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Revision 1.1 - (download) (as text) (annotate)
Fri Apr 9 14:48:10 2004 UTC (15 years, 6 months ago) by efrank
Branch: MAIN
CVS Tags: post-st-migration2, mass-spec-01, sc2004-3, mass-spec-02, post-st-migration, forRick-14Jul04-1, forRick-14Jul04-0, sc2004-4, sc04-finalDay, sc2004-2, sc2004-1, sc2004-0, HEAD
Modified files:
	adjustments in data sizes and little details
	destroyBss can probably be simplified.

Added files:
	ReloadBssData loads data into an empty database.  It calls
	the other guys to do the work:  Aiba*, glyc*, loadbuchnera*, testCas*

	buildNewBssCatalog.py:  copies data from old style catalog to new.


1. destroyBss                   deletes EVERYTHING
2. sqlplus
        @Rebuild                rebuilds schema.  reloads some reactions etc.
3. ReloadBssData                puts some data back in...OLD style catalog
4. buildNewBssCatalog.py        copies data from old style catalog to new.


import loadBss

b = loadBss.bss()

b.addMetabolite( '2OGLRT',	'2-oxoglutarate')
b.addMetabolite( '2PG',	'2-phospho-D-glycerate')
b.addMetabolite( '3PG',	'3-phospho-D-glycerate')
b.addMetabolite( '3PGLP',	'3-phospho-D-glyceroyl phosphate')
b.addMetabolite( 'ACCOA',	'acetyl-CoA')
b.addMetabolite( 'ACGLP',	'N-acetyl-5-glutamyl phosphate')
b.addMetabolite( 'ACGLU',	'N-acetyl-L-glutamate')
b.addMetabolite( 'ACGLUS',	'N-acetyl-L-glutamate 5-semialdehyde')
b.addMetabolite( 'ACORN',	'Nprime2-acetyl-L-ornithine')
b.addMetabolite( 'ACTT',	'acetate')
b.addMetabolite( 'ADGL',	'alpha-D-glucose')
b.addMetabolite( 'AGL1P',	'alpha-D-glucose 1-phosphate')
b.addMetabolite( 'AGL6P',	'alpha-D-glucose 6-phosphate')
b.addMetabolite( 'APAGN',	'(_-Asp-Arg),n')
b.addMetabolite( 'APAGN1',	'(_-Asp-Arg),(n-1)')
b.addMetabolite( 'ARG',	'L-arginine')
b.addMetabolite( 'ARGSCT',	'Nprime_(L-arginino)succinate')
b.addMetabolite( 'ASP',	'L-aspartate')
b.addMetabolite( 'BDGL',	'beta-D-glucose')
b.addMetabolite( 'BFR6P',	'beta-D-fructose 6-phosphate')
b.addMetabolite( 'BFRBP',	'beta-D-fructose 1,6-bisphosphate')
b.addMetabolite( 'BGL6P',	'beta-D-glucose 6-phosphate')
b.addMetabolite( 'CACTT',	'cis-aconitate')
b.addMetabolite( 'COA',	'CoA')
b.addMetabolite( 'CRBLP',	'carbamoyl phosphate')
b.addMetabolite( 'CTRL',	'L-citrulline')
b.addMetabolite( 'CTRT',	'citrate')
b.addMetabolite( 'DHAP',	'glycerone phosphate')
b.addMetabolite( 'FMRT',	'fumarate')
b.addMetabolite( 'GACACH',	'(glycogen amylose chain),n-(1,6-amylose chain),4')
b.addMetabolite( 'GACADG',	'glycogen amylose chain-1,6-alpha-D-glucose')
b.addMetabolite( 'GAP',	'D-glyceraldehyde 3-phosphate')
b.addMetabolite( 'GLACN3',	'(glycogen amylose chain),(n+3)')
b.addMetabolite( 'GLAMCH',	'glycogen amylose chain')
b.addMetabolite( 'GLAPCH',	'glycogen amylopectin chain')
b.addMetabolite( 'GLN',	'L-glutamine')
b.addMetabolite( 'GLU',	'L-glutamate')
b.addMetabolite( 'ICTRT',	'isocitrate')
b.addMetabolite( 'MAGPAP',	'multi-L-arginyl-poly-L-aspartate')
b.addMetabolite( 'MLT',	'L-malate')
b.addMetabolite( 'OFRD',	'oxidized ferredoxin')
b.addMetabolite( 'ORNT',	'L-ornithine')
b.addMetabolite( 'OXAC',	'oxaloacetate')
b.addMetabolite( 'OXFER',	'oxidized ferredoxin')
b.addMetabolite( 'OXFL',	'oxidized flavodoxin')
b.addMetabolite( 'PEP',	'phosphoenolpyruvate')
b.addMetabolite( 'PI',	'orthophosphate')
b.addMetabolite( 'PPI',	'pyrophosphate')
b.addMetabolite( 'PYR',	'pyruvate')
b.addMetabolite( 'RFER',	'reduced ferredoxin')
b.addMetabolite( 'RFL',	'reduced flavodoxin')
b.addMetabolite( 'RFRD',	'reduced ferredoxin')
b.addMetabolite( 'SCNT',	'succinate')
b.addMetabolite( 'SCNTS',	'succinate semialdehyde')
b.addMetabolite( 'UR',	'urea')

