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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (1 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0871 b2407 b0583 b2797 b3117 b1814 b4471 b2440 b3665 b3709 b2406 b3161 b0112 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b0494 b4141 b1798 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.751278 (mmol/gDw/h)
  Minimum Production Rate : 0.104039 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.125274
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.842013
  EX_pi_e : 1.036804
  EX_so4_e : 0.293226
  EX_k_e : 0.146644
  EX_fe2_e : 0.012066
  EX_mg2_e : 0.006517
  EX_ca2_e : 0.003910
  EX_cl_e : 0.003910
  EX_cu2_e : 0.000533
  EX_mn2_e : 0.000519
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000243
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.480783
  EX_co2_e : 25.832556
  EX_h_e : 7.215161
  Auxiliary production reaction : 0.104039
  DM_mththf_c : 0.000337
  DM_5drib_c : 0.000169
  DM_4crsol_c : 0.000168

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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