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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b4382 b4069 b4384 b3708 b3008 b2297 b2458 b2925 b2097 b2926 b0030 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b3945 b3709 b2406 b3161 b0112 b0114 b0886 b0509 b3125 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3821 b0594 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.585863 (mmol/gDw/h)
  Minimum Production Rate : 0.247082 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.692677
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.065119
  EX_pi_e : 1.309637
  EX_so4_e : 0.147532
  EX_k_e : 0.114356
  EX_fe2_e : 0.009410
  EX_mg2_e : 0.005082
  EX_ca2_e : 0.003049
  EX_cl_e : 0.003049
  EX_cu2_e : 0.000415
  EX_mn2_e : 0.000405
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.757385
  EX_co2_e : 27.321644
  EX_h_e : 8.333893
  EX_ac_e : 1.708586
  Auxiliary production reaction : 0.248170
  DM_oxam_c : 0.000656
  DM_5drib_c : 0.000393
  DM_4crsol_c : 0.000131

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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