Supplementary Material S1: Reactions and enzymes of metabolic pathwaysinH. salinarum.Reaction-Identifiers and equations have been retrieved from the KEGG ligand database (Kanehisa et al. 2004). Shaded reactionslikely exist in H. salinarum.While enzyme genes have been assigned for reactions highlighted in green, experimental but no genetic evidences are currently available for reactions with gray shading. Experimental evidences such as NMR studies or enzyme activity tests from external references (PMID) have been included within the comment field.
(Supplementary Material S1 will be published within Halolex:
1 Glycolytic pathways
Embden-Meyerhof pathway and gluconeogenesis
react_id / subsystem / EC-No / reaction / status / genes / references / commentR00199 / C / 2.7.9.2 / ATP + Pyruvate + H2O <=>
AMP + Phosphoenolpyruvate + Orthophosphate / YES
secure / OE1500R / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R00200 / C / 2.7.1.40 / ATP + Pyruvate <=>
ADP + Phosphoenolpyruvate / YES
secure / OE1495R / 3255682 / pos_enz_activ;
R00206 / C / 2.7.9.1 / ATP + Pyruvate + Orthophosphate <=>
AMP + Phosphoenolpyruvate + Pyrophosphate / YES
insecure / OE1500R / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R00299 / C / 2.7.1.1
2.7.1.2 / ATP + D-Glucose <=>
ADP + D-Glucose 6-phosphate / YES
insecure / OE4691R / 2256927
3255682
6642538 / NMR; labeled glc converted to glc-6P; neg_enz_activ for EC 2.7.1.1;
R00303 / C / 3.1.3.9 / D-Glucose 6-phosphate + H2O <=>
D-Glucose + Orthophosphate / YES
insecure / - / 3255682
9827332 / pos_enz_activ; NMR; no_genet_evid; labeled pyruvate converted to glc if TCA cycle blocked;
R00341 / C / 4.1.1.49 / ATP + Oxaloacetate <=>
ADP + Phosphoenolpyruvate + CO2 / NO
unlikely / - / - / no blastp hit with A. pernix enz.;
R00346 / C / 4.1.1.38 / Pyrophosphate + Oxaloacetate <=>
Orthophosphate + Phosphoenolpyruvate + CO2 / NO
unlikely / -
R00431 / C / 4.1.1.32 / GTP + Oxaloacetate <=>
GDP + Phosphoenolpyruvate + CO2 / NO
unlikely / -
R00658 / C / 4.2.1.11 / 2-Phospho-D-glycerate <=>
Phosphoenolpyruvate + H2O / YES
secure / OE2640F / 2256927
3255682
6642538
9827332 / pos_enz_activ; NMR; EA low compared with H. mediterranei and H. vallismortis; labeled pyruvate converted to glc if TCA cycle blocked;
R00756 / C / 2.7.1.11 / ATP + D-Fructose 6-phosphate <=>
ADP + D-Fructose 1,6-bisphosphate / NO
unlikely / - / 3255682
6642538 / neg_enz_activ;
R00762 / C / 3.1.3.11 / D-Fructose 1,6-bisphosphate + H2O <=>
D-Fructose 6-phosphate + Orthophosphate / YES
secure / OE2020F / 2256927
3255682
6642538
9827332 / pos_enz_activ; NMR; high activ. in glc-grown cells; low activ. in glycerol- and pyruvate-grown cells; labeled pyruvate converted to glc if TCA cycle blocked;
R00764 / C / 2.7.1.90 / Pyrophosphate + D-Fructose 6-phosphate <=>
Orthophosphate + D-Fructose 1,6-bisphosphate / NO
unlikely / - / - / no homology to and T. tenax enzymes;
R00771 / C / 5.3.1.9 / D-Glucose 6-phosphate <=>
D-Fructose 6-phosphate / YES
secure / OE3792F / 2256927
3255682
6642538
9827332 / pos_enz_activ; NMR; EA low compared with H. mediterranei and H. vallismortis; labeled pyruvate converted to glc-6P if TCA cycle blocked;
R00866 / C / 2.7.1.3 / ATP + D-Fructose <=>
ADP + D-Fructose 1-phosphate / NO
unlikely / -
R01015 / C / 5.3.1.1 / D-Glyceraldehyde 3-phosphate <=>
Glycerone phosphate / YES
secure / OE2500R / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R01058 / C / 1.2.1.9 / D-Glyceraldehyde 3-phosphate + NADP+ + H2O <=>
3-Phospho-D-glycerate + NADPH / YES
insecure / OE2133R
OE2190R
OE2367F
OE4529F / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R01061 / C / 1.2.1.12
