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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b3831 b2744 b3752 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b2361 b2291 b0411 b1701 b1805 b4138 b4123 b0621 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.682305 (mmol/gDw/h)
  Minimum Production Rate : 0.360356 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.968676
  EX_o2_e : 270.709758
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.336550
  EX_pi_e : 0.658156
  EX_so4_e : 0.171818
  EX_k_e : 0.133181
  EX_mg2_e : 0.005919
  EX_ca2_e : 0.003551
  EX_cl_e : 0.003551
  EX_cu2_e : 0.000484
  EX_mn2_e : 0.000471
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000220
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989041
  EX_h2o_e : 544.031894
  EX_co2_e : 22.888797
  EX_succ_e : 0.711502
  EX_ura_e : 0.483855
  Auxiliary production reaction : 0.360356
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000152

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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