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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b3399 b3846 b2341 b4069 b2744 b3708 b3926 b3115 b1849 b2296 b0160 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b3945 b1602 b2913 b3915 b0114 b2366 b2492 b0904 b1533 b3927 b3821 b1380 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465265 (mmol/gDw/h)
  Minimum Production Rate : 0.197085 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.551372
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.012324
  EX_pi_e : 0.842966
  EX_so4_e : 0.314248
  EX_k_e : 0.090816
  EX_fe3_e : 0.007474
  EX_mg2_e : 0.004036
  EX_ca2_e : 0.002422
  EX_cl_e : 0.002422
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.908050
  EX_co2_e : 37.242872
  EX_h_e : 5.146720
  EX_glyc_e : 0.381307
  EX_ac_e : 0.270872
  Auxiliary production reaction : 0.197085
  EX_hxan_e : 0.000521
  DM_5drib_c : 0.000312
  DM_4crsol_c : 0.000104

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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