1.2.1.59 / D-Glyceraldehyde 3-phosphate + Orthophosphate + NAD+ <=>
3-Phospho-D-glyceroyl phosphate + NADH + H+ / YES
secure / OE1154F / 2256927
3255682
6642538
9827332 / EC 1.2.1.59 typ. for arch.; pos_enz_activ; NMR; EA (EC 1.2.1.12) low compared with H. mediterranei and H. vallismortis; labeled pyruvate converted to glc if TCA cycle blocked;
R01063 / C / 1.2.1.13
1.2.1.59 / D-Glyceraldehyde 3-phosphate + Orthophosphate + NADP+ <=>
3-Phospho-D-glyceroyl phosphate + NADPH + H+ / YES
secure / OE1154F / 2256927
3255682
6642538
9827332 / EC 1.2.1.59 typ. for arch.; NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R01068 / C / 4.1.2.13 / D-Fructose 1,6-bisphosphate <=>
Glycerone phosphate + D-Glyceraldehyde 3-phosphate / YES
secure / OE1472F
OE2019F / 2256927
3255682
6642538
9827332 / pos_enz_activ; NMR; EA low compared with H. mediterranei and H. vallismortis; labeled pyruvate converted to glc if TCA cycle blocked;
R01512 / C / 2.7.2.3 / ATP + 3-Phospho-D-glycerate <=>
ADP + 3-Phospho-D-glyceroyl phosphate / YES
secure / OE2745R / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R01515 / C / 3.6.1.7 / 3-Phospho-D-glyceroyl phosphate + H2O <=>
3-Phospho-D-glycerate + Orthophosphate / NO
unlikely / - / - / no homology to A. fulgidus enzyme;
R01518 / C / 5.4.2.1 / 2-Phospho-D-glycerate <=>
3-Phospho-D-glycerate / YES
secure / OE3653R / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R02185 / C / 2.7.1.63 / (Phosphate)n + D-Glucose <=>
(Phosphate)n + D-Glucose 6-phosphate / NO
unlikely / -
R03232 / C / 2.7.1.69 / Protein N(pai)-phosphohistidine + D-Fructose <=>
Protein histidine + D-Fructose 1-phosphate / NO
unlikely / -
R05805 / C / 2.7.1.146 / ADP + D-Fructose 6-phosphate <=>
AMP + D-Fructose 1,6-bisphosphate / NO
unlikely / - / - / no homology to P. furiosus, T. litoralis and T. zilligii enzymes;
R10000 / C / 2.7.1.56 / ATP + D-Fructose 1-phosphate <=>
ADP + D-Fructose 1,6-bisphosphate / NO
unlikely / -
Entner-Douderoff pathway
react_id / subsystem / EC-No / reaction / status / genes / references / commentR00300 / C / 1.1.1.118
1.1.1.47 / D-Glucose + NAD+ <=>
D-Glucono-1,5-lactone + NADH / NO
unlikely / - / 2256927 / neg_enz_activ; hasal glc-1-dh does not prefer NAD+ as coenzyme; all known glc-1-dh seq seem to be assign. to EC 1.1.1.47 using beta-glucose;
R00305 / C / 1.1.5.2 / D-Glucose + Acceptor <=>
D-Glucono-1,5-lactone + Reduced acceptor / NO
unlikely / -
R00835 / C / 1.1.1.49 / D-Glucose 6-phosphate + NADP+ <=>
D-Glucono-1,5-lactone 6-phosphate + NADPH + H+ / YES
insecure / - / 11271421
5780095
10650712 / pos_enz_activ; no_genet_evid; enz_activ. with NAD and NADP; kinet. mech. studied;
R01519 / C / 3.1.1.17 / D-Glucono-1,5-lactone + H2O <=>
D-Gluconic acid / YES
insecure / - / 2256927 / NMR; no_genet_evid; labeled glc metabolized to gluconate in glc-grown HS cells;
R01538 / C / 4.2.1.39 / D-Gluconic acid <=>
2-Dehydro-3-deoxy-D-gluconate + H2O / YES
likely / OE1664R / 16794308
11271421
3255682
15869466 / OE1664R is homolog to Sulfolobus enzyme (SSO3198, PMID:16794308); OE1664R is part of ED pathway gene cluster; no enzyme activity observed in indirect test for 3-step ED reaction sequence from gluconate, but enzyme activity proven for H. mediterranei;
R01541 / C / 2.7.1.45 / ATP + 2-Dehydro-3-deoxy-D-gluconate <=>
ADP + 2-Dehydro-3-deoxy-6-phospho-D-gluconate / YES
likely / OE1266R / 11271421
3255682
15869466 / enz. activ. not found (test for a 3 step ED react. seq. done), but enz. activ. proven for H. mediterranei; likely homologue to H. mediterranei enz. found;
