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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b4069 b4384 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b4139 b1623 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b3927 b3029 b1380 b2660 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.355804 (mmol/gDw/h)
  Minimum Production Rate : 0.032881 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.097077
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.074810
  EX_pi_e : 0.441853
  EX_so4_e : 0.089599
  EX_k_e : 0.069450
  EX_fe3_e : 0.005715
  EX_mg2_e : 0.003087
  EX_ca2_e : 0.001852
  EX_cl_e : 0.001852
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 43.531948
  EX_co2_e : 28.071956
  EX_h_e : 9.053974
  EX_pyr_e : 5.405451
  EX_ac_e : 0.207144
  Auxiliary production reaction : 0.032881
  EX_ade_e : 0.000398
  DM_5drib_c : 0.000239
  DM_4crsol_c : 0.000079

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.

Last updated: 21-Sep-2023
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