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 : ap4a_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4069 b4384 b2744 b3708 b2297 b2458 b2779 b0030 b1238 b2883 b1982 b2797 b3117 b1814 b4471 b1623 b0261 b0411 b4381 b0452 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b2835 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.474240 (mmol/gDw/h)
  Minimum Production Rate : 0.100424 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.755169
  EX_o2_e : 287.460679
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.126531
  EX_pi_e : 0.859153
  EX_so4_e : 0.119423
  EX_k_e : 0.092568
  EX_mg2_e : 0.004114
  EX_ca2_e : 0.002468
  EX_cl_e : 0.002468
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992383
  EX_h2o_e : 553.203900
  EX_co2_e : 37.971810
  EX_ac_e : 0.276096
  Auxiliary production reaction : 0.100424
  DM_oxam_c : 0.000531
  DM_5drib_c : 0.000318
  DM_4crsol_c : 0.000106

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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