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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (87 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b2836 b3553 b4382 b3942 b1732 b4069 b3708 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b2463 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b1033 b3551 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b2406 b3915 b1727 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b1380 b1710 b2480 b1518 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.339826 (mmol/gDw/h)
  Minimum Production Rate : 0.477465 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.569032
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.193155
  EX_pi_e : 0.805263
  EX_so4_e : 0.085575
  EX_k_e : 0.066332
  EX_fe3_e : 0.005458
  EX_mg2_e : 0.002948
  EX_ca2_e : 0.001769
  EX_cl_e : 0.001769
  EX_cu2_e : 0.000241
  EX_mn2_e : 0.000235
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 43.090851
  EX_co2_e : 28.603461
  EX_h_e : 8.763243
  EX_pyr_e : 3.691741
  Auxiliary production reaction : 0.477465
  EX_mal__L_e : 0.372609
  EX_ac_e : 0.197842
  EX_etoh_e : 0.071686
  EX_ade_e : 0.009121
  EX_mththf_e : 0.000152
  DM_5drib_c : 0.000076
  DM_4crsol_c : 0.000076

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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