ATP:nucleoside-diphosphate phosphatransferase
O-Succinylbenzoate:CoA ligase (AMP-forming)
D-Glyceraldehyde-3-phosphate:NADP+ oxidoreductase(phosphorylating)
Prephenate hydro-lyase (decarboxylating)
Thymidine:orthophosphate deoxyribosyltransferase
5,10-Methylenetetrahydrofolate:glycine hydroxymethyltransferase
2-Deoxy-D-ribose-5-phosphate acetaldehyde-lyase
D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate hydro-lyase
Tetradecanoyl-CoA:(acceptor) 2,3-oxidoreductase
2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate phosphate-lyase
5,10-Methylenetetrahydrofolate:dUMP C-methyltransferase
(R)-Lactaldehyde:NAD+ oxidoreductase (glutathione-formylating)
Myristoyl-CoA:acetylCoA C-myristoyltransferase
2'-Deoxyuridine 5'-diphosphate:oxidized-thioredoxin
Hydorogen-peroxide:hydrogen-peroxide oxidoreductase
Guanosine:orthophosphate ribosyltransferase
Presqualene diphosphate:farnesyl-diphosphate farnesyltransferase
Guanosine 3'-diphosphate 5'-triphosphate
L-Tyrosine:2-oxoglutarate aminotransferase
L-Threonine:tRNA(Thr) ligase (AMP-forming)
Xanthosine 5'-phosphate phosphohydrolase
2,5-Diaminopyrimidine nucleoside triphosphate
Uridine:orthophosphate ribosyltransferase
2-Amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid
(S)-2-Aceto-2-hydroxybutanoate:NADP+ oxidoreductase (isomerizing)
2'-Deoxyadenosine 5'-diphosphate:oxidized-thioredoxin
L-Arogenate hydro-lyase (decarboxylating)
L-Glutamate:ammonia ligase (ADP-forming)
(R)-2,3-Dihydroxy-3-methylpentanoate:NADP+ oxidoreductase
3-Hydroxy-2-methylpropanoate:NAD+ oxidoreductase
Neurosporene, hydrogen-donor:oxygen oxidoreductase
L-Aspartic acid:oxygen oxidoreductase (deaminating)
L-Serine hydro-lyase (adding homocysteine)
ATP:2-dehydro-3-deoxy-D-gluconate 6-phosphotransferase
Decanoyl-CoA:acetyl-CoA C-acyltransferase
(S)-3-Hydroxydodecanoyl-CoA:NAD+ oxidoreductase
Hexanoyl-CoA:acetyl-CoA C-acyltransferase
5-Phosphoribosylamine:pyrophosphate phosphoribosyltransferase
L-Cysteine:tRNA(Cys) ligase (AMP-forming)
(S)-Hydroxyhexanoyl-CoA:NAD+ oxidoreductase
Substrate,reduced-flaboprotein:oxygen oxidoreductase
beta-D-Fructose 1,6-bisphosphate 1-phosphohydrolase
5-O-(1-Carboxyvinyl)-3-phosphoshikimate phosphate-lyase
L-Glutamine:D-fructose-6-phosphate aminotransferase (hexose
ATP phosphohydrolase (protein-secreting)
Nicotinate D-ribonucleotide:pyrophosphate phosphoribosyltransferase
UTP:alpha-D-hexose-1-phosphate uridylyltransferase
Acetyl-CoA:L-glutamate N-acetyltransferase
(S)-Hydroxyoctanoyl-CoA:NAD+ oxidoreductase
L-Aspartate:2-oxoglutarate aminotransferase
L-1-Pyrroline-5-carboxylate:NAD+ oxidoreductase
Adenosine 5'-monophosphate phosphohydrolase
Isopentenyl-diphosphate delta3-delta2-isomerase
Formamidopyrimidine nucleoside triphosphate 7,8-8,9-dihydrolase
3-Methyl-2-oxopentanoate:lipoamide oxidoreductase(decarboxylating
Acetyl-CoA:acetyl-CoA C-acetyltransferase
(S)-Hydroxydecanoyl-CoA:NAD+ oxidoreductase
(S)-2-Aceto-2-hydroxybutanoate pyruvate-lyase (carboxylating)
GTP 7,8-8,9-dihydrolase (pyrophosphate-forming)
Deamido-NAD+:L-glutamine amido-ligase (AMP-forming)
Prephytoene diphosphate:geranylgeranyl-diphosphate
ATP:adenylylsulfate 3'-phosphotransferase
3-Carboxy-3-hydroxy-4-methylpentanoate 3-methyl-2-oxobutanoate-lyase
Propinol adenylate:CoA ligase (AMP-forming)
(R)-4'-Phosphopantothenate:L-cysteine ligase
L-Alanine:2-oxoglutarate aminotransferase
ATP:pantetheine-4'-phosphate adenylyltransferase
Oxalosuccinate:NADP+ oxidoreductase (decarboxylating)
Glycine:lipoylprotein oxidoreductase (decarboxylating and
L-aspartate:L-glutamine amido-ligase (AMP-forming)
L-Phenylalanine:2-oxoglutarate aminotransferase
Carbon-dioxide:L-glutamine amido-ligase (ADP-forming,
beta-D-Glucose 6-phosphate ketol-isomerase
5-Phospho-D-ribosylamine:glycine ligase (ADP-forming)
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.
