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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 62
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3708 b3008 b0871 b0030 b2407 b1238 b1004 b3713 b1109 b0046 b3236 b0120 b0207 b3012 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b2799 b1602 b0507 b3709 b2913 b4381 b2406 b3161 b0112 b3915 b0452 b0886 b0755 b3612 b1539 b2492 b0904 b1781 b3001 b2578 b1533 b1380 b0325 b1473 b1771 b4141 b1798 b3662 b0606 b2285 b1008 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403917 (mmol/gDw/h)
  Minimum Production Rate : 0.219036 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.622801
  EX_o2_e : 285.365465
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.897767
  EX_pi_e : 1.046725
  EX_so4_e : 0.320750
  EX_k_e : 0.078842
  EX_mg2_e : 0.003504
  EX_ca2_e : 0.002102
  EX_cl_e : 0.002102
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993511
  EX_h2o_e : 552.013374
  EX_co2_e : 36.746050
  EX_acald_e : 0.598001
  Auxiliary production reaction : 0.219035
  EX_ade_e : 0.000452
  DM_5drib_c : 0.000271
  DM_4crsol_c : 0.000090

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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