GENE_ASSOCIATION: NA PROTEIN_ASSOCIATION: NA PROTEIN_CLASS: 3.5.1.18 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SUBSYSTEM: aspartate superpathway PROTEIN_CLASS: 3.5.1.18 SIDE: SUC SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_262_ilvC ) PROTEIN_ASSOCIATION: ( ketol-acid reductoisomerase ) PROTEIN_CLASS: 1.1.1.86 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: valine biosynthesis SIDE: PROTON SIDE: NADPH SIDE: NADP COFACTOR: NADPH COFACTOR: NADP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_122 ) or ( SMGWSS_121_trpA ) PROTEIN_ASSOCIATION: ( putative tryptophan synthase, beta subunit (trpB)/anthranilate isomerase activity of trpC (trpF) ) or ( Tryptophan synthase alpha chain//TRYPSYN-RXN//Tryptophan synthase ) PROTEIN_CLASS: 4.2.1.20 GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_210_aspC ) PROTEIN_ASSOCIATION: ( putative aspartate aminotransferase ) PROTEIN_CLASS: 2.6.1.1 SUBSYSTEM: aspartate degradation I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SUBSYSTEM: threonine biosynthesis SUBSYSTEM: aspartate biosynthesis SUBSYSTEM: isoleucine biosynthesis I SIDE: _2__45__KETOGLUTARATE COFACTOR: _2__45__KETOGLUTARATE COFACTOR: L__45__ASPARTATE COFACTOR: OXALACETIC_ACID COFACTOR: GLT GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_139_thrC ) PROTEIN_ASSOCIATION: ( threonine synthase ) PROTEIN_CLASS: 4.2.3.1 SUBSYSTEM: threonine biosynthesis from homoserine SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SUBSYSTEM: threonine biosynthesis SUBSYSTEM: isoleucine biosynthesis I SIDE: WATER SIDE: __124__Pi__124__ GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_110_argC ) PROTEIN_ASSOCIATION: ( N-acetyl-gamma-glutamyl-phosphate reductase (AGPR) (N- acetyl-glutamate semialdehyde dehydrogenase) (NAGSA dehydrogenase)//N-ACETYLGLUTPREDUCT-RXN//N-acetyl-gamma-glutamyl-phosphate reductase ) PROTEIN_CLASS: 1.2.1.38 SUBSYSTEM: ornithine biosynthesis SUBSYSTEM: arginine biosynthesis I SUBSYSTEM: arginine biosynthesis III SUBSYSTEM: arginine biosynthesis II (acetyl cycle) SIDE: NADPH SIDE: __124__Pi__124__ SIDE: NADP COFACTOR: NADPH COFACTOR: NADP GENERIC: false TYPE: small HOLE: false
N-acetyl-&gamma;-glutamyl-phosphate reductase
GENE_ASSOCIATION: ( SMGWSS_042_leuC ) or ( SMGWSS_041_leuD ) PROTEIN_ASSOCIATION: ( 3-isopropylmalate dehydratase large subunit ) or ( 3-isopropylmalate dehydratase small subunit (Isopropylmalate isomerase) (Alpha-IPM isomerase) (IPMI)//3-ISOPROPYLMALISOM-RXN//3-isopropylmalate dehydratase ) PROTEIN_CLASS: 4.2.1.33 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: leucine biosynthesis SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_264_ilvB ) or ( SMGWSS_263_ilvN ) PROTEIN_ASSOCIATION: ( putative acetolactate synthase large subunit ) or ( putative acetolactate synthase small subunit ) PROTEIN_CLASS: 2.2.1.6 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: isoleucine biosynthesis from threonine SUBSYSTEM: isoleucine biosynthesis I SIDE: PYRUVATE SIDE: CARBON__45__DIOXIDE GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_116 ) PROTEIN_ASSOCIATION: ( putative acetylornithine deacetylase (argE)/succinyl-diaminopimelate desuccinylase (dapE) ) PROTEIN_CLASS: 3.5.1.16 SUBSYSTEM: ornithine biosynthesis SUBSYSTEM: arginine biosynthesis I SIDE: WATER SIDE: ACET GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_264_ilvB ) or ( SMGWSS_263_ilvN ) PROTEIN_ASSOCIATION: ( putative acetolactate synthase large subunit ) or ( putative acetolactate synthase small subunit ) PROTEIN_CLASS: 2.2.1.6 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: valine biosynthesis SIDE: CARBON__45__DIOXIDE GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_116 ) PROTEIN_ASSOCIATION: ( putative acetylornithine deacetylase (argE)/succinyl-diaminopimelate desuccinylase (dapE) ) PROTEIN_CLASS: 3.5.1.16 SUBSYSTEM: arginine biosynthesis III SIDE: WATER SIDE: ACET GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_043_leuA ) PROTEIN_ASSOCIATION: ( 2-isopropylmalate synthase ) PROTEIN_CLASS: 2.3.3.13 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: leucine biosynthesis SIDE: WATER SIDE: ACETYL__45__COA SIDE: CO__45__A COFACTOR: ACETYL__45__COA COFACTOR: CO__45__A GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_257_gapA ) PROTEIN_ASSOCIATION: ( glyceraldehyde 3-phosphate dehydrogenase ) PROTEIN_CLASS: 1.2.1.12 SIDE: NAD SIDE: __124__Pi__124__ SIDE: NADH COFACTOR: NAD COFACTOR: NADH GENERIC: false TYPE: small HOLE: false
Glyceraldehyde 3-phosphate dehydrogenase (phosphorylating)
GENE_ASSOCIATION: ( SMGWSS_098_ilvE ) PROTEIN_ASSOCIATION: ( branched-chain amino acid aminotransferase ) PROTEIN_CLASS: 2.6.1.42 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: leucine biosynthesis SIDE: _2__45__KETOGLUTARATE SIDE: GLT COFACTOR: _2__45__KETOGLUTARATE COFACTOR: GLT GENERIC: false TYPE: small HOLE: false
Branched-chain amino acid aminotransferase
GENE_ASSOCIATION: ( SMGWSS_109 ) PROTEIN_ASSOCIATION: ( putative argininosuccinate synthase (argG)/acetyltransferase activity of N-acetylglutamate synthase (argA) ) PROTEIN_CLASS: 2.3.1.1 SUBSYSTEM: ornithine biosynthesis SUBSYSTEM: arginine biosynthesis I SUBSYSTEM: arginine biosynthesis III SUBSYSTEM: arginine biosynthesis II (acetyl cycle) SIDE: ACETYL__45__COA SIDE: CO__45__A COFACTOR: ACETYL__45__COA COFACTOR: CO__45__A GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_113_carB ) or ( SMGWSS_112_carA ) PROTEIN_ASSOCIATION: ( carbamyl phosphate synthase large subunit ) or ( carbamoyl phosphate synthase small subunit ) PROTEIN_CLASS: 6.3.5.5 SUBSYSTEM: arginine biosynthesis III SUBSYSTEM: arginine biosynthesis I SUBSYSTEM: arginine biosynthesis II (acetyl cycle) SIDE: WATER SIDE: ATP SIDE: GLN SIDE: GLT SIDE: ADP SIDE: __124__Pi__124__ COFACTOR: ATP COFACTOR: ADP COFACTOR: __124__Pi__124__ GENERIC: false TYPE: small HOLE: false
carbamoyl-phosphate synthetase (glutamine-hydrolysing)
GENE_ASSOCIATION: ( SMGWSS_122 ) or ( SMGWSS_121_trpA ) PROTEIN_ASSOCIATION: ( putative tryptophan synthase, beta subunit (trpB)/anthranilate isomerase activity of trpC (trpF) ) or ( Tryptophan synthase alpha chain//TRYPSYN-RXN//Tryptophan synthase ) PROTEIN_CLASS: 4.2.1.20 SUBSYSTEM: tryptophan biosynthesis SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_200 ) PROTEIN_ASSOCIATION: ( putative phospho-2-dehydro-3-deoxyheptonate aldolase (aroG)/chorismate mutase (pheA) ) PROTEIN_CLASS: 2.5.1.54 SUBSYSTEM: chorismate biosynthesis SIDE: WATER SIDE: PHOSPHO__45__ENOL__45__PYRUVATE SIDE: __124__Pi__124__ GENERIC: false TYPE: small HOLE: false
2-dehydro-3-deoxyphosphoheptonate aldolase
