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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 59
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2502 b2744 b3708 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1779 b0207 b3012 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b2799 b1602 b3709 b3161 b0112 b3915 b2975 b3603 b0509 b3125 b2366 b2492 b0904 b1781 b3001 b1533 b3821 b1380 b0325 b0508 b1473 b1600 b2660 b1771 b4141 b1798 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.336798 (mmol/gDw/h)
  Minimum Production Rate : 0.280679 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.848862
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.604011
  EX_pi_e : 1.166909
  EX_so4_e : 0.365490
  EX_k_e : 0.065741
  EX_fe3_e : 0.005411
  EX_mg2_e : 0.002922
  EX_ca2_e : 0.001753
  EX_cl_e : 0.001753
  EX_cu2_e : 0.000239
  EX_mn2_e : 0.000233
  EX_zn2_e : 0.000115
  EX_ni2_e : 0.000109

Product: (mmol/gDw/h)
  EX_h2o_e : 51.041328
  EX_co2_e : 34.848760
  EX_h_e : 5.396103
  EX_ac_e : 1.171468
  Auxiliary production reaction : 0.280677
  EX_ade_e : 0.000377
  DM_5drib_c : 0.000226
  DM_4crsol_c : 0.000075

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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