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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4069 b2744 b3708 b3008 b3115 b1849 b2296 b0160 b1982 b2688 b2797 b3117 b1814 b4471 b0595 b4374 b0675 b2361 b2291 b0261 b0507 b2943 b0452 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b0516 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.692732 (mmol/gDw/h)
  Minimum Production Rate : 0.439646 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.879934
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.243127
  EX_pi_e : 1.107859
  EX_so4_e : 0.174444
  EX_k_e : 0.135216
  EX_fe3_e : 0.011126
  EX_mg2_e : 0.006009
  EX_ca2_e : 0.003606
  EX_cl_e : 0.003606
  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 : 48.169005
  EX_co2_e : 25.039909
  EX_h_e : 9.420497
  Auxiliary production reaction : 0.439646
  EX_ac_e : 0.403299
  EX_alltn_e : 0.000775
  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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