GENE_ASSOCIATION: ( SMGWSS_098_ilvE ) PROTEIN_ASSOCIATION: ( branched-chain amino acid aminotransferase ) PROTEIN_CLASS: 2.6.1.42 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: isoleucine biosynthesis from threonine SUBSYSTEM: isoleucine biosynthesis I SIDE: _2__45__KETOGLUTARATE COFACTOR: _2__45__KETOGLUTARATE COFACTOR: GLT GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_180_aroE ) PROTEIN_ASSOCIATION: ( putative shikimate 5-dehydrogenase ) PROTEIN_CLASS: 1.1.1.25 SUBSYSTEM: chorismate biosynthesis SIDE: NADPH SIDE: NADP COFACTOR: NADPH COFACTOR: NADP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_210_aspC ) PROTEIN_ASSOCIATION: ( putative aspartate aminotransferase ) PROTEIN_CLASS: 2.6.1.57 SUBSYSTEM: phenylalanine biosynthesis I SIDE: GLT SIDE: _2__45__KETOGLUTARATE COFACTOR: GLT COFACTOR: _2__45__KETOGLUTARATE GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_202_asd ) PROTEIN_ASSOCIATION: ( aspartate semialdehyde dehydrogenase ) PROTEIN_CLASS: 1.2.1.11 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SUBSYSTEM: homoserine biosynthesis SUBSYSTEM: threonine biosynthesis SUBSYSTEM: isoleucine biosynthesis I SIDE: NADPH SIDE: __124__Pi__124__ SIDE: NADP COFACTOR: NADPH COFACTOR: NADP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_109 ) PROTEIN_ASSOCIATION: ( putative argininosuccinate synthase (argG)/acetyltransferase activity of N-acetylglutamate synthase (argA) ) PROTEIN_CLASS: 6.3.4.5 SUBSYSTEM: arginine biosynthesis III SUBSYSTEM: arginine biosynthesis I SUBSYSTEM: arginine biosynthesis II (acetyl cycle) SIDE: ATP SIDE: L__45__ASPARTATE SIDE: AMP SIDE: PPI COFACTOR: ATP COFACTOR: AMP COFACTOR: PPI GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_262_ilvC ) PROTEIN_ASSOCIATION: ( ketol-acid reductoisomerase ) PROTEIN_CLASS: 1.1.1.86 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: isoleucine biosynthesis from threonine SUBSYSTEM: isoleucine biosynthesis I SIDE: NADPH SIDE: NADP COFACTOR: NADPH COFACTOR: NADP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_265_ilvD ) PROTEIN_ASSOCIATION: ( dihydroxy-acid dehydratase ) PROTEIN_CLASS: 4.2.1.9 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: isoleucine biosynthesis from threonine SUBSYSTEM: isoleucine biosynthesis I SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_130_lysA ) PROTEIN_ASSOCIATION: ( diaminopimelate decarboxylase ) PROTEIN_CLASS: 4.1.1.20 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SIDE: CARBON__45__DIOXIDE GENERIC: false TYPE: small HOLE: false
2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase
GENE_ASSOCIATION: ( SMGWSS_097_dapD ) PROTEIN_ASSOCIATION: ( 2, 3, 4, 5-tetrahydropyridine-2, 6-dicarboxylate ) PROTEIN_CLASS: 2.3.1.117 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SIDE: SUC__45__COA SIDE: WATER SIDE: CO__45__A COFACTOR: SUC__45__COA COFACTOR: CO__45__A GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_040_leuB ) PROTEIN_ASSOCIATION: ( 3-isopropylmalate dehydrogenase ) PROTEIN_CLASS: 1.1.1.85 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: leucine biosynthesis SIDE: NAD SIDE: PROTON SIDE: NADH COFACTOR: NAD COFACTOR: NADH GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_114_argF ) PROTEIN_ASSOCIATION: ( putative ornithine carbamoyltransferase ) PROTEIN_CLASS: 2.1.3.9 SUBSYSTEM: arginine biosynthesis III SIDE: __124__Pi__124__ GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_114_argF ) PROTEIN_ASSOCIATION: ( putative ornithine carbamoyltransferase ) PROTEIN_CLASS: 2.1.3.3 SUBSYSTEM: citrulline degradation SUBSYSTEM: arginine biosynthesis I SUBSYSTEM: arginine biosynthesis II (acetyl cycle) SIDE: __124__Pi__124__ GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_140_thrB ) PROTEIN_ASSOCIATION: ( homoserine kinase ) PROTEIN_CLASS: 2.7.1.39 SUBSYSTEM: threonine biosynthesis from homoserine SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SUBSYSTEM: threonine biosynthesis SUBSYSTEM: isoleucine biosynthesis I SIDE: ATP SIDE: ADP COFACTOR: ATP COFACTOR: ADP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: NA PROTEIN_ASSOCIATION: NA PROTEIN_CLASS: NA SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: leucine biosynthesis SIDE: CARBON__45__DIOXIDE GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_028_prsA ) PROTEIN_ASSOCIATION: ( ribose-phosphate pyrophosphokinase ) PROTEIN_CLASS: 2.7.6.1 SUBSYSTEM: PRPP biosynthesis I SIDE: ATP COFACTOR: ATP COFACTOR: AMP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_177_dapB ) PROTEIN_ASSOCIATION: ( dihydrodipicolinate reductase ) PROTEIN_CLASS: 1.3.1.26 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SIDE: PROTON SIDE: NADH__45__P__45__OR__45__NOP SIDE: NAD__45__P__45__OR__45__NOP COFACTOR: NADH__45__P__45__OR__45__NOP COFACTOR: NAD__45__P__45__OR__45__NOP GENERIC: true TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_141_thrA ) or ( SMGWSS_038_lysC ) PROTEIN_ASSOCIATION: ( aspartokinase/homoserine dehydrogenase ) or ( putative aspartate kinase ) PROTEIN_CLASS: 2.7.2.4 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SUBSYSTEM: homoserine biosynthesis SUBSYSTEM: threonine biosynthesis SUBSYSTEM: isoleucine biosynthesis I SIDE: ATP SIDE: ADP COFACTOR: ATP COFACTOR: ADP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_138_menA ) PROTEIN_ASSOCIATION: ( 1,4-dihydroxy-2-naphthoate octaprenyltransferase ) PROTEIN_CLASS: 2.5.1.- SUBSYSTEM: menaquinone biosynthesis SIDE: CARBON__45__DIOXIDE SIDE: PPI GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_111_argD ) PROTEIN_ASSOCIATION: ( acetylornithine aminotransferase ) PROTEIN_CLASS: 2.6.1.11 COFACTOR: _2__45__KETOGLUTARATE COFACTOR: GLT GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_141_thrA ) PROTEIN_ASSOCIATION: ( aspartokinase/homoserine dehydrogenase ) PROTEIN_CLASS: 1.1.1.3 SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SUBSYSTEM: homoserine biosynthesis SUBSYSTEM: threonine biosynthesis SUBSYSTEM: isoleucine biosynthesis I SIDE: PROTON SIDE: NADH__45__P__45__OR__45__NOP SIDE: NAD__45__P__45__OR__45__NOP COFACTOR: NADH__45__P__45__OR__45__NOP COFACTOR: NAD__45__P__45__OR__45__NOP GENERIC: true TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_247_dapF ) PROTEIN_ASSOCIATION: ( diaminopimelate epimerase ) PROTEIN_CLASS: 5.1.1.7 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_111_argD ) PROTEIN_ASSOCIATION: ( acetylornithine aminotransferase ) PROTEIN_CLASS: 2.6.1.17 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SIDE: GLT SIDE: _2__45__KETOGLUTARATE COFACTOR: GLT COFACTOR: _2__45__KETOGLUTARATE GENERIC: false TYPE: small HOLE: false
