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 : ppa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (5 of 5: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b0351 b4069 b2926 b3844 b1004 b3713 b1109 b0046 b2463 b2210 b1033 b3551 b0335 b3945 b1602 b0153 b4219 b1832 b1778 b0590 b0728 b1380 b1710 b2480 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.584095 (mmol/gDw/h)
  Minimum Production Rate : 0.180456 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.147499
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.308181
  EX_pi_e : 0.563422
  EX_so4_e : 0.147087
  EX_k_e : 0.114011
  EX_fe2_e : 0.009381
  EX_mg2_e : 0.005067
  EX_ca2_e : 0.003040
  EX_cl_e : 0.003040
  EX_cu2_e : 0.000414
  EX_mn2_e : 0.000404
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.908544
  EX_co2_e : 35.484198
  EX_h_e : 5.547358
  Auxiliary production reaction : 0.180456
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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