R02035 / C / 3.1.1.31 / D-Glucono-1,5-lactone 6-phosphate + H2O <=>
6-Phospho-D-gluconate / NO
unlikely / -
R02036 / C / 4.2.1.12 / 6-Phospho-D-gluconate <=>
2-Dehydro-3-deoxy-6-phospho-D-gluconate + H2O / NO
unlikely / -
R05605 / C / 4.1.2.14 / 2-Dehydro-3-deoxy-6-phospho-D-gluconate <=>
D-Glyceraldehyde 3-phosphate + Pyruvate / YES
likely / OE1665R / 10760168
11271421
3255682
16794308
15869466 / OE1665R is homolog to bifunctional Sulfolobus KD(P)G aldolase (SSO3197, PMID:15869466); OE1665R is part of ED pathway gene cluster; H. salinarum contains no homolog of the classic KDPG aldolase, which is present in other haloarchaea, e.g. in H. mediterranei (GenBank: AAB40121); no enzyme activity observed in indirect test for 3-step ED reaction sequence from gluconate but enzyme activity proven for H. mediterranei;
R10001 / C / 1.1.1.119
1.1.1.47 / D-Glucose + NADP+ <=>
D-Glucono-1,5-lactone + NADPH / YES
likely / OE1669F / 2256927
8925901 / pos_enz_activ; NMR; labeled glucose is metabolized to gluconate in glucose-grown H. salinarum cells (PMID:2256927); NAD(P)-glucose dehydrogenase from H. mediterranei has been characterized and N-terminally sequenced (OE1669F matches) (PMID:8925901); OE1669F is part of ED pathway gene cluster;
R10002 / C / 4.1.2.20 / 2-Dehydro-3-deoxy-6-phospho-D-gluconate <=>
D-Glyceraldehyde + Pyruvate / NO
unlikely / -
2 Pentose-phosphate pathway and pentose metabolism
react_id / subsystem / EC-No / reaction / status / genes / references / commentR00024 / C / 4.1.1.39 / D-Ribulose 1,5-bisphosphate + CO2 + H2O <=>
2 3-Phospho-D-glycerate / NO
unlikely / - / 3255682
17303759 / negative enzyme activity; reaction of novel archaeal AMP recycling pathway; no homolog to N. pharaonis RuBisCO (NP2770A);
R00835 / C / 1.1.1.49 / D-Glucose 6-phosphate + NADP+ <=>
D-Glucono-1,5-lactone 6-phosphate + NADPH + H+ / YES
insecure / - / 11271421
5780095
10650712 / pos_enz_activ; no_genet_evid; enz_activ. with NAD and NADP; kinet. mech. studied;
R01056 / C / 5.3.1.6 / D-Ribose 5-phosphate <=>
D-Ribulose 5-phosphate / YES
secure / OE4185F
R01067 / C / 2.2.1.1 / D-Fructose 6-phosphate + D-Glyceraldehyde 3-phosphate <=>
D-Erythrose 4-phosphate + D-Xylulose 5-phosphate / NO
unlikely / - / - / no homologue to two M. jannaschii enzymes;
R01523 / C / 2.7.1.19 / ATP + D-Ribulose 5-phosphate <=>
ADP + D-Ribulose 1,5-bisphosphate / NO
questionable / - / 3255682
15375115 / positive enzyme activity but no genetic evidence; genetic evidence (OE4651F) for novel archaeal reaction from PRPP to ribulose 1,5-biphosphate found;
R01528 / C / 1.1.1.44 / 6-Phospho-D-gluconate + NADP+ <=>
D-Ribulose 5-phosphate + CO2 + NADPH + H+ / YES
insecure / OE4581F / 3255682 / enz. activ. of H. vallismortui and H. mediterranii inhib. by salt; only N-terminal domain conserved; C-terminal 6PGD-domain only feable conserved;
R01529 / C / 5.1.3.1 / D-Ribulose 5-phosphate <=>
D-Xylulose 5-phosphate / NO
unlikely / - / - / no homologue to M. jannaschii enzyme;
R01641 / C / 2.2.1.1 / D-Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate <=>
D-Ribose 5-phosphate + D-Xylulose 5-phosphate / NO
unlikely / - / - / no homologue to two M. jannaschii enzymes;
R01827 / C / 2.2.1.2 / D-Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate <=>
D-Erythrose 4-phosphate + D-Fructose 6-phosphate / NO
unlikely / - / - / no homologue to M. jannaschii, T. acidophilum and T. volcanium enzymes;
R02035 / C / 3.1.1.31 / D-Glucono-1,5-lactone 6-phosphate + H2O <=>
6-Phospho-D-gluconate / NO
unlikely / -
R05338 / C / - / D-Ribulose 5-phosphate + Formaldehyde <=>
D-Arabino-6-hexulose 3-phosphate / NO
questionable / - / 16237021
