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__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b4382 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3449 b1033 b0596 b0261 b3709 b2406 b3161 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b0494 b3447 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.697347 (mmol/gDw/h)
  Minimum Production Rate : 0.020222 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.072641
  EX_o2_e : 273.332109
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.499140
  EX_so4_e : 1.001124
  EX_pi_e : 0.733330
  EX_k_e : 0.136117
  EX_mg2_e : 0.006049
  EX_ca2_e : 0.003630
  EX_cl_e : 0.003630
  EX_cu2_e : 0.000494
  EX_mn2_e : 0.000482
  EX_zn2_e : 0.000238
  EX_ni2_e : 0.000225
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988800
  EX_h2o_e : 546.476211
  EX_co2_e : 26.009770
  EX_ac_e : 1.231504
  EX_cys__L_e : 0.825518
  Auxiliary production reaction : 0.020222
  DM_oxam_c : 0.000780
  DM_5drib_c : 0.000468
  DM_4crsol_c : 0.000156

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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