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amino_acid_pathways.tsv
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# KI data from Sander et al. Allosteric feedback inhibition enables robust amino acid biosynthesis
# in E. coli by enforcing enzyme overabundance. Cell. 2019.
# No annotated inhibition for L-ALPHA-ALANINE, L-ASPARTATE, GLT, GLN, GLY
# Other sources are noted in _notes and often come from EcoCyc
# Reverse and degradation enzymes are considered to be the same for calculation purposes but could be separated in the future with additional data
"Amino acid" "Enzymes" "Reverse enzymes" "kcat (1/units.s)" "KI, lower bound (units.mmol/units.L)" "KI, upper bound (units.mmol/units.L)" "Reverse amino acids" "KM, reverse (units.mmol/units.L)" "KM, degradation (units.mmol/units.L)" "Upstream amino acids" "KM, upstream (units.mmol/units.L)" "Downstream amino acids" "_notes"
"ARG" ["N-ACETYLTRANSFER-CPLX"] ["ARGSUCCTRAN-MONOMER"] 654 0.15 0.15 {"GLT": 2} NaN NaN {"GLT": 2} {"GLT": 2.65} {} (ArgA), (AstA), upstream KM: Takahara 2007, TODO: AdiA and SpeA can also degrade
"ASN" ["ASNSYNA-CPLX", "ASNSYNB-CPLX"] ["EG12407-MONOMER", "ANSA-CPLX"] NaN 0.12 0.12 {"L-ASPARTATE": 1} 4 NaN {"L-ASPARTATE": 1} {} {} (AsnA, AsnB), (IaaA, AnsA), reverse KM: Hejazi 2002 (for IaaA), AnsB can also degrade in the periplasm
"CYS" ["CYSSYNMULTI-CPLX", "CPLX0-237"] ["G7622-MONOMER", "TRYPTOPHAN-CPLX", "ACSERLYB-CPLX"] 772 0.001 0.001 {} NaN NaN {"SER": 1} {"SER": 1.17} {"MET": 1} (CysE), (CyuA, TnaA, CysM), upstream KM: Hindson 2003, TODO: AspC can also degrade to Glt
"HIS" ["CPLX0-7614"] ["TYRB-DIMER"] NaN 0.012 0.1 {} NaN 2.57 {"GLN": 1} {"GLN": 0.24} {} (HisG), (TyrB), upstream KM: Klem 1993 (for HisHF reaction step), degradation KM: Dolzan 2004 https://doi.org/10.1016/j.febslet.2004.06.075, TODO: add degradation reaction in metabolism, TODO: degradation not reverse enzyme
"ILE" ["THREDEHYDSYN-CPLX"] ["BRANCHED-CHAINAMINOTRANSFER-CPLX"] NaN 0.06 0.06 {"GLT": 1} 0.52 NaN {"GLT": 1} {} {} (IlvA), (IlvE), reverse KM: LeePeng 1979 (for IlvE), upstream KM: Eisenstein 1991
"LEU" ["2-ISOPROPYLMALATESYN-MONOMER"] ["BRANCHED-CHAINAMINOTRANSFER-CPLX"] NaN 0.28 0.28 {"GLT": 1} 0.58 NaN {"GLT": 1} {} {} (LeuA), (IlvE), reverse KM: LeePeng 1979 (for IlvE)
"LYS" ["DIHYDRODIPICSYN-CPLX"] ["LYSDECARBOX-CPLX", "LDC2-CPLX"] 104 0.21 3.9 {"GLT": 1} NaN NaN {"GLT": 1} {"GLT": 1.21} {} (DapA), (CadA, LdcC), ASP upstream KM: Keng 1996 (for LysC), GLT upstream KM: Cox 1996 (for ArgD)
"MET" ["HOMSUCTRAN-CPLX"] ["S-ADENMETSYN-CPLX"] 22 0.1 4 {} NaN 0.11 {"L-ASPARTATE": 1, "CYS": 1} {"L-ASPARTATE": 0.97, "CYS": 0.05} {} (MetA), (MetK), ASP upstream KM: Chassagnole 2001 (for ThrA), CYS upstream KM: Holbrook 1990 (for MetB), degradation KM: Taylor 2003 (for MetK), TODO: degradation not reverse enzyme
"PHE" ["CHORISMUTPREPHENDEHYDRAT-CPLX"] ["BRANCHED-CHAINAMINOTRANSFER-CPLX", "ASPAMINOTRANS-DIMER", "TYRB-DIMER"] 32 0.1 0.6 {"GLT": 1} 0.333 NaN {"GLT": 1} {} {} (PheA), (IlvE, AspC, TyrB), reverse KM: Mavrides 1975 (for TyrB)
