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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (98 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b2925 b2097 b3124 b2690 b1982 b2797 b3117 b1814 b4471 b0596 b4374 b0675 b2361 b2291 b0261 b3945 b3709 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b2413 b1473 b0494 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.701714 (mmol/gDw/h)
  Minimum Production Rate : 0.807190 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.040104
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.235887
  EX_pi_e : 1.484067
  EX_so4_e : 0.218977
  EX_k_e : 0.136970
  EX_fe2_e : 0.011270
  EX_mg2_e : 0.006087
  EX_ca2_e : 0.003652
  EX_cl_e : 0.003652
  EX_cu2_e : 0.000498
  EX_mn2_e : 0.000485
  EX_zn2_e : 0.000239
  EX_ni2_e : 0.000227
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.698214
  EX_co2_e : 25.238638
  EX_h_e : 8.472105
  Auxiliary production reaction : 0.807190
  EX_ac_e : 0.450799
  EX_met__L_e : 0.042271
  DM_oxam_c : 0.000785
  DM_5drib_c : 0.000471
  DM_4crsol_c : 0.000156

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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