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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1241 b0351 b4069 b4384 b3752 b2297 b2458 b3617 b2407 b3236 b3962 b3946 b2210 b0825 b4267 b3665 b0261 b2799 b2913 b4381 b0114 b0509 b3125 b0755 b3612 b0529 b1539 b2492 b0904 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406589 (mmol/gDw/h)
  Minimum Production Rate : 0.519599 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.783487
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.990491
  EX_pi_e : 1.950995
  EX_so4_e : 0.102387
  EX_k_e : 0.079363
  EX_fe2_e : 0.006530
  EX_mg2_e : 0.003527
  EX_cl_e : 0.002116
  EX_ca2_e : 0.002116
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.625290
  EX_co2_e : 34.611274
  EX_h_e : 7.047445
  EX_ac_e : 1.751377
  Auxiliary production reaction : 0.519599
  EX_ade_e : 0.000274
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000091

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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