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 : orot5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (111 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 64
  Gene deletion: b4467 b2242 b3399 b3846 b2341 b0474 b2518 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b2781 b0160 b0583 b1612 b1611 b4122 b1779 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b4161 b0675 b2361 b2291 b1415 b1014 b0822 b2799 b4138 b4123 b0621 b2913 b0112 b0452 b0511 b4265 b0114 b2366 b2492 b0904 b1533 b3028 b1380 b3918 b0789 b1249 b0508 b0515 b1511 b4266 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.330699 (mmol/gDw/h)
  Minimum Production Rate : 0.383449 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.516278
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.439069
  EX_pi_e : 0.702444
  EX_so4_e : 0.083277
  EX_k_e : 0.064550
  EX_fe2_e : 0.005311
  EX_mg2_e : 0.002869
  EX_ca2_e : 0.001721
  EX_cl_e : 0.001721
  EX_cu2_e : 0.000234
  EX_mn2_e : 0.000229
  EX_zn2_e : 0.000113
  EX_ni2_e : 0.000107

Product: (mmol/gDw/h)
  EX_h2o_e : 49.912267
  EX_co2_e : 32.020119
  EX_h_e : 10.216943
  EX_succ_e : 1.335316
  EX_ac_e : 1.256498
  EX_xan_e : 0.495233
  Auxiliary production reaction : 0.383449
  EX_ura_e : 0.059858
  EX_dxylnt_e : 0.000221
  DM_mththf_c : 0.000148
  DM_5drib_c : 0.000074
  DM_4crsol_c : 0.000074

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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