Succinyldiaminopimelate aminotransferase
GENE_ASSOCIATION: ( SMGWSS_123_trpC ) PROTEIN_ASSOCIATION: ( indole-3-glycerol phosphate synthase activity of trpC ) PROTEIN_CLASS: 4.1.1.48 SUBSYSTEM: tryptophan biosynthesis SIDE: CARBON__45__DIOXIDE SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_249_putA ) PROTEIN_ASSOCIATION: ( putative delta-1-pyrroline-5-carboxylate dehydrogenase//1-pyrroline-5-carboxylate dehydrogenase ) PROTEIN_CLASS: 1.5.1.12 SUBSYSTEM: proline degradation I SUBSYSTEM: arginine degradation I (arginase pathway) SIDE: NAD SIDE: WATER SIDE: NADH COFACTOR: NAD COFACTOR: NADH GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_205_aroA ) PROTEIN_ASSOCIATION: ( 3-phosphoshikimate 1-carboxyvinyltransferase ) PROTEIN_CLASS: 2.5.1.19 SUBSYSTEM: chorismate biosynthesis SIDE: PHOSPHO__45__ENOL__45__PYRUVATE SIDE: __124__Pi__124__ GENERIC: false TYPE: small HOLE: false
3-phosphoshikimate 1-carboxyvinyltransferase
GENE_ASSOCIATION: ( SMGWSS_124_trpG ) PROTEIN_ASSOCIATION: ( anthranilate phosphoribosyltransferase ) PROTEIN_CLASS: 2.4.2.18 SUBSYSTEM: tryptophan biosynthesis SIDE: PRPP SIDE: PPI GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_122 ) PROTEIN_ASSOCIATION: ( putative tryptophan synthase, beta subunit (trpB)/anthranilate isomerase activity of trpC (trpF) ) PROTEIN_CLASS: 5.3.1.24 SUBSYSTEM: tryptophan biosynthesis GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_007_aroB ) PROTEIN_ASSOCIATION: ( 3-dehydroquinate synthase ) PROTEIN_CLASS: 4.2.3.4 SUBSYSTEM: chorismate biosynthesis SIDE: __124__Pi__124__ GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_216_ubiE ) PROTEIN_ASSOCIATION: ( ubiquinone/menaquinone biosynthesis methyltransferase ) PROTEIN_CLASS: 2.1.1.- SUBSYSTEM: menaquinone biosynthesis SIDE: S__45__ADENOSYLMETHIONINE SIDE: ADENOSYL__45__HOMO__45__CYS COFACTOR: S__45__ADENOSYLMETHIONINE COFACTOR: ADENOSYL__45__HOMO__45__CYS GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_111_argD ) PROTEIN_ASSOCIATION: ( acetylornithine aminotransferase ) PROTEIN_CLASS: 2.6.1.11 SUBSYSTEM: ornithine biosynthesis SUBSYSTEM: arginine biosynthesis I SUBSYSTEM: arginine biosynthesis III SUBSYSTEM: arginine biosynthesis II (acetyl cycle) SIDE: _2__45__KETOGLUTARATE COFACTOR: GLT COFACTOR: _2__45__KETOGLUTARATE GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_201_pheA ) PROTEIN_ASSOCIATION: ( putative prephenate dehydratase ) PROTEIN_CLASS: 5.4.99.5 SUBSYSTEM: phenylalanine biosynthesis I GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_132_aroC ) PROTEIN_ASSOCIATION: ( Chorismate synthase (5-enolpyruvylshikimate-3-phosphate phospholyase)//CHORISMATE-SYNTHASE-RXN//Chorismate synthase ) PROTEIN_CLASS: 4.2.3.5 SUBSYSTEM: chorismate biosynthesis SIDE: __124__Pi__124__ GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_126_trpE ) or ( SMGWSS_125_trpD ) PROTEIN_ASSOCIATION: ( anthranilate synthase component I ) or ( anthranilate synthase component II ) PROTEIN_CLASS: 4.1.3.27 SUBSYSTEM: tryptophan biosynthesis SIDE: GLN SIDE: GLT SIDE: PYRUVATE GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: NA PROTEIN_ASSOCIATION: NA PROTEIN_CLASS: NA SUBSYSTEM: arginine degradation I (arginase pathway) SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_252_argH ) PROTEIN_ASSOCIATION: ( argininosuccinate lyase ) PROTEIN_CLASS: 4.3.2.1 SUBSYSTEM: arginine biosynthesis III SUBSYSTEM: arginine biosynthesis I SUBSYSTEM: arginine biosynthesis II (acetyl cycle) SIDE: FUM GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_265_ilvD ) PROTEIN_ASSOCIATION: ( dihydroxy-acid dehydratase ) PROTEIN_CLASS: 4.2.1.9 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: valine biosynthesis SIDE: WATER GENERIC: false TYPE: small HOLE: false