16788179 / ribulose monophosphate pathway substitutes the missing pentose phosphate pathway in several archaea; no homolog to 6-phospho-3-hexuloisomerase (COG0794) and 3-hexulose-6-phosphate synthase (COG0269) found in haloarchaea;
R05339 / C / - / D-Arabino-6-hexulose 3-phosphate <=>
D-Fructose 6-phosphate / NO
questionable / - / 16237021
16788179 / ribulose monophosphate pathway substitutes the missing pentose phosphate pathway in several archaea; no homolog to 6-phospho-3-hexuloisomerase (COG0794) and 3-hexulose-6-phosphate synthase (COG0269) found in haloarchaea;
R10008 / C / - / 5-Phospho-alpha-D-ribose 1-diphosphate <=>
D-Ribulose 1,5-bisphosphate / YES
secure / OE4651F / 15375115 / ribulose 1,5-biphosphate produced from PRPP and not from not ribulose 5-phosphate in archaea;
R10009 / P / - / AMP + Orthophosphate <=>
D-Ribose 1,5-bisphosphate + Adenine / NO
unlikely / - / 17303759 / reaction of novel archaeal AMP recycling pathway; no homolog to N. pharaonis AMP phosphorylase (NP3958A);
R10010 / P / - / D-Ribose 1,5-bisphosphate <=>
D-Ribulose 1,5-bisphosphate / YES
likely / OE3610R / 17303759 / reaction of novel archaeal AMP recycling pathway; all pathway enzymes encoded by N. pharaonis, but only ribose-1,5-biphosphate isomerase encoded by H. salinarum;
3 Glycerol metabolism
react_id / subsystem / EC-No / reaction / status / genes / references / commentR00841 / C / 3.1.3.21 / sn-Glycerol 3-phosphate + H2O <=>
Glycerol + Orthophosphate / NO
unlikely / - / - / Dunaliella enz. acts on sn-glycerol 1-phosphate, but also less rapidly on sn-glycerol 3-phosphate;
R00842 / C / 1.1.1.8
1.1.1.94 / sn-Glycerol 3-phosphate + NAD+ <=>
Glycerone phosphate + NADH + H+ / NO
unlikely / - / - / EC 1.1.1.94: no homologue to M. thermoautotrophicum and A. fulgidus enz.;
R00844 / C / 1.1.1.94 / sn-Glycerol 3-phosphate + NADP+ <=>
Glycerone phosphate + NADPH + H+ / NO
unlikely / - / - / no homologue to M. thermoautotrophicum and A. fulgidus enz.;
R00847 / C / 2.7.1.30 / ATP + Glycerol <=>
ADP + sn-Glycerol 3-phosphate / YES
secure / OE3762R / 3255682
3700337 / radioact; NMR; signals from labeled glycerol found in several aa and isoprenoids; EA test only performed for H. mediterranei and H. vallismortis yet (pos. result);
R00848 / C / 1.1.99.5 / sn-Glycerol 3-phosphate + FAD <=>
Glycerone phosphate + FADH2 / YES
secure / OE3763F
OE3764F
OE3765F / 3700337 / radioact; NMR; signals from labeled glycerol found in several aa and isoprenoids; H. salinarum only arch. with this enz.; enz. complex with 3 subunits pred.;
R00849 / C / 1.1.99.5 / sn-Glycerol 3-phosphate + Acceptor <=>
Glycerone phosphate + Reduced acceptor / YES
secure / OE3763F
OE3764F
OE3765F / 3700337 / radioact; NMR; signals from labeled glycerol found in several aa and isoprenoids; H. salinarum only arch. with this enz.; enz. complex with 3 subunits pred.;
R01010 / C / 3.1.3.1 / Glycerone phosphate + H2O <=>
Glycerone + Orthophosphate / YES
secure / OE5192R / - / H. salinarum only arch. with this enz.;
R01011 / C / 2.7.1.29 / ATP + Glycerone <=>
ADP + Glycerone phosphate / NO
unlikely / -
R01015 / C / 5.3.1.1 / D-Glyceraldehyde 3-phosphate <=>
Glycerone phosphate / YES
secure / OE2500R / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R01034 / C / 1.1.1.6 / Glycerol + NAD+ <=>
Glycerone + NADH / YES
secure / OE5160F / 3255682 / pos_enz_activ; high glycerol dh activ. found in H. salinarum, but no EA in H. mediterranei and H. vallismortis; H. salinarum only arch. with this enz.;
R01036 / C / 1.1.1.1
1.1.1.21 / Glycerol + NAD+ <=>
D-Glyceraldehyde + NADH + H+ / YES
insecure / OE3563R