"PRO" ["GLUTKIN-CPLX"] ["PUTA-CPLX", "PUTA-CPLXBND"] 53 0.02 0.15 {"GLT": 1} 2.7 NaN {"GLT": 1} {} {} (ProB), (PutA), upper limit from Perez-Arellano. 2010. https://doi.org/10.1016/j.jmb.2010.10.019, reverse KM: Abrahamson 1983 (for PutA)
"SER" ["PGLYCDEHYDROG-CPLX"] ["CPLX0-7622", "LSERINEDEAM1-MONOMER", "THREDEHYDCAT-CPLX", "LSERINEDEAM2-MONOMER"] 29 0.005 0.37 {} NaN NaN {"GLT": 1} {} {"CYS": 1, "GLY": 1, "MET": 1, "TRP": 1} (SerA), (TdcG, SdaA, TdcB, SdaB), TODO: degradation not reverse enzyme
"THR" ["ASPKINIHOMOSERDEHYDROGI-CPLX"] ["THREDEHYDCAT-CPLX", "EG12293-MONOMER", "THREODEHYD-CPLX", "LTAA-CPLX"] NaN 0.097 0.167 {} NaN 6.5 {"L-ASPARTATE": 1} {"L-ASPARTATE": 0.97} {} (ThrA), (TdcB, YiaY Tdh, LtaE), upstream KM: Chassagnole 2001, degradation KM: Anjem 2012 (for Tdh), TODO: degradation not reverse enzyme
"TRP" ["ANTHRANSYN-CPLX"] ["TRYPTOPHAN-CPLX"] NaN 0.17 0.17 {} NaN 0.12 {"GLN": 1, "SER": 1} {} {} (TrpDE), (TnaA), degradation KM: Kawata 1990 (for TnaA), TODO: degradation not reverse enzyme
"TYR" ["CHORISMUTPREPHENDEHYDROG-CPLX"] ["ASPAMINOTRANS-DIMER", "TYRB-DIMER"] 71 0.1 0.1 {"GLT": 1} 0.625 NaN {"GLT": 1} {} {} (TyrA), (AspC, TyrB), reverse KM: Mavrides 1975 (for TyrB)
"VAL" ["ACETOLACTSYNI-CPLX"] ["BRANCHED-CHAINAMINOTRANSFER-CPLX"] 38.5 0.078 0.1 {"GLT": 1} 3.13 NaN {"GLT": 1} {} {} (IlvB), (IlvE), reverse KM: LeePeng 1979 (for IlvE)
# Added from other sources
"L-ALPHA-ALANINE" ["CPLX0-7887", "CPLX0-7888", "VALINE-PYRUVATE-AMINOTRANSFER-MONOMER", "CPLX0-246", "CPLX0-248"] ["CPLX0-7887", "CPLX0-7888"] NaN NaN NaN {"GLT": 1} 4.9 NaN {"GLT": 1} {} {} (AlaC, AlaA, AvtA, SufS, IscS), (AlaC, AlaA), reverse KM: Kim 2010 (for AlaA), TODO: DadX, Alr, MetC and MalY can also degrade
"L-ASPARTATE" ["ASPAMINOTRANS-DIMER"] ["ASPAMINOTRANS-DIMER"] 670 NaN NaN {"GLT": 1} NaN NaN {"GLT": 1} {} {"ASN": 1, "MET": 1, "THR": 1} (AspC), (AspC)
"GLT" ["GLUTAMATESYN-CPLX", "GDHA-CPLX"] ["GLUTAMATESYN-CPLX", "GDHA-CPLX"] NaN NaN NaN {} NaN 2.3 {} {} {"L-ALPHA-ALANINE": 1, "ARG": 2, "ASN": 1, "L-ASPARTATE": 1, "CYS": 1, "GLN": 1, "GLY": 1, "HIS": 1, "ILE": 1, "LEU": 1, "LYS": 1, "MET": 2, "PHE": 1, "PRO": 1, "SER": 1, "THR": 1, "TRP": 2, "TYR": 1, "VAL": 1} (GltBD, GdhA), (GltBD, GdhA), degradation KM: Sharkey 2008, TODO: other degradation pathways exist
"GLN" ["GLUTAMINESYN-OLIGOMER"] ["ASNSYNB-CPLX", "CPLX0-7694", "CPLX0-7695", "GLUTAMATESYN-CPLX", "CARBPSYN-CPLX", "CTPSYN-CPLX", "GMP-SYN-CPLX", "GLUTAMIDOTRANS-CPLX"] 36 NaN NaN {"GLT": 1} 0.25 NaN {"GLT": 1} {"GLT": 3.3} {"HIS": 1, "TRP": 1} (GlnA), (AsnB, GlsA, GlsB, GltBD, CarBA, PyrG, GuaA, HisHF), reverse KM: Miller 1972 (for GltBD), upstream KM: Pearson 2005
"GLY" ["GLYOHMETRANS-CPLX"] ["GLYOHMETRANS-CPLX"] 11 NaN NaN {"SER": 1} 0.25 NaN {"SER": 1} {"SER": 0.14} {} (GlyA), (GlyA), reverse KM: Hopkins 1986, upstream KM: Florio 2009, TODO: degradation pathway exists
"L-SELENOCYSTEINE" ["CPLX0-246"] ["CPLX0-246"] NaN NaN NaN {} NaN NaN {} {} {} (SufS), (SufS), mainly just a placeholder for Selenocysteine because the model does not explicitly produce it