This is metabolic network reconstruction of Sulcia muelleri described in the article Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata. Cottret L, Milreu PV, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot MF. PLoS Comput Biol. 2010 Sep 2;6(9). pii: e1000904. PMID: 20838465 , DOI: 10.1371/journal.pcbi.1000904 Abstract: Endosymbiotic bacteria from different species can live inside cells of the same eukaryotic organism. Metabolic exchanges occur between host and bacteria but also between different endocytobionts. Since a complete genome annotation is available for both, we built the metabolic network of two endosymbiotic bacteria, Sulcia muelleri and Baumannia cicadellinicola, that live inside specific cells of the sharpshooter Homalodisca coagulata and studied the metabolic exchanges involving transfers of carbon atoms between the three. We automatically determined the set of metabolites potentially exogenously acquired (seeds) for both metabolic networks. We show that the number of seeds needed by both bacteria in the carbon metabolism is extremely reduced. Moreover, only three seeds are common to both metabolic networks, indicating that the complementarity of the two metabolisms is not only manifested in the metabolic capabilities of each bacterium, but also by their different use of the same environment. Furthermore, our results show that the carbon metabolism of S. muelleri may be completely independent of the metabolic network of B. cicadellinicola. On the contrary, the carbon metabolism of the latter appears dependent on the metabolism of S. muelleri, at least for two essential amino acids, threonine and lysine. Next, in order to define which subsets of seeds (precursor sets) are sufficient to produce the metabolites involved in a symbiotic function, we used a graph-based method, PITUFO, that we recently developed. Our results highly refine our knowledge about the complementarity between the metabolisms of the two bacteria and their host. We thus indicate seeds that appear obligatory in the synthesis of metabolites are involved in the symbiotic function. Our results suggest both B. cicadellinicola and S. muelleri may be completely independent of the metabolites provided by the co-resident endocytobiont to produce the carbon backbone of the metabolites provided to the symbiotic system (ie., thr and lys are only exploited by B. cicadellinicola to produce its proteins). This model was downloaded as a supplement to the article. The id of the Aspartate aminotransferase reactions, ASPAMINOTRANS__45__RXN, was duplicated and had to be changed to ASPAMINOTRANS__45__RXN_a and ASPAMINOTRANS__45__RXN_b, indicating reactions associated witht the genes GO2720342 and SMGWSS_210_aspC, respectively, to make the model valid SBML. 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.
