudouridine synthase: rluC 23S rRNA pseudouridine 2605 synthase: rluB [+ 2 isozymes] rRNA containing pseudouridine GTP guanosine5-phosphate

rRNA

a protein

coenzyme A

an apo-[acp]

DNAn

L-cysteine

ITP

ThiSCOAMP

FrlA

2-methylcitrate cycle I
propionate

CARBOXYLATES DEGRADATION L-ascorbate degradation, anaerobic


L-ascorbate6-phosphate

a proteinL-glutamine

a protein L-glutamate

conversion of succinate to propionate


succinyl-CoA

ITPase: yjjX

OmpR-Pasp

OmpR

TorSR Two-Component Signal Transduction System BasSR TwoComponent Signal Transduction System
BasR BasR-Pasp

HMP-PP hydrolase / thiamin pyrophosphate hydrolase: nudJ

YhfC

PII-UMP YhhJ

ArcAB TwoComponent Signal Transduction System


ArcB CheA-Phis

NarQ Nitrate/Nitrite-Dependent Two-Component Regulatory System


NarQ NarQ-Phis

TorS

TorSPhis443

TorSPasp723

TorR

TorSPhis850

phosphoTorR

TorS

acetyl-CoA synthetase (AMPforming): acs

IDP

propionyl-CoA

phosphodiesterase / predicted L-ascorbate 6-phosphate lactonase: ulaG 3-keto-Lgulonate 6phosphate 3-keto-Lgulonate 6phosphate decarboxylase: ulaD L-xylulose5-phosphate L-xylulose 5phosphate 3-epimerase: ulaE L-ribulose5-phosphate L-ribulose 5phosphate 4-epimerase: ulaF D-xylulose5-phosphate

methylmalonyl pathway
propionylCoA propionylCoA carboxylase (S)methylmalonylCoA methylmalonylCoA epimerase (R)methylmalonylCoA methylmalonylCoA mutase: scpA succinylCoA

methylmalonylCoA mutase: scpA propionyl-CoA:succinate CoA transferase: scpC (R)-methylmalonyl-CoA propionyl-CoA

2-oxopentenoate 2-oxopent4-enoate hydratase: mhpD 4-hydroxy2-oxovalerate 4-hydroxy-2ketovalerate aldolase: mhpE

guanosine5-phosphate

CheA

YhjV

NtrB

NtrB-P PhoQ CheY CheY-Pasp CheB CheB-Pasp

PhoQP TwoComponent Signal Transduction System


PhoQ-Phis RstA

TorT

TorT-TMAO

methylcitrate synthase: prpC (2S,3S)-2methylcitrate 2-methylcitrate dehydratase: prpD cis-2methylaconitate bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase: acnB methylisocitrate

GTPase associated with the 50S subunit of the ribosome: hflX ribosome small subunitdependent GTPase A: rsgA GTPase that interacts with methylmalonylCoA mutase: argK

purine nucleotidase: yrfG broad specificity 5(3)nucleotidase and polyphosphatase: surE ribonucleotide monophosphatase: nagD

16S rRNA m2G966 phosphotyrosinemethyltransferase: protein rsmD phosphatase: etp 23S rRNA m2G2445 tyrosine methyltransferase: phosphatase: rlmL wzb 23S rRNA m2G1835 proteinmethyltransferase: tyrosinerlmG phosphatase: 16S rRNA m2G1207 pphB methyltransferase: protein phosphatase rsmC 1 modulates phosphoproteins, rRNA signals protein containing N2misfolding: pphA methylguanine hydroquinone a protein L-tyrosine

ClpAXP: clpX clpA clpP ClpXP: clpX clpP ClpAP: clpA clpP ClpP serine protease: clpP

holo-[acyl carrier protein] synthase 2: acpT holo-[acylcarrierprotein] synthase: acpS adenosine 3,5bisphosphate

ThiI: thiI thiamin (thiazole moiety) biosynthesis protein: thiF

YdeE

YhaU AMP L-alanine ThiS-COSH oligopeptide ABC transporter

a peptide

a holo-[acp]

a peptide

guanosine

RstBA TwoComponent Signal Transduction System


RstA-Pasp

NarP-Pasp BasS-Phis BasS

NarP

NarL-Pasp

NarL

methylmalonyl-CoA decarboxylase: scpB

acetyl-CoA biosynthesis (from pyruvate)


lipoate acetyltransferase N6-(lipoyl)lysine

guanosine-5diphosphate

YhaO

HdeB

FliY

MdoD

SohB

YihO NtrC-P NtrC ArcBPhis292 KdpD PhoP-Pasp PhoP

NarX Nitrate/Nitrite-Dependent Two-Component Regulatory System


RstB-Phis RstB

superpathway of acetate utilization and formation


acetate

YihP

HdeA

YdhX

EnvC

MalM

acetaldehyde

pyruvate

adenylylglutamine synthase ArcB-Pasp uridylyltransferase: glnD

CpxAR TwoComponent Signal Transduction System


CpxA

KdpDE TwoComponent Signal Transduction System


KdpD KdpD-Phis

pyruvate dehydrogenase: aceE 3-oxoadipyl-CoA lipoamide dehydrogenase: lpd lipoate acetyltransferase N6lipoate acetyltransferase (S-acetyldihydrolipoyl)lysine N6-(dihydrolipoyl)lysine acetate kinase: ackA acetate kinase B: ackB acetyl-CoA synthetase (AMP-forming): acs

