Hexanoyl-CoA:acetyl-CoA C-acyltransferase
L-Cystathionine Lysteine-lyase (deaminating)
ATP:nucleoside-diphosphate phosphatransferase
O-Phospho-L-homoserine phospho-lyase (adding water)
(3S)-3-Hydroxyacyl-CoA:NAD+ oxidoreductase
Inosine 5'-monophosphate phosphohydrolase
3-Methyl-2-oxobutanoate:lipoamide oxidoreductase(decarboxylating and
Xanthosine:orthophosphate ribosyltransferase
(S)-3-Hydroxybutanoyl-CoA:NAD+ oxidoreductase
Acetyl-CoA:D-glucosamine-6-phosphate N-acetyltransferase
(S)-Hydroxydecanoyl-CoA:NAD+ oxidoreductase
(R)-Mevalonate:NADP+ oxidoreductase (CoA acylating)
Isopentenyl-diphosphate delta3-delta2-isomerase
L-Serine hydro-lyase (adding homocysteine)
Chorismate pyruvate-lyase (amino-accepting)
O3-Acetyl-L-serine acetate-lyase (adding hydrogen sulfide)
(S)-3-Hydroxytetradecanoyl-CoA:NAD+ oxidoreductase
3-Phosphoserine:2-oxoglutarate aminotransferase
(S)-3-Hydroxytetradecanoyl-CoA hydro-lyase
2,5-Diaminopyrimidine nucleoside triphosphate
AMP:pyrophosphate phosphoribosyltransferase
N2-Acetyl-L-ornithine:2-oxoglutarate aminotransferase
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
2-(alpha-Hydroxyethyl)thiamine diphosphate
3-Methylbutanoyl-CoA:(acceptor) 2,3-oxidoreductase
2'-Deoxyguanosine 5'-monophosphate phosphohydrolase
1-(2-Carboxyphenylamino)-1'-deoxy-D-ribulose 5'-phosphate
L-Threonine:tRNA(Thr) ligase (AMP-forming)
L-Cysteine:tRNA(Cys) ligase (AMP-forming)
3-Phospho-D-glyceroyl phosphate phosphohydrolase
L-Phenylalanine:2-oxoglutarate aminotransferase
Nicotinate D-ribonucleotide:pyrophosphate phosphoribosyltransferase
2'-Deoxyadenosine 5'-monophosphate phosphohydrolase
D-Glyceraldehyde-3-phosphate:NADP+ oxidoreductase(phosphorylating)
(S)-2-Acetolactate pyruvate-lyase (carboxylating)
Carbamoyl-phosphate:L-aspartate carbamoyltransferase
2-Hydroxybutane-1,2,4-tricarboxylate 2-oxoglutarate-lyase
5-Amino-6-(5-phosphoribitylamino)uracil:NADP+ 1'-oxidoreductase
L-Aspartate-4-semialdehyde:NADP+ oxidoreductase (phosphorylating)
5,6,7,8-Tetrahydrofolate:NADP+ oxidoreductase
3-Carboxy-3-hydroxy-4-methylpentanoate 3-methyl-2-oxobutanoate-lyase
2-Methylpropanoyl-CoA:(acceptor) 2,3-oxidoreductase
(S)-Malate:NADP+ oxidoreductase(oxaloacetate-decarboxylating)
Uridine:orthophosphate ribosyltransferase
Farnesyl-diphosphate:farnesyl-diphosphate farnesyltransferase
O-Succinyl-L-homoserine succinate-lyase (adding cysteine)
N-Acetyl-L-glutamate-5-semialdehyde:NADP+ 5-oxidoreductase
GMP:pyrophosphate phosphoribosyltransferase
2,3,4,5-Tetrahydrodipicolinate:NAD+ oxidoreductase
(2S,3S)-3-Hydroxy-2-methylbutanoyl-CoA:NAD+ oxidoreductase
Citrate oxaloacetate-lyase ((pro-3S)-CH2COO- -->acetate)
L-Glutamine:D-fructose-6-phosphate aminotransferase (hexose
D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate
Formamidopyrimidine nucleoside triphosphate
meso-2,6-Diaminoheptanedioate carboxy-lyase
(R)-2,3-Dihydroxy-3-methylbutanoate:NADP+ oxidoreductase
5-Phosphoribosylamine:pyrophosphate phosphoribosyltransferase
L-1-Pyrroline-5-carboxylate:NAD+ oxidoreductase
O-Succinylbenzoate:CoA ligase (AMP-forming)
