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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2836 b3846 b2341 b3831 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2407 b2688 b2797 b3117 b1814 b4471 b3665 b4381 b2406 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.721367 (mmol/gDw/h)
  Minimum Production Rate : 0.459726 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.641606
  EX_o2_e : 275.019114
  EX_nh4_e : 10.089333
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.155561
  EX_so4_e : 0.181655
  EX_k_e : 0.140806
  EX_mg2_e : 0.006258
  EX_ca2_e : 0.003755
  EX_cl_e : 0.003755
  EX_cu2_e : 0.000511
  EX_mn2_e : 0.000498
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988414
  EX_h2o_e : 549.512610
  EX_co2_e : 25.412107
  Auxiliary production reaction : 0.459726
  EX_ac_e : 0.419970
  DM_mththf_c : 0.000323
  DM_5drib_c : 0.000162
  DM_4crsol_c : 0.000161

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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