L-Glutamate:NADP+ oxidoreductase (deaminating)
N-[(R)-4'-Phosphopantothenoyl]-L-cysteine carboxy-lyase
Riboflavin-5-phosphate phosphohydrolase (acid optimum)
Orotidine-5'-phosphate:pyrophosphate phosphoribosyltransferase
Citrate oxaloacetate-lyase ((pro-3S)-CH2COO- -->acetate)
2'-Deoxycytidine 5'-monophosphate phosphohydrolase
Propanoyl-CoA:(acceptor) 2,3-oxidoreductase
alpha-D-Glucose 6-phosphate ketol-isomerase
(R)-2,3-Dihydroxy-3-methylbutanoate:NADP+ oxidoreductase
2'-Deoxyguanosine 5'-diphosphate:oxidized-thioredoxin
O3-Acetyl-L-serine acetate-lyase (adding hydrogen sulfide)
Inosine:orthophosphate ribosyltransferase
L-Valine:2-oxoglutarate aminotransferase
O-Phospho-L-homoserine phospho-lyase (adding water)
(S)-3-Hydroxyhexadecanoyl-CoA:NAD+ oxidoreductase
(S)-Dihydroorotate:oxygen oxidoreductase
O-Acetyl-L-homoserine succinate-lyase (adding cysteine)
N-Succinyl-LL-2,6-diaminoheptanedioate amidohydrolase
D-Fructose-2,6-bisphosphate 2-phosphohydrolase
L-Leucine:2-oxoglutarate aminotransferase
(R)-2-Methyl-3-oxopropanoyl-CoA 2-epimerase
(S)-3-Hydroxyhexadecanoyl-CoA hydro-lyase
(S)-3-Hydroxytetradecanoyl-CoA:NAD+ oxidoreductase
NADPH:oxidized-thioredoxin oxidoreductase
L-Isoleucine:2-oxoglutarate aminotransferase
(R)-2,3-Dihydroxy-3-methylbutanoate hydro-lyase
Farnesyl-diphosphate:farnesyl-diphosphate farnesyltransferase
2-Methylpropanoyl-CoA:(acceptor) 2,3-oxidoreductase
N-(5-Phospho-beta-D-ribosyl)anthranilate ketol-isomerase
L-Glutamate-5-semialdehyde:NADP+ 5-oxidoreductase (phosphorylationg)
NADH:guanosine-5'-phosphate oxidoreductase(deaminating)
(R)-Pantoate:beta-alanine ligase (AMP-forming)
N-Acetyl-L-glutamate-5-semialdehyde:NADP+ 5-oxidoreductase
Citrate oxaloacetate-lyase ((pro-3S)-CH2COO- -> acetyl-CoA)
Acetyl-CoA:L-homoserine O-acetyltransferase
(R)-Mevalonate:NADP+ oxidoreductase (CoA acylating)
Formamidopyrimidine nucleoside triphosphate
(S)-2-Methyl-3-oxopropanoyl-CoA carboxy-lyase
Pyruvate:carbon-dioxide ligase (ADP-forming)
(3S)-3-Hydroxyacyl-CoA:NAD+ oxidoreductase
1-(5-Phospho-D-ribosyl)-ATP:pyrophosphate phosphoribosyl-transferase
Cystathionine L-homocysteine-lyase (deaminating)
Geranylgeranyl diphosphate:sn-3-O-(geranylgeranyl)glycerol
Lauroyl-CoA:(acceptor) 2,3-oxidoreductase
AMP:pyrophosphate phosphoribosyltransferase
Lauroyl-CoA:acetyl-CoA C-acyltransferase
D-Fructose 1-phosphate D-glyceraldehyde-3-phosphate-lyase
Succinate-semialdehyde:NADP+ oxidoreductase
Cytidine-5'-monophosphate phosphohydrolase
Indole hydro-lyase (adding indoleglycerol-phosphate)
4-amino-4-deoxychorismate pyruvate-lyase
3-Methyl-2-oxobutanoate:lipoamide oxidoreductase(decarboxylating and
