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 (106 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b0474 b2518 b3831 b3752 b2930 b4232 b3697 b3925 b4152 b0871 b3115 b1849 b2296 b2779 b2926 b1612 b1611 b4122 b1525 b3946 b0825 b4161 b2661 b4014 b2976 b0726 b4138 b4123 b0621 b0114 b0509 b3125 b0508 b1206 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.614183 (mmol/gDw/h)
  Minimum Production Rate : 0.324378 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.428529
  EX_o2_e : 276.643060
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.504219
  EX_pi_e : 0.592445
  EX_so4_e : 0.154664
  EX_k_e : 0.119884
  EX_mg2_e : 0.005328
  EX_ca2_e : 0.003197
  EX_cl_e : 0.003197
  EX_cu2_e : 0.000435
  EX_mn2_e : 0.000424
  EX_zn2_e : 0.000209
  EX_ni2_e : 0.000198
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990136
  EX_h2o_e : 546.514673
  EX_co2_e : 26.602703
  EX_for_e : 0.852796
  EX_succ_e : 0.640465
  EX_pyr_e : 0.555447
  EX_ac_e : 0.357569
  Auxiliary production reaction : 0.324378
  EX_ura_e : 0.111169
  EX_glyclt_e : 0.000411
  DM_5drib_c : 0.000138
  DM_4crsol_c : 0.000137

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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