Propanoyl-CoA:(acceptor) 2,3-oxidoreductase
Nicotinate-nucleotide:pyrophosphate phosphoribosyltransferase
ATP:pantetheine-4'-phosphate adenylyltransferase
Guanosine 3'-diphosphate 5'-triphosphate
Propanoyl-CoA:carbon-dioxide ligase (ADP-forming)
alpha-D-Glucose 6-phosphate ketol-isomerase
CDPdiacylglycerol:L-serine 3-O-phosphatidyltransferase
Adenosine 3',5'-bisphosphate 3'(2')-phosphohydrolase
Lauroyl-CoA:acetyl-CoA C-acyltransferase
NADH:guanosine-5'-phosphate oxidoreductase(deaminating)
Thymidine:orthophosphate deoxyribosyltransferase
(R)-2-Methyl-3-oxopropanoyl-CoA CoA-carbonylmutase
Guanosine 5'-monophosphate phosphohydrolase
Substrate,reduced-flaboprotein:oxygen oxidoreductase
Oxalosuccinate:NADP+ oxidoreductase (decarboxylating)
L-Aspartate:2-oxoglutarate aminotransferase
ATP:2-dehydro-3-deoxy-D-gluconate 6-phosphotransferase
N-(5-Phospho-beta-D-ribosyl)anthranilate ketol-isomerase
(S)-3-Hydroxydodecanoyl-CoA:NAD+ oxidoreductase
ATP:nicotinamide-nucleotide adenylyltransferase
(R)-2,3-Dihydroxy-3-methylpentanoate:NADP+ oxidoreductase
UMP:pyrophosphate phosphoribosyltransferase
(R)-2-Methyl-3-oxopropanoyl-CoA 2-epimerase
(S)-Methylmalonate semialdehyde:NAD+ oxidoreductase
N-Methylimidazolidine-2,4-dione amidohydrolase (ATP-hydrolysing)
(R)-2,3-Dihydroxy-3-methylpentanoate hydro-lyase
(S)-2-Methyl-3-oxopropanoyl-CoA carboxy-lyase
L-Arogenate hydro-lyase (decarboxylating)
2'-Deoxycytidine diphosphate:oxidized-thioredoxin 2'-oxidoreductase
sn-3-O-(Geranylgeranyl)glycerol 1-phosphate
5,10-Methylenetetrahydrofolate:dUMP C-methyltransferase
D-Glyceraldehyde-3-phosphate ketol-isomerase
5'-Phosphoribosylformylglycinamide:L-glutamine amido-ligase
L-Cystathionine L-homocysteine-lyase (deaminating)
Hexanoyl-CoA:(acceptor) 2,3-oxidoreductase
Cystathionine L-homocysteine-lyase (deaminating)
3-Phospho-D-glycerate:NAD+ 2-oxidoreductase
5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase
L-Leucine:2-oxoglutarate aminotransferase
D-Fructose 1-phosphate D-glyceraldehyde-3-phosphate-lyase
Adenosine 3',5'-bisphosphate,sulfite:oxidized-thioredoxin
Carbon-dioxide:L-glutamine amido-ligase (ADP-forming,
Prephenate:NAD+ oxidoreductase(decarboxylating)
Acetyl-CoA:acetyl-CoA C-acetyltransferase
D-Fructose-2,6-bisphosphate 2-phosphohydrolase
Formamidopyrimidine nucleoside triphosphate 7,8-8,9-dihydrolase
L-Tyrosine:2-oxoglutarate aminotransferase
Octanoyl-CoA:acetyl-CoA C-acyltransferase
(S)-3-Hydroxy-3-methylglutaryl-CoA acetoacetyl-CoA-lyase
Tetrahydrofolate:L-glutamate gamma-ligase (ADP-forming)
Prephytoene diphosphate:geranylgeranyl-diphosphate
L-Glutamate:tRNA(Gln) ligase (AMP-forming)
(R)-2,3-Dihydroxy-3-methylbutanoate hydro-lyase
Citrate oxaloacetate-lyase ((pro-3S)-CH2COO- -> acetyl-CoA)
ATP:adenylylsulfate 3'-phosphotransferase
2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate
2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate phosphate-lyase
(S)-Dihydroorotate:oxygen oxidoreductase
L-Methionine:tRNAMet ligase (AMP-forming)
(R)-Lactaldehyde:NAD+ oxidoreductase (glutathione-formylating)
2'-Deoxycytidine 5'-monophosphate phosphohydrolase
