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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b2066 b0474 b2518 b1241 b0351 b4384 b1479 b3752 b0871 b2926 b1850 b3617 b2407 b3236 b2463 b2498 b2210 b3665 b0114 b0529 b2492 b0904 b1380 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.541730 (mmol/gDw/h)
  Minimum Production Rate : 0.587254 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.248445
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.201475
  EX_pi_e : 1.109809
  EX_so4_e : 0.136418
  EX_k_e : 0.105742
  EX_fe2_e : 0.008701
  EX_mg2_e : 0.004700
  EX_ca2_e : 0.002820
  EX_cl_e : 0.002820
  EX_cu2_e : 0.000384
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.530077
  EX_co2_e : 29.761052
  EX_h_e : 7.328468
  EX_acald_e : 1.063925
  Auxiliary production reaction : 0.587254
  EX_ade_e : 0.000365
  DM_mththf_c : 0.000243
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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