OE4674F / - / H. salinarum and Sulfolobus only arch. with this enz.;
R01039 / C / 1.1.1.156 / Glycerol + NADP+ <=>
Glycerone + NADPH + H+ / YES
insecure / OE5160F / - / as EC 1.1.1.6, only NADP+ as cofact.;
R01041 / C / 1.1.1.1
1.1.1.2
1.1.1.21
1.1.1.72 / Glycerol + NADP+ <=>
D-Glyceraldehyde + NADPH + H+ / YES
insecure / OE3563R
OE4674F / - / H. salinarum and Sulfolobus only arch. with this enz.;
R01059 / C / 2.7.1.28 / ATP + D-Glyceraldehyde <=>
ADP + D-Glyceraldehyde 3-phosphate / NO
unlikely / -
R01514 / C / 2.7.1.31 / ATP + D-Glycerate <=>
ADP + 3-Phospho-D-glycerate / NO
unlikely / -
R01752 / C / 1.2.1.3 / D-Glyceraldehyde + NAD+ + H2O <=>
D-Glycerate + NADH + H+ / YES
secure / OE2133R
OE2190R
OE2367F
OE4529F
R05679 / C / 1.1.1.261 / Glycerol 1-phosphate + NAD+ <=>
Glycerone phosphate + NADH + H+ / YES
secure / OE1602F / 9419225 / enz. requ. for formation of sn-glycerol 1-phosphate used for arch.-spec. lipids; stereospec. diff. from glycerol 3-phosphate dh (EC 1.1.1.8);
R05680 / C / 1.1.1.261 / Glycerol 1-phosphate + NADP+ <=>
Glycerone phosphate + NADPH + H+ / YES
secure / OE1602F / - / enz. requ. for formation of arch.-spec. glycero-1-phosphate used for phospholipids; stereospec. diff. from EC sn-glycerol-3-phosphate dh;
4 Pyruvate metabolism and tricarboxylic acid cycle
Pyruvate metabolism
react_id / subsystem / EC-No / reaction / status / genes / references / commentR00014 / C / 1.2.4.1
2.2.1.6 / 2-(alpha-Hydroxyethyl)thiamine diphosphate + CO2 <=>
Thiamin diphosphate + Pyruvate / NO
unlikely / - / 15556640
6266826 / TU_oxdhA1B_dsa_lpdA; 4 subunits likely to form a 2-oxoacid dehydrogenase complex; not pyruvate or 2-oxoglutarate dh complex (lipoic acid absent in H. salinarum pyruvate and 2-oxoglutarate synthase); 2-oxoacid dehydrogenase complex might be involved in branched-chain amino acid degradation as in T. acidophilum;
R00196 / C / 1.1.2.3 / (S)-Lactate + 2 Ferricytochrome c <=>
Pyruvate + 2 Ferrocytochrome c / NO
unlikely / -
R00199 / C / 2.7.9.2 / ATP + Pyruvate + H2O <=>
AMP + Phosphoenolpyruvate + Orthophosphate / YES
secure / OE1500R / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R00200 / C / 2.7.1.40 / ATP + Pyruvate <=>
ADP + Phosphoenolpyruvate / YES
secure / OE1495R / 3255682 / pos_enz_activ;
R00206 / C / 2.7.9.1 / ATP + Pyruvate + Orthophosphate <=>
AMP + Phosphoenolpyruvate + Pyrophosphate / YES
insecure / OE1500R / 2256927
9827332 / NMR; labeled pyruvate converted to glc if TCA cycle blocked;
R00207 / C / 1.2.3.3 / Pyruvate + Orthophosphate + Oxygen <=>
Acetyl phosphate + H2O2 + CO2 / NO
unlikely / -
R00210 / C / 1.2.1.51 / Pyruvate + CoA + NADP+ <=>
Acetyl-CoA + CO2 + NADPH / NO
unlikely / - / 6266826 / flavin nucleotides absent in Hasal pyruvate synthase; enzyme purified from Euglena (PNO_EUGGR);
R00211 / C / 1.2.3.6 / Pyruvate + CoA + Oxygen <=>
H2O2 + Acetyl-CoA + CO2 / NO
unlikely / -
R00212 / C / 2.3.1.54 / Acetyl-CoA + Formate <=>
CoA + Pyruvate / NO
unlikely / -
R00214 / C / 1.1.1.38
1.1.1.39
4.1.1.3 / (S)-Malate + NAD+ <=>
Pyruvate + CO2 + NADH / YES
likely / OE3308F / - / enz. activ. only tested with NADP yet; EC 4.1.1.3 not likely;
R00216 / C / 1.1.1.40
4.1.1.3 / (S)-Malate + NADP+ <=>
Pyruvate + CO2 + NADPH / YES
secure / OE3308F / 8157586
9827332 / pos_enz_activ; NMR; NADP-dep. malic enz_activ found; 7% of labeled pyruvate entering TCA cycle converted back to pyruvate by malic enz.; H. salinarum only archaea with this enz.; EC 4.1.1.3 not likely;
R00217 / C / 1.1.1.38
1.1.1.40
4.1.1.3 / Oxaloacetate <=>
Pyruvate + CO2 / YES
likely / OE3308F / - / malic enz. (EC 1.1.1.38/40) often also decarb. added oxaloacetate; EC 4.1.1.3 not likely;