1-(2-Carboxyphenylamino)-1'-deoxy-D-ribulose 5'-phosphate
XMP:pyrophosphate phosphoribosyltransferase
(2S,3S)-3-Hydroxy-2-methylbutanoyl-CoA:NAD+ oxidoreductase
4-Methyl-2-oxopentanoate:lipoamide oxidoreductase(decarboxylating
3-Phosphoserine:2-oxoglutarate aminotransferase
Acetyl-CoA:orthophosphate acetyltransferase
3-Oxopropanoate:NAD+ oxidoreductase (decarboxylating,
3-Methylbutanoyl-CoA:(acceptor) 2,3-oxidoreductase
O-Succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase
L-Cystathionine L-homocysteine-lyase (deaminating)
CDPdiacylglycerol:L-serine 3-O-phosphatidyltransferase
beta-D-Fructose 1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase
Uridine 5'-monophosphate phosphohydrolase
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate
2-Methylbutanoyl-CoA:(acceptor) 2,3-oxidoreductase
(S)-3-Hydroxy-3-methylglutaryl-CoA acetoacetyl-CoA-lyase
L-Serine hydro-lyase (adding indoleglycerol-phosphate)
L-Alanine:tRNA(Ala) ligase (AMP-forming)
L-Glutamate:tRNA(Glu) ligase (AMP-forming)
O-Succinyl-L-homoserine succinate-lyase (adding cysteine)
(S)-3-Hydroxybutanoyl-CoA:NAD+ oxidoreductase
(R)-2,3-Dihydroxy-3-methylpentanoate hydro-lyase
L-Aspartate-4-semialdehyde hydro-lyase (adding pyruvate and
L-Malate glyoxylate-lyase (CoA-acetylating)
2,3-Bis-O-(geranylgeranyl)glycerol 1-phosphate
ATP:nicotinamide-nucleotide adenylyltransferase
2'-Deoxyadenosine 5'-monophosphate phosphohydrolase
Acetyl-CoA:D-glucosamine-6-phosphate N-acetyltransferase
Nicotinate D-ribonucleotide phosphohydrolase
(S)-Methylmalonate semialdehyde:NAD+ oxidoreductase
Nicotinate-nucleotide:pyrophosphate phosphoribosyltransferase
UDPglucose:alpha-D-galactose-1-phosphate uridylyltransferase
5'-Phosphoribosylformylglycinamide:L-glutamine amido-ligase
Prephenate:NAD+ oxidoreductase(decarboxylating)
Decanoyl-CoA:(acceptor) 2,3-oxidoreductase
Adenosine:orthophosphate ribosyltransferase
O-Acetyl-L-homoserine acetate-lyase (adding methanethiol)
Adenosine 3',5'-bisphosphate 3'(2')-phosphohydrolase
sn-3-O-(Geranylgeranyl)glycerol 1-phosphate
D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate
Acetyl adenylate:CoA ligase (AMP-forming)
(S)-Malate:NADP+ oxidoreductase(oxaloacetate-decarboxylating)
beta-Carotene:oxygen 15,15'-oxidoreductase (bond-cleaving)
(2S,3S)-3-Hydroxy-2-methylbutanoyl-CoA hydro-liase
L-Aspartate:tRNA(Asp) ligase (AMP-forming)
2-Hydroxybutane-1,2,4-tricarboxylate 2-oxoglutarate-lyase
alpha-D-Glucose 1-phosphate 1,6-phosphomutase
Geranylgeranyl diphosphate:sn-glyceryl phosphate
1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate carboxy-lyase
