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Table 3 Unannotated metabolic reactions in the T. erythraeum genome but included in the model based on homology to related organisms and/or to close gaps for biomass formation

From: The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum

Pathway Proposed function E.C. Number Gene Annotated function Closest organism
Newly/Improved Annotated
 Amino Acid Metabolism L-alanine: glyoxylate aminotransferase 2.6.1.44 Tery_3167 Serine: glyoxylate transaminase Leptolyngbya sp. NIES 3755
L-serine: pyruvate aminotransferase 2.6.1.44, 2.6.1.45, 2.6.1.51 Tery_3167 Serine: glyoxylate transaminase Leptolyngbya sp. NIES 3755
L-aspartase 4.3.1.1 Tery_1328 Fumarase Nitrosococcus oceani
L-arogenate: 2-oxoglutarate aminotransferase 2.6.1.79 Tery_0293 L-aspartate aminotransferase Pleurocapsa sp. PCC 7327
L-threonine ammonium-lyase 4.3.1.19 Tery_4742 Pyridoxal-5’-phosphate-dependent enzyme, beta subunit/cysteine synthase A Zymomonas mobilis subsp. NRRL B-12526
 Isoprenoid Synthesis Tocopherol phytyltransferase 2.5.1.117 Tery_3881 Homogentisate phytyltransferase Nostoc sp. NIES-3756
 Pigment Metabolism Chlorophyllide-a: NADP+ oxidoreductase 1.1.5.31.3.1.75 18445Tery_3563 NmrA-like Amborella trichopoda
 Secondary Carbon Metabolism Citramalate synthase 2.3.1.182 Tery_2253 2-Isopropylmalate synthase Dehalococcoides mccartyi VS
 Sulfur Metabolism O-succinylhomoserine thiol lyase 2.5.1.48 Tery_0352 8-Amino-7-oxononanoate synthase Nostoc sp. PCC 7524
 Tricarboxylic Acid Cycle Isocitrate lyase 4.1.3.1 Tery_4268 2,3-Dimethylmalate lyase/methylisocitrate lyase Candidatus Nitrososphaera gargensis
Assumed Promiscuous
 Amino Acid Metabolism 4-Hydroxyglutamate transaminase 2.6.1.23 Tery_0293 L-aspartate aminotransferase T. erythraeum
 Cofactor and Energy Carrier Metabolism Dihydroneopterin P i dephosphorylase 3.6.1.1 Tery_1519 Inorganic diphosphatase
Dihydroneopterin PPP i dephosphorylase 3.6.1.1 Tery_1519 Inorganic diphosphatase
 Lipid Metabolism/Secondary Carbon Metabolism Glycoaldehyde dehydrogenase 1.2.1.21 Tery_2599 Aldehyde dehydrogenase
 Nucleotide Metabolism 3’-5’-Nucleotide phosphodiesterase: cAMP 3.1.4.17 Many 3’-5’-Nucleotide phosphodiesterase: NMP
Missing (but Essential) Gene
 Cofactor and Energy Carrier Metabolism (R)-Pantoate:NADP+2-oxidoreductase 1.1.1.169 None None None
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BMC Systems Biology

ISSN: 1752-0509

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