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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b4069 b2744 b3708 b0871 b3115 b1849 b2296 b2925 b2097 b2926 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b2690 b2797 b3117 b1814 b4471 b2210 b1033 b2799 b3945 b1602 b4381 b2406 b3915 b2366 b2492 b0904 b1533 b1380 b2660 b1518 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.348459 (mmol/gDw/h)
  Minimum Production Rate : 0.527763 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.586216
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.292034
  EX_pi_e : 0.863889
  EX_so4_e : 0.087749
  EX_k_e : 0.068017
  EX_fe3_e : 0.005597
  EX_mg2_e : 0.003023
  EX_ca2_e : 0.001814
  EX_cl_e : 0.001814
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000241
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 43.579138
  EX_co2_e : 29.006458
  EX_h_e : 8.254941
  EX_pyr_e : 3.788228
  Auxiliary production reaction : 0.527763
  EX_ac_e : 0.202868
  EX_acald_e : 0.084321
  EX_hxan_e : 0.000235
  DM_mththf_c : 0.000156
  DM_5drib_c : 0.000078
  DM_4crsol_c : 0.000078

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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