R00220 / C / 4.3.1.19 / L-Serine <=>
Pyruvate + NH3 / YES
insecure / OE3941F / - / NMR; Ser signals detected from labeled substrates; pathways via hydroxypyruvate/3P-hydroxypyruvate incomplete; pathway via 3P-hydroxypyruvate likely, since genes for EC 1.1.1.95 and EC 3.1.3.3 adjacent to each other; missing EC 2.6.1.52 potentially coded by OE4391F; serine dehydratation to pyruvate by EC 4.3.1.19 might be possible;
R00224 / C / 4.1.1.1 / Pyruvate <=>
Acetaldehyde + CO2 / NO
unlikely / -
R00258 / C / 2.6.1.2 / L-Alanine + 2-Oxoglutarate <=>
Pyruvate + L-Glutamate / YES
secure / OE1755F
OE1944R
OE2619F / 8157586
9827332 / NMR; NMR studies indicate that Ala is not synthesized from pyruvate by glutamate:pyruvate transaminase (alanine aminotransferase, EC 2.6.1.2), but by aspartate:pyruvate transaminase (aspartate aminotransferase, EC 2.6.1.1) (PMID: 8157586); Ala signals were detected from labeled glycerol (if Ala was omitted from the growth medium), but not from labeled acetate (PMID: 3700337); labeled pyruvate was converted to Ala primarly under anaerobic conditions (TCA cycle less active) and in absence of glucose in the growth medium (PMID: 8157586);
R00341 / C / 4.1.1.49 / ATP + Oxaloacetate <=>
ADP + Phosphoenolpyruvate + CO2 / NO
unlikely / - / - / no blastp hit with A. pernix enz.;
R00344 / C / 6.4.1.1 / ATP + Pyruvate + HCO3- <=>
ADP + Orthophosphate + Oxaloacetate / YES
insecure / - / 11195096
8157586
9827332 / NMR; 10\\% of labeled pyruvate flows into TCA cycle via PYC; haloarchaea do not encode archaeal-type pyruvate carboxylase (MJ1229/MJ1231); OE3177F is a biotin carboxylase, but the enzyme is more likely involved in propionate metabolism; N. pharaonis homolog found within fatty-acid degradation cluster;
R00345 / C / 4.1.1.31 / Orthophosphate + Oxaloacetate <=>
H2O + Phosphoenolpyruvate + CO2 / NO
unlikely / -
R00346 / C / 4.1.1.38 / Pyrophosphate + Oxaloacetate <=>
Orthophosphate + Phosphoenolpyruvate + CO2 / NO
unlikely / -
R00369 / C / 2.6.1.44 / L-Alanine + Glyoxylate <=>
Pyruvate + Glycine / YES
insecure / OE4391F / - / NMR; serine--pyruvate aminotransferase (EC 2.6.1.51) might also function as alanine--glyoxylate aminotransferase (EC 2.6.1.44) as shown for the human enzyme; Ala signals were detected from labeled glycerol (if Ala was omitted from the growth medium), but not from labeled acetate (PMID: 3700337); labeled pyruvate was converted to Ala primarly under anaerobic conditions (TCA cycle less active) and in absence of glucose in the growth medium (PMID: 8157586);
R00400 / C / 2.6.1.12 / L-Alanine + Oxaloacetate <=>
Pyruvate + L-Aspartate / NO
unlikely / -
R00431 / C / 4.1.1.32 / GTP + Oxaloacetate <=>
GDP + Phosphoenolpyruvate + CO2 / NO
unlikely / -
R00703 / C / 1.1.1.27 / (S)-Lactate + NAD+ <=>
Pyruvate + NADH + H+ / YES
insecure / - / 8157586
9827332 / pos_enz_activ; NMR; no_genet_evid; NADH-dep. EA proven in HS cell extract; labeled pyruvate converted to lactate under anaerobic condit.;
R01196 / C / 1.2.7.1 / Reduced ferredoxin + Acetyl-CoA + CO2 <=>
Oxidized ferredoxin + Pyruvate + CoA / YES
secure / OE2622R
OE2623R / 6266826
6266827
8157586
9827332 / pos_enz_activ; NMR; enz. complex with 2 subunits proven; cat. cycle of the enzyme invest.; 90% of labeled pyruvate flows into TCA cycle via POR; only 53% of acetyl-CoA produced from labeled pyruvate, rest generated endogenously;
R01698 / C / 1.8.1.4 / Dihydrolipoamide + NAD+ <=>
Lipoamide + NADH / YES
secure / OE4116F / 15556640
