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 : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (116 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 62
  Gene deletion: b4467 b2242 b3399 b0474 b2518 b1241 b0351 b4069 b2744 b1278 b3708 b3115 b1849 b2296 b2926 b2781 b0160 b1612 b1611 b4122 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b4161 b0675 b2361 b2291 b1415 b1014 b0261 b0822 b4138 b4123 b0621 b2913 b0112 b3915 b0452 b0511 b0114 b0529 b1539 b2492 b0904 b3028 b1380 b3918 b0325 b0508 b0516 b4266 b2842 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.316497 (mmol/gDw/h)
  Minimum Production Rate : 0.231402 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.094568
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.423772
  EX_pi_e : 0.305295
  EX_so4_e : 0.079701
  EX_k_e : 0.061778
  EX_fe3_e : 0.005085
  EX_mg2_e : 0.002746
  EX_ca2_e : 0.001647
  EX_cl_e : 0.001647
  EX_cu2_e : 0.000224
  EX_mn2_e : 0.000219
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_h2o_e : 50.014072
  EX_co2_e : 32.976381
  EX_h_e : 10.608281
  EX_ac_e : 1.601522
  EX_succ_e : 1.543865
  EX_xan_e : 0.606912
  Auxiliary production reaction : 0.231392
  EX_ura_e : 0.057599
  EX_dxylnt_e : 0.000212
  DM_5drib_c : 0.000071
  DM_4crsol_c : 0.000071

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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