GENE_ASSOCIATION: ( SMGWSS_115_argB ) PROTEIN_ASSOCIATION: ( acetylglutamate kinase ) PROTEIN_CLASS: 2.7.2.8 SUBSYSTEM: ornithine biosynthesis SUBSYSTEM: arginine biosynthesis I SUBSYSTEM: arginine biosynthesis III SUBSYSTEM: arginine biosynthesis II (acetyl cycle) SIDE: ATP SIDE: ADP COFACTOR: ATP COFACTOR: ADP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_174_dapA ) PROTEIN_ASSOCIATION: ( Dihydrodipicolinate synthase (DHDPS)//DIHYDRODIPICSYN-RXN//Dihydrodipicolinate synthase ) PROTEIN_CLASS: 4.2.1.52 SUBSYSTEM: lysine biosynthesis I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SIDE: PYRUVATE SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_201_pheA ) PROTEIN_ASSOCIATION: ( putative prephenate dehydratase ) PROTEIN_CLASS: 4.2.1.51 SUBSYSTEM: phenylalanine biosynthesis I SIDE: CARBON__45__DIOXIDE SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_014_aroD ) PROTEIN_ASSOCIATION: ( 3-dehydroquinate dehydratase ) PROTEIN_CLASS: 4.2.1.10 SUBSYSTEM: chorismate biosynthesis SIDE: WATER GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_119_aroK ) PROTEIN_ASSOCIATION: ( shikimate kinase ) PROTEIN_CLASS: 2.7.1.71 SUBSYSTEM: chorismate biosynthesis SIDE: ATP SIDE: ADP COFACTOR: ATP COFACTOR: ADP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_261_ilvA ) PROTEIN_ASSOCIATION: ( threonine dehydratase ) PROTEIN_CLASS: 4.3.1.19 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: isoleucine biosynthesis from threonine SUBSYSTEM: isoleucine biosynthesis I SIDE: AMMONIA GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( GO2720342 ) PROTEIN_ASSOCIATION: ( GO2720342-MONOMER ) SUBSYSTEM: aspartate degradation I SUBSYSTEM: superpathway of lysine, threonine and methionine biosynthesis I SUBSYSTEM: threonine biosynthesis SUBSYSTEM: aspartate biosynthesis SUBSYSTEM: isoleucine biosynthesis I PROTEIN_CLASS: 2.6.1.1 COFACTOR: OXALACETIC_ACID COFACTOR: _2__45__KETOGLUTARATE COFACTOR: GLT COFACTOR: L__45__ASPARTATE GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_121_trpA ) PROTEIN_ASSOCIATION: ( Tryptophan synthase alpha chain//TRYPSYN-RXN//Tryptophan synthase ) PROTEIN_CLASS: NA SUBSYSTEM: tryptophan biosynthesis SIDE: GAP GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_098_ilvE ) PROTEIN_ASSOCIATION: ( branched-chain amino acid aminotransferase ) PROTEIN_CLASS: 2.6.1.42 SUBSYSTEM: superpathway of leucine, valine, and isoleucine biosynthesis SUBSYSTEM: valine biosynthesis SIDE: _2__45__KETOGLUTARATE SIDE: GLT COFACTOR: _2__45__KETOGLUTARATE COFACTOR: GLT GENERIC: false TYPE: small HOLE: false
GENE_ASSOCIATION: ( SMGWSS_249_putA ) PROTEIN_ASSOCIATION: ( putative delta-1-pyrroline-5-carboxylate dehydrogenase//1-pyrroline-5-carboxylate dehydrogenase ) PROTEIN_CLASS: 1.5.1.12 SIDE: NAD__45__P__45__OR__45__NOP SIDE: WATER SIDE: PROTON SIDE: NADH__45__P__45__OR__45__NOP COFACTOR: NAD__45__P__45__OR__45__NOP COFACTOR: NADH__45__P__45__OR__45__NOP GENERIC: true TYPE: small HOLE: false