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Table 3 The coefficients (mmol/g CDW) used in the biomass equation of the T. reesei model

From: Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Kegg Id Compound name Coefficient
C00133 Alanine −0.382a
C00062 Arginine −0.253a
C00152 Asparagine −0.141a
C00049 Aspartate −0.233a
C00097 Cysteine −0.053a
C00064 Glutamine −0.161a
C00025 Glutamate −0.248a
C00037 Glycine −0.289a
C00135 Histidine −0.098a
C00407 Isoleucine −0.193a
C00123 Leucine −0.362a
C00047 Lysine −0.202a
C00073 Methionine −0.092a
C00079 Phenylalanine −0.151a
C00148 Proline −0.243a
C00065 Serine −0.322a
C00188 Threonine −0.233a
C00078 Tryptophan −0.061a
C00082 Tyrosine −0.113a
C00183 Valine −0.254a
C06424 Myristic acid −0.00015b
C08362 Palmitoleic acid −0.00043b
C06427 \(\alpha\)−Linolenic acid −0.01b
C00219 Arachidic acid −0.00013b
C08320 Lignoceric acid −0.00014b
C00249 Palmitic acid −0.026c
C01530 Stearic acid −0.003c
C00712 Oleic acid −0.008c
C01595 Linoleic acid −0.061c
C01694 Ergosterol −0.007d
C00093 Glycerol−3−P −0.04e
C00588 Phosphocholine −0.014e
C00346 Phosphoethanolamine −0.007e
C00031 d−Glucose −0.385f
C00140 N-acetyl-d-glucosamine −0.948f
C00360 Deoxyadenosine monophosphate −0.007g
C00239 Deoxycytidine monophosphate −0.008g
C00362 Deoxyguanosine monophosphate −0.008g
C00364 Deoxythymidine monophosphate −0.007g
C00020 Adenosine-monophosphate −0.047h
C00055 Cytidine monophosphate −0.045h
C00144 Guanosine monophosphate −0.053h
C00105 Uridine monophosphate −0.045h
C00001 Water −59.276i
C00002 Adenosine triphosphate −59.276i
C00008 Adenosine diphosphate 59.276i
C00009 Organic phosphorous 59.305i
C00059 Sulfate −0.02i
C00255 Riboflavin −0.001i
C00010 Coenzyme A −0.000001j
C00003 Nicotinamide adenine dinucleotide (NAD) −0.000001j
C00016 Flavin adenine dinucleotide (FAD) −0.000001j
C00051 Glutathione −0.000001j
C00101 tetrahydrofolate −0.000001j
C00575 3′,5′-cyclic AMP −0.000001j
C00096 GDP-mannose −0.000001j
C01083 \(\alpha\),\(\alpha\)-Trehalose −0.000001j
  1. The coefficients correspond to the measured or estimated molar amounts of the compound in the cells, as described in "Methods" section
  2. aThe amount of amino acids calculated based on the measured cellular protein and the ratio of amino acids in cellular proteins calculated based on the codon abundancy in the RNAseq data of transcriptome
  3. b Esterified fatty acid measured using GC-MS
  4. c Sum of measured esterified and free fatty acid measured using GC-MS
  5. d Measured using GC-MS
  6. e The amount estimated to be needed for synthesis of triacylglycerols, phophatidylethanolamines or phosphatidylcholines (1 mol of glycerol-3-P, phosphoethanolamine or phosphocholine per 1 mol of triacylglycerol, phosphatidylethanolamine or phosphatidylcholine, respectively)
  7. f The measured total carbohydrate was assumed to consist of polymers of d-glucose subunits (glucan) and polymers of N-acetyl-d-glucosamine (chitin). Chitin content of the cells was estimated based on the amount of chitin in Aspergillus oryzae [8], and the rest of the measured carbohydrate as glucan
  8. g The amount of deoxyribonucleotides in DNA calculated based on the cellular DNA amount and the GC content of the genome
  9. h The amount of ribonucleotides in RNA was estimated based on the measured total RNA amount the nucleotide ratio in genome region encoding ribosomal 18S-28S pre-rRNA
  10. i As in S. cerevisiae model iMM904 [42]
  11. j Trace amount of the compound was added