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 : nac_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b0474 b2518 b3831 b0910 b3752 b4152 b0871 b2297 b2458 b2925 b2097 b1232 b1612 b1611 b4122 b1779 b2690 b4015 b0614 b3945 b4138 b4123 b0621 b0452 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.487278 (mmol/gDw/h)
  Minimum Production Rate : 0.257353 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.881571
  EX_o2_e : 282.101955
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.696313
  EX_pi_e : 0.470031
  EX_so4_e : 0.122706
  EX_k_e : 0.095113
  EX_mg2_e : 0.004227
  EX_ca2_e : 0.002536
  EX_cl_e : 0.002536
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992174
  EX_h2o_e : 548.138940
  EX_co2_e : 32.218172
  EX_succ_e : 1.329253
  EX_ac_e : 0.283686
  Auxiliary production reaction : 0.257353
  EX_ura_e : 0.088199
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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