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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (117 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 63
  Gene deletion: b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b1479 b0871 b2926 b0030 b2407 b1238 b1747 b3236 b0120 b3962 b1982 b1302 b2662 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1014 b4014 b0261 b2976 b3945 b0507 b2342 b3845 b4381 b2406 b0112 b0452 b4265 b2975 b0114 b3603 b0886 b2366 b0306 b3605 b2492 b0904 b3035 b2578 b1533 b1380 b0325 b0508 b4266 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.404142 (mmol/gDw/h)
  Minimum Production Rate : 0.067810 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.225881
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.191234
  EX_pi_e : 0.593267
  EX_so4_e : 0.520992
  EX_k_e : 0.078886
  EX_fe2_e : 0.006491
  EX_mg2_e : 0.003506
  EX_ca2_e : 0.002104
  EX_cl_e : 0.002104
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.391315
  EX_co2_e : 37.659113
  EX_h_e : 3.566614
  EX_acald_e : 1.182527
  EX_met__L_e : 0.351411
  Auxiliary production reaction : 0.067810
  DM_oxam_c : 0.000452
  DM_5drib_c : 0.000271
  EX_dxylnt_e : 0.000270
  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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