CybB CpxP Asr ZraP FimC

NarX

NarX-Phis

beta-ketoadipylCoA thiolase: paaJ

acetylphosphate lipoate acetyltransferase: aceF

acetyl-CoA succinyl-CoA acetyl-CoA DcrB HlyE MdoG Eco

NarL-Pasp

NarL

NarP-Pasp

NarP

[GlnK]

uridylyl-[GlnK] ArcBPhis717 UhpB

UhpBA TwoComponent Signal Transduction System


UhpB-Phis PhoR

2-methylisocitrate lyase: prpB

phosphate acetyltransferase: pta

PhoRB TwoComponent Signal Transduction System


PhoR-Phis ZraR

KdpE-Pasp

KdpE

pyruvate

succinate

L-glutamate

glutamine synthetase: glnA

phosphohistidine phosphatase: sixA L-glutamine ArcB

ZraSR TwoComponent Signal Transduction System

CpxR

CpxA-Phis

UhpA-Pasp

UhpA PhoB-Pasp PhoB

ZraRphosphate

AtoSC TwoComponent Signal Transduction System


AtoS AtoS-Phis RcsF

YraP

LolA

YceI

CybC

RcsCB Two-Component Signal Transduction System


ZinT RcsF-P RcsC RcsC-Phis YbcL GltF

adenylyl[glutamine synthetase] 4-hydroxybenzoate

glutamine synthetase deadenylylating enzyme: glnE

UhpC GlnA multidrug

UhpCglucose-6-P ferric enterobactin iron (III) hydroxamate complex

ZraS-Phis

ZraS

AtoC-Pasp

AtoC

phosphoRcsB

RcsB

YedY

Ivy

OsmY

multidrug

multidrug

ferric dicitrate

cob(I)alamin spermidine an O-antigen an aromatic amino acid fosmidomycin a macrolide antibiotic

enterobactin succinate EntS-TolC Enterobactin Efflux Transport System succinate

L-ascorbate6-phosphate

MQH2 MQ

MQH2 MQ

gammabutyrobetaine

N-acetyl-Dglucosamine6-phosphate

phosphate

cellobiose-6-phosphate salicin-6-phosphate arbutin-6-phosphate

H+

salicin-6-phosphate arbutin-6-phosphate

AaeAB Hydroxylated, Aromatic Carboxylic Acid Efflux Transport System

YjhF

NlpA

YigG

YijP

NrfE

RseA

YafY

YkgB

YbjO

YcdU

RsxA

RsxG

Cld

Hda

FtsB

pryidoxine tranporter

FxsA

Blr

pyridoxal transporter

YmgF

RodZ

BioP

TrxA

AsmA

MdtABCTolC multidrug efflux transport system

AcrAD-TolC multidrug efflux transport system

AcrAB-TolC multidrug efflux transport system

ferric enterobactin ABC transporter

iron dicitrate ABC transporter

iron (III) hydroxamate ABC transporter

vitamin B12 ABC transporter

YicJ

aliphatic sulfonate ABC transporter

nickel ABC transporter

dipeptide ABC transporter

molybdate ABC transporter

arabinose ABC transporter

MdtJI spermidine SMR transporter

CadB

BetT

RfbX

YddG

Fsr

YbjYZ

UidB

potassium ion P-type ATPase transporter

YidK

KgtP

phosphate ABC transporter

YjdL

CitT

YchM

thiosulfate ABC transporter

sulfate ABC transporter

TtdT

EIISga

FDH-O

Fdh-N

CynX

NupX

CaiT

EIINag

YjcG

TrkA

YjcG

GlpT

glycerol3-P ABC transporter

GlcA

LldP

GlpF

YhcB

Aer

RseC

YfbV

YebS

RsxC

YcfT

EIIAsc

ATP synthase

EIIBgl

YejA/ YejB/YejE/ YejF ABC transporter

peptide uptake ABC transporter

DegS

FtsL

LepA

YifK

YaaU

YhjX

pyridoxine

pyridoxal

biotin Outer Membrane Ferric Enterobactin Transport System Outer Membrane Ferric Citrate Transport System Outer Membrane Ferrichrome Transport System vitamin B12 outer membrane transport complex isethionate

Ni2+

a dipeptide

molybdate

alpha-Larabinose

cadaverine

choline

a glucoronide K+

2-oxoglutarate phosphate

citrate

sulfate

thiosulfate sulfate

thiosulfate sulfate

L-tartrate

L-ascorbate

formate

formate CO2

cyanate CO2

L-carnitine

N-acetyl-Dglucosamine

acetate

glycolate

sn-glycerol3-phosphate

sn-glycerol3-phosphate

glycolate L-lactate

L-lactate

glycerol

cellobiose salicin arbutin

salicin arbutin a peptide a peptide

ferric enterobactin

ferric dicitrate

iron (III) hydroxamate complex

cob(I)alamin

Copyright ' 2009 SRI International. All Rights Reserved.

This diagram was automatically generated by SRI International Pathway Tools version 13.0, authors S. Paley and P. Karp.

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