2'-Deoxyguanosine 5'-monophosphate phosphohydrolase
(S)-2-Acetolactate pyruvate-lyase (carboxylating)
2-(Formamido)-N1-(5-phosphoribosyl)acetamidine cyclo-ligase
5-Amino-2-oxopentanoate:2-oxoglutarate aminotransferase
3-Aminopropanoate:2-oxoglutarate aminotransferase
Tetrahydrofolate:L-glutamate gamma-ligase (ADP-forming)
Geranyl-diphosphate:isopentenyl-diphosphate geranyltrans-transferase
5,6,7,8-Tetrahydrofolate:NADP+ oxidoreductase
Inosine 5'-monophosphate phosphohydrolase
L-Citrulline:L-aspartate ligase (AMP-forming)
L-Glutamate:tRNA(Gln) ligase (AMP-forming)
3-Phospho-D-glyceroyl phosphate phosphohydrolase
Propanoyl-CoA:carbon-dioxide ligase (ADP-forming)
(S)-3-Hydroxytetradecanoyl-CoA hydro-lyase
(R)-2-Methyl-3-oxopropanoyl-CoA CoA-carbonylmutase
Xanthosine-5'-phosphate:L-glutamine amido-ligase (AMP-forming)
2'-Deoxycytidine diphosphate:oxidized-thioredoxin 2'-oxidoreductase
UTP:alpha-D-glucose-1-phosphate uridylyltransferase
ATP:nucleoside-phosphate phosphotransferase
2-(alpha-Hydroxyethyl)thiamine diphosphate
Adenosine 3',5'-bisphosphate,sulfite:oxidized-thioredoxin
ATP:N-acetyl-L-glutamate 5-phosphotransferase
ATP:3-phospho-D-glycerate 1-phosphotransferase
3-Phospho-D-glycerate:NAD+ 2-oxidoreductase
Chorismate pyruvate-lyase (amino-accepting)
Succinate-semialdehyde:NAD+ oxidoreductase
Octanoyl-CoA:acetyl-CoA C-acyltransferase
N-Methylimidazolidine-2,4-dione amidohydrolase (ATP-hydrolysing)
2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate
meso-2,6-Diaminoheptanedioate carboxy-lyase
UMP:pyrophosphate phosphoribosyltransferase
Carbamoyl-phosphate:L-aspartate carbamoyltransferase
1-(5-Phosphoribosyl)-5-amino-4-carboxyimidazole:L-aspartate ligase
Carbamoyl-phosphate:L-ornithine carbamoyltransferase
2,3,4,5-Tetrahydrodipicolinate:NADP+ oxidoreductase
2,3,4,5-Tetrahydrodipicolinate:NAD+ oxidoreductase
L-Aspartate:tRNAAsp ligase (AMP-forming)
L-Methionine:tRNAMet ligase (AMP-forming)
6-Phospho-D-gluconate:NADP+ 2-oxidoreductase (decarboxylating)
D-Glyceraldehyde-3-phosphate ketol-isomerase
Hexanoyl-CoA:(acceptor) 2,3-oxidoreductase
5-Amino-6-(5-phosphoribitylamino)uracil:NADP+ 1'-oxidoreductase
(R)-S-Lactoylglutathione methylglyoxal-lyase (isomerizing)
Guanosine 5'-monophosphate phosphohydrolase
N2-Acetyl-L-ornithine:2-oxoglutarate aminotransferase
GMP:pyrophosphate phosphoribosyltransferase
ATP:D-ribose-5-phosphate pyrophosphotransferase
L-Aspartate-4-semialdehyde:NADP+ oxidoreductase (phosphorylating)
4-Aminobutanoate:2-oxoglutarate aminotransferase
Xanthosine:orthophosphate ribosyltransferase
Isocitrate:NADP+ oxidoreductase (decarboxylating)
L-Cystathionine Lysteine-lyase (deaminating)