###############################################################################

b.addEnzymeRole( 'EC5.1.3.3_k', 'EC 5.1.3.3', 'Aldose 1-epimerase' )
b.addEnzymeRole( 'EC5.4.2.2_k', 'EC 5.4.2.2', 'Phosphoglucomutase' )
b.addEnzymeRole( 'EC2.7.1.2_k', 'EC 2.7.1.2', 'Glucokinase' )
b.addEnzymeRole( 'EC5.3.1.9_k', 'EC 5.3.1.9', 'Glucose 6-phosphate Isomerase' )
b.addEnzymeRole( 'EC2.7.9.2_k', 'EC 2.7.9.2', 'Pyruvate, Water Dikinase' )
b.addEnzymeRole( 'EC4.1.1.31_k', 'EC 4.1.1.31', 'Phosphoenolpyruvate Carboxylase' )
b.addEnzymeRole( 'EC3.5.3.1_k', 'EC 3.5.3.1', 'Arginase' )
b.addEnzymeRole( 'EC3.5.1.5_k', 'EC 3.5.1.5', 'Urease' )
b.addEnzymeRole( 'EC1.4.1.2_k', 'EC 1.4.1.2', 'Glutamate Dehydrogenase' )
b.addEnzymeRole( 'EC1.4.1.4_k', 'EC 1.4.1.4', 'Glutamate Dehydrogenase (NADP+)' )
b.addEnzymeRole( 'EC1.4.1.14_k', 'EC 1.4.1.14', 'Glutamate Synthase (NADH)' )
b.addEnzymeRole( 'EC1.4.7.1_k', 'EC 1.4.7.1', 'Glutamate Synthase (ferredoxin)' )
b.addEnzymeRole( 'EC6.3.1.2_k', 'EC 6.3.1.2', 'Glutamate--Ammonia Ligase' )
b.addEnzymeRole( 'EC3.5.1.2_k', 'EC 3.5.1.2', 'Glutaminase' )



###############################################################################
b.addReco( "EE Glycogen Degradation--Cyanophycin Biosynthesis", "top of EE Glyc-Cyanophycin" )
###############################################################################


b.addREChild( "Glycogen Degradation", "top of EE Glyc-Cyanophycin" )

b.addRx( "Glycogen Degradation", "GLAPCH +  PI ->   GACACH +  AGL1P"  )
b.addRx( "Glycogen Degradation", "GACACH -> GLACN3 + GACADG" )
b.addRx( "Glycogen Degradation", "GACADG +  H2O ->  ADGL + GLAMCH" )
b.addRx( "Glycogen Degradation", "EC5.1.3.3_k: ADGL -> BDGL" )
b.addRx( "Glycogen Degradation", "EC5.4.2.2_k: AGL1P ->  AGL6P" )
b.addRx( "Glycogen Degradation", "EC2.7.1.2_k:  ADGL + ATP  ->    AGL6P +  ADP" )
b.addRx( "Glycogen Degradation", "EC5.3.1.9_k:     AGL6P ->  BGL6P" )


b.addREChild( "Glycolysis", "top of EE Glyc-Cyanophycin" )

b.addRx( "Glycolysis", "BDGL +  ATP  -> ADP  +  BGL6P" )
b.addRx( "Glycolysis", "BGL6P -> BFR6P" )
b.addRx( "Glycolysis", "BFR6P + ATP  -> ADP + BFRBP" )
b.addRx( "Glycolysis", "BFRBP -> DHAP + GAP" )
b.addRx( "Glycolysis", "DHAP -> GAP" )
b.addRx( "Glycolysis", "GAP + PI + NAD -> H + NADH + 3PGLP" )
b.addRx( "Glycolysis", "ADP + 3PGLP -> ATP + 3PG" )
b.addRx( "Glycolysis", "3PG -> 2PG" )
b.addRx( "Glycolysis", "2PG -> H2O + PEP" )
b.addRx( "Glycolysis", "ADP + PEP -> ATP + PYR" )
b.addRx( "Glycolysis", "EC2.7.9.2_k: PYR + ATP + H2O -> ADP + PI + PEP" )
b.addRx( "Glycolysis", "EC4.1.1.31_k: PEP + H2O + CO2 -> PI + OXAC" )


b.addREChild( "Pyruvate--Acetyl-CoA Interconversion",  "top of EE Glyc-Cyanophycin" )

