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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4069 b4384 b3708 b3008 b2297 b2458 b2925 b2097 b0030 b2407 b1238 b2690 b2797 b3117 b1814 b4471 b3449 b0596 b3665 b3945 b4381 b2406 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b0494 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.728097 (mmol/gDw/h)
  Minimum Production Rate : 0.011735 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.917503
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.814889
  EX_pi_e : 0.737531
  EX_so4_e : 0.629763
  EX_k_e : 0.142119
  EX_fe2_e : 0.011694
  EX_mg2_e : 0.006316
  EX_ca2_e : 0.003790
  EX_cl_e : 0.003790
  EX_cu2_e : 0.000516
  EX_mn2_e : 0.000503
  EX_zn2_e : 0.000248
  EX_ni2_e : 0.000235
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.129871
  EX_co2_e : 25.917691
  EX_h_e : 7.595554
  EX_ac_e : 0.870301
  EX_cgly_e : 0.434678
  Auxiliary production reaction : 0.011735
  DM_mththf_c : 0.000326
  DM_5drib_c : 0.000164
  DM_4crsol_c : 0.000162

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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