Succinate-semialdehyde:NADP+ oxidoreductase
ATP:D-ribose-5-phosphate pyrophosphotransferase
L-Alanine:2-oxoglutarate aminotransferase
Acetyl adenylate:CoA ligase (AMP-forming)
ATP:N-acetyl-L-glutamate 5-phosphotransferase
Succinate-semialdehyde:NAD+ oxidoreductase
Propinol adenylate:CoA ligase (AMP-forming)
2'-Deoxyadenosine 5'-diphosphate:oxidized-thioredoxin
3-Aminopropanoate:2-oxoglutarate aminotransferase
beta-D-Fructose 1,6-bisphosphate 1-phosphohydrolase
L-Valine:2-oxoglutarate aminotransferase
Myristoyl-CoA:acetylCoA C-myristoyltransferase
Cytidine-5'-monophosphate phosphohydrolase
1-(5-Phosphoribosyl)-5-amino-4-carboxyimidazole:L-aspartate ligase
Nicotinate D-ribonucleotide phosphohydrolase
This is metabolic network reconstruction of Natronomonas pharaonis described in the article Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis. Gonzalez O, Oberwinkler T, Mansueto L, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D. PLoS Comput Biol. 2010 Jun 3;6(6):e1000799. PMID: 20543878 , DOI: e1000799. doi:10.1371/journal.pcbi.1000799 Abstract: Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment. This model was downloaded from the supplemetary materials to the article. To make this file valid SBML, some minor changes had to be done. The reaction Test_sink and empty lists were removed. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
(R)-S-Lactoylglutathione methylglyoxal-lyase (isomerizing)
Indole hydro-lyase (adding indoleglycerol-phosphate)
(R)-4'-Phosphopantothenate:L-cysteine ligase
N-Succinyl-LL-2,6-diaminoheptanedioate amidohydrolase
Acetyl-CoA:L-glutamate N-acetyltransferase
L-Serine hydro-lyase (adding indoleglycerol-phosphate)
Prephenate hydro-lyase (decarboxylating)
Guanosine:orthophosphate ribosyltransferase
(R)-Pantoate:beta-alanine ligase (AMP-forming)
O-Acetyl-L-homoserine succinate-lyase (adding cysteine)
(S)-3-Hydroxyhexadecanoyl-CoA:NAD+ oxidoreductase
Inosine:orthophosphate ribosyltransferase
5-Amino-2-oxopentanoate:2-oxoglutarate aminotransferase
2,3-Bis-O-(geranylgeranyl)glycerol 1-phosphate
Geranylgeranyl diphosphate:sn-3-O-(geranylgeranyl)glycerol
O-Acetyl-L-homoserine acetate-lyase (adding methanethiol)
Decanoyl-CoA:acetyl-CoA C-acyltransferase
2-Methylbutanoyl-CoA:(acceptor) 2,3-oxidoreductase
N-[(R)-4'-Phosphopantothenoyl]-L-cysteine carboxy-lyase
1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate carboxy-lyase
Pyruvate:carbon-dioxide ligase (ADP-forming)
2-Amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid
GTP 7,8-8,9-dihydrolase (pyrophosphate-forming)
(S)-2-Aceto-2-hydroxybutanoate:NADP+ oxidoreductase (isomerizing)
2-(Formamido)-N1-(5-phosphoribosyl)acetamidine cyclo-ligase
Acetyl-CoA:orthophosphate acetyltransferase
O-Succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase
UDPglucose:alpha-D-galactose-1-phosphate uridylyltransferase
Riboflavin-5-phosphate phosphohydrolase (acid optimum)
UTP:alpha-D-hexose-1-phosphate uridylyltransferase
Acetyl-CoA:L-homoserine O-acetyltransferase
L-Glutamate:tRNA(Glu) ligase (AMP-forming)
