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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 61
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b1479 b3115 b1849 b2296 b0030 b2407 b3236 b1779 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1014 b4014 b0261 b2976 b2799 b3945 b0507 b3709 b1907 b2406 b3161 b0112 b4265 b2975 b0114 b3603 b2366 b0755 b3612 b0306 b3605 b2492 b0904 b3035 b1533 b3927 b3825 b1380 b0508 b1473 b0494 b1600 b0514 b4266 b3662 b1985 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.232232 (mmol/gDw/h)
  Minimum Production Rate : 0.445283 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.781266
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.874975
  EX_pi_e : 1.559862
  EX_so4_e : 0.753408
  EX_k_e : 0.045330
  EX_fe2_e : 0.003730
  EX_mg2_e : 0.002015
  EX_ca2_e : 0.001209
  EX_cl_e : 0.001209
  EX_cu2_e : 0.000165
  EX_mn2_e : 0.000160
  EX_zn2_e : 0.000079
  EX_ni2_e : 0.000075

Product: (mmol/gDw/h)
  EX_h2o_e : 49.329198
  EX_co2_e : 33.345832
  EX_h_e : 5.590716
  EX_ac_e : 2.369993
  Auxiliary production reaction : 0.445283
  EX_met__L_e : 0.249644
  DM_oxam_c : 0.000260
  DM_5drib_c : 0.000156
  EX_dxylnt_e : 0.000155
  DM_4crsol_c : 0.000052

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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