b.addRx( "Pyruvate--Acetyl-CoA Interconversion", "PYR + NADH + H + COA -> NAD + CO2 + ACCOA" )
b.addRx( "Pyruvate--Acetyl-CoA Interconversion", "PYR + COA + OXFER -> CO2 + RFER + ACCOA" )
b.addRx( "Pyruvate--Acetyl-CoA Interconversion", "PYR + COA + OXFL -> CO2 + RFL + ACCOA" )


b.addREChild( "TCA Cycle (via EC 4.1.1.71)", "top of EE Glyc-Cyanophycin" )

b.addRx( "TCA Cycle (via EC 4.1.1.71)", "OXAC + ACCOA + H2O -> COA + CTRT" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "CTRT -> H2O + CACTT" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "H2O + CACTT -> ICTRT" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "ICTRT + NADP -> NADPH + H + CO2 + 2OGLRT" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "2OGLRT -> CO2 + SCNTS" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "H2O + NADP + SCNTS -> NADPH + H + SNCT" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "SCNT + PQ -> PQH2 + FMRT" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "H20 + FMRT -> MLT" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "MLT + NAD -> OXAC + H + NADH" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "MLT + NAD -> NADH + H + CO2 + PYR" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "ACTT + ATP + COA -> AMP + PPI + ACCOA" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "GLN + 2 ATP + CO2 + H2O -> 2 ADP + PI + GLU + CRBLP" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "GLU + OXAC -> 2OGLRT + ASP" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "EC3.5.3.1_k: ORNT + UR -> H2O + ARG" )
b.addRx( "TCA Cycle (via EC 4.1.1.71)", "EC3.5.1.5_k: UR + H2O -> NH3 + CO2" )

##
# the following enzymes were not defined in the spreadsheet and have been dropped
##
#b.addRx( "TCA Cycle (via EC 4.1.1.71)", "EC1.1.1.38_k: MLT + NAD -> NADH + H + CO2 + PYR" )
#b.addRx( "TCA Cycle (via EC 4.1.1.71)", "EC4.1.1.71_k: ACTT + ATP + COA -> AMP + PPI + ACCOA" )
#b.addRx( "TCA Cycle (via EC 4.1.1.71)", "EC6.3.5.5_k: GLN + 2 ATP + CO2 + H2O -> 2 ADP + PI + GLU + CRBLP" )
#b.addRx( "TCA Cycle (via EC 4.1.1.71)", "EC2.6.1.1_k: GLU + OXAC -> 2OGLRT + ASP" )



b.addREChild( "Ornithine Biosynthesis", "top of EE Glyc-Cyanophycin" )

b.addRx( "Ornithine Biosynthesis", "GLU + ACCOA -> COA + ACGLU" )
b.addRx( "Ornithine Biosynthesis", "ACGLU + ATP -> ADP + ACGLP" )
b.addRx( "Ornithine Biosynthesis", "ACGLP + NADPH + H -> NADP + PI + ACGLUS" )
b.addRx( "Ornithine Biosynthesis", "GLU + ACGLUS -> 2OGLRT + ACORN" )
b.addRx( "Ornithine Biosynthesis", "GLU + ACORN -> ACGLU + ORNT" )
b.addRx( "Ornithine Biosynthesis", "ACORN + H2O -> ACTT + ORNY" )


b.addREChild( "Arginine Biosynthesis", "top of EE Glyc-Cyanophycin" )

b.addRx( "Arginine Biosynthesis", "ORNT + CRBLP -> PI + CTRL" )
b.addRx( "Arginine Biosynthesis", "CTRL + ASP + ATP -> AMP + PPI + ARGSCT" )
b.addRx( "Arginine Biosynthesis", "ARGSCT -> FMRT + ARG" )
b.addRx( "Arginine Biosynthesis", "EC1.4.1.2_k: 2OGLRT + NH3 + NADH + H -> NAD + H2O + GLU" )
b.addRx( "Arginine Biosynthesis", "EC1.4.1.4_k: 2OGLRT + NH3 + NADPH + H -> NADP + H2O + GLU" )
b.addRx( "Arginine Biosynthesis", "EC1.4.1.14_k: 2OGLRT + GLN + NADH + H -> NADP + H2O + GLU" )
b.addRx( "Arginine Biosynthesis", "EC1.4.7.1_k: 2OGLRT + GLN + RFRD -> OFRD + 2 GLU" )
b.addRx( "Arginine Biosynthesis", "EC6.3.1.2_k: GLU + ATP + NH3 -> ADP + PI + GLN" )
b.addRx( "Arginine Biosynthesis", "EC3.5.1.2_k: GLN + H2O -> NH3 + GLU" )


b.addREChild( "Cyanophycin Biosynthesis", "top of EE Glyc-Cyanophycin" )

b.addRx("Cyanophycin Biosynthesis", "APAGN1 + ASP + ARG + ATP -> ADP + PI + APAGN" )
b.addRx("Cyanophycin Biosynthesis", "ASP + ARG + ATP + APAGN -> ADP + PI + MAGPAP" )

b.writeAndClear()

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