Lauroyl-CoA:(acceptor) 2,3-oxidoreductase
4-Methyl-2-oxopentanoate:lipoamide oxidoreductase(decarboxylating
Adenosine 5'-monophosphate phosphohydrolase
2,3,4,5-Tetrahydrodipicolinate:NADP+ oxidoreductase
Isocitrate:NADP+ oxidoreductase (decarboxylating)
beta-D-Glucose 6-phosphate ketol-isomerase
L-Alanine:tRNA(Ala) ligase (AMP-forming)
Geranyl-diphosphate:isopentenyl-diphosphate geranyltrans-transferase
L-Aspartate:tRNA(Asp) ligase (AMP-forming)
5-O-(1-Carboxyvinyl)-3-phosphoshikimate phosphate-lyase
(S)-3-Hydroxyhexadecanoyl-CoA hydro-lyase
Xanthosine-5'-phosphate:L-glutamine amido-ligase (AMP-forming)
2-Deoxy-D-ribose-5-phosphate acetaldehyde-lyase
Adenosine:orthophosphate ribosyltransferase
6-Phospho-D-gluconate:NADP+ 2-oxidoreductase (decarboxylating)
Decanoyl-CoA:(acceptor) 2,3-oxidoreductase
Deamido-NAD+:L-glutamine amido-ligase (AMP-forming)
3-Methyl-2-oxopentanoate:lipoamide oxidoreductase(decarboxylating
XMP:pyrophosphate phosphoribosyltransferase
L-Glutamate-5-semialdehyde:NADP+ 5-oxidoreductase (phosphorylationg)
4-Aminobutanoate:2-oxoglutarate aminotransferase
Presqualene diphosphate:farnesyl-diphosphate farnesyltransferase
ATP phosphohydrolase (protein-secreting)
L-Malate glyoxylate-lyase (CoA-acetylating)
Geranylgeranyl diphosphate:sn-glyceryl phosphate
ATP:nucleoside-phosphate phosphotransferase
D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate hydro-lyase
L-Aspartic acid:oxygen oxidoreductase (deaminating)
(S)-2-Aceto-2-hydroxybutanoate pyruvate-lyase (carboxylating)
ATP:3-phospho-D-glycerate 1-phosphotransferase
beta-Carotene:oxygen 15,15'-oxidoreductase (bond-cleaving)
NADPH:oxidized-thioredoxin oxidoreductase
2'-Deoxyguanosine 5'-diphosphate:oxidized-thioredoxin
L-Glutamate:NADP+ oxidoreductase (deaminating)
L-aspartate:L-glutamine amido-ligase (AMP-forming)
alpha-D-Glucose 1-phosphate 1,6-phosphomutase
L-Aspartate:tRNAAsp ligase (AMP-forming)
L-Aspartate-4-semialdehyde hydro-lyase (adding pyruvate and
Carbamoyl-phosphate:L-ornithine carbamoyltransferase
L-Glutamate:ammonia ligase (ADP-forming)
Tetradecanoyl-CoA:(acceptor) 2,3-oxidoreductase
Hydorogen-peroxide:hydrogen-peroxide oxidoreductase
1-(5-Phospho-D-ribosyl)-ATP:pyrophosphate phosphoribosyl-transferase
(S)-Hydroxyhexanoyl-CoA:NAD+ oxidoreductase
L-Citrulline:L-aspartate ligase (AMP-forming)
Orotidine-5'-phosphate:pyrophosphate phosphoribosyltransferase
Xanthosine 5'-phosphate phosphohydrolase
UTP:alpha-D-glucose-1-phosphate uridylyltransferase
4-amino-4-deoxychorismate pyruvate-lyase
3-Oxopropanoate:NAD+ oxidoreductase (decarboxylating,
Uridine 5'-monophosphate phosphohydrolase
(2S,3S)-3-Hydroxy-2-methylbutanoyl-CoA hydro-liase
beta-D-Fructose 1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase
Neurosporene, hydrogen-donor:oxygen oxidoreductase
2'-Deoxyuridine 5'-diphosphate:oxidized-thioredoxin
Glycine:lipoylprotein oxidoreductase (decarboxylating and
(S)-Hydroxyoctanoyl-CoA:NAD+ oxidoreductase
5-Phospho-D-ribosylamine:glycine ligase (ADP-forming)
3-Hydroxy-2-methylpropanoate:NAD+ oxidoreductase
L-Isoleucine:2-oxoglutarate aminotransferase