MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b0474 b2518 b1241 b0351 b3831 b4069 b4384 b3708 b2297 b2458 b2781 b0030 b2407 b3236 b0651 b2162 b1759 b3962 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0596 b4161 b0261 b3945 b4381 b2406 b0112 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3821 b3918 b0325 b4042 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410570 (mmol/gDw/h)
  Minimum Production Rate : 0.384756 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.000019
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.046018
  EX_pi_e : 1.550307
  EX_so4_e : 0.488146
  EX_k_e : 0.080140
  EX_fe2_e : 0.006594
  EX_mg2_e : 0.003562
  EX_ca2_e : 0.002137
  EX_cl_e : 0.002137
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 48.634557
  EX_co2_e : 27.801135
  EX_h_e : 7.945942
  EX_ac_e : 2.099855
  EX_thym_e : 0.459071
  Auxiliary production reaction : 0.384756
  DM_oxam_c : 0.000459
  DM_5drib_c : 0.000275
  EX_glyclt_e : 0.000275
  DM_4crsol_c : 0.000092

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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