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 : ap4a_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b2913 b0114 b0755 b3612 b0529 b1539 b2492 b0904 b2947 b2578 b1533 b3927 b3821 b2413   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.692568 (mmol/gDw/h)
  Minimum Production Rate : 0.079484 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.901330
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.274524
  EX_pi_e : 0.985993
  EX_so4_e : 0.174403
  EX_k_e : 0.135184
  EX_fe2_e : 0.011123
  EX_mg2_e : 0.006008
  EX_cl_e : 0.003605
  EX_ca2_e : 0.003605
  EX_cu2_e : 0.000491
  EX_mn2_e : 0.000479
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.416913
  EX_co2_e : 29.982017
  EX_h_e : 6.840501
  Auxiliary production reaction : 0.079484
  DM_5drib_c : 0.000465
  DM_4crsol_c : 0.000154

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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