6266826 / haloarchaea are the only archaea with this enzyme, which is secure to function as a dihydrolipoamide dehydrogenase in reactions of a 2-oxoacid dehydrogenase complex (TU_oxdhA1B_dsa_lpdA); not part of pyruvate or 2-oxoglutarate dehydrogenase complex;
R02569 / C / 2.3.1.12 / Acetyl-CoA + Dihydrolipoamide <=>
CoA + S-Acetyldihydrolipoamide / NO
unlikely / - / 15556640
6266826 / haloarchaea are the only archaea with a dihydrolipoamide S-acyltransferase (EC 2.3.1.-), which is likely to function in reactions of a 2-oxoacid dehydrogenase complex (TU_oxdhA1B_dsa_lpdA); not part of pyruvate (EC 2.3.1.12) or 2-oxoglutarate (EC 2.3.1.61) dehydrogenase complex;
R03145 / C / 1.2.2.2 / Ferricytochrome b1 + Pyruvate + H2O <=>
Ferrocytochrome b1 + Acetate + CO2 / YES
insecure / - / 8157586 / NMR; no_genet_evid; acetate signals found from labeled pyruvate if growth without glc;
R03270 / C / 1.2.4.1 / 2-(alpha-Hydroxyethyl)thiamine diphosphate + Lipoamide <=>
S-Acetyldihydrolipoamide + Thiamin diphosphate / NO
unlikely / - / 15556640
6266826 / TU_oxdhA1B_dsa_lpdA; 4 subunits likely to form a 2-oxoacid dehydrogenase complex; not pyruvate or 2-oxoglutarate dh complex (lipoic acid absent in H. salinarum pyruvate and 2-oxoglutarate synthase); 2-oxoacid dehydrogenase complex might be involved in branched-chain amino acid degradation as in T. acidophilum;
Tricarboxylic acid and glyoxylate cycle
react_id / subsystem / EC-No / reaction / status / genes / references / commentR00267 / C / 1.1.1.42 / Isocitrate + NADP+ <=>
2-Oxoglutarate + CO2 + NADPH + H+ / YES
secure / OE3634F / 4393394
5058691
5780095
5802601
9827332 / pos_enz_activ; NMR; first enz_act (EC 1.1.1.42) tested; later enz. purified, enz_act measured and inactivation investig.; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R00268 / C / 1.1.1.42 / Oxalosuccinate <=>
2-Oxoglutarate + CO2 / YES
secure / OE3634F
R00342 / C / 1.1.1.37 / (S)-Malate + NAD+ <=>
Oxaloacetate + NADH + H+ / YES
secure / OE4323F / 5780095
9827332 / pos_enz_activ; NMR; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R00351 / C / 2.3.3.3
2.3.3.1 / Citrate + CoA <=>
Acetyl-CoA + H2O + Oxaloacetate / YES
insecure / OE3934R / 5780095
9827332 / pos_enz_activ; NMR; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R00352 / C / 2.3.3.8 / ATP + Citrate + CoA <=>
ADP + Orthophosphate + Acetyl-CoA + Oxaloacetate / YES
insecure / OE1942F / - / can be dissoc. into compon., 2 are ident. with EC 4.1.3.34 (found by sim. search) and EC 6.2.1.18;
R00354 / C / 4.1.3.34 / (3S)-Citryl-CoA <=>
Acetyl-CoA + Oxaloacetate / YES
secure / OE1942F / - / compon. of EC 2.3.3.8 and EC 4.1.3.6; H. salinarum only archaea with this enz.;
R00362 / C / 4.1.3.6 / Citrate <=>
Acetate + Oxaloacetate / YES
insecure / OE1942F / - / can be dissoc. into compon., 2 are ident. with EC 2.8.3.10 and EC 4.1.3.34 (found by sim. search);
R00405 / C / 6.2.1.5 / ATP + Succinate + CoA <=>
ADP + Orthophosphate + Succinyl-CoA / YES
secure / OE3195F
OE3196F / 5780095
9827332 / pos_enz_activ; NMR; enz. complex with 2 subunits pred.; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R00407 / C / 3.1.2.3 / Succinyl-CoA + H2O <=>
CoA + Succinate / NO
unlikely / -
R00408 / C / 1.3.99.1 / Succinate + FAD <=>
FADH2 + Fumarate / YES
secure / OE2865R
OE2866R
OE2867R
OE2868R / 5780095 / pos_enz_activ; enz. complex with 4 subunits pred.;
R00412 / C / 1.3.99.1 / Succinate + Acceptor <=>
Fumarate + Reduced acceptor / YES
secure / OE2865R
OE2866R
OE2867R
OE2868R / 5780095
9827332 / pos_enz_activ; NMR; enz. complex with 4 subunits pred.; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R00432 / C / 6.2.1.4 / GTP + Succinate + CoA <=>
