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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b1238 b1982 b2797 b3117 b1814 b4471 b1033 b0595 b0675 b2361 b0261 b0507 b3709 b4381 b2406 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b1473 b0494 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.698733 (mmol/gDw/h)
  Minimum Production Rate : 0.221986 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.241805
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.100936
  EX_pi_e : 1.339959
  EX_so4_e : 0.397941
  EX_k_e : 0.136388
  EX_fe2_e : 0.011222
  EX_mg2_e : 0.006062
  EX_cl_e : 0.003637
  EX_ca2_e : 0.003637
  EX_cu2_e : 0.000495
  EX_mn2_e : 0.000483
  EX_zn2_e : 0.000238
  EX_ni2_e : 0.000226
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 47.846761
  EX_co2_e : 24.953884
  EX_h_e : 7.716533
  EX_ac_e : 0.628778
  Auxiliary production reaction : 0.221986
  DM_oxam_c : 0.000782
  DM_5drib_c : 0.000469
  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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