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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b0238 b0125 b2744 b1278 b3614 b0910 b4152 b0871 b2781 b1850 b1612 b1611 b4122 b1779 b1759 b0477 b2440 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b0452 b0114 b2492 b0904 b1380 b3918 b0418 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.582151 (mmol/gDw/h)
  Minimum Production Rate : 0.307413 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.294414
  EX_o2_e : 277.861139
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.420303
  EX_pi_e : 0.868960
  EX_so4_e : 0.146597
  EX_k_e : 0.113632
  EX_mg2_e : 0.005050
  EX_cl_e : 0.003030
  EX_ca2_e : 0.003030
  EX_cu2_e : 0.000413
  EX_mn2_e : 0.000402
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990650
  EX_h2o_e : 547.605944
  EX_co2_e : 28.029338
  EX_succ_e : 0.607062
  Auxiliary production reaction : 0.307413
  EX_ura_e : 0.105418
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130
  EX_etha_e : 0.000047

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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