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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2407 b1238 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b0261 b4381 b2406 b0112 b0452 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.520286 (mmol/gDw/h)
  Minimum Production Rate : 0.519325 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.897243
  EX_o2_e : 270.595456
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.254316
  EX_pi_e : 1.540520
  EX_so4_e : 0.650343
  EX_k_e : 0.101556
  EX_mg2_e : 0.004513
  EX_ca2_e : 0.002708
  EX_cl_e : 0.002708
  EX_cu2_e : 0.000369
  EX_mn2_e : 0.000360
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991644
  EX_h2o_e : 545.310149
  EX_co2_e : 22.227171
  EX_ac_e : 2.755832
  Auxiliary production reaction : 0.519325
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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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