GDP + Orthophosphate + Succinyl-CoA / YES
insecure / OE3195F
OE3196F / 5780095
9827332 / pos_enz_activ; NMR; enz. complex with 2 subunits pred.; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R00472 / C / 2.3.3.9 / (S)-Malate + CoA <=>
Acetyl-CoA + H2O + Glyoxylate / YES
insecure / - / 5780095 / pos_enz_activ; no_genet_evid;
R00479 / C / 4.1.3.1 / Isocitrate <=>
Succinate + Glyoxylate / YES
insecure / - / 5780095 / pos_enz_activ; no_genet_evid;
R00621 / C / 1.2.4.2 / 2-Oxoglutarate + Thiamin diphosphate <=>
3-Carboxy-1-hydroxypropyl-ThPP + CO2 / NO
unlikely / - / 15556640
6266826 / TU_oxdhA1B_dsa_lpdA; 4 subunits likely to form a 2-oxoacid dehydrogenase complex; not pyruvate or 2-oxoglutarate dh complex (lipoic acid absent in H. salinarum pyruvate and 2-oxoglutarate synthase); 2-oxoacid dehydrogenase complex might be involved in branched-chain amino acid degradation as in T. acidophilum;
R00709 / C / 1.1.1.41 / Isocitrate + NAD+ <=>
2-Oxoglutarate + CO2 + NADH + H+ / YES
insecure / OE3634F / 4393394
5058691
5802601 / enz. purified, enz_act measured and inactivation investig.;
R01082 / C / 4.2.1.2 / (S)-Malate <=>
Fumarate + H2O / YES
secure / OE2935R / 5780095
9827332 / pos_enz_activ; NMR; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R01197 / C / 1.2.7.3 / Reduced ferredoxin + Succinyl-CoA + CO2 <=>
Oxidized ferredoxin + 2-Oxoglutarate + CoA / YES
secure / OE1710R
OE1711R / 5780095
6266826
6266827
9827332 / pos_enz_activ; NMR; enz. complex with 2 subunits proven; cat. cycle of the enzyme invest.; also found in bact., e.g. H. pylori; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R01322 / C / 6.2.1.18 / ATP + Citrate + CoA <=>
ADP + Orthophosphate + (3S)-Citryl-CoA / NO
possible / - / - / compon. of EC 2.3.3.8;
R01323 / C / 2.8.3.10 / Acetyl-CoA + Citrate <=>
Acetate + (3S)-Citryl-CoA / NO
possible / - / - / compon. of EC 4.1.3.6;
R01324 / C / 4.2.1.3 / Citrate <=>
Isocitrate / YES
secure / OE4613F / 5780095
9827332 / pos_enz_activ; NMR; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R01325 / C / 4.2.1.3 / Citrate <=>
cis-Aconitate + H2O / YES
secure / OE4613F
R01899 / C / 1.1.1.42 / Isocitrate + NADP+ <=>
Oxalosuccinate + NADPH + H+ / YES
secure / OE3634F
R01900 / C / 4.2.1.3 / Isocitrate <=>
cis-Aconitate + H2O / YES
secure / OE4613F
R02164 / C / 1.3.5.1 / Ubiquinone + Succinate <=>
Ubiquinol + Fumarate / YES
insecure / OE2865R
OE2866R
OE2867R
OE2868R / 4004256
5780095
9827332 / pos_enz_activ; NMR; enz. complex with 4 subunits pred.; 13C NMR studies with labeled pyruvate fully consistent with active TCA cycle;
R02570 / C / 2.3.1.61 / Succinyl-CoA + Dihydrolipoamide <=>
CoA + S-Succinyldihydrolipoamide / NO
unlikely / - / 15556640
6266826 / haloarchaea are the only archaea with a dihydrolipoamide S-acyltransferase (EC 2.3.1.-), which is likely to function in reactions of a 2-oxoacid dehydrogenase complex (TU_oxdhA1B_dsa_lpdA); not part of pyruvate (EC 2.3.1.12) or 2-oxoglutarate (EC 2.3.1.61) dehydrogenase complex;
R03316 / C / 1.2.4.2 / 3-Carboxy-1-hydroxypropyl-ThPP + Lipoamide <=>
S-Succinyldihydrolipoamide + Thiamin diphosphate / NO
unlikely / - / 15556640
6266826 / TU_oxdhA1B_dsa_lpdA; 4 subunits likely to form a 2-oxoacid dehydrogenase complex; not pyruvate or 2-oxoglutarate dh complex (lipoic acid absent in H. salinarum pyruvate and 2-oxoglutarate synthase); 2-oxoacid dehydrogenase complex might be involved in branched-chain amino acid degradation as in T. acidophilum;
R04450 / C / 3.1.2.16 / Citrate (pro-3S)-lyase (acetyl form) + H2O <=>
Citrate (pro-3S)-lyase (thiol form) + Acetate / NO
unlikely / -
5 Nucleotide Metabolism