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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b2744 b1479 b0871 b2779 b3617 b1851 b3236 b2883 b2463 b3962 b2210 b4267 b1415 b3551 b0261 b0411 b2913 b4219 b1832 b1778 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b0325 b1710 b2480 b0508 b4266 b0606 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359878 (mmol/gDw/h)
  Minimum Production Rate : 0.585099 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.423949
  EX_o2_e : 283.522102
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.228257
  EX_pi_e : 0.347140
  EX_so4_e : 0.090624
  EX_k_e : 0.070246
  EX_mg2_e : 0.003122
  EX_ca2_e : 0.001873
  EX_cl_e : 0.001873
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000249
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994220
  EX_h2o_e : 549.875746
  EX_co2_e : 32.600123
  EX_acald_e : 1.465848
  EX_fum_e : 0.960861
  Auxiliary production reaction : 0.585099
  EX_ade_e : 0.000242
  EX_dxylnt_e : 0.000241
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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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